The urban development in the Yellow River basin (YRB) varies widely. Therefore, it is necessary to choose a development path that fits the characteristics of each city to achieve high-quality development. The purpose of this paper is to address the problem of how to choose a characteristic path for high-quality development and clarify its suitability for YRB cities. Firstly, based on data from 50 YRB cities from 2011 to 2020, the suitability evaluation was carried out from the perspective of an ecological niche, followed by the measurement of sub-dimensional niche breadth and overlap. The results confirmed the great diversity of development between cities and the intense competition for resources. Then, based on the classification approach using the k-means method, this study proposes a method for selecting a suitable path for high-quality development. It classifies the suitable paths into 3 major types with 7 minor types and recommends policies for the suitable paths for YRB cities. The systematic thinking and specific path selection method for the high-quality development of YRB cities is not only of practical significance for implementing city classification strategies but also provides a reference for the sustainable development of basin cities in other countries. The Yellow River basin (YRB) covers an area of 795,000 square kilometers, spanning 9 Chinese provinces within 60 cities, accounting for 8.3% of China’s land area ,2. As thPrevious scholars have conducted fruitful research studies on the high-quality development of the YRB, focusing on two aspects, for example, the level of high-quality development. As research progressed, scholars began to explore quantitative methods to analyze the weaknesses of high-quality development in the basin, among which the measurement of the high-quality development level was the earliest area of concern. Some scholars have constructed a measurement system of high-quality development in the YRB based on the new development concept ,8,9. ForFrom the perspective of ecology, the region through which the Yellow River flows is a special natural–economic–social composite ecosystem, and its high-quality development is constrained and limited by several factors, such as natural resource endowment and infrastructure. Each city in the basin occupies different resources and is in a different niche in this ecosystem, and has different paths and strategies for its development. The ecological niche concept in ecology was first defined by Grinnell, who considered ecological niche as “the ecological space occupied by an individual or a population” . WhittakBased on the research background analysis and literature review, this study argues that the high-quality development of cities in the YRB starts from the actual current situation of the overall basin, aims to solve the current main contradictions of cities in the YRB, and determines the all-around development of suitable development paths by combining the regional resource endowments. Based on factor endowment and ecological niche theory, this paper explores a suitability evaluation system that can comprehensively and accurately assess the environment and conditions for high-quality development in YRB cities. The suitability development of YRB cities is evaluated and measured using ecological niche-related theories and models, and then the K-means classification method is applied to classify the evaluation and measurement results; the selection methods of suitability paths for high-quality development are proposed on the basis of the classification results. In this way, this study attempts to address the problems of “how to choose”, “what to choose”, and “how to do” the paths of high-quality development of YRB cities. This will provide a theoretical basis and policy recommendations for the classification of the YRB to achieve high-quality development.The main innovations of this study are as follows: (1) An index system for evaluating the niche suitability of the high-quality development of cities in the YRB is created based on the ecological niche theory and the factor endowments of the cities in the YRB, in which the 7 sub-dimensional innovatively reflect the reality of the resource elements on which the cities’ development depends. This makes the process of evaluating the high-quality development more refined and the results more intuitive. Thus, it clarifies the resources and competitive advantages of each city in the basin from the perspective of sub-dimensional ecological niche, and provides a basis for finding the path that fits their own development characteristics. (2) In the method of selecting suitable paths, we propose a suitable path classification method based on the niche suitability evaluation results, which classify the high-quality development paths of cities in the YRB into 3 major types (including 7 minor types): (1) the leading development path ; (2) the characteristic development path ; (3) the livelihood development path. The suitability path selection method allows this study to scientifically and feasibly identify the suitable paths for the high-quality development of cities in the YRB, referencing other basin cities domestically and internationally.The current research focuses on the prefecture-level cities located in the YRB watershed. To facilitate the study, the selection of the research objects was based on the criteria of the classification of cities in the basin by Yang et al. A city is considered a YRB city if one of the following 3 criteria is fulfilled : (1) MorBased on the above criteria, a total of 60 prefecture-level cities  distributed in 9 provinces were selected. Due to missing data on individual cities, 50 cities in the basin were finally studied in this study. The map of YRB cities is shown in As shown in After determining the study area, according to the evaluation index system established in The study on the niche suitability evaluation and path selection for the high-quality development of cities in the YRB involves a combination of theoretical foundations and methodological innovations that are generalizable and replicable. In this study, the niche suitability of high-quality development refers to the suitability level of each ecological factor for the high-quality development of cities in the YRB, reflecting the resources of each sub-dimension and the relative position of a city in its environment for high-quality development. When evaluating the niche suitability of the high-quality development of cities in the YRB, this study first constructs a niche suitability index system for high-quality development. Then, the suitability values of sub-dimensional niche of each city is measured by using the niche suitability model. Finally, the results are rationally classified according to the measurement results and classification methods.First, this paper constructs a niche suitability index system to evaluate the high-quality development of cities in the YRB. Combined with related research studies, this paper defines the niche of YRB cities as the sum of various resources, their economic and social functions, and relationships required for the high-quality development of YRB cities at certain times and spaces.Based on the above definition and combined with the niche classification in related research ,34, combAfter constructing the index system for evaluating the niche suitability of the high-quality development in the YRB, the entropy-weighted TOPSIS-integrated evaluation method was adopted to calculate the niche suitability; the specific steps are as follows ,37,38:First, the raw data are standardized to obtain the normalization matrix jth index of the ith city value, create matrix Let Second, calculate the information entropy of each index.jth index.Third, calculate the weight coefficient ith city in the jth indicator among the objects, i.e., the positive ideal solution. Set ith city in the jth indicator among the objects, i.e., the negative ideal solution. After determining the weight coefficient, use the TOPSIS method to select the decision-making plan. Establish the weighted matrix Fourth, calculate the Euclidean distance i city to the ideal solution by using Formula (9). According to the score of Finally, calculate the relative proximity The niche breadth in the current research refers to the collection of all ecological factors possessed or available for high-quality development in YRB cities. The wider the niche breadth, the greater the diversity of resources utilized by the city, and the greater the demand for that dimension of resources for high-quality development. Similarly, the narrower the niche breadth, the more constrained the city’s development is.Niche breadth is generally measured using methods such as Levins, the Shannon–Wiener niche breadth index, and the niche theory of state and potential. In this study, the niche breadth is measured using a combination of state and potential. The “state” describes the reality for high-quality development in YRB cities. Here, the niche suitability evaluation values of 50 YRB cities in 2015 and 2020 are measured. The “potential” describes the future development trend for high-quality development in YRB cities. In this paper, the increases of the niche suitability evaluation values from 2011 to 2015 and from 2016 to 2020 are used as the “potential”. The “potential” is measured on a time scale of n years and the dimension conversion coefficient is 1/n. Therefore, the dimension conversion coefficient for this study is 0.25. Thus, the niche breadth is calculated as follows .(10)Ni=i and j. n is the number of cities. i, and i.In the formula: Niche overlap refers to the similarity of the high-quality development niche of any two cities in the YRB, which includes a measure of the similarity in the ability to utilize the same ecological factor. Using the niche overlap model, we can observe the similarities and differences in resource utilization in the YRB cities. In this study, the Pianka model was used to calculate the degree of niche overlap ,41, and i and k on resource j; the domain value is . i to the jth indicator to its utilization of the total resource status. k to the jth indicator to its utilization of the total resource status. The larger the value of i and city k. The larger the value of i and city k, and the higher the potential competition degree between them.In the formula, The K-means clustering method is applied to classify the results of niche suitability, niche breadth, and niche overlap measures for high-quality development in YRB cities in a reasonable way. The K-means clustering method is an objective dynamic clustering method . The metBased on the K-means clustering method, this paper proposes a path selection method for the suitability of high-quality development. The niche suitability, the niche breadth, and the niche overlap in the YRB cities are classified into four levels, and the four levels are assigned values according to the criteria stated above; the larger the value, the stronger the degree. Thus, the suitability path selection criteria for the high-quality development of 50 YRB cities were obtained.The suitability paths for high-quality development in YRB cities are divided into 3 categories (including 7 subcategories). The selection criteria are as follows:The first major path is the leading development path.Central-leading path:The number of niche sub-dimensions with niche suitability levels of 4 are greater than or equal to 1, the number of niche sub-dimensions with niche overlap levels of 4 are less than or equal to 4, and the number of niche sub-dimensions with niche breadth levels of 4 are greater than or equal to 3.Regional-leading path:Under the premise of considering location conditions, the number of niche sub-dimensions with niche suitability level greater than or equal to 2 are greater than or equal to 1, the number of niche sub-dimensions with niche overlap levels of 3 are less than or equal to 2, and the number of niche sub-dimensions with niche breadth levels of 2 are greater than or equal to 3.The second major path is the characteristic development path.Agriculturally featured development path:The niche suitability level of the sub-dimensional niche of agricultural resources is greater than or equal to 2, the niche overlap level of the sub-dimensional niche of agricultural resources is less than or equal to 3, and the niche breadth level of the sub-dimensional niche of agricultural resources is greater than or equal to 2.Industrially featured development path:The niche suitability level of the sub-dimensional niche of industrial resources is greater than or equal to 2, the niche overlap level of the sub-dimensional niche of industrial resources is less than or equal to 3, and the niche breadth level of the sub-dimensional niche of industrial resources is greater than or equal to 2.Service-featured development path:The niche suitability level of the sub-dimensional niche of service resources is greater than or equal to 2, the niche overlap level of the sub-dimensional niche of service resources is less than or equal to 3, and the niche breadth level of the sub-dimensional niche of service resources is greater than or equal to 2.Ecological function path:The niche suitability level of the sub-dimensional ecological environment resources niche is greater than or equal to 2, the niche overlap level of the sub-dimensional ecological environment resources niche is less than or equal to 3, and the niche breadth level of the sub-dimensional ecological environment resources niche is greater than or equal to 2.The third major path is the livelihood development path.Livelihood development path: The number of niche sub-dimensions with niche suitability levels of 1 are greater than or equal to 6, the number of niche sub-dimensions with niche overlap levels of 1 are less than or equal to 3, and the number of niche sub-dimensions with niche breadth levels of 1 are greater than or equal to 4.According to the index system of niche suitability evaluation for high-quality development in YRB cities constructed in According to the method in As can be seen from For service industry resources, the proportion of cities that are very suitable (“****”) and relatively suitable (“***”) are the lowest, while the proportion of cities that are not suitable (“*”) is relatively high. This shows that there is a serious division between the two levels in this niche dimension. The development of the service industry is more prominent in cities such as Lanzhou.For industrial resources, the proportion of cities that are very suitable (“****”) and relatively suitable (“***”) are relatively high, while the proportion of cities that are not suitable (“*”) is the lowest. This niche dimension has the most balanced development among the YRB cities. The industrial developments of cities such as Yulin are more prominent.For agricultural resources, the proportion of cities that are very suitable (“****”) and relatively suitable (“***”) are relatively high. Among these, agricultural development is more prominent in cities such as Bayannur.For ecological environmental resources, ecological positions that are very suitable (“****”) and relatively suitable (“***”) are relatively less. Guyuan is more suitable regarding ecological environment resources.As can be seen from The 7 sub-dimensional niche breadth values of the 50 YRB cities from 2011 to 2020 were derived based on Equation , and theIn terms of the basins, only more than half of the cities in the industrial resource ecotone and agricultural resource ecotone increased their ecotone width values during the study period, which indicates that the resources available for the high-quality development of the basin as a whole is gradually decreasing.In the basins, it was only in 2 sub-dimensional niches  where the niche breadth values of more than half of the cities increased during the study period. This indicates that the resources available for high-quality development in the YRB (as a whole) are on a decreasing trend. In addition, more than half of the niche breadth values of the cities in service industry resources and infrastructure resources decreased during the study period. This indicates that the competitiveness for the high-quality development in the YRB increased in industrial resources and agricultural resources, while the competitiveness of service resources and infrastructure resources decreased.In order to deeply analyze the spatial distribution patterns of the niche breadth for the high-quality development of YRB cities, this study used ArcGIS software to map the spatial distribution of niche breadth for 50 YRB cities for the period 2011 to 2020, as shown in From Specifically, it can be seen from The sub-dimensional niche overlap values for each YRB city in 2020 were calculated and statistically analyzed according to Equation  in SectiMeanwhile, in terms of spatial distribution, the overlap of ecological niches in the YRB cities (as a whole) goes from high to low in the downstream, midstream, and upstream. Specifically, we analyze the spatial relationship of the overlap degree of ecological niches in 7 sub-dimensions. The niche overlap of infrastructure resources is higher among downstream cities than upstream and midstream cities. The overall niche overlap of service industry resources is the highest in the YRB cities. The niche overlap degree of openness resources is the lowest in the sub-dimensional niches, especially among cities in upstream Gansu Province. Meanwhile, the niche overlap of innovative resources is low in this section of the province and among cities in the midstream. The niche overlap of industrial resources is high, especially between upstream and downstream cities. The niche overlap of agricultural resources and ecological environment resources is high among cities in the downstream.Based on the calculation results of the sub-dimensional niche suitability, niche breadth, and niche overlap of 50 cities, it is clear that the resource endowment for the high-quality development varies widely and unevenly among cities in the YRB. Therefore, to achieve the national strategic goal for high-quality development, the selection of suitability path differs among cities. According to the above analysis results and the path selection method in Leading Development PathThe leading development path is a high-quality development strategy that gives full play to the city’s strengths as a driver. The high-quality development of this city plays a key role in leading and demonstrating the formation of the high-quality development pattern of the YRB. The development of cities suitable for this path is not only outstanding but also relatively balanced in all niche aspects. Therefore, the city selecting this path has a strong development drive and is the most mature core area for urban development in the YRB at this stage. According to the different scopes of influence and radiation, the leading development path is further subdivided into the central-leading path and regional- leading path.The cities selected for the central-leading path include Xi’an, Zhengzhou, and Jinan. These 3 provincial capitals have much higher levels of development than other cities in their provinces in terms of infrastructure resources, service resources, openness resources, innovative resources, industrial resources, agricultural resources, and ecological environment resources, and they also have greater advantages over other cities throughout the whole basin.The cities selected for the regional-leading path include Taiyuan, Luoyang, Jining, Baotou, and Xining, which are ranked relatively high among the 50 YRB cities in terms of their high-quality development levels. Although their development levels are slightly lower compared to the central-leading cities, they have absolute advantages in their provinces.Characteristic development pathThe characteristic development path refers to the development strategy that gives full play to the characteristic industrial advantages of cities and plays a key role in promoting the regional division of labor for the high-quality development of YRB cities. The cities that selected this path are those with significant competitive advantages in a certain sub-dimensional niche in the basin. Compared with the leading developmental cities, the development of these cities is not that balanced, but the characteristic development and regional division of urban labor are also important driving forces for high-quality development. There are 35 cities in this study that were selected for the characteristic development path. According to the differences in advantageous features, they are subdivided into the agriculturally featured development path, industrially feature development path, Service-featured development path, and ecological function path.There are 10 suitable cities for the agriculturally featured development path, i.e., Bayannur, Weinan, Heze, Dezhou, Liaocheng, Xinxiang, Kaifeng, Tai’an, Yuncheng, and Puyang. As can be seen in There are 14 suitable cities for the industrially feature development path, i.e., Yulin, Erdos, Binzhou, Zibo, Lvliang, Dongying, Changzhi, Yinchuan, Jiaozuo, Xianyang, Jincheng, Baoji, Shuozhou, and Jinzhong. These cities are concentrated in the middle stream of the YRB.There are 4 suitable cities for the service-featured development path, i.e., Lanzhou, Yan’an, Hohhot, and Linfen, which are spatially distributed.There are 7 suitable cities for the ecological function path, i.e., Guyuan, Tianshui, Qingyang, Dingxi, Shangluo, Tongchuan and Sanmenxia. These cities are economically backward and relatively weak in overall development but have high ecological function value.The livelihood development pathThe livelihood development path is a development strategy that focuses on securing and improving the living and development conditions of low- and middle-income members of society in cities and focuses on improving the living standards of the people.There are 7 suitable cities for the livelihood development path, i.e., Wuhai, Baiyin, Pingliang, Shizuishan, Zhongwei, Xinzhou, and Wuzhong. These cities are mostly clustered in the upper stream of the YRB. These cities are lagging in the development of each sub-dimensional niche in the basin. On the basis of improving people’s livelihoods, exploring and cultivating special advantageous industries is the focus of the high-quality development of these cities.Studying the high-quality development of the YRB is a popular topic, but few scholars have used quantitative methods to investigate the high-quality development paths from a theoretical perspective. Therefore, this study introduces the ecological niche theory from ecology to examine the path selection for high-quality development in the YRB. The paper measures the suitability of YRB cities for high-quality development from the perspective of an ecological niche to explore how to choose suitable paths for achieving high-quality development.Unlike other evaluation systems guided by the “Five Development Concepts” ,46, thisThe breadth and overlap of ecological niches in each sub-dimension of cities in the YRB vary greatly, with the most competitive ecological niches for service and industrial resources in mid- and downstream cities. Unlike previous studies that focused on the high-quality development paths of the entire YRB or individual industries or cities, this paper includes all cities in the YRB in the research system.Although the research results all confirm that there are huge differences in the levels of high-quality development among cities in the upper and middle reaches of the YRB, and that zoning and classification are needed to implement policies, the research perspectives based on the ecological niche theory make the path classification more refined. Most of the previous studies have classified the paths with the help of some main functional areas, and the subsequent development paths are mainly divided into 4 types, i.e., optimized development zones, key development zones, restricted development zones, and prohibited development zones. In contrast, this study classifies the path types based on the resource endowment characteristics derived from the results of the sub-dimensional ecological niche adaptation of the YRB cities, which is more convenient for the basin cities to clarify their directions for high-quality development.The cities suitable for the leading development path should first make full use of their own advantages to drive the development of high-quality and all-dimensional niches of neighboring cities, especially to strengthen the leading role in innovation. Second, these cities should focus on improving their “shortcomings”. The suitability of agricultural and ecological environment resources for these cities is relatively low; thus, the rational development and utilization of agricultural and ecological resources should be top priorities. Local authorities should make good use of the city’s location according to local conditions, and at the same time regulate macro policies, to expand the ecological niches of agricultural and ecological environment resources. A typical city, such as Xi’an, while strengthening infrastructure construction, may use advanced manufacturing and electronic information industries and other advantageous industries as carriers, promote the expansion of urban development spaces to the periphery through industrial chain clustering, etc., and smooth the mechanisms of sharing and cooperation with other regions in terms of knowledge and technology, so as to improve the level of industrial development in the peripheral regions. In addition, in terms of ecological environment construction, ecological restoration, improvement of energy utilization, and transformation of green lifestyles can be promoted to enable the sustainable improvement of ecological environment quality;The cities that are suitable for characteristic development paths should first make their characteristic industries bigger, stronger, and more refined to form their own barriers to advantageous development. Through the specialization strategy, the development and utilization of the city’s regional advantages and resource advantages can be specialized and divided. This helps to reach the local monopoly of the city in the sub-dimensional niche of being advantageous in a short period of time, thus forming a natural advantage. Second, these cities should expand the number of niche resources and enhance the suitability of new sub-dimensional niches. At the same time, it ought to mitigate the phenomenon of vicious competition for resources caused by niche overlapping in similar characteristic development cities. For example, Erdos promotes the development of a new energy industry and expands the proportion of high-tech industries, such as energy-saving, environmental protection, and new materials in the industrial system. Meanwhile, it can develop a high-quality cultural tourism industry by relying on its historical and geomorphological features.Cities that choose the path of livelihood development should first improve their livelihoods to raise their living standards. In addition, these cities should actively open up to the outside world and reach a resource-parasitic relationship with other advantageous cities. The focus of this path is to implement ecological location specialization strategy. Cities should accurately locate their own advantageous development points. First, they should improve the suitability of certain resource niches in the region, drive the improvement of the suitability of other resource niches, and finally realize high-quality comprehensive development. The local government will transform disadvantages into advantages by increasing investments, so as to realize the transformation of resource advantages into economic advantages. A typical city, such as Wuhai, should increase the local government’s investment and use the city’s special topography to focus on developing international ecotourism, so as to realize the transformation of resource advantages into economic advantages and promote the improvement of the city’s livelihood in multiple directions.Based on the above analysis and discussion, the following countermeasures are proposed for the implementation strategy of the suitability path for the high-quality development of YRB cities:The current research is a path study based on the resource endowment and high-quality development status of the YRB cities themselves, without considering the cooperation between the basin cities, which have certain limitations. The subsequent study should add relevant elements to enhance the synergy of the high-quality development paths of the basin cities.This study addresses the lack of theoretical and quantitative research on high-quality development paths of YRB cities by introducing the ecological niche theory. The proposed classification criteria for high-quality development paths provide more scientific and systematic ways for cities to select their suitable paths. An index system for evaluating niche suitability of high-quality development in the YRB was constructed and used to evaluate niche suitability from 2011 to 2020. The study proposes a method for selecting suitable development paths, leading to the following conclusions.In terms of temporal evolution, the niche suitability of the high-quality development of YRB cities decreased during 2011–2020. Infrastructure resources and service industry resources did not change much, while openness to resources and industrial resources increased. In addition, innovative resources, agricultural resources, and ecological environment resources continued to decrease.In terms of spatial evolution, there are relatively few links between cities in the upper YRB and other cities, and the competition is less intense than that between cities in the lower and middle basins; however, ecological environment resources in the upper stream developed. The unevenness of infrastructure resources and service industry resources for the high-quality development of YRB cities are strong; most are centered in provincial capital cities and radiate outward.The suitability paths for the high-quality development of YRB cities can be divided into 3 major categories: (1) the leading development type, including central-leading type and regional-leading type; (2) the characteristic development type, including agriculturally featured development type, industrially featured development type, service-featured development type, and ecological function type; and (3) the livelihood development type.The current research provides a systematic consideration of the problem of selecting the suitable paths for the high-quality development of basin cities in China. The study of watershed city development problems using the ecological niche theory and targeted suggestions are also significant for the development of watershed cities in other countries.


Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity  and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars. Eleusine coracana (L.) Gaertn. (finger millet) is an annual crop that belongs to the Chloridoideae subfamily of the Poaceae grass family. There are nine species under the genus Eleusine Gaertn., among which E. coracana is the only domesticated species  and used for research and breeding purposes. In Zimbabwe, it is a major crop in regions IV and V, which are the driest agro-ecological regions in the country  crop. The diploid species E. indica (L.) Gaertn.  and E. floccifolia (Forssk.) Spreng  are considered the genome donors of E. coracana  is a widely used next-generation sequencing (NGS) method developed for the simultaneous discovery of new markers and genotyping of target germplasm . It is aThis study used two hundred eighty-eight finger millet accessions composed of 274 landrace accessions (228 from Ethiopia and 46 from Zimbabwe) and 14 improved cultivars released in Ethiopia. The 228 Ethiopian landrace accessions were originally collected from Amhara (130), Benishangul-Gumuz (2), Oromia (51), Southern Nations, Nationalities and Peoples’ Region (SNNPR) (4), Tigray (32), and unknown locations in Ethiopia (9) . Landrac3+) stress tolerance of the accessions was initially screened using the hydroponic nutrient solution. The solution containing 500 µM KNO3, 500 µM CaCl2, 500 µM NH4NO3, 150 µM MgSO4.7H2O, 10 µM KH2PO4, 2 µM FeCl3 (III), and 75 µM Al2 (SO4)3.18H2O was prepared according to Zhou et al. (2013). The pH of the nutrient solution was adjusted to 4.3 (using 1 M HCl or NaOH) and renewed every day to maintain the pH and Al3+ concentration relatively constant. For this experiment, similar-sized seeds from each accession were selected and surface-sterilized by soaking in 3% sodium hypochlorite solution for 5 min and rinsed thoroughly with water. The sterilized seeds of each accession were then wrapped in tissue paper, moistened with distilled water, and placed in a Petri dish for 36 h under dark conditions to initiate germination. Then, the seeds of each accession were grouped into two, and one group was grown in the hydroponic nutrient solution containing 100 μM Al. In contrast, the other group was grown as a control in the nutrient solution without aluminum for 10 days. This was followed by measuring the root length of the seedlings in cm using a ruler and calculating the relative root length (RRL) in percent as follows:Aluminum (Alhttps://biosearchassets.blob.core.windows.net/assetsv6/guide_bioark-leaf-collection-kit.pdf), as described in In order to ensure at least one germinating seeds of each of the 288 accessions, five seeds were planted in a 5 L plastic pot for each accession in a greenhouse at the Swedish University of Agricultural Sciences . After seed germination, extra seedlings were removed, and only a single seedling was maintained for each accession. Three weeks after planting, the leaf tissue of each accession was separately sampled using the BioArk Leaf collection kit from LGC, Biosearch Technologies (https://biosearch-cdn.azureedge.net/assetsv6/sbeadex-plant-data-sheet.pdf) for the GBS analysis. For the construction of a GBS library, Pstl  and ApeKl  restriction enzymes were used following the recommendations of the experts at LGC, Biosearch Technologies, who optimized restriction enzymes for various crops. The combined use of Pstl-ApeKl produced a fragment size distribution suitable for sequencing on Illumina platforms with a mean insert size of ∼220 bp. The GBS was conducted in 2 × 150 bp (paired-end) sequencing mode using NexSeq 500/550 v2 and NovaSeq SP FC NGS platforms to generate the reads. This produced about 1.5 million read pairs per sample. The reads were then adapter clipped, and those containing Ns were discarded along with reads whose 5′ ends did not match the restriction enzyme site. This was followed by trimming the 3′-end of the remaining reads using Trimmomatic v. 0.3 (A high molecular weight genomic DNA of the 288 accessions was extracted using the Sbeadex plant kit (c v. 0.3  to obtaiEleusine coracana subsp. coracana cultivar ML-365 scaffold-level genome assembly (https://www.ncbi.nlm.nih.gov/assembly/GCA_002180455.1/) was used as a reference genome, as there is no chromosome-level assembly available for finger millet yet. BWA-MEM v. 0.7.12 software package  from here on for the sake of simplicity. Pop-1 to Pop-5 represent Ethiopian landrace accessions, and their descriptions are as follows: Pop-1 represents accessions collected from Agew-Awi, Gojam, Bahrdar, and Metekel (northwestern accessions); Pop-2 represents accession from western Tigray and Gonder (northern accessions); Pop-3 represents accessions collected from Wellega and IIluababora (western accessions); Pop-4 represents accessions from central, eastern, and southern Tigray and northern Wello (northeastern accessions); Pop-5 represents accessions with unknown sampling location; and Pop-6 represents the 14 improved cultivars whereas the 46 Zimbabwean landrace accessions form Pop-7.Second, the accessions were grouped based on days to flowering, as early flowering and late flowering types . Third, The genetic diversity of the 288 accessions grouped based on different criteria was assessed using different statistical programs. For this data analysis, 5,226 SNPs with minor allele frequency (MAF) above 5% and no missing values were used. Polymorphism information content (PIC) of the SNPs was calculated as described by Neighbor-joining (NJ) cluster analysis was done based on Nei’s genetic distance using the MEGA7 program . GeneAlEA total of 5,226 SNP markers with MAF above 5% and without missing data were used for genetic diversity analyses of the finger millet accessions . The 5,2p < 0.01) with 10.7% and 86.4% of them showing heterozygosity excess and deficit, respectively (The Hardy–Weinberg equilibrium (HWE) test was conducted using 1000,000 steps in the Markov chain and 100,000 steps in dememorization by assuming that the 288 accessions are random samples from a single population. This analysis revealed that 2.5% of the loci were at HWE, 11% were with excess heterozygosity, and 86.5% were with heterozygosity deficit. Interestingly, the vast majority of the loci deviated from HWE at a highly significant level  varied from 1.19 (Pop-4) to 1.44 (Pop-1), with an overall mean of 1.33 . ShannonThe genetic analyses of the accessions grouped based on panicle type revealed that accession with open panicle had higher mean values for most of the diversity parameters  than semi-compact accessions  and compact accessions  . The earp < 0.01). The estimates for the differentiation among the groups (FST) were 0.31 (for the seven populations), 0.43 (for country of origin), 0.30 (for panicle type), 0.09 (for days to flowering), and 0.28   was conducted to estimate the genetic variation within and among different groups of finger millet accessions grouped based on different criteria. AMOVA for the seven populations revealed that the variation within and among the populations accounted for 70% and 30% of the total variation, respectively . When aclerance) .Pairwise Nei’s standard genetic distance among the seven finger millet populations ranged from 0.01 to 0.48. The lowest genetic distance was found between Pop-2 and Pop-5 (0.01), followed by Pop-1 vs. Pop-2 (0.04) and Pop-1 vs. Pop-5 (0.06) , which iThe Nei’s standard genetic distance-based neighbor-joining (NJ) cluster analysis of the 288 accessions revealed seven clusters with a good clustering pattern according to their geographic origin, except that few accessions collected from different regions were clustered together . ClusterPrincipal coordinate analysis (PCoA) was used to visualize the differentiation among the 288 accessions . The anaAccording to the admixture model-based population genetic structure analysis conducted using the 5,226 SNP markers, three genetic populations represent the 288 accessions the best . This anPstl/ApeKl methylation-sensitive restriction enzyme combination. Hence, the SNPs identified in this study represent a novel genomic resource for finger millet as the target genomic regions were different from those in the previous study. The final set of 5,226 SNP markers used in this study were distributed across 2,500 scaffolds with only one SNP per scaffold in most cases, indicating a wide distribution of these SNPs across the finger millet genome. Hence, the Pstl/ApeKl enzyme combination is suitable for GBS-based SNP discovery in finger millet and closely related species. The allele frequencies of most of these SNPs exceed 10%, with a quarter exceeding 27%, which makes them ideal for population genetics and genome-wide association studies (GWAS). The polymorphism information content (PIC) is a measure of the informativeness of molecular markers, and the higher the PIC value of a locus is, the more informative it is  is expected to be higher than the observed heterozygosity (Ho) if all other HWE assumptions are met. In line with the expectation, the mean He value (0.28) was higher than the mean Ho value (0.10) in the present study. A recent study in sorghum  using 3001 SNP markers reported mean He and Ho values of 0.10 and 0.06 . The lowThe genetic characterization of germplasm using codominant DNA markers is a crucial step toward developing stable and productive cultivars with various desirable traits. In the present study, 5,226 GBS-based SNP markers were used to examine the pattern and level of genetic diversity across 288 finger millet accessions representing the finger millet gene pool in Ethiopia and Zimbabwe. According to the result of site-frequency spectrum analysis, there is substantial genetic diversity among the seven finger millet populations, as evidenced by variation in minor allele frequency distributions between them. However, individual accessions in different populations generally bear minor alleles at fewer loci compared to results obtained in a similar study in sorghum . More thin situ conservation because finger millet is cultivated in large quantities in this region. The average values of different estimates of genetic variation of the four Ethiopian landrace populations (Pop-1 to Pop-4) were similar to those of the Zimbabwean landrace population (Pop-7). Hence, the finger millet gene pools in the two countries can be considered equally diverse. The level of genetic diversity of the population representing the cultivars (Pop-6) was within the diversity range of the landrace populations, which suggests that at least some cultivars were developed based on different finger millet genetic resources. It is noteworthy that the observed heterozygosity (Ho) of the cultivars was quite similar to that of the landraces, indicating that the cultivars are not pure lines. This indicates that their further improvement is possible through self-pollination.The level of genetic diversity observed across the populations in this study was comparable to that of earlier studies in finger millet based on SSR markers . Among tAmong the three groups of accessions classified based on the panicle types, the genetic diversity of those with open panicles was slightly higher than that of the other two groups. This could be mainly because of the sample size effects as accessions with open panicles accounted for two-thirds of the 288 accessions, representing wider geographic areas. Finger millet with open panicles is preferred for cultivation in Ethiopia due to its better grain yield, drought tolerance, resistance to bird attack and shattering, and ease to thresh . Hence, p < 0.01). The significant differentiation among groups of finger millet accessions was in agreement with the previously published research using EST and genomic SSR markers  revealed highly significant genetic differentiations among groups of accessions classified based on the geographic region of origin, country of origin, flowering time, panicle shape, and Al tolerance  and Pop-2 (northern accessions) were poorly differentiated, suggesting stronger gene flow between them. However, some of the accessions in these populations are different from those in other populations, as shown in Cluster-I of the PCoA . Pop-4 iAn important feature of the Bayesian statistical approach to population structure analysis is that it enables the identification of genotypes that originate purely from one genetic population or are the results of genetic admixture . This stIn the present study, over ten thousand SNP markers were detected using GBS, providing a new genomic resource for finger millet. The characterization of 5,226 of these SNPs in diverse finger millet populations from Ethiopia and Zimbabwe shows that they are highly informative and, therefore, suitable for different applications, such as genome-wide association studies and population genetics. The observed heterozygosity among landraces and cultivars is low, agreeing with the crop’s reproductive mechanism. However, there was excess heterozygosity at about one-tenth of the SNP loci, although the crop is mainly self-pollinating, suggesting evolutionary forces favoring heterozygosity may be at play at these loci. Future research focusing on these loci will provide more insight into their role. In order to determine whether private alleles found in different accession groups have potential associations with desired traits, further investigation is needed. Within Ethiopia, finger millet landrace accessions from different geographic regions differ moderately in terms of genetic diversity, with those from northeastern Ethiopia being the least diverse. The fact that some accessions from different regions clustered closely together suggests a countrywide gene flow, though to a different extent. The genetic differentiation among accessions classified by geographic region, country of origin, days to flowering, panicle type, and Al tolerance is significantly high, with differentiation among countries being the highest. In the case of improved cultivars, most of them clustered tightly together, suggesting that they were developed from similar germplasm and/or selected for the same traits, mainly grain yield. In addition, the level of their heterozygosity suggests that they can be further improved through self-pollination-based breeding. By using genetically distinct accessions from different geographic regions or countries, crossbreeding can potentially lead to the development of superior cultivars due to the recombination of alleles.


Cenchrus ciliaris. Between four and five samples per site (n = 93) were genotyped using the DArTseq platform, and we filtered the data to produce panels of 15,965 neutral and 5030 non‐neutral single nucleotide polymorphism (SNP) markers. Using fastSTRUCTURE, we detected three distinct genetic clusters with extremely high FST values among them (0.94–0.97) suggesting three different cultivars. We found high rates of asexual reproduction, possibly related to clonality or apomixis common in this species. At three locations, burnt and unburnt sites were genetically different, but genetic structure was not consistently related to fire management across the study region. Burning was associated with high genetic diversity and sexual reproduction in one genetic cluster, but with low genetic diversity and clonality in another. Individual SNPs were associated with longitude and genetic clustering, but not with recent fire management. Overall, we found limited evidence that roadside burning consistently increased genetic diversity and adaptive potential in C. ciliaris; evolutionary and breeding history more strongly shaped genetic structure. Roadside burning could therefore continue to be used for managing biomass in this species, with continued monitoring. Our study provides a framework for detecting fire‐related changes on a genetic level–a process that could be used as an early warning system to detect the invasive grass–fire cycle in future.The invasive grass–fire cycle is a widely documented feedback phenomenon in which invasive grasses increase vegetation flammability and fire frequency, resulting in further invasion and compounded effects on fire regimes. Few studies have examined the role of short‐term adaptation in driving the invasive grass–fire cycle, despite invasive species often thriving after introduction to new environments. We used a replicated (nine locations), paired sampling design (burn vs unburnt sites) to test the hypothesis that roadside burning increases genetic diversity and thus adaptive potential in the invasive, high‐biomass grass  Prescribed burning is commonly used to manage C. ciliaris biomass  (buffel grass) is a perennial C4 grass, native to Africa, India and the Middle East, which has become invasive in the Americas and Australia , which can tolerate fire and germinate rapidly after erratic rain events in arid climates  . Replicate samples were processed to assess call rate (mean = 75%), reproducibility (mean = 99%) and polymorphic information content (mean = 29%).Samples were genotyped at Diversity Arrays Technology P/L  using double‐restriction enzyme (PstI and HpaII) complexity reduction and high‐throughput sequencing (DArTseq). This method was developed for crop plants and has been widely used on polyploid genomes to detect DNA polymorphism with high reproducibility . The data comprised 20,995 SNPs after applying these filters . LFMM is spatially and environmentally explicit and, in addition to testing model assumptions, we also used this test to investigate whether specific loci were related to the burn status of sampled individuals. If a variation at a locus was strongly related to whether individuals had experienced recent fire, it could elucidate the genetic basis underlying fire‐related genetic changes at a population level . To control for the false discovery rate, we calculated q values from p values and classed SNPs as outliers where q < 0.05. When combined with quality control filters our non‐neutral (putatively adaptive) data set comprised 5030 SNPs and, after filtering these loci, our neutral dataset comprised 15,965 SNPs  that would maximize Hardy–Weinberg and linkage equilibrium. We investigated K = 1 to K = 11 and assigned each individual to a cluster based on the model complexity that maximized marginal likelihood and the model components used to explain structure in data . We also calculated FST values between the three genetic clusters identified by fastSTRUCTURE.To further explore genetic differences among individuals, we conducted principal components analysis on neutral SNPs using the ade4 package  with boxplots to summarize overall trends. Changes in neutral background genetic variation can reflect demographic processes such as admixture arising from nonrandom mating  but is standardized for sample size. We analysed the influence of fire category on allelic richness using linear regression in base R. Fire category was treated as a two‐level factor: roadside burnt and roadside unburnt (excluding location 11 with fewer replicates and a different management regime). To account for background genetic structure, we assigned each individual to one of K genetic clusters identified by fastSTRUCTURE and assigned site‐level K as the most common K among individuals at each site. We then fit an interactive model between fire category and K to test our hypothesis that fire would influence genetic diversity, while allowing this response to vary among genetic clusters. The model was fit separately to neutral and non‐neutral allelic richness data.We calculated site‐level allelic richness in hierfstat  on heterozygosity using a linear mixed‐effects model in lme4  with SNPrelate  and calculated the mean and interlocus standard deviation of FIS for each cluster separately  was between K = 3  and K = 4 (model components used to explain structure in the data). We based our interpretation and downstream analyses on K = 3  and orange (K2) clusters were genetically distinct, but more strongly related to each other than individuals from the green cluster (K3). Three individuals from sites 7b and 8b formed a distinct branch that was related at a higher level to the orange cluster (K2). All individuals except one in the orange cluster and this distinct branch were from burnt sites.Hierarchical clustering revealed higher‐level relationships corresponding largely to the three clusters identified by fastSTRUCTURE Figure . The majFST revealed strong genetic structure in the data. Three principal components (PC) explained almost all of the variation in the data (89%) and showed strong differences among samples , 0.022 in cluster K1 (range = −0.037 to 0.087) and 0.046 in cluster K3 (range = −0.004 to 0.212). There was no relationship between FST and geographic distance (isolation by distance) in either the overall sample   Figure b,c. FST3.3K genetic clusters identified by fastSTRUCTURE and K2 had lower levels of intercluster variation in all response variables  and non‐neutral (p = 0.024) allelic richness  main effect of K   values less than zero: K1 = −0.631 (–0.746); K2 = –0.022 (–0.864); K3 = –0.123 (–0.824)  was 0.20 in the whole data set, 0.32 within locations (burnt/unburnt sites combined) and 0.46 within sites Figure . Thus, w p < 0.00  Figure . This in4Cenchrus ciliaris showed inconsistent effects of roadside burning on genetic structure, genetic diversity and the mode of reproduction. Some burnt sites were genetically distinct from paired unburnt sites, but this was not consistent across the whole study region. Burning was associated with high genetic diversity and sexual reproduction in one cluster, but with low genetic diversity and clonality in another. We found individual SNPs associated with longitude and genetic clustering, but not with recent fire management history. Thus, genetic structure appeared to be more to strongly related to evolutionary or breeding history than fire management. We were unable to quantify fire history at our study sites beyond very recent burning, and it is possible that too few fires had occurred to detect consistent fire‐related changes or that the long‐term fire history between burnt and unburnt sites were not strongly different. It might take repeated burning over several years for genetic changes to be detected.Our replicated study of the high‐biomass invasive grass FST values (0.94–0. 97) among genetic clusters identified by fastSTRUCTURE and hierarchical clustering suggested three different cultivars of C. ciliaris in the data. High levels of FST can be driven by extremely low heterozygosity  has an evolutionary history that favoured drought tolerance with limited exposure to frequent or high‐intensity fire that would select for fire‐tolerant seed  had intermediate levels of genetic diversity and clonality , even within genetic clusters. In a different bioregion of Australia, Fensham et al.  had higher site‐level genetic diversity than the roadside locations. Individuals from this area comprised two different genetic clusters, which probably led to the overall higher allelic richness. However, this site also appeared to have higher rates of outcrossing, with a lower rate of asexual reproduction and fewer clonal individuals. The different management regime at this site has not had profound effects on genetic structure as genetic clustering was not strongly distinct from the roadside locations.K3, we might have concluded that fire would enhance sexual reproduction and adaptive potential. Our study shows, however, that we cannot draw such general conclusions. Our data also gives insights into the type of management appropriate for different populations. For example, managing a population with generally high rates of clonality (e.g. K1) using mechanical methods such as slashing or burning might not be as effective as for more sexually reproducing populations. Our study was limited to only one year of sampling per site and, even though our sampling spanned 100 km of central Australia, we sampled only three of at least 10 cultivars that have been introduced into the country. The species has an enormous distribution in Australia, covering all mainland states (Marshall et al., While we did not find consistent effects of fire in our study, the finding of strong genetic structure within the overall sample highlights the importance of understanding cryptic genetic variation within invasive species (Ward et al., C. ciliaris, with evolutionary and breeding history having a more dominant role in shaping population genetic structure. Roadside burning could continue to be used as a method for managing biomass in Central Australia and elsewhere but monitoring should continue as more generations and a longer exposure to burning might be required to see a change. Fire regimes are changing rapidly in Australia and globally (Abram et al., We found limited evidence that roadside burning consistently contributes to increased genetic diversity and thus adaptive potential in The authors declare no conflict of interest.Figure S1–S7Click here for additional data file.


The aim of this paper was to present the current situation of native sheep breeding in Poland, in terms of the significance and the effects of genetic resources protection programmes. The sheep farming tradition in Poland is deeply rooted in culture, particularly in the mountain and foothill regions. Sheep are permanently linked to many areas of country, not only playing an indispensable part in shaping the landscape, but also providing unique products. The most effective method of conserving native breeds is their sustainable management. It is important to maintain and develop the promotion and certification of high-quality products from native breeds and to control the endangered status of local breeds, which must be monitored and updated on an ongoing basis.The sheep population of native breeds, despite their unique features and the ability to adapt to harsh environmental conditions, has significantly decreased in recent years. Due to the low profitability of breeding, many local breeds of sheep in Poland were exposed to the risk of extinction. Many years of crisis in sheep farming have exacerbated this situation. The aim of this paper was to present the current situation of native sheep breeding in Poland, in terms of significance and effects of genetic resources protection programmes. The conservation of genetic resources of sheep aims to maintain and increase the population size while striving to maintain the greatest possible genetic variability. There are 17 native breeds included in the Polish sheep genetic resources conservation programme. A positive element of the implementation of the conservation of genetic resources programme for sheep is the accompanying measures which are based on the use of the non-productive role of the species. Extensive sheep grazing, as a form of nature conservation, serves to preserve valuable natural landscapes and the culture of local communities associated with sheep farming. Production and promotion of quality products, especially using niche markets and short production chains, are essential to ensure the economic viability of farms. These activities must be accompanied by raising public awareness of indigenous breeds and their alternative use in environmental activities, as well as their role in preserving the cultural heritage of local communities, for example through mountain grazing and the production of traditional products. Native breeds of sheep, despite their unique characteristics and ability to adapt to difficult environmental conditions, have declined in number, and this decline exposes them to the threat of extinction due to the low profitability of breeding. This fate has befallen 5 local breeds of sheep in Poland, and years of crisis in sheep farming have exacerbated this situation. Today, the significance of native breeds is growing, due to their role in the history of development of the regions from which they originate. Through fulfilling important natural, landscape, as well as social and cultural functions, native breeds are a testimony to the traditions and material culture of local communities. Programmes for the conservation of farm animal genetic resources implemented in many countries make it possible to preserve native breeds for future generations. The aim of this paper was to present the current situation of native sheep breeding in Poland, in terms of the significance and the effects of genetic resources protection programmes.Ovis aries) are one of the most numerous and earliest domesticated animal species. Since the beginning of domestication, which probably dates back approximately 11,000–9000 years ago in central or Southwestern Asia [Domestic sheep  databases and information system, Domestic Animal Diversity Information System (DAD-IS) , the divIn 1996 Poland joined the group of implementers of the World Conservation Strategy for Animal Genetic Resources undertaken by FAO, as a result of which it was obliged to establish appropriate national structures. A National Coordination Centre for the Preservation of Animal Genetic Resources was established which, along with the authorisation to collect and store biological material subject to cryopreservation, was transferred to the National Research Institute of Animal Production (NRIAP) . The advIn 1999, based on the working team activities, efforts were undertaken on the National Programme for the Protection of Animal Genetic Resources. As a result, by the decision of the Minister of Agriculture and Rural Development, the implementation of breeding programmes for the conservation of genetic resources of farm animal populations was undertaken. At that time, 32 programmes for the conservation of genetic resources were approved, covering 75 breeds, varieties, lines, and lineages of farm animals, including fish. The programmes specified objectives and schedules of activities, as well as the scope of in-situ and ex-situ conservation . As part of national programmes, a gene bank is envisaged for cattle, sheep, fish, and horses. The programmes also include methods of breeding and indicate the bodies responsible for their implementation. They are subject to amendment and extension when necessary [In June 2001, the Minister of Agriculture and Rural Development declared Poland’s participation in the process initiated by FAO to prepare a Report on the State of Animal Genetic Resources in the World. The definitive version of the Report, which emerged after numerous discussions during the National Workshop and the meetings of the Consultative Team, was drafted at the NRIAP and the Report was approved by the Ministry in August 2002 .The sheep farming tradition in Poland is deeply rooted in culture, particularly in the mountain and foothill regions. Sheep are permanently linked to many areas in Poland, not only playing an indispensable part in shaping the landscape, but also providing unique products such as wool, leather, meat, and dairy products . The proIn the 1990s, there was a drastic reduction in the overall sheep population in Poland, and thus many breeds that were less productive were at risk of being eliminated from breeding. The programme for the protection of genetic resources of sheep, as well as the farm and environment programmes of the Rural Development Programme, implemented since 2004, have made it possible to protect breeds in danger of extinction. In 1999, the Programme for the Protection of Genetic Resources included twelve sheep breeds such as Świniarka and Wrzosówka, which have been bred in Poland for centuries, as well as the following breeds: Olkuska, Pomorska, Coloured Merino, Uhruska, Wielkopolska, Corriedale, Żelaźnieńska, and Kamieniecka. Due to the low interest of breeders, the protection of the Leine and Booroola breeds was abandoned during the implementation of the programs. In 2000, coloured mountain sheep originated from the Zackel sheep were added to the programme. In 2008, the old-type Polish Merino and the Podhale Zackel were also incorporated into the programme. In 2015, Polish foothill sheep and the Black-headed sheep became part of the programme ,12. As oThe native breeds are adapted to often difficult and demanding environmental conditions of the regions from which they originate. They are distinguished by lower productivity than high-performance and commercial breeds, however, it is compensated by their resistance to diseases and stress, high fertility and prolificacy, longevity and low nutritional requirements with good use of feed .The implementation of conservation programmes requires the provision of financial support, since populations of native breeds are distinguished by lower productivity and, consequently, lower profitability of breeding in relation to breeds used in intensive production. Prior to Poland’s accession to the European Union (EU), financial support for the implementation of projects resulting from the maintenance of local breeds in accordance with adopted conservation programmes was covered under the national budget. Since 2005, funding for activities related to the protection of animal genetic resources has come from two sources and provided directly to the breeders. Support for breeders of horses, cattle, sheep, goats, and pigs is covered by farm and environment payments as part of the Rural Development Programme (to a considerable extent these are EU funds). Breeders of poultry, fur animals, bees, and fish covered by the genetic resources protection programme benefit from national aid ,13.https://www.gov.pl/web/arimr/informacje---pakiet-7-zachowanie-zagrozonych-zasobow-genetycznych-zwierzat-w-rolnictwie, accessed on 1 March 2022). The NRIAP, which is authorised to implement or coordinate activities in the field of genetic resources protection, defines criteria and abundance thresholds at which a given breed becomes endangered, creates a protection programme the implementation of which is to ensure the protection of individual endangered breeds, supervises the implementation, and coordinates genetic resources protection programmes [Since 2004, breeders who keep sheep, horses, cattle, pigs, and since 2015, those who keep goats covered by conservation programmes, have benefited from EU funds . The number of subsidies for animals of conservation breeds has been estimated to calculate the opportunity costs in these payments. Package 7 under the farm, environment, and climate programme of Rural Development Programme 2014–2020 supports programmes for the conservation of animal genetic resources, including sheep and goats. The aim of the package is to financially support the protection of particularly valuable breeds of selected farm animal species in case of which a low or decreasing number of breeding individuals results in the risk of their extinction (ogrammes .www.bioroznorodnosc.izoo.krakow.pl (accessed on 1 March 2022). Participation in the conservation programme is voluntary. The payment under this package is granted to a recipient who owns a farm located in Poland, with arable land of not less than 1 ha. The payments under the measure are granted annually, for the period of 5-year commitment, to farmers who voluntarily accept the farm, environmental, and climate obligation within the scope of the package or variant concerned. The payment fully or partially compensates for lost income and additional costs incurred. Currently, The farm, environment, and climate payment under the package “Conservation of local sheep breeds” amounts to around €100 per ewe per year [Farm, environmental, and climate payments are granted for ewes, which, depending on the breed, range from 10 to 30 animals per flock. The general conditions for participation in the programme for the conservation of genetic resources of sheep, hereafter referred to as the programme, are set out in a procedure available at per year .-selection of sheep breeds for the conservation programme when it is necessary to include an endangered breed-selection for the purpose of the conservation programme of animals and flocks when new breeds are introduced-drawing up complete documentation necessary for the implementation of measures under the programme, procedures, sample documents to be submitted by recipients under farm and environment programmes-maintenance and management of a database on national genetic resources of sheep-maintaining a website devoted to the implementation of sheep and goat genetic resources protection programmes -updating data on Polish sheep and goat breeding in the European Farm Animal Biodiversity Information System (EFABIS) -cooperation with FAO and other international organisations on the implementation of the World Action Plan for Animal Genetic Resources-activities related to the popularisation of native sheep breeds through publication of scientific research results on native sheep breeds, organisation of national and regional exhibitions of native animal breeds, symposia, trainings, and scientific conferences.-research: the currently conducted scientific research concerns the characteristics of the quality of products from native breeds of sheep in terms of nutritional and health-promoting values, their use in maintaining the biodiversity of naturally valuable areas, as well as the assessment of genetic variability of the population with the use of modern molecular biology tools-projects: the research project “BIOSTRATEG—The directions of use and the conservation of farm animal genetic resources under sustainable development” carried out in the recent period at the NRIAP. It was an interdisciplinary concept of comprehensive research related to the protection and the use of the potential of native animal breeds, including sheep, in low-input production systems, paying particular attention to the dietary and health-promoting properties of products and the development of naturally valuable areas. The impact of animal, biotechnological, and economic sciences on the socio-economic and natural environment by enabling the use of the latest technologies and solutions for the protection of animal genetic resources in order to optimally use their production potentialThe NRIAP in Cracow performs and coordinates tasks related to the protection of genetic resources  , assigneThe programme for the conservation of genetic resources in sheep has been a useful tool to protect the biodiversity of this species. Since the beginning of the programme for the conservation of sheep genetic resources, there has been a steady increase in the protected population. Within 15 years of the implementation of the programme , the numA positive element in the implementation of the programme for the conservation of genetic resources of sheep is the accompanying measures that are based on the use of the non-productive role of this species. Extensive sheep grazing, as a form of nature conservation, serves to preserve valuable natural landscapes and the culture of local communities associated with sheep farming.The native breeds of sheep are adapted to extensive grazing in nature-value areas and areas under nature conservation intended to control vegetation and maintain the landscape. This is carried out on wet meadows, fallow land, grasslands in mountain and foothill areas, in river valleys and forest clearings where, after abandoning grazing and haymaking, overgrowth has been observed along with consequent damage to the plants and animal species. Grazing helps preserve the specific nature of ecosystems and biodiversity of free-living species . GrazingEasement grazing, understood as limited collective grazing of sheep and comprehensive pastoral management, is a special form of farming carried out in the mountains, in legally protected areas or in their immediate vicinity. In Poland, easement grazing is practised in all national mountain parks, where it is only permitted in accordance with a number of restrictions. Only shepherds who obtain a permit and sign a lease agreement with the national park authorities may graze sheep. The density of the sheep must be appropriate to the land area, and only native breeds of sheep, mainly mountain sheep , may be grazed. Shepherds are obliged to observe traditional rituals, cheese-making rules, use traditional equipment, wear traditional clothes, which allow them to cultivate the heritage of the region .Grazing animals in mountain areas fulfils a specific cultural function that distinguishes these areas from other parts of the country, giving a specific character to the entire highland culture. The shepherding events that accompany sheep farming, the production of sheep’s milk products, the cultivation of traditions in shepherd’s huts and sheep grazing by the trails are an unusual attraction for tourists visiting the Polish mountains . ShepherA critical issue related to conservation breeding is the development of a market for traditional and regional products related to local sheep breeds . Producthttps://www.gov.pl/web/rolnictwo/lista-produktow-tradycyjnych12, accessed on 1 March 2022). The List includes products whose unique features and properties or quality result from the application of traditional (used for at least 25 years) production methods. A product applying for inclusion in the List should be an element of the local community’s identity and belong to the cultural heritage of a specific region. The most numerous groups of products on the List are cheese made from goat’s milk and traditional products of mountain sheep farming. Some of them, such as the most recognizable regional cheese—Oscypek, as well as Redykołka and Bryndza Podhalańska .The meat product included in the List which has been granted Protected Geographical Indication (PGI) status is the Podhale lamb. The List of Traditional Products includes more items from native breeds of sheep. These are both dairy products, such as traditional żentyca; and diverse types of cheese, such as bundz, grudka, bryndza żywiecka and wołoska smoked cheese, wołoski smoked cheese and klagany cheese; as well as meat products, such as Beskidzka lamb, Świniarka lamb, lamb from Wielkopolska sheep, Jurassic lamb from Olkuska sheep, or sheep leg from Pomeranian sheep with garlic .Considering the valuable properties of raw materials and products derived from local breeds, efforts have been made in many European countries to promote them through certification with unique quality marks. The NRIAP develops a certification system for native breeds and their products. As part of the project “Directions of use and protection of animal genetic resources under the conditions of sustainable development”, the Native Breed logo was developed as a collective symbol , as wellThe logo system is not a quality system as defined by EU regulations, but it meets similar requirements. It is expected that the logo will promote the products of specific Polish native breeds kept under traditional  systems on local markets. The main purpose of using the logo for producers of native breeds is to promote and raise public awareness of the role and importance of native breeds as an important part of our national heritage. This promotion is intended to highlight the importance of Polish native breeds, their historical as well as social and cultural value, the role they play in environmental and landscape renewal, and the potentials represented by their genetic resources. The logo is also intended to indicate products having a higher nutritional and health-promoting value. It may be used for all types of products  obtained from animals covered by the genetic resources protection programme. The logo is owned by the NRIAP, which establishes the principles and conditions for granting rights to its use. The right to mark products with the logo, based on an agreement with the Institute, belongs to breeders of domestic breeds participating in the programme, breeders-processors and processing plants producing products from the aforementioned breeds. The Institute maintains a register of participants in the certification programme, a website dedicated to it and an information campaign on the Native Breed logo .Keeping native breeds is popular among organic and farm-tourism farms, where they play an important popularising, promotional, and educational role not only for the animals themselves, but also for the region they come from . Such faThe dissemination of information on the benefits of preserving the animal’s genetic diversity and popularisation of the use of animal raw materials from domestic conservation breeds for the production of regional, organic products on small farms, gives breeders great opportunities to increase the profitability of their production. It may also constitute a form of income diversification. To this end, numerous promotional activities are undertaken, such as conferences, exhibitions, fairs, study tours, training courses, seminars, expert networks, and publications. An effective form of promotion of native breeds and products derived from them is animal exhibitions and thematic fairs and events, organised both as part of local and national events. The NRIAP holds regional and national exhibitions of native breeds in Poland, which are very popular among breeders and tourists. As shown in n = 181) (n = 129). The species with the largest number of breeds (n = 183) reported as extinct are cattle, as well as pigs (n = 93) and horses (n = 92); some breeds may have become extinct before they were documented [n = 780), so it is important to continuously monitor the status of endangered species in order to implement appropriate conservation mechanisms to save valuable genotypes.Sheep, apart from cattle and horses, are the species with the largest number of endangered breeds (n = 181) ; a largeds n = 18 reportedIn Poland, and throughout the EU, in order to determine the endangered status of breeds until 2014, European Commission Regulation 1974/2006 was in force, setting out the criteria for the number of females within individual species . It setsIn Poland, a model based on three factors was proposed: demographic, genetic, and socio-economic . Taking The conservation of genetic resources of sheep breeding animals aims to maintain and increase the population size while striving to maintain the greatest possible genetic variability. The most effective method of conserving native breeds is their sustainable management. Keeping native breeds of animals on farms, in organic and tourism farms, as well as organising national and regional exhibitions, provides an opportunity to learn about and come into direct contact with the animals. Production, promotion, and marketing of quality products (using niche markets and short production chains) are essential to ensure the economic viability of farms. These activities must be accompanied by raising public awareness of indigenous breeds and their alternative use in environmental activities, as well as their role in preserving the cultural heritage of local communities, for example through mountain grazing and the production of traditional products. The certification of products from native breeds is a good form of direct promotion and a way of showing consumers the distinctiveness of local breeds and the high quality of the raw materials obtained from them. Certification increases consumer confidence in products derived from native breeds, and thus increases the interest in breeds themselves and the demand for these products. The endangered status of local breeds should be monitored and updated on an ongoing basis in order to respond to changes and to strengthen ongoing measures.The programme for the protection of genetic resources of sheep is an important tool for the protection of biodiversity of this species, and its most visible effect is the constant growth of the protected population. Thanks to the implementation of the protection programme, after a long period of stagnation, sheep breeding is gaining more and more importance as one of the main field of livestock production in Poland.


Arvicola scherman, located in a bocage landscape in Atlantic NW Spain were studied using DNA microsatellite markers and a graph-based model. The results showed a strong isolation-by-distance pattern with a significant genetic correlation at smaller geographic scales, while genetic differentiation at larger geographic scales indicated a hierarchical pattern of up to eight genetic clusters. A metapopulation-type structure was observed, immersed in a landscape with a low proportion of suitable habitats. Matrix scale rather than matrix heterogeneity per se may have an important effect upon gene flow, acting as a demographic sink. The identification of sub-populations, considered to be independent management units, allows the establishment of feasible population control efforts in this area. These insights support the use of agro-ecological tools aimed at recreating enclosed field systems when planning integrated managements for controlling patch-dependent species such as grassland voles.The population dynamics of most animal species inhabiting agro-ecosystems may be determined by landscape characteristics, with agricultural intensification and the reduction of natural habitats influencing dispersal and hence limiting gene flow. Increasing landscape complexity would thus benefit many endangered species by providing different ecological niches, but it could also lead to undesired effects in species that can act as crop pests and disease reservoirs. We tested the hypothesis that a highly variegated landscape influences patterns of genetic structure in agricultural pest voles. Ten populations of fossorial water vole,  Landscape characteristics are a key factor in the population dynamics of most animal species ,2,3. TheSmall mammals may provide valuable ecosystem services in agricultural areas: being a key component of the food web and acting as pollinators or seed dispersers . Voles, Microtus arvalis, and fossorial water voles, Arvicola scherman  and Nava    a,b. The ® Andermatt Biocontrol, Grossdietwil, Switzerland) were placed in galleries for five consecutive days to collect specimens. A variable number of traps was set in each sampling plot according to surface signs of activity, using one trap per group of earth mounds observed. Shortly after capture, each specimen was cryopreserved at −20 °C until necropsy. Then, a sample of muscle tissue was preserved in 70% ethanol at −20 °C. Specimens gathered from each orchard were georeferenced and initially considered as belonging to independent populations (demes). Further favourable inhabited patches were found to exist close to our sampled demes. The recommendations of the Directive of the European Parliament and the Council on the Protection of Animals Used for Scientific Purposes  and its rate of change (∆K). Given that the geographical position of samples may have an impact on the outcome of clustering approaches [K, was allowed to vary between 1 and 10. MCMC convergence was assessed by comparing the number of clusters across replicate runs, with a single run chosen for presentation on the basis of the mean posterior probability as a criterion. Genetic subdivision within the area studied was assessed using non-spatial and spatial clustering methods. First, we used the non-spatial model-based Bayesian clustering method implemented in Structure 2.3.4 . This soarvester  was usedproaches ,71, Geneproaches  was usedST-like estimator under the infinite alleles model (IAM) [The distribution of genetic variation and the significance of differentiation was also examined through the analysis of molecular variance (AMOVA) based on the clusters inferred by Structure and Geneland  (Meirmanel (IAM) ,73. We tST/(1 − FST). In addition, partial Mantel tests were used in a causal modelling framework to identify which variable best explained the observed genetic structure [ST) for each pair of demes and a matrix describing hierarchical structure was examined using a third matrix of each landscape variable as an indicator [Mantel tests , with 10tructure ,77. Thusndicator ,78. Liker) was calculated comparing the genetic similarity of pairs of multilocus genotypes from individuals within each distance class  with the mean genetic similarity of all pairs of individuals [r [r for that distance class [Genetic spatial autocorrelation analysis at the individual level was conducted in Genealex 6.5 . The genividuals . In totaduals [r ,81. Distce class ,81.p < 0.001). As a result, locus AV14 was excluded prior to further analyses being performed as it had a lower number of alleles than AV13P. A total of 137 fossorial water voles  were successfully genotyped at 12 microsatellite loci . The numIS = 0.183, p < 0.001; Oles: FIS = 0.180, p < 0.001). The software Geneclass indicated seven first-generation immigrants in the studied demes: Vegadali (1), Ceceda (1), Serida (1), Priesca (2), Rozada (1) and Oles (1). The immigrant in Ceceda was a home-assigned immigrant, meaning that it was genetically closer to its deme of capture than others sampled. Priesca and Rozada received immigrants from demes genetically closer to Teleña and Marina. The number of genotyped voles per deme ranged between 11 and 18 . Allelicp < 0.05) for 38 of 45 pairs of fossorial water vole demes. Estimates of FST ranged between 0.003 and 0.281 . The estimation of the number of genetic clusters with Geneland across all runs yielded K = 4 (K = 3 (K = 8 (K) from K = 1 to K = 8  resulted in an increase in the proportion of genetic variation explained  and from 1.50 to 42.23 km (Mean 20.28 ± 12.51 SD), respectively . Resistap = 0.736). Fossorial water voles within sampling locations were significantly more closely related to each other than random individuals . SpatialWe present here the first landscape genetics study for an agricultural pest rodent in a highly variegated landscape, testing the hypothesis that landscape affects successful dispersal and thus influences the genetic structure pattern at the local scale. The results showed a strong IBD pattern supported by a high and a significant genetic correlation between fossorial water voles at smaller geographic scales. This distance-dependence of dispersal on genetic differentiation can also be expected at larger geographical scales, where the direct exchange of migrants is unlikely to occur ,38. HoweA. amphibius, [This metapopulation structure may be determined by kin clustering such as occurs in northern water voles  and those that are not specialised  [Landscape configuration is considered a key factor in determining gene flow between fossorial water vole populations ,37. Indesurfaces . The stu species . Consecu species . Convers species . Surroun species ,32, altho buteo) ,95 may po buteo) . In homogeneous agricultural landscapes from Western Europe, multiannual fluctuations of density and outbreaks of fossorial water voles occur at the regional scale ,32 becau