Abstract
Genomic technologies are making it possible to strategically exploit genetic diversity in crops to map complex agronomic and physiological traits and improve these traits for grain and biomass production. Sorghum is well positioned to benefit from these association genetics strategies, and essential components of association mapping have been established. Research in sorghum association mapping contributes to a better understanding of genetics of complex traits and improved breeding methods to exploit genetic diversity.
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References
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631
Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265
Bernai JH, Clark RB (1998) Growth traits among sorghum genotypes in response to aluminium. J Plant Nutr 21:297–305
Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Brown PJ, Rooney WL, Franks C, Kresovich S (2008) Efficient mapping of plant height quantitative trait loci in a sorghum association population with introgressed dwarfing genes. Genetics 180:629–637
Bucheyeki TL, Shenkalwa EM, Mapunda TX, Matata LW (2010) Yield performance and adaptation of four sorghum cultivars in Igunga and Nzega districts of Tanzania. Commun Biometry Crop Sci 5:4–10
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718
Carpita NC, McCann MC (2008) Maize and sorghum: genetic resources for bioenergy grasses. Trends Plant Sci 13:415–420
Casa AM, Pressoira G, Brown PJ, Mitchell SE, Rooney WL, Tuinstrac MR, Franks CD, Kresovicha S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48:30–40
Casas AM, Kononowicz AK, Zehr UB, Tomes DT, Axtell JD, Butler LG, Bressan RA, Hasegawa PM (1993) Transgenic sorghum plants via microprojectile bombardment. Proc Natl Acad Sci U S A 90:11212–11216
de Alencar Figueiredo LF, Calatayud C, Dupuits C, Billot C, Rami JF, Brunel D, Perrier X, Courtois B, Deu M, Glaszmann JC (2008) Phylogeographic evidence of crop neodiversity in sorghum. Genetics 179:997–1008
Deu M, Rattunde F, Chantereau J (2006) A global view of genetic diversity in cultivated sorghums using a core collection. Genome 49:168–180
Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Gowda CLL, Serraj R, Srinivasan G, Chauhan YS, Reddy BVS, Rai KN, Nigam SN, Gaur PM, Reddy LJ, Dwivedi SL, Upadhyaya HD, Zaidi PH, Rai HK, Maniselvan P, Folkerstma R, Nalini M (2009) Opportunities for improving crop water productivity through genetic enhancement of dryland crops. In: Wani SP, Rockström J, Oweis T (eds) Rainfed agriculture: unlocking the potential. CAB International, Wallingford, pp 133–163
Hamblin MT, Casa AM, Sun H, Murray SC, Paterson AH, Aquadro CF, Kresovich S (2006) Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics 173:953–964
Hamblin MT, Fernandez MGS, Tunistra MR, Rooney WL, Kresovich S (2007) Sequence variation at candidate loci in the starch metabolism pathway in sorghum: prospects for linkage disequilibrium mapping. Crop Sci 47:S125–S134
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 167:471–483
Hamblin MT, Salas Fernandez MG, Casa AM, Mitchell SE, Paterson AH, Kresovich S (2005) Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171:1247–1256
Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319:330–333
Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases. Nature 461:747–753
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, Brown P, Browne C, Eller M, Guill K, Harjes C, Kroon D, Lepak N, Mitchell SE, Peterson B, Pressoir G, Romero S, Oropeza Rosas M, Salvo S, Yates H, Hanson M, Jones E, Smith S, Glaubitz JC, Goodman M, Ware D, Holland JB, Buckler ES (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740
Miller FR (1984) Registration of RTx430 sorghum parental line. Crop Sci 24:1224
Murray SC, Rooney WL, Hamblin MT, Mitchell SE, Kresovich S (2009) Sweet sorghum genetic diversity and association mapping for brix and height. Plant Genome 2:48–62
Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202
Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90
Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723
Paterson AH, Bowers JE, Bruggmann R, Dubchak I et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517
Rooney WL, Blumenthal J, Bean B, Mullet JE (2007) Designing sorghum as a dedicated bioenergy feedstock. Biofuels Bioprod Bioref 1:147–157
Schmutz J, Cannon SB, Schlueter J, Ma J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Schnable PS, Ware D, Fulton RS, Stein JC et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Shehzad T, Iwata H, Okuno K (2009a) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breed Sci 59:217–227
Shehzad T, Okuizumi H, Kawase M, Okuno K (2009b) Development of SSR-based sorghum (Sorghum bicolor (L.) Moench) diversity research set of germplasm and its evaluation by morphological traits. Genet Resour Crop Evol 56:809–827
Sorrells ME, Yu J (2009) Linkage disequilibrium and association mapping in the Triticeae. In: Feuillet C, Muehlbauer GJ (eds) Genetics and genomics of the Triticeae, plant genetics/genomics. Springer, New York, pp 655–684
Sun G, Zhu C, Kramer MH, Yang SS, Song W, Piepho HP, Yu J (2010) Variation explained in mixed-model association mapping. Heredity 105:333–340
Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D, Wang Y, Yu J, Gu M, Li J (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci U S A 106:21760–21765
Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S (2009) Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci 49:1769–1780
Visscher PM (2008) Sizing up human height variation. Nat Genet 40:489–490
Wang ML, Zhu C, Barkley NA, Chen Z, Erpelding JE, Murray SC, Tuinstra MR, Tesso T, Pederson GA, Yu J (2009) Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theor Appl Genet 120:13–23
Wang WY, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 6:109–118
Yan J, Kandianis CB, Harjes CE, Bai L, Kim EH, Yang X, Skinner DJ, Fu Z, Mitchell S, Li Q, Fernandez MG, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, Dellapenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T (2010) Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nat Genet 42:322–327
Yu J (2009) The potential of ultrahigh throughput genomic technologies in crop improvement. Plant Genome 2:2
Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160
Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92
Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
Yu J, Zhang Z, Zhu C, Tabanao DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES (2009) Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome 2:63–77
Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355–360
Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4
Zhao ZY, Cai T, Tagliani L, Miller M, Wang N, Pang H, Rudert M, Schroeder S, Hondred D, Seltzer J, Pierce D (2000) Agrobacterium-mediated sorghum transformation. Plant Mol Biol 44:789–798
Zhu C, Gore MA, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20
Zhu C, Yu J (2009) Nonmetric multidimensional scaling corrects for population structure in whole genome association studies. Genetics 182:875–888
Acknowledgments
This project is supported by the Kansas State University Targeted Excellence Program, National Research Initiative (NRI) Plant Genome Program of the USDA Cooperative State Research, Education and Extension Service (CSREES) (2006-35300-17155), Kansas Grain Sorghum Commission, International Sorghum and Millet Collaborative Research Support Program (INTSORMIL-CRSP), and Institute for Genomic Diversity at Cornell University.
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Yu, J., Hamblin, M.T., Tuinstra, M.R. (2013). Association Genetics Strategies and Resources. In: Paterson, A. (eds) Genomics of the Saccharinae. Plant Genetics and Genomics: Crops and Models, vol 11. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-5947-8_9
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