Abstract
Any type of genetic mapping is limited by the number of recombinations since the last common ancestor of the mapping population. Traditionally, genetic linkage mapping has been conducted within families derived from two parents after one or two generations. In contrast, association mapping, or linkage disequilibrium mapping (LD mapping), is conducted within populations in which relatedness is not established. Thus, the genetic resolution, as defined by the number of recombinations since the last common ancestor, are magnitudes higher in ‘population-mapping’ as compared to ‘family-mapping’. Recent efforts are seeking to combine population- and family-mapping methodology, thus creating unprecedented genetic resolution. This chapter describes the current status and prospects of LD mapping in crops.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abdurakhmonov IY, Abdukarimov A (2008) Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics 2008:574927
Abecasis GR, Cardon LR, Cookson WO (2000) A general test of association for quantitative traits in nuclear families. Am J Hum Genet 66:279–292
Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560
Andersen JR, Schrag T, Melchinger AE, Zein I, Lübberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111:206–217
Andersen JR, Zein I, Wenzel G, Krützfeldt B, Eder J, Ouzunova M, Lübberstedt T (2007) High levels of linkage disequilibrium and associations with forage quality at a phenylalanine ammonia-lyase locus in European maize (Zea mays L.) inbreds. Theor Appl Genet 114:307–319
Atwell S, Huang YS, Vilhjálmsson 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
Badu R, Nair SK, Prasanna BM, Gupta HS (2004) Integrating marker-assisted selection in crop breeding-prospects and challenges. Curr Sci 87:607–619
Balding DJ (2006) A tutorial on statistical methods for population studies. Nat Rev Genet 7:781–791
Beer SC, Siripoonwiwat W, O’donoughue LS, Souza E, Matthews D, Sorrels ME (1997) Associations between molecular markers and quantitative traits in an oat germplasm pool: can we infer linkages. J Agric Genom 3:197
Beló A, Zheng P, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A (2008) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279:1–10
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
Brenner EA (2011) Diagnostic DNA markers for lignocellulosic conversion of maize stover into biofuels. Ph.D. thesis, Iowa State University, Ames
Brenner EA, Zein I, Chen Y, Andersen JR, Wenzel G, Ouzunova M, Eder J, Darnhofer B, Frei U, Barrière Y, Lübberstedt T (2010) Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea mays L.). BMC Plant Biol 10:27
Brenner EA, Blanco M, Gardner C, Lübberstedt T (2012) Genotypic and phenotypic characterization of isogenic doubled haploid exotic introgression lines in maize. Mol Breed. doi:1.1007/s11032-001-9684-5
Campos H, Cooper M, Habben JE, Edmeades GO, Schussler JR (2004) Improving drought tolerance in maize: a view from industry. Field crops Res 90:19–34
Camus-Kulandaivelu L, Veyrieras JB, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449–2463
Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10
Chen Y (2011) Pleiotropic effects of genes involved in cell wall lignification on agronomic characters. Ph.D. thesis, Iowa State University, Ames
Chen Y, Lübberstedt T (2010) Molecular basis of trait correlations. Trends Plant Sci 15:454–461
Chen Y, Zein I, Brenner EA, Andersen JR, Landbeck M, Ouzunova M, Lubberstedt T (2010) Polymorphisms in monolignol biosynthetic genes are associated with biomass yield and agronomic traits in European maize (Zea mays L.). BMC Plant Biol 10:12
Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19
Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Sterernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, AGOUEB Consortium, Waugh R, O’Sullivan DM (2010) Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome. Proc Natl Acad Sci USA 107:21611–21616
Devlin B, Roeder K, Wasserman L (2001) Genomic control, a new approach to genetic-based association studies. Thero Popul Biol 60:155–166
Ding J, Araki H, Wang Q, Zhang P, Yang S, Chen JQ, Tian D (2007) Highly asymmetric rice genomes. BMC Genomics 8:154
Doebley J (2006) Unfallen grains: how ancient farmers turned weeds into crops. Science 312:1318–1319
Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11:446–450
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci 16:77–89
Gebhardt C, Ballvora A, Walkemeier B, Oberhagemann P, Schüler K (2004) Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol Breed 13:93–102
Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, Narechania A, Harkins TT, Grills GS, Ware DH, Buckler ES (2009) Large-scale discovery of gene-enriched SNPs. Plant Genome 2:121–133
Gupta P, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485
Hall IM, Quinlan AR (2012) Detection and interpretation of genomic structural variation in mammals. Methods Mol Biol 838:225–248
Hamblin MT, Close TJ, Bhat PR, Chao S, King JG, Abraham KJ, Blake T, Brooks WS, Cooper B, Griffey CA, Hayes PM, Hole DJ, Horsley RD, Obert DE, Smith KP, Ullrich SE, Muehlbauer GJ, Jannink J (2010) Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Sci 50:556–566
Hamblin MT, Buckler ES, Jannink JL (2011) Population genetics of genomics-based crop improvement methods. Trends Genet 27:98–106
Hardy OJ, Vekemans X (2002) spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
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
Herbst AL, Ulfelder H, Poskanzer DC (1971) Adenocarcinoma of the vagina: association of maternal stilbestrol therapy with tumor appearance in young women. N Engl J Med 284:878–881
Hospital F (2009) Challenges for effective marker-assisted selection in plants. Genetica 136:303–310
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299–314
Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723
Köhler K, Bickeböller H (2006) Case-control association tests correcting for population stratification. Ann Hum Genet 70:89–115
Kump KL, Bradbury PJ, Buckler ES, Belcher AR, Oropeza-Rosas M, Wisser RJ, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168
Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030
Lander ES, Schork N (1994) Genetic dissection of complex traits. Science 265:2037–2048
Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63
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
McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457
McIntyre CL, Whan VA, Croft B, Magarey R, Smith GR (2005) Identification and validation of molecular markers associated with Pachymetra root rot and brown rust resistance in sugarcane using map- and association-based approaches. Mol Breed 16:151–161
McMullen MD, Kresovich S, Villeda HS, Bradbury PJ, 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
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
Newell MA, Cook D, Tinker NA, Jannink JL (2011) Population structure and linkage disequilibrium in oat (Avena Sativa L.): implications for genome-wide association studies. Theor Appl Genet 122:623–632
Palaisa KA, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15:1795–1806
Passador-Gurgel G, Hsieh WP, Hunt P, Deighton N, Gibson G (2007) Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster. Nat Genet 39:264–268
Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275–291
Poland JA, Bradbury PJ, Buckler ES, Nelson RJ (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci 108:6893–6898
Pollak LM (2003) The history and success of the public-private project on germplasm enhancement of maize (GEM). Adv Agron 78:45–87
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Rafalski A, Ananiev E (2009) Genetic diversity, linkage disequilibrium and association mapping. In: Bennetzen JL, Hake S (eds) Handbook of maize: genetics and genomics. Springer, New York, pp 201–220
Rakshit S, Kanzaki H, Matsumura H, Rakshit A, Fujibe T, Okuyama Y, Yoshida K, Tamiru MO, Shenton M, Utsushi H, Mitsuoka C, Abe A, Kiuchi Y, Terauchi R (2010) Use of TILLING for reverse and forward genetics of rice. In: Meksem K, Kahl G (eds) The handbook of plant mutation screening: mining of natural and induced alleles. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. doi:10.1002/9783527629398.ch11
Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661
SAS Institute (1999) SAS/STAT user’s guide. Version 8 SAS Institute, Inc, Cary, NC
Searle SR (1987) Linear models for unbalanced data. Wiley, New York
Spielman RS, McGinnes RE, Ewens WJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506–516
Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5(11):e1000734
Stich B, Melchinger AE, Piepho HP, Heckenberger M, Maurer HP, Reif JC (2006) A new test for family-based association mapping with inbred lines from plant breeding programs. Theor Appl Genet 113:1121–1130
Stich B, Piepho HP, Schulz B, Melchinger AE (2008) Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor Appl Genet 117:947–954
Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from elite maize inbred lines using molecular markers. Genetics 132:823–829
Stuber CW, Polacco M, Lynn M (1999) Synergy of empirical breeding, marker assisted selection and genomics to increase crop yield potential. Crop Sci 39:1571–1583
Sun FZ, Flanders WD, Yang QH, Zhao HY (2000) Transmission/disequilibrium tests for quantitative traits. Ann Hum Genet 64:555–565
Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES 4th (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530
Virk PS, Ford-Lloyd BV, Jackson MT, Pooni HS, Clemeno TP, Newbury HJ (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304
Waugh R, Marshall D, Thomas B, Comadran J, Russell J, Close T, Stein N, Hayes P, Muehlbauer G, Cockram J, O’Sullivan D, Mackay I, Flavell A, Agoueb A, Barleycap, Ramsay L (2010) Whole-genome association mapping in elite inbred crop varieties. Genome 53: 967–972
Weigel D, Mott R (2009) The 1001 genome project for Arabidopsis thaliana. Genome Biol 10:107
Wen W, Araus JL, Shah T, Carirns J, Mahuku G, Bänziger M, Torres JL, Sánchez C, Yan J (2011) Molecular characterization of a diverse maize inbred line collection and its potential utilization for stress tolerance improvement. Crop Sci. doi:10.2135
Xia X, Melchinger AE, Kuntze L, Lübberstedt T (1999) Quantitative trait loci mapping of resistance to sugarcane mosaic virus in maize. Phytopathology 89:660–667
Xu ML, Melchinger AE, Xia XC, Lübberstedt T (1999) High-resolution mapping of loci conferring resistance to sugarcane mosaic virus in maize using RFLP, SSR, and AFLP markers. Mol Gen Genet 261:574–581
Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767
Yan J, Bermudez Kandianis C, Harjes CE, Bai L, Kim E, Yang X, Skinner DJ, Fu Z, Mitchell SE, Li Q, Salas 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 ß-carotene in maize grain. Nat Genet 42:322–327
Yang X, Gao S, Xu S, Zhang Z, Prasanna BM, Li L, Li J, Yan J (2011) Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed 28:511–526
Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160
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
Zhang YX, Wang Q, Jiang L, Liu LL, Wang BX, Shen YY, Cheng XN (2011) Fine mapping of qSTV11(KAS), a major QTL for rice stripe disease resistance. Theor Appl Genet 122:1591–1604
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467
Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20
Zondervan KT, Cardon LR (2007) Designing candidate gene and genome-wide case-control association studies. Nat Protoc 2:2492–2501
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Chen, Y. (2013). Dissection of Agronomic Traits in Crops by Association Mapping. In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_6
Download citation
DOI: https://doi.org/10.1007/978-94-007-5687-8_6
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-5686-1
Online ISBN: 978-94-007-5687-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)