Family-based association mapping in crop species

Theoretical and Applied Genetics

Volumn 126, Issue 6, 2013, Pages 1419-1430

  Guo, Baohong ^a   Wang, Daolong ^a   Guo, Zhigang ^a   Beavis, William D ^b  

^a SYNGENTA BIOTECHNOLOGY INC   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELIC VARIANTS; ASSOCIATION MAPPING; LINKAGE DISEQUILIBRIUM; MOLECULAR GENETICS; NATURAL SELECTION; NEXT-GENERATION SEQUENCING; TECHNICAL ADVANCEMENT; TECHNOLOGICAL ADVANCEMENT;

AGRONOMY; CHROMOSOMES; GENETIC ENGINEERING;

GENES;

AGRICULTURE; BREEDING; CROP; CROSS BREEDING; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETICS; HUMAN; METHODOLOGY; POPULATION GENETICS; REVIEW; SPECIES DIFFERENCE;

AGRICULTURE; BREEDING; CROPS, AGRICULTURAL; CROSSES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; HUMANS; LINKAGE DISEQUILIBRIUM; SPECIES SPECIFICITY;

EID: 84878347234     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-013-2100-2     Document Type: Review

References (60)

1. Abecasis GR, Cardon LR, Cookson WOC (2000) A general test of association for quantitative traits in nuclear families. Am J Hum Genet 66: 279-292.
2. Allison DB, Heo M, Kaplan N, Martin ER (1999) Sibling based tests of linkage and association for quantitative traits. Am J Hum Genet 64: 1754-1764.
3. Anderson L, Georges M (2004) Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genetics 5: 202-212.
4. 2 plants. Theor Appl Genet 119: 255-262.
5. Bernardo R (2010) Breeding for quantitative traits in plants. Stemma Press, Minnesota.
6. 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.
7. Bordes J, Dumas de Vaul R, Lapierre A, Pollacsek M (1997) Haplodiploidization of maize (Zea mays L.) through induced gynogenesis assisted by glossy markers and its use in breeding. Agronomie 17: 291-297.
8. Buckler E, Gore M (2007) An Arabidopsis haplotype map takes root. Nat Genet 39: 1056-1057.
9. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C et al (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
10. Burdick JT, Chen W, Abecasis GR, Cheung VG (2006) In silico method for inferring genotypes in pedigrees. Nat Genet 38: 1002-1004.
11. Burgueno J, Campos G, Weigel K, Crossa J (2012) Genomic prediction of breeding values when modeling genotype x environment interaction using pedigree and dense molecular markers. Crop Sci 52: 707-719.
12. Chase SS (1951) Production of homozygous diploids of maize from monoploids. Agron J 44: 263-267.
13. Churchill GA et al (2004) The collaborative cross: a community resource for the genetic analysis of complex traits. Nat Genet 36d: 1133-1137.
14. Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole genome sequencing. Nat Rev Genet 11: 415-425.
15. Darvasi A, Weinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134: 943-951.
16. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB (2010) Rare variants create synthetic genome wide associations. PLoS Biol 6: e1000294.
17. Farnir F, Grisart B, Coppieters W, Riquet J, Berzi P, Cambisano N, Karim L et al (2002) Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred hal-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14. Genetics 161: 275-287.
18. Fulker DW, Cherny SS, Sham PC, Hewitt JK (1999) Combined linkage and association sib-pair analysis for quantitative traits. Am J Hum Genet 64: 259-267.
19. Gale MD, Youssefian S (1985) Dwarfing genes in wheat. In: Russell GE (ed) Progress in plant breeding 1. Butterworths, London, pp 1-35.
20. George AW, Visscher PM, Haley CS (2000) Mapping quantitative trait loci in complex pedigree: a two- step variance component approach. Genetics 156: 2081-2092.
21. Guo B, Beavis WD (2011) In silico genotyping of the maize nested association mapping population. Mol Breed 27: 107-113.
22. Guo B, Sleper DA, Sun J, Nguyen HT, Arelli PR, Shannon JG (2006) Pooled analysis of data from multiple quantitative trait locus mapping populations. Theor Appl Genet 113: 39-48.
23. Guo B, Sleper DA, Beavis WD (2010) Nested association mapping for identification of functional markers. Genetics 186: 373-383.
24. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 89: 315-324.
25. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108.
26. Horvath S, Xu X, Lake SL, Silverman EK, Weiss ST, Laird NM (2004) Family based tests for associating haplotypes with general phenotype data: application to asthma genetics. Genet Epidemiol 26: 61-69.
27. 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.
28. International Hapmap Consortium (2003) The international HapMap project. Nature 426: 789-796.
29. 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.
30. Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM et al (2012) Exome sequencing and the genetic basis of complex traits. Nat Genet 44: 623-630.
31. Kingsmore SF, Lindquist IE, Mudge J, Gesler DD, Beavis WD (2008) Genome-wide association studies: progress and potential for drug discovery and development. Nat Rev Drug Discov 7: 221-230.
32. Kump KL, Bradbury PJ, Buckler ES, Belcher AR, Oropeza-Rosas M et al (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163-168.
33. Laird NM, Lange C (2006) Family based designs in the age of large scale gene association studies. Nat Rev Genetics 7: 385-394.
34. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SM, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059.
35. Lander ES, Bostein (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
36. Lange C, DeMeo DL, Laird NM (2002) Power and design considerations for a general class of family based association tests: quantitative traits. Am J Hum Genet 71: 1330-1341.
37. Lee SH, Werf JHJ (2004) The efficiency of designs for fine mapping of quantitative trait loci using combined linkage disequilibrium and linkage. Genet Sel Evol 36: 145-161.
38. Li R, Lyons MA, Wittenburg H, Paigen B, Churchill GA (2005) Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping. Genetics 169: 1699-1709.
39. Lund MS, Sorensen P, Guldbrandtsen B, Sorensen DA (2003) Multi fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis. Genetics 163: 405-410.
40. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Inc, Sunderland.
41. Martin ER, Monks SA, Warren LL, Kaplan NL (2000) A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am J Hum Genet 67: 146-154.
42. Metzker M (2010) Sequencing technologies-the next generation. Nat Rev Genetics 11: 31-46.
43. 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.
44. Monks SA, Kaplan NL (2000) Removing the sampling restrictions from family based tests of association for a quantitative trait locus. Am J Hum Genet 66: 576-592.
45. Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genetics 13: 85-96.
46. Rabinowitz D, Laird N (2000) A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum Hered 50: 211-223.
47. Rival MA, Beaudoin M, Gardet A, Stevens C, Sharma Y et al (2011) Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet 43: 1066-1073.
48. SAS Institute (2004) SAS/STAT 9. 1 user's guide. SAS institute, Cary, NC.
49. Snape JW (1988) The detection and estimation of linkage using doubled haploid or single seed descent populations. Theor Appl Genet 76: 125-128.
50. So Y, Edwards J (2011) Predictive ability assessment of linear mixed models in multi-environment trials in corn. Crop Sci 51: 542-552.
51. Stanklewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61: 437-455.
52. Steen KV, McQueen MB, Herbert A, Raby B, Lyon H et al (2005) Genomic screening and replication using the same data set in family based association testing. Nat Genet 37: 683-691.
53. Stich B, Melchinger AE, Piepho H, Heckenberger M, Manurer 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.
54. Tian F, Bradbury PJ, Brown PJ, Sun Q, Flint-Garcia S et al (2011) Genome-wide association study of maize identifies genes affecting leaf architecture. Nat Genet 43: 159-162.
55. Valdar W, Holmes CC, Mott R, Flint J (2009) Mapping in structured populations by resample model averaging. Genetics 182: 1263-1277.
56. VSN international (2010) ASReml 3. VSSN international Ltd., Hemel Hempstead.
57. Xu S (1998) Mapping quantitative trait loci using multiple families of lines crosses. Genetics 148: 517-524.
58. Yan J, Kandianis CB, Harjes CE, Bai L, Kim EH et al (2010) Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nat Genet 42: 322-327.
59. Yu J, Pressoir G, Briggs WH, Bi IV, 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.
60. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.