Genetic characterization of the wheat association mapping initiative (WAMI) panel for dissection of complex traits in spring wheat

Theoretical and Applied Genetics

Volumn 128, Issue 3, 2015, Pages 453-464

  Lopes, M S ^a   Dreisigacker, S ^b   Pena R J ^b   Sukumaran, S ^b   Reynolds, M P ^b  

^a CIMMYT   (Turkey)

^b INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

DISSECTION; MAPPING;

ASSOCIATION MAPPING; GENE DIVERSITY; GENETIC BACKGROUNDS; GENETIC CHARACTERIZATION; GENOME-WIDE ASSOCIATION STUDIES; GENOTYPE BY ENVIRONMENTS; POPULATION STRUCTURES; SINGLE-NUCLEOTIDE POLYMORPHISM MARKERS;

GENES;

GENETIC MARKER;

CHROMOSOME MAP; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC MARKER; GENETICS; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; PLANT CHROMOSOME; PLANT GENOME; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; WHEAT;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENE-ENVIRONMENT INTERACTION; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; GENETICS, POPULATION; GENOME, PLANT; GENOTYPE; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; TRITICUM;

EID: 84925462836     PISSN: 00405752     EISSN: 14322242     Source Type: Journal    
DOI: 10.1007/s00122-014-2444-2     Document Type: Article

References (50)

1. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733. doi:10.1007/s00122-007-0603-4
2. Bennett D, Izanloo A, Edwards J, Kuchel H, Chalmers K, Tester M, Reynolds M, Schnurbusch T, Langridge P (2012a) Identification of novel quantitative trait loci for days to ear emergence and flag leaf glaucousness in a bread wheat (Triticum aestivum L.) population adapted to southern Australian conditions. Theor Appl Genet 124:697–711. doi:10.1007/s00122-011-1740-3
3. Bennett D, Reynolds M, Mullan D, Izanloo A, Kuchel H, Langridge P, Schnurbusch T (2012b) Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments. Theor Appl Genet 125:1473–1485. doi:10.1007/s00122-012-1927-2
4. Berloo RV (2008) Computer note: GGT 2.0: versatile software for visualization and analysis of genetic data. J Hered 99:232–236. doi:10.1093/jhered/esm109
5. Bonneau J, Taylor J, Parent B, Bennett D, Reynolds M, Feuillet C, Langridge P, Mather D (2013) Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat. Theor Appl Genet 126:747–761. doi:10.1007/s00122-012-2015-3
6. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
7. Cavanagh CR, Chao S, Wang HBE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Matthew Reynolds M, Lopez MS, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Nat Acad Sci 110:8062–8067
8. Chao S, Zhang W, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market class. Crop Sci 47:1018–1030. doi:10.2135/cropsci2006.06.0434
9. Chao S, Dubcovsky J, Dvorak J, Luo MC, Baezinger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED (2010) Population and genome specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genom 11:727. doi:10.1186/1471-2164-11-727
10. Charmet G, Masood-Quraishi U, Ravel C, Romeuf I, Balfourier F, Perretant MR, Joseph JL, Rakszegi M, Guillon F, Sado PE, Bedo Z, Saulnier L (2009) Genetics of dietary fibre in bread wheat. Euphytica 170:155–168. doi:10.1007/s10681-009-0019-0
11. Chen X, Min D, Yasir TA, Hu YG (2012) Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS ONE 7:e44510. doi:10.1371/journal.pone.0044510
12. 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. doi:10.1534/genetics.107.078659
13. Diaz A, Zikhali M, Turner AS, Isaac P, Laurie DA (2012) Copy number variation affecting the photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS ONE 7(3):e33234. doi:10.1371/journal.pone.0033234
14. Dodig D, Zoric M, Kobiljski B, Savic J, Kandic V, Quarrie S, Barnes J (2012) Genetic association mapping study of wheat agronomic traits under contrasting water regimes. Int J Mol Sci 13:6167–6188. doi:10.3390/ijms13056167
15. Dreisigacker S, Shewayrga H, Crossa J, Arief VN, DeLacy IH, Singh RP, Dieters MJ, Braun HJ (2012) Genetic structures of the CIMMYT international yield trial targeted to irrigation environments. Mol Breed 29:529–541. doi:10.1007/s11032-011-9569-7
16. Edae EA, Byrne PF, Haley SD, Lopes MS, Reynolds MP (2014) Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theor Appl Genet in press doi:10.1007/s00122-013-2257-8
17. Ellis MH, Spielmeyer W, Gale KR, Rebetzke GJ, Richards RA (2002) Perfect markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105:1038–1042. doi:10.1007/s00122-002-1048-4
18. Everitt B (2007) Principal component analysis. In: An R and S-Plus companion to multivariate analysis. London, Springer-Verlag pp 41–62
19. Fu DL, Szücs P, Yan LL, Helguera M, Skinner JS, Zitzewitz JV, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Gen Genomics 273:54–65. doi:10.1007/s00438-004-1095-4
20. Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15:1502–1506. doi:10.1105/tpc.150730
21. 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. doi:10.1534/genetics.107.080101
22. Lipka AE, Tian F, Wang Q, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang Z. (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics pp 1–2. doi:10.1093/bioinformatics/bts444
23. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi:10.1093/bioinformatics/bti282
24. Liu L, He ZH, Yan J, Zhang Y, Xia X, Peña RJ (2005) Allelic variation at the Glu-1 and Glu-3 loci, presence of the 1B.1R translocation, and their effects on mixographic properties in Chinese bread wheats. Euphytica 142:197–204. doi:10.1007/s10681-005-1682-4
25. Lobell DB, Schlenker W, Costa-Roberts J (2011) Climate trends and global crop production since 1980. Science 333:616–620. doi:10.1126/science.1204531
26. Lopes MS, Reynolds MP, Jalal-Kamali MR, Moussa M, Feltaous Y, Tahir ISA, Barma N, Vargas M, Mannes Y, Baum M (2012) The yield correlations of selectable physiological traits in a population of advanced spring wheat lines grown in warm and drought environments. Field Crops Res 128:129–136. doi:10.1016/j.fcr.2011.12.017
27. Lopes MS, Reynolds MP, McIntyre CL, Mathews KL, Jalal Kamali MR, Mossad M, Feltaous Y, Tahir ISA, Chatrath R, Ogbonnaya F, Baum M (2013) QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions. Theor Appl Genet 126:971–984. doi:10.1007/s00122-012-2030-4
28. Lopes MS, Rebetzke G, Reynolds M (2014) Integration of phenotyping and genetic platforms for a better understanding of wheat performance under drought. J Exp Bot in press doi:10.1093/jxb/eru384
29. Lu Y, Xu J, Yuan Z, Hao Z, Xie C, Li X, Shah T, Lan H, Zhang S, Rong T, Xu Y (2012) Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize. Mol Breeding 30:407–418. doi:10.1007/s11032-011-9631-5
30. Maccaferri M, Samguineti MC, Demontis A, El-Ahmed A, del Moral LG, Maalouf F, Nachit M, Nserallah N, Ouabbou H, Rhouma S, Royo C, Villegas D, Tuberosa R (2011) Association mapping in durum wheat grown across a broad range of water regimes. J Exp Bot 62:409–438. doi:10.1093/jxb/erq287
31. Olesen JE, Trnka M, Kersebaum KC, Skjelvåg AO, Seguin B, Peltonen-Sainio P, Rossi F, Kozyra J, Micale F (2011) Impacts and adaptation of European crop production systems to climate change. Eur J Agron 34:96–112. doi:10.1016/j.eja.2010.11.003
32. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:e190. doi:10.1371/journal.pgen.0020190
33. Pinto RS, Reynolds MP, Mathews KL, McIntyre CL, Olivares-Villegas JJ, Chapman SC (2010) Heat and drought adaptive QTL in a wheat population designed to minimize confounding. Theor Appl Genet 121:1001–1021. doi:10.1007/s00122-010-1351-4
34. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181
35. Rebetzke GJ, Rattey AR, Farquahar GD, Richards RA, Condon AG (2012) Genomic regions of canopy temperature and their genetic association with stomatal conductance and grain yield in wheat. Funct Plant Biol 40:14–33
36. Rehman Arif MA, Nagel N, Newmann K, Kobiljski B, Lohwasser U, Borner A (2012) Genetic studies of seed longevity in hexaploid wheat using segregation and association mapping approaches. Euphytica 1869:1–13. doi:10.1007/s10681-011-0471-5
37. Reynolds MP, Manes Y, Izanloo A, Langridge P (2009) Phenotyping for physiological breeding and gene discovery in wheat. Ann Appl Biol 155:309–320. doi:10.1111/j.1744-7348.2009.00351.x
38. Richards RA, Rebetzke GJ, Watt M, Condon AG, Spielmeyer W, Dolferus R (2010) Breeding for improved water–productivity in temperate cereals: phenotyping, quantitative trait loci, markers and the selection environment. Funct Plant Biol 37:1–13
39. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517. doi:10.1126/science.273.5281.1516
40. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Nat Acad Sci 81:8014–8018
41. Samonte SOPB, Wilson LT, McClung AM, Medley JC (2005) Targeting cultivars onto rice growing environments using AMMI and SREG GGE biplot analysis. Crop Sci 45:2414–2424. doi:10.2135/cropsci2004.0627
42. Schwarz EG (1978) Estimating the dimension of a model. Ann Stat 6:461–464. doi:10.1214/aos/1176344136
43. Sharma RC, Crossa J, Velu G, Huerta-Espino J, Vargas M, Payne TS, Singh RP (2012) Genetic gains for grain yield in CIMMYT spring bread wheat across international environments. Crop Sci 52:1522–1533. doi:10.2135/cropsci2011.12.0634
44. Trevaskis B, Bagnall DJ, Ellis MH, Peacock WJ, Dennis ES (2003) MADS box genes control vernalization-induced flowering in cereals. Proc Natl Acad Sci USA 100:130–13104. doi:10.1073/pnas.1635053100
45. Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland
46. Wilhelm EP, Turner AS, Laurie DA (2009) Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet 118:285–294. doi:10.1007/s00122-008-0898-9
47. Yan W, Hunt LA (2001) Interpretation of genotype x environment interaction for winter wheat yield in Ontario. Crop Sci 41:19–25. doi:10.2135/cropsci2001.41119x
48. Yan LL, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J (2004) Allelic variation at the VRN-1 promoter region in polyploid wheat. Theor Appl Genet 109:1677–1686. doi:10.1007/s00122-004-1796-4
49. Zhang P, Dreisigacker S, Melchinger AE, Reif JC, Mujeeb Kazi A, Van Ginkel M, Hoisington D, Warburton ML (2005) Quantifying novel sequence variation and selective advantage in synthetic hexaploid wheats and their backcross-derived lines using SSR markers. Mol Breed 15:1–10. doi:10.1007/s00122-004-1796-4
50. Zhang LY, Liu DC, Guo XL, Yang WL, Sun JZ, Wang DW (2011) Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genet 12:42. doi:10.1186/1471-2156-12-42