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Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population

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Abstract

Genome-wide association studies have become a wide spread method of quantitative trait locus identification for many crops, including wheat (Triticum aestivum L.). Its benefit over traditional biparental mapping approaches depends on the extent of linkage disequilibrium (LD) in natural populations. We estimated the genetic diversity, population structure, and LD decay rate in a winter wheat association mapping panel (n = 205) and identified markers associated with thousand-kernel weight (TKW) and related traits. The panel was genotyped with a high-density Illumina iSelect 90 K single nucleotide polymorphism assay. PIC values were 0.047–0.375 with a mean of 0.277. Structural analysis suggested the association mapping panel contained four subpopulations. LD decay rates extended to longer genetic distances within the D genome (11.0 cM) relative to the A and B genomes (1.5 and 1.8 cM, respectively). A total of 271 marker-trait associations (MTAs) were identified for TKW and related traits, explaining 5.49–9.86 % of variation in individual traits. Among them, 11 highly significant markers (p < 0.0001), eight stable markers and twelve multi-trait MTAs were detected. Two stable markers, Ku_c9210_105 for KL and BS00023893_51 for TKW, were detected in three environments. These MTAs could be used for developing cleaved amplified polymorphic sequence markers for molecular marker-assisted selection in wheat breeding programs.

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References

  • Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 119:507–517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Al-Maskri AH, Sajjad M, Khan SH (2012) Association mapping: a step forward to discovering new alleles for crop improvement. Int J Agric Biol 14:1537–1546

    Google Scholar 

  • Botstein D, Wlllte RL, Skolinck M (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–319

    CAS  PubMed  PubMed Central  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 23:2637–2645

    Article  CAS  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

    Article  PubMed  PubMed Central  Google Scholar 

  • Buckler ES IV, Thornsberry JM (2002) Plant molecular diversity and applications to genomics. Curr Opin Plant Biol 5:107–111

    Article  CAS  PubMed  Google Scholar 

  • Chao S, Zhang W, Akhunov E, Sherman J, Ma Y (2009) Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breed 23:23–33

    Article  CAS  Google Scholar 

  • Chen XJ, Min DH, Tauqeer AY, Hu YG (2012) Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR Markers. PLoS ONE 7:e44510

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colasuonno P, Gadaleta A, Giancaspro A, Nigro D, Giove S, Incerti O, Mangini G, Signorile A, Simeone R, Blanco A (2014) Development of a high-density SNP-based linkage map and detection of yellow pigment content QTLs in durum wheat. Mol Breed 34:1563–1578

    Article  CAS  Google Scholar 

  • Cormier F, Gouis JL, Dubreuil P, Lafarge S, Praud S (2014) A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.). Theor Appl Genet 127:2679–2693

    Article  CAS  PubMed  Google Scholar 

  • Cui F, Ding A, Li J, Zhao C, Li X, Feng D, Wang X, Wang L, Gao J, Wang H (2011) Wheat kernel dimensions: how do they contribute to kernel weight at an individual QTL? J Genet 90:409–425

    Article  PubMed  Google Scholar 

  • Cui F, Fan X, Chen M, Zhang N, Zhao C, Zhang W, Han J, Ji J, Zhao X, Yang L, Wang T, Li J (2015) QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress. Theor Appl Genet. doi:10.1007/s00122-015-2641-7

    Google Scholar 

  • Eric M, James JM, Frank AM, Benjamin N, Stephen VF (2011) Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Prog Neuro-Psychopharmacol Biol Psychiatr 35:4667–4672

    Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  CAS  PubMed  Google Scholar 

  • Gegas VC, Nazari A, Griffiths S, Simmonds J, Fish L, Orford S, Sayers L, Doonan JH, Snape JW (2010) A genetic framework for grain size and shape variation in wheat. Plant Cell 22:1046–1056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta PK, Mir RR, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genom 896451

  • Hao CY, Wang LF, Ge HM, Dong YC, Zhang XY (2011) Genetic diversity and linkage disequilibrium in chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS ONE 6:1–13

    Google Scholar 

  • Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, Noll JS, Somers DJ, Brown PD (2006) Molecular detection of QTLs for agronomic and quality traits in adoubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet 113:753–766

    Article  CAS  PubMed  Google Scholar 

  • Huang XH, Wei XH, Sang T, Zhao Q, Feng Q, Zhao Y (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Gene 42:961–967

    Article  CAS  Google Scholar 

  • Li QF, Zhang Y, Liu TT, Wang FF, Liu K, Chen JS, Tian JC (2015) Genetic analysis of kernel weight and kernel size in wheat (Triticum aestivum L.) using unconditional and conditional QTL mapping. Mol Breed 35:194

  • Liu K, Muse SV (2005) Power Marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  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. Theor Appl Genet. doi:10.1007/s00122-014-2444-2

    Google Scholar 

  • Lu YL, Yan JB, Claudia T, Guimaraes Suketoshi T, Hao ZF (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115

    Article  CAS  PubMed  Google Scholar 

  • Nyquist WE, Nyquist RJ, Baker RJ (1991) Estimation of heritability and prediction of selection response in plant populations. Crit Rev Plant Sci 10:235–254

    Article  Google Scholar 

  • Patil RM, Tamhankar SA, Oak MD, Raut AL, Honrao BK, Rao VS, Misra SC (2013) Mapping of QTL for agronomic traits and kernel characters in durum wheat (Triticum durum Desf.). Euphytica 190:117–129

    Article  Google Scholar 

  • Peng J, Ronin Y, Fahima T, Röder 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

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ramya P, Chaubal A, Kulkarni K, Gupta L, Kadoo N, Dhaliwal HS, Chhuneja P, Lagu M, Gupt P (2010) QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.). J Appl Genet 51:421–429

    Article  CAS  PubMed  Google Scholar 

  • Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, Würschum T (2011) Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet. doi:10.1007/s00122-011-1583-y

    Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 80:1516–1517

    Article  Google Scholar 

  • Sajjad M, Khan SH, Kazi AM (2012) The low down on association mapping in hexaploid wheat (Triticum aestivum L.). J. Crop Sci. Biotech. (September) 15:147–158

    Article  Google Scholar 

  • Snape JW, Foulkes MJ, Simmonds J, Leverington M, Fish LJ, Wang Y, Ciavarrella M (2007) Dissecting gene 9 environmental effects on wheat yields via QTL and physiological analysis. Euphytica 154:401–408

    Article  Google Scholar 

  • Sorrells ME, Yu J (2009) Linkage disequilibrium and association mapping in the Triticeae. In: Muehlbaucer GJ (ed) Genetics and Genomics of the Triticeae Feuillet C. Springer, Gatersleben, pp 655–683

    Chapter  Google Scholar 

  • Sukumaran S, Yu J (2014) Association mapping of genetic resources: achievements and future perspectives. Genomics of plant genetic resources. Springer, Netherlands, pp 207–235

    Chapter  Google Scholar 

  • Sukumaran S, Dreisigacker S, Lopes M, Chavez P, Reynolds MP (2014) Genome wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor Appl Genet. doi:10.1007/s00122-014-2435-3

    Google Scholar 

  • Sun XY, Wu K, Zhao Y, Kong FM, Han GZ, Jiang HM, Huang XJ, Li RJ, Wang HG, Li SS (2009) QTL analysis of kernel shape and weight using recombinant inbred lines in wheat. Euphytica 165:615–624

    Article  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  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 115:6977–6995

    Article  Google Scholar 

  • Tsilo TJ, Hareland GA, Simsek S, Chao S, Anderson JA (2010) Genome mapping of kernel characteristics in hard red spring wheat breeding lines. Theor Appl Genet 121:717–730

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Ge H, Hao C, Dong Y, Zhang X (2012) Identifying loci influencing 1,000-kernel weight in wheat by microsatellite screening for evidence of selection during breeding. PLoS ONE 7(2)

  • Wang SC, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Guedira GB, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, 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 90000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene associations. Plant Cell 16:2719–2733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC (2011) Genome-wide association mapping of agronomic traits in sugar beet. Theor Appl Genet 123:1121–1131

    Article  PubMed  Google Scholar 

  • Yao J, Wang L, Liu L, Zhao C, Zheng Y (2009) Association mapping of agronomic traits on chromosome 2A of wheat. Genetica 137:677–687

    Article  CAS  Google Scholar 

  • Zanke CD, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Neumann F, Eichhorn A, Polley A, Jaenecke C, Ganal MW, Röder MS (2015) Analysis of main effect QTL for thousand grain weight in European winter wheat (Triticum aestivum L.) by genome-wide association mapping. Frontiers. Plant Sci 6:644

    Google Scholar 

  • Zhang D, Bai G, Zhu C, Yu J, Carver BF (2010) Genetic diversity, population structure, linkage disequilibrium in U.S. elite winter wheat. Plant Genome 3:1177–1186

    Article  CAS  Google Scholar 

  • Zhang KP, Wang JJ, Zhang LY, Rong CW, Zhao FW, Peng T (2013) Association Analysis of Genomic Loci Important for Grain Weight Control in Elite Common Wheat Varieties Cultivated with Variable Water and Fertiliser Supply. PLoS ONE 8:e57853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang XY, Deng ZY, Wang YR, Li JF, Tian JC (2014) Unconditional and conditional QTL analysis of kernel weight related traits in wheat (Triticum aestivum L.) in multiple genetic backgrounds. Genetica 142:371–379

    Article  CAS  PubMed  Google Scholar 

  • Zheng BS, Le GJ, Leflon M, Rong WY, Laperche A, Brancourt HM (2010) Using probe genotypes to dissect QTL × environment interactions for grain yield components in winter wheat. Theor Appl Genet 121:1501–1517

    Article  PubMed  Google Scholar 

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Acknowledgments

This research was supported by the Shandong Provincial Agriculture Liangzhong Project Foundation of China (2014 No. 96) and National Natural Science Foundation of China (No. 31171554 and 31301315).

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    Authors and Affiliations

    1. State Key Laboratory of Crop Biology, Group of Quality Wheat Breeding of Shandong Agricultural University, Tai’an, 271018, China

      Guangfeng Chen, Han Zhang, Zhiying Deng & Jichun Tian

    2. College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023, China

      Guangfeng Chen, Dongmei Li & Mingyou Wang

    3. Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China

      Han Zhang

    4. Dezhou Academy of Agricultural Sciences, Dezhou, 253015, China

      Rugang Wu

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    1. Guangfeng Chen
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    Correspondence to Jichun Tian.

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    Guangfeng Chen and Han Zhang contributed equally to this study.

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    Chen, G., Zhang, H., Deng, Z. et al. Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population. Euphytica 212, 173–185 (2016). https://doi.org/10.1007/s10681-016-1750-y

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