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Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments

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Abstract

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Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum).

Abstract

Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m2. The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated.

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Abbreviations

GWAS:

Genome-wide association study

SNP:

Single nucleotide polymorphism

LD:

Linkage disequilibrium

References

  • Bradbury PJ, Zhang Z, Kroon DE et al (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635. doi:10.1093/bioinformatics/btm308

    Article  CAS  PubMed  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177. doi:10.1534/genetics.105.044586

    Article  PubMed Central  PubMed  Google Scholar 

  • Chao S, Dubcovsky J, Dvorak J et al (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

    Article  CAS  Google Scholar 

  • Cossani CM, Reynolds MP (2012) Physiological traits for improving heat tolerance in wheat. Plant Physiol 160:1710–1718. doi:10.1104/pp.112.207753

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Curtis T, Halford NG (2014) Food security: the challenge of increasing wheat yield and the importance of not compromising food safety. Ann Appl Biol. doi:10.1111/aab.12108

    PubMed Central  PubMed  Google Scholar 

  • Dhaliwal AS, Mares DJ, Marshall DR (1987) Effect of 1B-1R chromosome translocation on milling and quality characteristics of bread wheats. Cereal Chem 64:72–76

    Google Scholar 

  • Dodig D, Zoric M, Kobiljski B et al (2012) Genetic and association mapping study of wheat agronomic traits under contrasting water regimes. Int J Mol Sci 13:6167–6188. doi:10.3390/ijms13056167

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dreisigacker S, Tiwari R, Sheoran S (2013) Laboratory manual: ICAR-CIMMYT molecular breeding course in wheat. ICAR/BMZ/CIMMYT, Haryana, India, p 36

  • Edae EA, Byrne PF, Manmathan H, Haley SD, Moragues M, Lopes MS, Reynolds MP (2013) Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat. Plant Genome 6(2). doi:10.3835/plantgenome2013.04.0010

  • 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 127(4):791–807. doi:10.1007/s00122-013-2257-8

    PubMed  Google Scholar 

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620. doi:10.1046/j.1471-8286.2002.00305.x

    Article  Google Scholar 

  • Heidari B, Saeidi G, SayedTabatabaei BE, Suenaga K (2012) QTLs involved in PH, peduncle length and heading date of wheat (Triticum aestivum L.). J Agric Sci Technol 14(5):1090–1104

    Google Scholar 

  • Hoffmann B (2008) Alteration of drought tolerance of winter wheat caused by translocation of rye chromosome segment 1RS Cereal Research Communications. Cereal Res Commun 36(2):269–278. doi:10.1556/CRC.36.2008.2.7

    Article  Google Scholar 

  • Jackson RD, Reginato RJ, Idso SB (1977) Wheat canopy temperature: a practical tool for evaluating water requirements. Water Resour Res 13:651. doi:10.1029/WR013i003p00651

    Article  Google Scholar 

  • 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 28(18):2397–2399

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129. doi:10.1093/bioinformatics/bti282

    Article  CAS  PubMed  Google Scholar 

  • Loiselle BA, Sork VL, Nason JD, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82:1420–1425. doi:10.2307/2445869

    Article  Google Scholar 

  • Lopes MS, Reynolds MP, Jalal-Kamali MR, Moussa M, Feltaous Y, Tahir ISA, Barma N, Vargas M, Mannes Y, Baum, M (2012a) The yield correlations of selectable physiological traits in a population of advanced spring wheat lines grown in warm and drought environments. Field Crop Res 128:129–136

    Article  Google Scholar 

  • Lopes MS, Reynolds MP, Manes Y et al (2012b) Genetic yield gains and changes in associated traits of CIMMYT spring bread wheat in a “historic” set representing 30 years of breeding. Crop Sci 52:1123. doi:10.2135/cropsci2011.09.0467

    Article  Google Scholar 

  • Lopes MS, Reynolds MP, McIntyre CL et al (2012c) 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. doi:10.1007/s00122-012-2030-4

    PubMed  Google Scholar 

  • Lopes MS, Dreisigacker S, Peña RJ, Sukumaran S, Reynolds MP (2014) Genetic characterization of the Wheat Association Mapping Initiative (WAMI) panel for dissection of complex traits in spring wheat (submitted)

  • Malik R, Tiwari R, Arora A, Kumar P, Sheoran S, Sharma P, Singh R, Sharma I (2013) Genotypic characterization of elite Indian wheat genotypes using molecular markers and their pedigree analysis. Aust J Crop Sci 7(5):561

    Google Scholar 

  • Mason RE, Hays DB, Mondal S et al (2013) QTL for yield, yield components and canopy temperature depression in wheat under late sown field conditions. Euphytica 194:243–259. doi:10.1007/s10681-013-0951-x

    Article  Google Scholar 

  • Pask AJD, Pietragalla J, Mullan, Reynolds MP (eds) (2012) Physiological breeding II: a field guide to wheat phenotyping. International Wheat and Maize Improvement Centre (CIMMYT), DF, Mexico

    Google Scholar 

  • Pearson K (1901) LIII. On lines and planes of closest fit to systems of points in space. Philos Mag Ser 6(2):559–572. doi:10.1080/14786440109462720

    Article  Google Scholar 

  • Pena RJ, Amaya A, Rajaram S, Mujeeb-Kazi A (1990) Variation in quality characteristics associated with some spring 1B/1R translocation wheats. J Cereal Sci 12:105–112. doi:10.1016/S0733-5210(09)80092-1

    Article  Google Scholar 

  • Pinto RS, Reynolds MP, Mathews KL et al (2010) Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects. Theor Appl Genet 121:1001–1021. doi:10.1007/s00122-010-1351-4

    Article  PubMed Central  PubMed  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. doi:10.1073/pnas.1010894108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. doi:10.1111/j.1471-8286.2007.01758.x

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rashid A, Stark JC, Tanveer A, Mustafa T (1999) Use of canopy temperature measurements as a screening tool for drought tolerance in spring wheat. J Agron Crop Sci 182:7. doi:10.1046/j.1439-037x.1999.00335.x

    Google Scholar 

  • Reynolds MP, Singh RP, Ibrahim A et al (1998) Evaluating physiological traits to complement empirical selection for wheat. Euphytica 100:85–94. doi:10.1023/A:1018355906553

    Article  Google Scholar 

  • Risch N, Merikangas K (1996) The Future of Genetic Studies of Complex Human Diseases. Science 80(273):1516–1517. doi:10.1126/science.273.5281.1516

    Article  Google Scholar 

  • 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 Natl Acad Sci 81(24):8014–8018

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Saint Pierre C, Crossa J, Manes Y, Reynolds MP (2010) Gene action of canopy temperature in bread wheat under diverse environments. Theor Appl Genet 120:1107–1117. doi:10.1007/s00122-009-1238-4

    Article  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. doi:0737-4038/87/0404-0007$02.00

  • SAS Institute (2000) SAS 9.1.3 help and documentation. SAS Institute Inc, Cary

    Google Scholar 

  • Sharma RC, Crossa J, Velu G et al (2012) Genetic gains for YLD in CIMMYT spring bread wheat across international environments. Crop Sci 52:1522. doi:10.2135/cropsci2011.12.0634

    Article  Google Scholar 

  • Snape JW, Foulkes MJ, Simmonds J et al (2007) Dissecting gene × environmental effects on wheat yields via QTL and physiological analysis. Euphytica 154:401–408. doi:10.1007/s10681-006-9208-2

    Article  Google Scholar 

  • Sukumaran S, Yu J (2014) Association mapping of genetic resources: achievements and future perspectives. In: Genomics of plant genetic resources, Springer, Netherlands, pp 207–235. doi: 10.1007/978-94-007-7572-5_9

  • Sukumaran S, Xiang W, Bean SR et al (2012) Association mapping for grain quality in a diverse sorghum collection. Plant Genome J 5:126. doi:10.3835/plantgenome2012.07.0016

    Article  CAS  Google Scholar 

  • Sylvester-Bradley R, Lunn G, Foulkes J, Shearman V, Spink J, Ingram J (2002) Management strategies for high yields of cereals and oilseed rape. In: HGCA R and D conference-agronomic intelligence: the basis for profitable production, pp 8–1

  • Wang S, Wong D, Forrest K, Allen A, Chao S, Huang E, Maccaferri M, Salvi S, Milner S, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, IWGSC, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnol J (in press)

  • Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Assoc Sunderl MA 376. doi:10.1111/j.1365-2052.2009.01970.x

  • Wieser H, Kieffer R, Lelley T (2000) The influence of 1B/1R chromosome translocation on gluten protein composition and technological properties of bread wheat. J Sci Food Agric 80:1640–1647. doi:10.1002/1097-0010(20000901)80:11<1640:AID-JSFA688>3.0.CO;2-4

    Article  CAS  Google Scholar 

  • Würschum T, Langer SM, Longin CFH et al (2013) Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet 126:1477–1486. doi:10.1007/s00122-013-2065-1

    Article  PubMed  Google Scholar 

  • Yu J, Pressoir G, Briggs WH et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208. doi:10.1038/ng1702

    Article  CAS  PubMed  Google Scholar 

  • Yu L-X, Lorenz A, Rutkoski J et al (2011) Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet 123:1257–1268. doi:10.1007/s00122-011-1664-y

    Article  CAS  PubMed  Google Scholar 

  • Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome J 1:5. doi:10.3835/plantgenome2008.02.0089

    Article  CAS  Google Scholar 

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Acknowledgments

We would like to thank Araceli Torres, Yei Nayeli Quiche, and Mayra Jacqueline Barcelo for help in data collection. Mike Listman of CIMMYT provided editorial input. Financial support is acknowledged from ADAPTAWHEAT consortium and SAGARPA.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT Int.), Apdo. Postal 6‑641, 06600, Mexico, DF, Mexico

    Sivakumar Sukumaran, Susanne Dreisigacker, Perla Chavez & Matthew P. Reynolds

  2. CIMMYT, PO Box 39, Emek, Ankara, 06511, Turkey

    Marta Lopes

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  1. Sivakumar Sukumaran
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  2. Susanne Dreisigacker
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  3. Marta Lopes
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  4. Perla Chavez
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  5. Matthew P. Reynolds
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Correspondence to Sivakumar Sukumaran.

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Communicated by Mark E. Sorrells.

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Sukumaran, S., Dreisigacker, S., Lopes, M. et al. Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor Appl Genet 128, 353–363 (2015). https://doi.org/10.1007/s00122-014-2435-3

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