Mapping QTL for agronomic traits in breeding populations

Theoretical and Applied Genetics - Tập 125 - Trang 201-210 - 2012
Tobias Würschum1
1State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany

Tóm tắt

Detection of quantitative trait loci (QTL) in breeding populations offers the advantage that these QTL are of direct relevance for the improvement of crops via knowledge-based breeding. As phenotypic data are routinely generated in breeding programs and the costs for genotyping are constantly decreasing, it is tempting to exploit this information to unravel the genetic architecture underlying important agronomic traits in crops. This review characterizes the germplasm from breeding populations available for QTL detection, provides a classification of the different QTL mapping approaches that are available, and highlights important considerations concerning study design and biometrical models suitable for QTL analysis.

Tài liệu tham khảo

Alheit KV, Reif JC, Maurer HP, Hahn V, Weissmann EA et al (2011) Detection of segregation distortion loci in triticale (× Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map. BMC Genomics 12:380 Bauer AM, Hoti F, von Korff M, Pillen K, Léon J et al (2009) Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials. Theor Appl Genet 119:105–123 Bernardo R (2008) Molecular marker and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664 Bink MCAM, Uimari P, Sillanpää MJ, Janss LLG, Jansen RC (2002) Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor Appl Genet 104:751–762 Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE et al (2008) Bayesian analysis of complex traits in pedigreed plant populations. Euphytica 161:85–96 Blanc G, Charcosset A, Mangin B, Gallais A, Moreau L (2006) Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize. Theor Appl Genet 113:206–224 Bradbury P, Parker T, Hamblin MT, Jannink JL (2011) Assessment of power and false discovery rate in genome-wide association studies using the BarleyCAP germplasm. Crop Sci 51:52–59 Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177 Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325:714–718 Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5:618–625 Coles ND, McMullen MD, Balint-Kurti PJ, Pratt RC, Holland JB (2010) Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis. Genetics 184:799–822 Dekkers JCM, Hospital F (2002) Multifactorial genetics: the use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3:22–32 Dudley JW, Johnson GR (2009) Epistatic models improve prediction of performance in corn. Crop Sci 49:763–770 Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Addison Wesley Longman, Harlow Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374 Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217 Gasbarra D, Pirinen M, Sillanpää MJ, Arjas E (2009) Bayesian quantitative trait locus mapping based on reconstruction of recent genetic histories. Genetics 183:709–721 Harjes CE, Rocheford TR, Bai L, Brutnell TP, Bermudez Kandianis C et al (2008) Natural genetic variation in epsilon lycopene cyclase tapped for maize biofortification. Science 319:300–333 Heckenberger M, Maurer HP, Melchinger AE, Frisch M (2008) The plabsoft database: a comprehensive database management system for integrating phenotypic and genomic data in academic and commercial plant breeding programs. Euphytica 161:173–179 Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161 Jannink JL, Bink M, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342 Jansen RC (2007) Quantitative trait loci in inbred lines. In: Handbook of Statistical Genetics, 3rd edn. Wiley, New York. ISBN: 978-0-470-05830-5 Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455 Jansen RC, Jannink JL, Beavis WD (2003) Mapping quantitative trait loci in plant breeding populations: use of parental haplotype sharing. Crop Sci 43:829–834 Lander ES, Schork NJ (1994) Genetic dissection of complex traits. Science 265:2037–2048 Li L, Paulo MJ, Van Eeuwijk F, Gebhardt C (2010) Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato. Theor Appl Genet 121:1303–1310 Li H, Bradbury P, Ersoz E, Buckler ES, Wang J (2011) Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS ONE 6(3):e17573. doi:10.1371/journal.pone.0017573 Liu W, Gowda M, Steinhoff J, Maurer HP, Würschum T et al (2011) Association mapping in an elite maize breeding population. Theor Appl Genet 123:847–858 Liu W, Maurer HP, Reif JC, Cossic F, Würschum T (2012a) Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses (in review) Liu W, Reif JC, Cossic F, Würschum T (2012b) Comparison of biometrical approaches for QTL detection in multiple segregating populations. Theor Appl Genet (accepted) Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Assoc, Sunderland Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577 Malosetti M, Van der Linden CG, Vosman B, Van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175:879–889 Malosetti M, Van Eeuwijk FA, Boer MP, Casas AM, Elía M et al (2011) Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs. Theor Appl Genet 122:1605–1616 Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R et al (2011) Genome-wide association mapping of fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breeding 27:439–454 McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740 Melchinger AE, Orsini E, Schön CC (2012) QTL mapping under truncation selection in homozygous lines derived from biparental crosses. Theor Appl Genet 124:543–553 Meuwissen THE, Karlsen A, Lien S, Olsaker I, Goddard ME (2002) Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 161:373–379 Miedaner T, Wilde F, Korzun V, Ebmeyer E, Schmolke M et al (2009) Marker selection for Fusarium head blight resistance based on quantitative trait loci (QTL) from two European sources compared to phenotypic selection in winter wheat. Euphytica 166:219–227 Miedaner T, Würschum T, Maurer HP, Korzun V, Ebmeyer E, Reif JC (2011) Association mapping for Fusarium head blight resistance in soft European winter wheat. Mol Breed 28:647–655 Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z et al (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202 Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723 Parisseaux B, Bernardo R (2004) In silico mapping of quantitative trait loci in maize. Theor Appl Genet 109:508–514 Phillips PC (2008) Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9:855–867 Powell JE, Visscher PM, Goddard ME (2010) Reconciling the analysis of IBD abd IBS in complex trait studies. Nat Rev Genet 11:800–805 Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA et al (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909 Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100 Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T et al (2011) Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123:283–292 Steinhoff J, Liu W, Maurer HP, Würschum T, Longin FH et al (2011) Multiple-line cross QTL-mapping in European elite maize. Crop Sci 51:2505–2516 Steinhoff J, Liu W, Reif JC, Ranc N, Würschum T (2012) Detection of QTL for flowering time in multiple families of elite maize (in review) Thornsberry JM, Goodman MM, Doebley H, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289 Van Eeuwijk FA, Boer M, Totir LR, Bink M, Wright D et al (2010a) Mixed model approaches for the identification of QTLs within a maize hybrid breeding program. Theor Appl Genet 120:429–440 Van Eeuwijk FA, Bink MCAM, Chenu K, Chapman SC (2010b) Detection and use of QTL for complex traits in multiple environments. Cur Opin Plant Biol 13:193–205 Van Inghelandt D, Reif JC, Dhillon BS, Flament P, Melchinger AE (2011) Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm. Theor Appl Genet 123:11–20 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 Verhoeven KJF, Jannink JL, McIntyre LM (2006) Using mating designs to uncover QTL and the genetic architecture of complex traits. Heredity 96:139–149 Von der Ohe C, Ebmeyer E, Korzun V, Miedaner T (2010) Agronomic and quality performance of winter wheat backcross populations carrying non-adapted Fusarium head blight resistance QTL. Crop Sci 50:2283–2290 Wang H, Smith KP, Combs E, Blake T, Horsley RD et al (2011) Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor Appl Genet. doi:10.1007/s00122-011-1691-8 Wu R, Zheng ZB (2001) Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157:899–909 Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C et al (2011a) Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123:1121–1131 Würschum T, Maurer HP, Schulz B, Möhring J, Reif JC (2011b) Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet. Theor Appl Genet 123:109–118 Würschum T, Maurer HP, Dreyer F, Reif JC (2012a) Effect of inter- and intragenic epistasis on the heritability of complex traits (in review) Würschum T, Liu W, Gowda M, Maurer HP, Fischer S et al (2012b) Comparison of biometrical models for joint linkage association mapping. Heredity 108:332–340 Würschum T, Liu W, Maurer HP, Abel S, Reif JC (2012c) Dissecting the genetic architecture of agronomic traits in multiple segregating populations in rapeseed (Brassica napus L.). Theor Appl Genet 124:153–161 Yu J, Arbelbide M, Bernardo R (2005) Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program. Theor Appl Genet 110:1061–1067 Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208 Yu LX, Lorenz A, Rutkoski J, Singh RP, Bhavani S et al (2011) Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet. doi:10.1007/s00122-011-1664-y Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468 Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK et al (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 et al (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4