QTL Mapping: Methodology and Applications in Cereal Breeding (original) (raw)

References

• Adhikari TB, Jackson EW, Gurung S, Hansen JM, Bonman JM (2011) Association mapping of quantitative resistance to Phaeosphaeria nodorum in spring wheat landraces from the USDA national small grains collection. Phytopathol 11:1301–1310
  Google Scholar
• Agrama HA, Yan WG (2009) Association mapping of straighthead disorder induced by arsenic in Oryza sativa. Plant Breeding 128:551–558
  Google Scholar
• Apotikar DB, Venkateswarlu D, Ghorade RB, Wadaskar RM, Patil JV, Kulwal PL (2011) Mapping of shoot fly tolerance loci in sorghum using SSR markers. J Genet 90:59–66
  PubMed CAS Google Scholar
• Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745
  PubMed CAS Google Scholar
• Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant-Microbe Interact 21:859–868
  PubMed CAS Google Scholar
• Bandillo NB, Muyco PA, Redona E, Gregorio G, Singh KK, Leung H (2011) Population development through multiparent advanced generation intercrosses (MAGIC) among diverse genotypes to facilitate gene discovery for various traits in rice. Phill J Crop Sci 36:32–33
  Google Scholar
• Bauer AM, Hoti F, von Korff M, Pillen K, Leon J, Sillanpaa MJ (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
  PubMed CAS Google Scholar
• Beaumont MA, Rannala B (2004) The Bayesian revolution in genetics. Nat Rev Genet 5:251–261
  PubMed CAS Google Scholar
• Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, New York, pp 145–162
  Google Scholar
• Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci 48:1649–1664
  Google Scholar
• Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE, van de Weg WE (2008) Bayesian analysis of complex traits in pedigreed plant populations. Euphytica 161:85–96
  Google Scholar
• Bink Marco CAM, van Eeuwijk FA (2009) A Bayesian QTL linkage analysis of the common dataset from the 12th QTL-MAS workshop. BMC Proc 3:S4
  PubMed Google Scholar
• Boer MP, Wright D, Feng L, Podlich DW, Luo L, Cooper M, van Eeuwijk FA (2007) A mixed-model quantitative trait loci (QTL) analysis for multiple-environment trial data using environmental covariables for QTL-by-environment interactions, with an example in maize. Genetics 177:1801–1813
  PubMed Google Scholar
• de Borba TCO, Brondani RPV, Breseghello F et al (2010) Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Genet Mol Biol 33:515–524
  Google Scholar
• Borevitz JO, Chory J (2004) Genomics tools for QTL analysis and gene discovery. Curr Opin Plant Biol 7:132–136
  PubMed CAS Google Scholar
• Borner A, Schumann E, Furste A, Coster H, Leithold B, Roder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L). Theor Appl Genet 105:921–936
  PubMed Google Scholar
• 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
  PubMed CAS Google Scholar
• Breseghello F, Sorrells ME (2006a) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46:1323–1330
  Google Scholar
• Breseghello F, Sorrells ME (2006b) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177
  PubMed Google Scholar
• Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890
  PubMed CAS Google Scholar
• Bryant R, Proctor A, Hawkridge M, Jackson A, Yeater K, Counce P, Yan W, McClung A, Fjellstrom R (2011) Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection. Genetica 139:1383–1398
  PubMed CAS Google Scholar
• Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325:714–718
  PubMed CAS Google Scholar
• Buckler ES, Thornsberry JM (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111
  PubMed CAS Google Scholar
• Buckler ES (2012) Uniting the world’s maize diversity for detection of complex traits and accelerating breeding. 4th international conference on quantitative genetics: understanding variation in complex traits (Edinburgh, UK; 17–22 June 2012). Book of abstracts, p 29
  Google Scholar
• Cadalen T, Sourdille P, Charmet G, Tixier MH, Gay G, Boeuf C, Bernard S, Leroy P, Bernard M (1998) Molecular markers linked to genes affecting plant height in wheat using a doubled-haploid population. Theor Appl Genet 96:933–940
  CAS Google Scholar
• Canas RA, Quillere I, Gallais A, Hirel B (2012) Can genetic variability for nitrogen metabolism in the developing ear of maize be exploited to improve yield? New Phytol 194:440–452
  PubMed CAS Google Scholar
• Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Currt Opin Plant Biol 11:215–221
  Google Scholar
• CGIAR Generation Challenge Programme (2009) 2009 project updates. Generation challenge programme, Texcoco, Mexico
  Google Scholar
• Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169–2185
  PubMed CAS Google Scholar
• Chen X, Hackett CA, Niks RE, Hedley PE, Booth C, Druka A, Marcel TC, Vels A, Bayer M, Milne I, Morris J, Ramsay L, Marshall D, Cardle L, Waugh R (2010) An eQTL analysis of partial resistance to Pucciniahordei in barley. PLoS ONE 5:e8598
  PubMed Google Scholar
• Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
  PubMed CAS Google Scholar
• Cockram J, White J, Zuluaga DL, Smith S et al (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci USA 107:21611–21616
  PubMed CAS Google Scholar
• Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
  CAS Google Scholar
• Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P, Ross-Ibarra J, Buckler ES, Flint-Garcia SA (2012) Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol 158:824–834
  PubMed CAS Google Scholar
• Coque M, Martin A, Veyrieras JB, Hirel B, Gallais A (2008) Genetic variation for N-remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. Theor Appl Genet 117:729–747
  PubMed CAS Google Scholar
• Crepieux S, Lebreton C, Servin B, Charmet G (2004) Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data. Genetics 168:1737–1749
  PubMed CAS Google Scholar
• Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913
  PubMed CAS Google Scholar
• Damerval C, Maurice A, de Josse JM, Vienne D (1994) Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137:289–301
  PubMed CAS Google Scholar
• Danan S, Jean-Baptiste V, Véronique L (2011) Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 11:16
  PubMed Google Scholar
• Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141:1199–1207
  PubMed CAS Google Scholar
• de Vienne D, Leonardi A, Damerval C, Zivy M (1999) Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize. J Exp Bot 50:303–309
  Google Scholar
• Doebley J, Stec A, Gustus C (1995) Teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346
  PubMed CAS Google Scholar
• Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc Natl Acad Sci USA 87:9888–9892
  PubMed CAS Google Scholar
• Doebley J, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386:485–488
  PubMed CAS Google Scholar
• Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3:43–52
  PubMed CAS Google Scholar
• Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142:285–294
  PubMed CAS Google Scholar
• Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936
  PubMed CAS Google Scholar
• Eleuch L, Jilal A, Grando S, Ceccarelli S, Schmising MK, Tsujimoto H, Hajer A, Daaloul A, Baum M (2008) Genetic diversity and association analysis for salinity tolerance, heading date and plant height of barley germplasm using simple sequence repeat markers. J Integr Plant Biol 50:1004–1014
  PubMed CAS Google Scholar
• Emrich K, Price A, Piepho HP (2008) Assessing the importance of genotype x environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models. Euphytica 161:229–240
  Google Scholar
• Famoso AN, Zhao K, Clark RT, Tung C-W, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7:e1002221
  PubMed CAS Google Scholar
• Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110:1445–1452
  PubMed CAS Google Scholar
• Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171
  PubMed CAS Google Scholar
• Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374
  PubMed CAS Google Scholar
• Friedt W, Ordon F (2007) Molecular markers for gene pyramiding and disease resistance breeding in barley. In: Varshney RK, Tuberosa T (eds) Genomics-assisted crop improvement, vol 2. Genomics applications in crops, Springer, Berlin, pp 81–101
  Google Scholar
• Fu DL, Uauy C, Distelfeld A, Blechl A, Epstein L, Chen XM, Sela H, Fahima T, Dubcovsky J (2009) A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323:1357–1360
  PubMed CAS Google Scholar
• Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K, Hayashi N, Takahashi A, Hirochika H, Okuno K, Yano M (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325:998–1001
  PubMed CAS Google Scholar
• Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcros of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894
  CAS Google Scholar
• Gardiner JM, Coe EH, Melia-Hancock S, Hoisington DA, Chao S (1993) Development of a core RFLP map in maize using an immortalized F2 population. Genetics 154:917–930
  Google Scholar
• Gill KS, Lubbers EL, Gill BS, Raupp WJ, Cox TS (1991) A genetic linkage map of Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome 34:362–374
  Google Scholar
• Glemin S, Bataillon T (2009) A comparative view of the evolution of grasses under domestication. New Phytol 183:273–290
  PubMed CAS Google Scholar
• Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Herrmann RG (1991) Construction of an RFLP map of barley. Theor Appl Genet 83:250–256
  Google Scholar
• Griffiths S, Simmonds J, Leverington M, Wang Y, Fish L, Sayers L, Alibert L, Orford S, Wingen L, Herry L, Faure S, Laurie D, Bilham L, Snape J (2009) Meta-QTL analysis of the genetic control of ear emergence in elite European winter wheat germplasm. Theor Appl Genet 119:383–395
  PubMed CAS Google Scholar
• Griffiths S, Simmonds J, Leverington M, Wang Y, Fish L, Sayers L, Alibert L, Orford S, Wingen L, Snape J (2012) Meta-QTL analysis of the genetic control of crop height in elite European winter wheat germplasm. Mol Breeding 29:159–171
  Google Scholar
• Gupta PK, Kulwal PL (2006) Methods of QTL analysis in crop plants: present status and future prospects. In: Trivedi PC (ed) Biotechnology and biology of plants. Avishkar Publishers, Jaipur, pp 1–23
  Google Scholar
• Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485
  PubMed CAS Google Scholar
• Gupta PK, Kumar J, Mir RR, Kumar A (2010a) Marker-assisted selection as a component of conventional plant breeding. Plant Breeding Rev 33:145–217
  Google Scholar
• Gupta PK, Langridge P, Mir RR (2010b) Marker-assisted wheat breeding: present status and future possibilities. Mol Breeding 26:145–161
  Google Scholar
• Haberle J, Holzapfel J, Schweizer G, Hartl L (2009) A major QTL for resistance against Fusarium head blight in European winter wheat. Theor Appl Genet 119:325–332
  PubMed Google Scholar
• Hall D, Tegstrom C, Ingvarsson PK (2010) Using association mapping to dissect the genetic basis of complex traits in plants. Brief Funct Genomics 9:157–165
  PubMed CAS Google Scholar
• Hackett CA (2002) Statistical methods of QTL mapping in cereals. Plant Mol Biol 48:585–599
  PubMed CAS Google Scholar
• Hackett CA, Weller JI (1995) Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 51:1252–1263
  PubMed CAS Google Scholar
• Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324
  PubMed CAS Google Scholar
• Hamzehzarghani H, Paranidharan V, Abu-Nada Y, Kushalappa AC, Mamer O, Somers D (2008) Metabolic profiling to discriminate wheat near isogenic lines, with quantitative trait loci at chromosome 2DL, varying in resistance to fusarium head blight. Can J Plant Sci 88:789–797
  Google Scholar
• Hanocq E, Laperche A, Jaminon O, Laine AL, Gouis JL (2007) Most significant genome regions involved in the control of earliness traits in bread wheat, as revealed by QTL meta-analysis. Theor Appl Genet 114:569–584
  PubMed CAS Google Scholar
• Hansen BG, Halkier BA, Kliebenstein DJ (2008) Identifying the molecular basis of QTLs: eQTLs add a new dimension. Trends Plant Sci 13:72–77
  PubMed CAS Google Scholar
• Hao Z, Li X, Liu X, Xie C, Li M, Zhang D, Zhang S (2010) Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize. Euphytica 174:165–177
  Google Scholar
• Harushima Y, Yano M, Shomura A, Sato M et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494
  PubMed CAS Google Scholar
• Ho J, McCouch S, Smith M (2002) Improvement of hybrid yield by advanced backcross QTL analysis in elite maize. Theor Appl Genet 105:440–448
  PubMed CAS Google Scholar
• Hua J, Xing Y, Wu W, Xu C, Sun X et al (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 100:2574–2574
  PubMed CAS Google Scholar
• Huang XQ, Coster H, Ganal MW, Roder MS (2003) Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (Triticum aestivum L.). Theor Appl Genet 106:1379–13
  PubMed CAS Google Scholar
• Huang X, Paulo M-J, Boer M, Effgen S, Keizer P, Koornneef M, van Eeuwijk FA (2011) Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc Natl Acad Sci USA 108:4488–4493
  PubMed CAS Google Scholar
• Huang X, Wei X, Sang T, Zhao Q, Feng Q et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
  PubMed CAS Google Scholar
• Isobe S, Nakaya A, Tabata S (2007) Genotype matrix mapping: searching for quantitative trait loci interactions in genetic variation in complex traits. DNA Res 14:217–225
  PubMed CAS Google Scholar
• Jahoor A, Eriksen L, Backes G (2004) QTLs and genes for disease resistance in barley and wheat. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer Academic Publishers, The Netherlands, pp 199–251
  Google Scholar
• Jaiswal V, Mir RR, Mohan A, Balyan HS, Gupta PK (2012) Association mapping for pre-harvest sprouting tolerance in common wheat (Triticum aestivum L.). Euphytica 188:89–102
  CAS Google Scholar
• Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129:440–450
  PubMed CAS Google Scholar
• Jansen RC, Nap J-P (2001) Genetical genomics: the added value from segregation. Trends Genet 17:388–391
  PubMed CAS Google Scholar
• 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
  Google Scholar
• Jansen RC, Tesson BM, Fu J, Yang Y, McIntyre LM (2009) Defining gene and QTL networks. Curr Opin Plant Biol 12:241–246
  PubMed CAS Google Scholar
• Jia L, Yan W, Zhu C, Agrama HA, Jackson A et al (2012) Allelic analysis of sheath blight resistance with association mapping in rice. PLoS ONE 7(3):e32703
  PubMed CAS Google Scholar
• Jordan MC, Somers DJ, Banks TW (2007) Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci. Plant Biotechnol J 5:442–453
  PubMed CAS Google Scholar
• Jourjon M-F, Jasson S, Marcel J, Ngom B, Mangin B (2005) MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics 21:128–130
  PubMed CAS Google Scholar
• 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
  PubMed Google Scholar
• Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203–1216
  PubMed CAS Google Scholar
• Katja W, Pietsch C, Strickert M, Matros A, Roder MS, Weschke W, Wobus U, Mock H-P (2011) Mapping of quantitative trait loci associated with protein expression variation in barley grains. Mol Breeding 27:301–314
  Google Scholar
• Keller B, Bieri S, Bossolini E, Yahiaoui N (2007) Cloning genes and QTLs for disease resistance in cereals. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement, vol 2. Genomics applications in crops, Springer, Berlin, pp 103–128
  Google Scholar
• Keurentjes JJ, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M (2006) The genetics of plant metabolism. Nat Genet 38:842–849
  PubMed CAS Google Scholar
• Khowaja FS, Gareth NJ, Brigitte C, Adam PH (2009) Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics 10:276
  PubMed Google Scholar
• Kleinhofs A, Kilian A, Saghai Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ (1993) A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705–712
  CAS Google Scholar
• Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters; power and genetic variances for unreplicated and replicated progeny. Genetics 126:769–777
  PubMed CAS Google Scholar
• Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43:1096–1105
  PubMed CAS Google Scholar
• Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
  PubMed CAS Google Scholar
• Korol AB, Ronin YI, Kirzhner VM (1995) Interval mapping of quantitative trait loci employing correlated trait complexes. Genetics 140:1137–1147
  PubMed CAS Google Scholar
• Korol AB, Ronin YI, Nevo E, Hays PM (1998) Multi-interval mapping of correlated trait complexes. Heredity 80:273–284
  Google Scholar
• Kou Y, Wang S (2010) Broad-spectrum and durability: understanding of quantitative disease resistance. Curr Opin Plant Biol 13:181–185
  PubMed CAS Google Scholar
• Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) Multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551
  PubMed Google Scholar
• Kraakman ATW, Martínez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breeding 17:41–58
  CAS Google Scholar
• Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446
  PubMed CAS Google Scholar
• Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009a) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1362
  PubMed CAS Google Scholar
• Krattinger S, Wicker T, Keller B (2009b) Map-based cloning of genes in triticeae (wheat and barley). In: Feuillet C, Muehlbauer GJ (eds) Genetics and genomics of the triticeae, plant genetics and genomics: crops and model 7. Springer, Berlin, pp 337–357
  Google Scholar
• Krill AM, Kirst M, Kochian LV, Buckler ES, Hoekenga OA (2010) Association and linkage analysis of aluminum tolerance genes in maize. PLoS ONE 5:e9958
  PubMed Google Scholar
• Kulwal PL, Ishikawa G, Benscher D, Feng Z, Yu L-X, Jadhav A, Mehetre S, Sorrells ME (2012) Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet 125:793–805
  PubMed CAS Google Scholar
• Kulwal PL, Singh R, Balyan HS, Gupta PK (2004) Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analyses in bread wheat. Funct Integr Genomics 4:94–101
  PubMed CAS Google Scholar
• Kulwal PL, Roy JK, Balyan HS, Gupta PK (2003) QTL analysis for growth and leaf characters in bread wheat. Plant Sci 164:267–277
  CAS Google Scholar
• Kulwal PL, Kumar N, Kumar A, Gupta RK, Balyan HS, Gupta PK (2005) Gene networks in hexaploid wheat: interacting quantitative trait loci for grain protein content. Funct Integr Genomics 5:254–259
  PubMed CAS Google Scholar
• Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL analysis for yield and yield contributing traits in two mapping populations of bread wheat. Mol Breeding 19:163–177
  Google Scholar
• Kumar N, Kulwal PL, Gaur A, Tyagi AK, Khurana JP, Khurana P, Balyan HS, Gupta PK (2006) QTL analysis for grain weight in bread wheat. Euphytica 151:135–144
  CAS Google Scholar
• Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, 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 43:163–169
  PubMed CAS Google Scholar
• Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
  PubMed CAS Google Scholar
• Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
  PubMed CAS Google Scholar
• Langridge P, Karakousis A, Collins N, Kretschmer J, Manning S (1995) A consensus linkage map of barley. Mol Breeding 1:389–395
  CAS Google Scholar
• Larièpe A, Mangin B, Jasson S, Combes V, Dumas F, Jamin P, Lariagon C, Jolivot D, Madur D, Fiévet JB, Gallais A, Dubreuil P, Charcosset A, Moreau L (2012) The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics 190:795–811
  PubMed Google Scholar
• Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A (2002) Expanding the genetic map of maize with the intermated B73 3 Mo17 (IBM) population. Plant Mol Biol 48:453–461
  PubMed CAS Google Scholar
• Lehmensiek A, Bovill W, Wenzl P, Langridge P, Rudi A (2009) Genetics and genomics of the triticeae. In: Feuillet C, Muehlbauer GJ (eds) Plant genetics and genomics: crops and models 7, DOI 10.1007/978-0-387-77489-3_7
  Google Scholar
• Li C, Zhou A, Sang T (2006a) Rice domestication by reducing shattering. Science 311:1936–1939
  PubMed CAS Google Scholar
• Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three yield components in rice Oryza sativa L. Genetics 145:453–465
  PubMed CAS Google Scholar
• Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CHM, Liu GF, Wang GC, Shashidhar HE, Zhuang JY, Zheng KL, Singh VP, Sidhu JS, Srivantaneeyakul S, Khush GS (2003) QTL× environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108:141–153
  PubMed CAS Google Scholar
• Li C, Zhou A, Sang T (2006b) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194
  PubMed CAS Google Scholar
• Li H, Hearne S, Banziger M, Li Z, Wang J (2010) Statistical properties of QTL linkage mapping in biparental genetic populations. Heredity 105:257–267
  PubMed CAS Google Scholar
• Li H, Ribaut J-M, Li Z, Wang J (2008) Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theor Appl Genet 116:243–260
  PubMed Google Scholar
• Li H, Ye G, Wang J (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175:361–374
  PubMed Google Scholar
• Li J, Wang S, Zeng ZB (2006) Multiple-interval mapping for ordinal traits. Genetics 173:1649–1663
  PubMed CAS Google Scholar
• Li JZ, Zhang ZW, Li YL, Wang QL, Zhou YG (2011) QTL consistency and meta-analysis for grain yield components in three generations in maize. Theor Appl Genet 122:771–782
  PubMed CAS Google Scholar
• Li X, Yan W, Agrama H, Jia L et al (2012) Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS ONE 7:e29350
  PubMed CAS Google Scholar
• Lincoln S, Daly M, Lander E (1993) Mapping genes controlling quantitative traits using MAPMAKER/QTL. Version 1.1, 2nd edn. Whitehead Institute for Biomedical Research, Technical report
  Google Scholar
• Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore M, Buckler ES, Zhang Z (2011) User manual of GAPIT: genome association and prediction integrated tool. http://www.maizegenetics.net/gapit
• Liu BH (1998) Statistical genomics: linkage mapping and QTL analysis. CRC Press, Boca Raton
  Google Scholar
• Liu S, Pumphrey MO, Gill BS, Trick HN, Zhang JX, Dolezel J, Chalhoub B, Anderson JA (2008) Toward positional cloning of Fhb1, a major QTL for Fusarium head blight resistance in wheat. Cereal Res Commun 36:195–201
  CAS Google Scholar
• Liu R, Zhang H, Zhao P, Zhang Z, Liang W, Tian Z, Zheng Y (2012) Mining of candidate maize genes for nitrogen use efficiency by integrating gene expression and QTL data. Plant Mol Biol Rep 30:297–308
  CAS Google Scholar
• Liu SC, Kowalski SP, Lan TH, Feldmann KA, Paterson AH (1996) Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics 142:247–258
  PubMed CAS Google Scholar
• Loffler M, Schon CC, Miedaner T (2009) Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Mol Breeding 23:473–488
  Google Scholar
• Lu C, Shen L, Tan Z, Xu Y, He P, Chen Y, Zhu L (1996) Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population. Theor Appl Genet 93:1211–1217
  CAS Google Scholar
• Lu Y, Zhang S, Shah T, Xie C, Hao Z, Li X, Farkhari M, Ribaut J-M, Cao M, Rong T, Xu Y (2010) Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci USA 107:19585–19590
  PubMed CAS Google Scholar
• Ma XQ, Tang JH, Teng WT, Yan JB, Meng YJ, Li JS (2007) Epistatic interaction is an important genetic basis of grain yield and its components in maize. Mol Breeding 20:41–51
  Google Scholar
• Mackay TFC (2001) The genetic architecture of quantitative traits. Annu Rev Genet 33:303–339
  Google Scholar
• Malosetti M, Boer MP, Bink MCAM, van Eeuwijk FA (2006) Multi-trait QTL analysis based on mixed models with parsimonious covariance matrices. In: Proceedings of the 8th world congress on genetics applied to livestock production, August 13–18, Belo Horizonte, MG, Brasil. http://www.wcgalp8.org.br/wcgalp8. Article 25–04
• Malosetti M, Ribaut JM, Vargas M, Crossa J, van Eeuwijk FA (2008) A multi-trait multi-environment QTL mixed model with an application to drought and nitrogen stress trials in maize (Zea mays L.). Euphytica 161:241–257
  Google Scholar
• Malosetti M, Voltas J, Romagosa I, Ullrich SE, van Eeuwijk FA (2004) Mixed models including environmental covariables for studying QTL by environment interaction. Euphytica 137:139–145
  CAS Google Scholar
• Manly KF, Olson JM (1999) Overview of QTL mapping software and introduction to map manager QTL. Mamm Genome 10:327–334
  PubMed CAS Google Scholar
• Mauricio R (2001) Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nat Rev Genet 2:370–381
  PubMed CAS Google Scholar
• Martinez O, Curnow RN (1992) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480–488
  Google Scholar
• Massman J, Cooper B, Horsley R, Neate S, Dill-Macky R, Chao S, Dong Y, Schwarz P, Muehlbauer GJ, Smith KP (2011) Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm. Mol Breeding 27:439–454
  Google Scholar
• McMullen MD, Stephen K, Hector SV, Peter B et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740
  PubMed CAS Google Scholar
• Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
  PubMed CAS Google Scholar
• 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
  PubMed CAS Google Scholar
• Meuwissen THE, Goddard ME (2004) Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genet Sel Evol 36:261–279
  PubMed CAS Google Scholar
• Meyer RC, Steinfath M, Lisec J et al (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci USA 104:4759–4764
  PubMed CAS Google Scholar
• Michelmore WR, Paran I, Kesseli RV (1991) Identification of marker linked to diseases resistance genes by bulked segregant analysis, a rapid method to detect the markers in specific genetic region by using the segregating population. Proc Natl Acad Sci USA 88:9828–9832
  PubMed CAS Google Scholar
• Michelmore RW (2003) The impact zone: genomics and breeding for durable disease resistance. Curr Opin Plant Biol 6:397–404
  PubMed Google Scholar
• Miedaner T, Wurschum T, Maurer HP, Korzun V, Ebmeyer E, Reif JC (2011) Association mapping for Fusarium head blight resistance in European soft winter wheat. Mol Breeding 28:647–655
  Google Scholar
• Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012) Genetic dissection of grain weight in bread wheat through quantitative trait locus interval and association mapping. Mol Breeding 29:963–972
  Google Scholar
• Mohan A, Kulwal PL, Singh S, Kumar V, Mir RR, Kumar J, Prasad M, Balyan HS, Gupta PK (2009) Genome-wide QTL analysis for pre-harvest sprouting tolerance in bread wheat. Euphytica 168:319–329
  CAS Google Scholar
• Moncada P, Martinez CP, Borrero J, Chatel M, Gauch Jr-H, Guimareaes E, Tohmem J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52
  CAS Google Scholar
• Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969–977
  PubMed CAS Google Scholar
• Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13:85–96
  CAS Google Scholar
• 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
  PubMed CAS Google Scholar
• Narasimhamoorthy B, Gill BS, Fritz AK, Nelson JC, Brown-Guedira GL (2006) Advanced backcross QTL analysis of a hard winter wheat × synthetic wheat population. Theor Appl Genet 112:787–796
  PubMed CAS Google Scholar
• Nelson JC (1997) QGENE: software for marker-based genomic analysis and breeding. Mol Breeding 3:239–245
  CAS Google Scholar
• Neumann K, Kobiljski B, Dencic S, Varshney RK, Borner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breeding 27:37–58
  Google Scholar
• Nishimura A, Ashikari M, Lin S, Takashi T, Angeles ER, Yamamoto T, Matsuoka M (2005) Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. Proc Natl Acad Sci USA 102:11940–11944
  PubMed CAS Google Scholar
• Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456:720–723
  PubMed CAS Google Scholar
• Norton GJ, Aitkenhead MJ, Khowaja FS, Whalley WR, Price AH (2008) A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. Genomics 92:344–352
  PubMed CAS Google Scholar
• Peleg Z, Fahima T, Korol AB, Abbo S, Saranga Y (2011) Genetic analysis of wheat domestication and evolution under domestication. J Expt Bot 62:5051–5061
  CAS Google Scholar
• Peng J, Ronin Y, Fahima T, Roder MS, Li Y, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494
  PubMed CAS Google Scholar
• Perretant MR, Cadalen T, Charmet G, Sourdille P, Nicolas P, Boeuf C, Tixier MH, Branlard G, Bernard S (2000) QTL analysis of bread-making quality in wheat using a doubled haploid population. Theor Appl Genet 100:1167–1175
  CAS Google Scholar
• Piepho HP (2000) A mixed-model approach to mapping quantitative trait loci in barley on the basis of multiple environment data. Genetics 156:2043–2050
  PubMed CAS Google Scholar
• Pillen K, Zacharias A, Leon J (2003) Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor Appl Genet 105:1253–125
  Google Scholar
• Podlich DW, Winkler CR, Cooper M (2004) Mapping as you go: an effective approach for marker-assisted selection of complex traits. Crop Sci 44:1560–1571
  Google Scholar
• Poland JA, Nelson RJ (2011) In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping. Phytopath 101:290–298
  Google Scholar
• Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 11:21–29
  Google Scholar
• 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 USA 108:6893–6898
  PubMed CAS Google Scholar
• Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253
  PubMed CAS Google Scholar
• Potokina E, Druka A, Luo Z, Moscou M, Wise R, Waugh R, Kearsey M (2008a) Tissue-dependent limited pleiotropy affects gene expression in barley. Plant J 56:287–296
  PubMed CAS Google Scholar
• Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M (2008b) Gene expression quantitative trait locus analysis of 16000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. The Plant J 53:90–101
  CAS Google Scholar
• Pozzi C, Rossini L, Vecchietti A, Salamini F (2004) Gene and genome changes during domestication of cereals. In: Gupta PK, Varshney RK (eds) Cereal genomics. Springer, Berlin, pp 165–198
  Google Scholar
• Prasad M, Kumar N, Kulwal PL, Röder M, Balyan HS, Dhaliwal HS, Gupta PK (2003) QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat. Theor Appl Genet 106:659–667
  PubMed CAS Google Scholar
• Prasad M, Varshney RK, Kumar A, Balyan HS, Sharma PC, Edwards KJ, Singh H, Dhaliwal HS, Roy JK, Gupta PK (1999) A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat. Theor Appl Genet 99:341–345
  Google Scholar
• Price AH (2006) Believe it or not, QTLs are accurate. Trends Plant Sci 11:213–216
  PubMed CAS Google Scholar
• Price A, 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
  PubMed CAS Google Scholar
• Pritchard JK, Stephens M, Donnelly PJ (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
  PubMed CAS Google Scholar
• Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:843–848
  PubMed CAS Google Scholar
• Quraishi UM, Murat F, Abrouk M, Pont C, Confolent C, Oury FX, Ward J, Boros D, Gebruers K, Delcour JA, Courtin CM, Bedo Z, Saulnier L, Guillon F, Balzergue S, Shewry PR, Feuillet C, Charmet G, Salse J (2011) Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct Integr Genomics 11:71–83
  PubMed CAS Google Scholar
• Quarrie SA, Laurie DA, Zhu J, Lebreton C, Semikhodskii A, Steed A, Witsenboer H, Calestani C (1997) QTL analysis to study the association between leaf size and abscisic acid accumulation in droughted rice leaves and comparisons across cereals. Plant Mol Biol 35:155–165
  PubMed CAS Google Scholar
• Quarrie SA, Vesna LJ, Dragan K, Andy S, Sofija P (1999) Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize. J Expt Bot 50:1299–1306
  CAS Google Scholar
• Rakshit S, Rakshit A, Patil JV (2012) Multiparent intercross populations in analysis of quantitative traits. J Genet 91:111–117
  PubMed Google Scholar
• Raman H, Stodart B, Ryan PR et al (2010) Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistance. Genome 53:957–966
  PubMed CAS Google Scholar
• Rao S, Xu S (1998) Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity 81:214–224
  PubMed Google Scholar
• Rehman Arif MA, Neumann K, Nagel M, Kobiljski B, Lohwasser U, Borner A (2012) An association mapping analysis of dormancy and pre-harvest sprouting in wheat. Euphytica 188:409–417
  CAS Google Scholar
• Reif JC, Gowda M, Maurer HP, Longin CFH, Korzun V, Ebmeyer E, Bothe R, Pietsch C, Wurschum T (2011) Association mapping for quality traits in soft winter wheat. Theor Appl Genet 122:961–970
  PubMed Google Scholar
• Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146
  PubMed CAS Google Scholar
• Rockman MV, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–1078
  PubMed Google Scholar
• Rode J, Ahlemeyer J, Friedt W, Ordon F (2012) Identification of marker-trait associations in the German winter barley breeding gene pool (Hordeum vulgare L.). Mol Breeding 30:831–843
  Google Scholar
• Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023
  PubMed Google Scholar
• Rong J, Feltus FA, Waghmare VN, Pierce GJ, Chee PW, Draye X, Saranga Y, Wright RJ, Wilkins TA, May OL, Smith CW, Gannaway JR, Wendel JF, Paterson AH (2007) Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176:2577–2588
  PubMed CAS Google Scholar
• Ross-Ibarra J (2005) Quantitative trait loci and the study of plant domestication. Genetica 123:197–204
  PubMed Google Scholar
• Ross-Ibarra J, Morrell PL, Gaut BS (2007) Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci USA 104:8641–8648
  PubMed CAS Google Scholar
• Rousset M, Bonnin I, Remoue C et al (2011) Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.). Theor Appl Genet 123:907–926
  PubMed Google Scholar
• Rostoks N, Ramsay L, MacKenzie K, Cardle L et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661
  PubMed CAS Google Scholar
• Rowe HC, Hansen BG, Halkier BA, Kliebenstein DJ (2008) Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. Plant Cell 20:1199–1216
  PubMed CAS Google Scholar
• Roy JK, Smith KP, Muehlbauer GJ, Chao S, Close TJ, Steffenson BJ (2010) Association mapping of spot blotch resistance in wild barley. Mol Breeding 26:243–256
  Google Scholar
• Salunkhe AS, Poornima R, Prince KS, Kanagaraj P, Sheeba JA, Amudha K, Suji KK, Senthil A, Babu RC (2011) Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis. Mol Biotechnol 49:90–95
  PubMed CAS Google Scholar
• Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10:297–304
  PubMed CAS Google Scholar
• Salvi S, Tuberosa R (2007) Cloning QTLs in plants. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement, vol 1., Genomics approaches and platformsSpringer, Berlin, pp 207–225
  Google Scholar
• Salvi S, Sponza G, Morgante M, Tomes D, Xiaomu NX, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E, Li B, Haney CF, Radovic S, Zaina G, Rafalski J-A, Tingey SV, Miao G-H, Phillips RL, Tuberosa R (2007) Conserved non-coding genomic sequences controlling flowering time differences in maize. Proc Natl Acad Sci USA 104:11376–11381
  PubMed CAS Google Scholar
• Satagopan JM, Yandell BS, Newton MA, Osborn TC (1996) A Bayesian approach to detect quantitative trait loci using Markov Chain Monte Carlo. Genetics 144:805–816
  PubMed CAS Google Scholar
• Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560
  PubMed CAS Google Scholar
• Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422:297–302
  PubMed CAS Google Scholar
• Schauer N, Semel Y, Roessner U et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454
  PubMed CAS Google Scholar
• Seaton G, Haley CS, Knott SA, Kearsey M, Visscher PM (2002) QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18:339–34
  PubMed CAS Google Scholar
• Servin B, Stephens M (2007) Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3:e114
  PubMed Google Scholar
• Setter TL, Yan J, Warburton M, Ribaut J-M, Xu Y, Mark S, Buckler ES, Zhang Z, Gore MA (2011) Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. J Expt Bot 62:701–716
  CAS Google Scholar
• Sharma S, Xu S, Ehdaie B, Hoops A, Close TJ, Lukaszewski AJ, Waines JG (2011) Dissection of QTL effects for root traits using a chromosome arm-specific mapping population in bread wheat. Theor Appl Genet 122:759–769
  PubMed Google Scholar
• Shoemaker JS, Painter IS, Weir BS (1999) Bayesian statistics in genetics: a guide for the uninitiated. Trends Genet 15:354–358
  PubMed CAS Google Scholar
• Sillanpaa MJ, Arjas E (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148:1373–1388
  PubMed CAS Google Scholar
• Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630
  PubMed CAS Google Scholar
• Stich B, Melchinger AE (2010) An introduction to association mapping in plants. CAB Reviews 5:039
  Google Scholar
• Stich B, Piepho H-P, Schulz B, Melchinger AE (2008) Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor Appl Genet 117:947–954
  PubMed Google Scholar
• Stracke S, Haseneyer G, Veyrieras JB, Geiger HH, Sauer S, Graner A, Piepho HP (2009) Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor Appl Genet 118:259–273
  PubMed CAS Google Scholar
• Swanson-Wagner RA, DeCook R, Jia Y, Bancroft T, Ji T, Zhao X, Nettleton D, Schnable PS (2009) Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science 326:1118–1120
  PubMed CAS Google Scholar
• St.Clair DA (2010) Quantitative disease resistance and quantitative resistance loci in breeding. Annu Rev Phytopath 48:247–268
  CAS Google Scholar
• Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci USA 107:5792–5797
  PubMed CAS Google Scholar
• Sun D, Ren W, Sun G, Peng J (2011) Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm. Euphytica 178:31–43
  Google Scholar
• Szalma SJ, Buckler ES, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333
  PubMed CAS Google Scholar
• Tanhuanpää P, Kalendar R, Schulman AH, Kiviharju E (2008) The first doubled haploid linkage map for cultivated oat. Genome 51:560–569
  PubMed Google Scholar
• Tanhuanpää P, Manninen O, Kiviharju E (2010) QTLs for important breeding characteristics in the doubled haploid oat progeny. Genome 53:482–493
  PubMed Google Scholar
• Takai T, Yoshimichi F, Tatsuhiko S, Takeshi H (2005) Time-related mapping of quantitative trait loci controlling grain-filling in rice (Oryza sativa L.). J Expt Bot 56:2107–2118
  CAS Google Scholar
• Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233
  PubMed CAS Google Scholar
• Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck BT (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–222
  CAS Google Scholar
• Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203
  Google Scholar
• Tang J, Yan J, Ma X, Teng W, Wu W, Dai J, Dhillon BS, Melchinger AE, Li J (2010) Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population. Theor Appl Genet 120:333–340
  PubMed Google Scholar
• Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the a-subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927
  PubMed CAS Google Scholar
• Tinker NA, Mather DE (1995) MQTL: software for simplified composite interval mapping of QTL in multiple environments. J Quant Trait Loci 1:2
  Google Scholar
• Thomson MJ, Tai TH, McClung AM, Lai X-H, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493
  PubMed CAS Google Scholar
• Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289
  PubMed CAS Google Scholar
• 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
  PubMed CAS Google Scholar
• Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708
  PubMed CAS Google Scholar
• Truntzler M, Barrière Y, Sawkins MC, Lespinasse D, Betran J, Charcosset A, Moreau L (2010) Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes. Theor Appl Genet 121:1465–1482
  PubMed CAS Google Scholar
• Tuberosa R, Salvi S (2004) QTLs and genes for tolerance to abiotic stress in cereals. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer Academic Publishers, The Netherlands, pp 253–315
  Google Scholar
• Tuberosa R, Salvi S (2007) From QTLs to genes controlling root traits in maize. In: Spiertz JHJ, Struik PC, van Laar HH (eds) Scale and complexity in plant systems research: gene-plant-crop relations. Springer, Berlin, pp 15–24
  Google Scholar
• Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudo-response regulator _Ppd_-H1 provides adaptation to photoperiod in barley. Science 310:1031–1034
  PubMed CAS Google Scholar
• Tyagi S, Gupta PK (2012) Meta-analysis of QTLs involved in pre-harvest sprouting tolerance and dormancy in bread wheat. Triticeae Genomics Genet 3:9–24
  Google Scholar
• Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314:1298–1301
  PubMed CAS Google Scholar
• Ueda T, Sato T, Hidema J, Hirouchi T, Yamamoto K, Kumagai T, Yano M (2005) _qUVR_-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics 171:1941–1950
  PubMed CAS Google Scholar
• Utz H, Melchinger A (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2:1
  Google Scholar
• van Dyk MM, Kullan ARK, Mizrachi E, Hefer CA, van Rensburg LJ, Tschaplinski TJ, Cushman KC, Engle NE, Tuskan GA, Jones N, Kanzler A, Myburg AA (2011) Genetic dissection of transcript, metabolite, growth and wood property traits in an F2 pseudo-backcross pedigree of Eucalyptus grandis x E. urophylla. BMC Proc 5:O7
  Google Scholar
• van Eeuwijk FA, Bink MCAM, Chenu K, Chapman SC (2010) Detection and use of QTL for complex traits in multiple environments. Cur Opin Plant Biol 13:193–205
  Google Scholar
• van Ooijen JW, Maliepaard C (1996) MapQTL™ version 3.0: software for the calculation of QTL positions on genetic maps. Plant Research International, Wageningen
  Google Scholar
• Varshney RK, Paulo MJ, Grando S, van Eeuwijk FA, Keizer LCP, Guo P, Ceccarelli S, Kilian A, Baum M, Graner A (2012) Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Res 126:171–180
  Google Scholar
• Varshney RK, Prasad M, Roy JK, Kumar N, Singh H, Dhaliwal HS, Balyan HS, Gupta PK (2000) Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTLs for grain weight in bread wheat. Theor Appl Genet 100:1290–1294
  CAS Google Scholar
• Veyrieras J-B, Goffinet B, Charcosset A (2007) MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinfor 8:49
  Google Scholar
• von Zitzewitz J, Cuesta-Marcos A, Condon F, Castro AJ, Chao S, Corey A, Filichkin T, Fisk SP, Gutierrez L, Haggard K, Karsai I, Muehlbauer GJ, Smith KP, Veisz O, Hayes PM (2011) The genetics of winterhardiness in barley: perspectives from genome-wide association mapping. Plant Genome 4:76–91
  Google Scholar
• Wang DL, Zhu J, Li ZK, Paterson AH (1999) Mapping QTLs with epistatic effects and QTL × environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255–1264
  Google Scholar
• Wang H, Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley J (2005) The origin of the naked grains of maize. Nature 436:714–719
  PubMed CAS Google Scholar
• Wang M, Jiang N, Jia T, Leach L, Cockram J, Waugh R, Ramsay L, Thomas B, Luo Z (2012) Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet 124:233–246
  PubMed Google Scholar
• Wang S, Basten CJ, Zeng Z-B (2011) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm)
• Wang Y, Yao J, Zhang ZF, Zheng YL (2006b) The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs. Chin Sci Bull 51:2219–2230
  CAS Google Scholar
• Wang Y-M, Kong W-Q, Tang Z-X, Lu X, Xu C-W (2009) Bayesian statistics-based multiple interval mapping of qtl controlling endosperm traits in cereals. Acta Agron Sinica 35:1569–1575
  CAS Google Scholar
• Wen W, Mei H, Feng F, Yu S, Huang Z, Wu J, Chen L, Xu X, Luo L (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet 119:459–470
  PubMed Google Scholar
• Whitkus R, Doebley J, Lee M (1992) Comparative genome mapping of sorghum and maize. Genetics 132:1119–1130
  PubMed CAS Google Scholar
• Wisser RJ, Sun Q, Hulbert SH, Kresovich S, Nelson RJ (2005) Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance. Genetics 169:2277–2293
  PubMed CAS Google Scholar
• Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS (2005) The effects of artificial selection on the maize genome. Science 308:1310–1314
  PubMed CAS Google Scholar
• Wu W-R, Li W-M, Tang D-Z, Lu H-R, Worland AJ (1999) Time-related mapping of quantitative trait loci underlying tiller number in rice. Genetics 151:297–303
  PubMed CAS Google Scholar
• Wu R, Lin M (2006) Functional mapping—how to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 7:229–237
  PubMed CAS Google Scholar
• Wu D, Qiu L, Xu L, Ye L, Chen M et al (2011) Genetic variation of HvCBF genes and their association with salinity tolerance in Tibetan annual wild barley. PLoS ONE 6:e22938
  PubMed CAS Google Scholar
• Wu RL, Zeng Z-B (2001) Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157:899–909
  PubMed CAS Google Scholar
• Wu R, Chang-Xing M, George C (2002) Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160:779–792
  PubMed CAS Google Scholar
• Wurschum T (2012) Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet 125:201–210
  PubMed Google Scholar
• Xie C, Gessler DDG, Xu S (1998) Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method. Genetics 149:1139–1146
  PubMed CAS Google Scholar
• Xu S (2003a) Estimating polygenic effects using markers of the entire genome. Genetics 163:789–801
  PubMed CAS Google Scholar
• Xu S (2003b) Theoretical basis of the Beavis effect. Genetics 165:2259–2268
  PubMed Google Scholar
• Xu S, Jia Z (2007) Genome wide analysis of epistatic effects for quantitative traits in barley. Genetics 175:1955–1963
  PubMed CAS Google Scholar
• Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545
  PubMed CAS Google Scholar
• Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail MA, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature 442:705–708
  PubMed CAS Google Scholar
• Xu Y (2010) Molecular plant breeding. CABI, Oxfordshire
  Google Scholar
• Yan WG, Li Y, Agrama HA, Luo D, Gao F, Lu X, Ren G (2009) Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.). Mol Breeding 24:277–292
  Google Scholar
• Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484
  PubMed CAS Google Scholar
• Yao J, Wang L, Liu L, Zhao C, Zheng Y (2009) Association mapping of agronomic traits on chromosome 2A of wheat. Genetica 137:67–75
  PubMed CAS Google Scholar
• Yi N, George V, Allison DB (2003a) Stochastic search variable selection for identifying multiple quantitative trait loci. Genetics 164:1129–1138
  PubMed CAS Google Scholar
• Yi N, Xu S, Allison DB (2003b) Bayesian model choice and search strategy for mapping interacting quantitative trait loci. Genetics 165:867–883
  PubMed CAS Google Scholar
• Yi N, Banerjee S, Pomp D, Yandell BS (2007) Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits. Genetics 176:1855–1864
  PubMed Google Scholar
• Yi N, Xu Z (2002) Linkage analysis of quantitative trait loci in multiple line crosses. Genetica 114:217–230
  PubMed CAS Google Scholar
• Yoshida K, Saitoh H, Fujisawa S et al (2009) Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell 21:1573–1591
  PubMed CAS Google Scholar
• Young ND (1996) QTL mapping and quantitative disease resistance in plants. Ann Rev Phytopath 34:479–501
  CAS Google Scholar
• Youens-Clark K, Buckler E, Casstevens T, Chen C, DeClerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094
  PubMed CAS Google Scholar
• Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551
  PubMed Google Scholar
• Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160
  PubMed CAS Google Scholar
• Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2005) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
  PubMed Google Scholar
• Yu L-X, Lorenz A, Rutkoski J, Singh RP, Bhavani S, Huerta-Espino J, Sorrells ME (2011) Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet 123:1257–1268
  PubMed CAS Google Scholar
• Yu L-X, Morgounov A, Wanyera R et al (2012) Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis. Theor Appl Genet 125:749–758
  PubMed Google Scholar
• Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468
  PubMed CAS Google Scholar
• Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genet Res 74:279–289
  PubMed CAS Google Scholar
• Zhang Y-M, Gai J (2009) Methodologies for segregation analysis and QTL mapping in plants. Genetica 136:311–318
  PubMed Google Scholar
• Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW, Zhang A (2010) Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat. J Integr Plant Biol 52:996–1007
  PubMed Google Scholar
• Zhang YM, Mao Y, Xie C, Smith H, Luo L, Xu S (2005) Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.). Genetics 169:2267–2275
  PubMed CAS Google Scholar
• Zhao K, Tung C-W, Eizenga GC et al (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467
  PubMed Google Scholar
• Zheng S, Byrne PF, Bai G et al (2009) Association analysis reveals effects of wheat glutenin alleles and rye translocations on dough-mixing properties. J Cereal Sci 50:283–290
  CAS Google Scholar
• Zhou J, You A, Ma Z, Zhu L, He G (2012) Association analysis of important agronomic traits in japonica rice germplasm. Afr J Biotechnol 11:2957–2970
  Google Scholar
• Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20
  CAS Google Scholar

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