Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor
Martha T. Hamblin, Sharon E. Mitchell, Gemma M. White, Javier Gallego, Rakesh Kukatla, Rod A Wing, Andrew H. Paterson, Stephen Kresovich
Plant Sciences, School of
Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.
https://doi.org/10.1534/genetics.167.1.471
Hamblin, M. T., Mitchell, S. E., White, G. M., Gallego, J., Kukatla, R., Wing, R. A., ... Kresovich, S. (2004). Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics, 167(1), 471-483. https://doi.org/10.1534/genetics.167.1.471
Comparative population genetics of the panicoid grasses : Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. / Hamblin, Martha T.; Mitchell, Sharon E.; White, Gemma M.; Gallego, Javier; Kukatla, Rakesh; Wing, Rod A; Paterson, Andrew H.; Kresovich, Stephen.
In: Genetics, Vol. 167, No. 1, 05.2004, p. 471-483.
Hamblin, MT, Mitchell, SE, White, GM, Gallego, J, Kukatla, R, Wing, RA, Paterson, AH & Kresovich, S 2004, 'Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor', Genetics, vol. 167, no. 1, pp. 471-483. https://doi.org/10.1534/genetics.167.1.471
Hamblin MT, Mitchell SE, White GM, Gallego J, Kukatla R, Wing RA et al. Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics. 2004 May;167(1):471-483. https://doi.org/10.1534/genetics.167.1.471
Hamblin, Martha T. ; Mitchell, Sharon E. ; White, Gemma M. ; Gallego, Javier ; Kukatla, Rakesh ; Wing, Rod A ; Paterson, Andrew H. ; Kresovich, Stephen. / Comparative population genetics of the panicoid grasses : Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. In: Genetics. 2004 ; Vol. 167, No. 1. pp. 471-483.
@article{c7ab6b1ef9854639944633d61aee7541,
title = "Comparative population genetics of the panicoid grasses: Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor",
abstract = "Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.",
author = "Hamblin, {Martha T.} and Mitchell, {Sharon E.} and White, {Gemma M.} and Javier Gallego and Rakesh Kukatla and Wing, {Rod A} and Paterson, {Andrew H.} and Stephen Kresovich",
doi = "10.1534/genetics.167.1.471",
journal = "Genetics",
publisher = "Genetics Society of America",
T1 - Comparative population genetics of the panicoid grasses
T2 - Sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor
AU - Hamblin, Martha T.
AU - Mitchell, Sharon E.
AU - White, Gemma M.
AU - Gallego, Javier
AU - Kukatla, Rakesh
AU - Wing, Rod A
AU - Paterson, Andrew H.
AU - Kresovich, Stephen
N2 - Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.
AB - Levels of genetic variation and linkage disequilibrium (LD) are critical factors in association mapping methods as well as in identification of loci that have been targets of selection. Maize, an outcrosser, has a high level of sequence variation and a limited extent of LD. Sorghum, a closely related but largely self-pollinating panicoid grass, is expected to have higher levels of LD. As a first step in estimation of population genetic parameters in sorghum, we surveyed 27 diverse S. bicolor accessions for sequence variation at a total of 29,186 bp in 95 short regions derived from genetically mapped RFLPs located throughout the genome. Consistent with its higher level of inbreeding, the extent of LD is at least severalfold greater in sorghum than in maize. Total sequence variation in sorghum is about fourfold lower than that in maize, while synonymous variation is fivefold lower, suggesting a smaller effective population size in sorghum. Because we surveyed a species-wide sample, the mating system, which primarily affects population-level diversity, may not be primarily responsible for this difference. Comparisons of polymorphism and divergence suggest that both directional and diversifying selection have played important roles in shaping variation in the sorghum genome.
U2 - 10.1534/genetics.167.1.471
DO - 10.1534/genetics.167.1.471
JO - Genetics
JF - Genetics
10.1534/genetics.167.1.471