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Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat

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Abstract

We recently reported genomic regions associated with resistance to four wheat diseases and insensitivity to three Pyrenophora tritici-repentis toxins in an association mapping panel consisting of 81 diverse Canadian western spring wheat (Triticum aestivum L.) cultivars. Here, we report genomic regions and SNPs associated with days to heading, plant maturity, plant height, test weight (grain volume weight), grain yield, and grain protein content in the same population using genome-wide association studies (GWAS). The 81 spring wheat cultivars were evaluated for the above six traits across six environments and genotyped with 19,919 polymorphic SNPs and 14 gene-specific markers. Using mixed liner model and a threshold of p ≤ 3.1 × 10−4, we identified a total of 139 significant marker-trait associations that were mapped at 19 genomic regions on 11 chromosomes for heading (3 regions), maturity (2), plant height (3), test weight (3), grain yield (6), and grain protein (2). Each region consisted of clusters of markers ranging from 2 to 33 and individually explained from 4.5 to 26.1% of the phenotypic variation averaged over six environments. Some the genomic regions identified in the present study are novel, while others, such as the regions for grain protein on 1B, days to heading on 5A, plant height on 4B, and test weight on 7A, were located close to either known genes or QTLs reported in previous studies, but direct comparisons in some cases were challenging due to lack of common set of markers and reliable physical positions among the different studies. Results from this study provide additional information to wheat researchers developing improved spring wheat cultivars.

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Abbreviations

90K:

Wheat 90K SNP array

DAPC:

Discriminant analysis of principal components

DH:

Doubled haploid lines

GWAS:

Genome-wide association studies

LD:

Linkage disequilibrium

MABC:

Marker-assisted backcrossing

MARS:

Marker-assisted recurrent selection

MLM:

Mixed linear model

MTAs:

Significant marker-trait associations

NILs:

Near isogenic lines

Ptr:

Pyrenophora tritici-repentis

QTL:

Quantitative trait loci

RIL:

Recombinant inbred lines

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

References

  • Asif M, Yang RC, Navabi A, Iqbal M, Kamran A, Lara EP, Randhawa H, Pozniak C, Spaner D (2015) Mapping QTL, selection differentials, and the effect of Rht-B1 under organic and conventionally managed systems in the Attila × CDC go spring wheat mapping population. Crop Sci 55:1129–1142

    Article  Google Scholar 

  • Babiker EM, Gordon TC, Chao S, Newcomb M, Rouse MN, Jin Y, Wanyera R, Acevedo M, Brown-Guedira G, Williamson S, Bonman JM (2015) Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace. Theor Appl Genet 128:605–612

    Article  CAS  PubMed  Google Scholar 

  • Baga M, Fowler DB, Chibbar RN (2009) Identification of genomic regions determining the phenological development leading to floral transition in wheat (Triticum Aestivum L.) J Exp Bot 60:3575–3585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  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

    Article  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

    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

    Article  PubMed  PubMed Central  Google Scholar 

  • Cavanagh CR, Chao S, Wang S, Huang BE, 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, Reynolds M, da Silva ML, 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 Natl Acad Sci U S A 110:8057–8062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen F, Gao M, Zhang J, Zuo A, Shang X, Cui D (2013) Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China. BMC Plant Biol 13:199

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen H, Moakhar NP, Iqbal M, Pozniak C, Hucl P, Spaner D (2016) Genetic variation for flowering time and height reducing genes and important traits in western Canadian spring wheat. Euphytica 208:377–390

    Article  CAS  Google Scholar 

  • Chen J, Chu C, Souza EJ, Guttieri MJ, Chen X, Xu S, Hole D, Zemetra R (2012) Genome-wide identification of QTL conferring high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici) in wheat. Mol Breed 29:791–800

    Article  CAS  Google Scholar 

  • Dilbirligi M, Erayman M, Campbell BT, Randhawa HS, Baenziger PS, Dweikat I, Gill KS (2006) High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A. Genomics 88:74–87

    Article  CAS  PubMed  Google Scholar 

  • Dong L, Wang F, Liu T, Dong Z, Li A, Jing R, Mao L, Li Y, Liu X, Zhang K, Wang D (2014) Natural variation of TaGASR7-A1 affects grain length in common wheat under multiple cultivation conditions. Mol Breed 34:937–947

    Article  CAS  Google Scholar 

  • Dubcovsky J, Lijavetzky D, Appendino L, Tranquilli G (1998) Comparative RFLP mapping of Triticum monococcum genes controlling vernalization requirement. Theor Appl Genet 97:968–975

    Article  CAS  Google Scholar 

  • Elouafi I, Nachit MM (2004) A genetic linkage map of the Durum x Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits. Theor Appl Genet 108:401–413

    Article  CAS  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Emebiri LC, Oliver JR, Mrva K, Mares D (2010) Association mapping of late maturity α-amylase (LMA) activity in a collection of synthetic hexaploid wheat. Mol Breed 26:39–49

    Article  CAS  Google Scholar 

  • Ewens WJ, Spielman RS (2001) Locating genes by linkage and association. Theor Popul Biol 60:135–139

    Article  CAS  PubMed  Google Scholar 

  • Falconer DS, MacKay TFC (1996) Introduction to quantitative genetics. Longman Group Limited

  • Fowler DB, N’Diaye A, Laudenci-Chingcuanco D, Pozniak CJ (2016) Quantitative trait loci associated with phenological development, low-temperature tolerance, grain quality, and agronomic characters in wheat (Triticum aestivum L.) PLoS One 11:e0152185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Galiba G, Quarrie SA, Sutka J, Morgounov A, Snape JW (1995) RFLP mapping of the vernalization (Vrn1) and frost resistance (Fr1) genes on chromosome 5A of wheat. Theor Appl Genet 90:1174–1179

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

  • Gurung S, Mamidi S, Bonman JM, Xiong M, Brown-Guedira G, Adhikari TB (2014) Genome-wide association study reveals novel quantitative trait loci associated with resistance to multiple leaf spot diseases of spring wheat. PLoS One 9:e108179

    Article  PubMed  PubMed Central  Google Scholar 

  • Gut IG (2001) Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17:475–492

    Article  CAS  PubMed  Google Scholar 

  • Holland JB (2006) Estimating genotypic correlations and their standard errors using multivariate restricted maximum likelihood estimation with SAS Proc MIXED. Crop Sci 46:642–654

    Article  Google Scholar 

  • Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161

    Article  CAS  PubMed  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 a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.) Theor Appl Genet 113:753–766

    Article  CAS  PubMed  Google Scholar 

  • Inostroza L, Ad P, Matus I, Castillo D, Hayes P, Machado S, Corey A (2009) Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol Breed 23:365–376

    Article  Google Scholar 

  • Iqbal M, Navabi A, Salmon DF, Yang RC, Murdoch BM, Moore SS, Spaner D (2007) Genetic analysis of flowering and maturity time in high latitude spring wheat: genetic analysis of earliness in spring wheat. Euphytica 154:207–218

    Article  CAS  Google Scholar 

  • Jannink JL, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342

    Article  CAS  PubMed  Google Scholar 

  • Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:99

    Article  Google Scholar 

  • Kamran A, Iqbal M, Navabi A, Randhawa H, Pozniak C, Spaner D (2013) Earliness per se QTLs and their interaction with the photoperiod insensitive allele Ppd-D1a in the Cutler × AC Barrie spring wheat population. Theor Appl Genet 126:1965–1976

    Article  CAS  PubMed  Google Scholar 

  • Kollers S, Rodemann B, Ling J, Korzun V, Ebmeyer E, Argillier O, Hinze M, Plieske J, Kulosa D, Ganal MW, Röder MS (2014) Genome-wide association mapping of tan spot resistance (Pyrenophora tritici-repentis) in European winter wheat. Mol Breed 34:363–371

    Article  CAS  Google Scholar 

  • Kollers S, Rodemann B, Ling J, Korzun V, Ebmeyer E, Argillier O, Hinze M, Jr P, Kulosa D, Ganal MW, R\ d MS (2013) Whole genome association mapping of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.) PLoS One 8:e57500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Law CN, Sutka J, Worland AJ (1978) A genetic study of day-length response in wheat. Heredity 41:185–191

    Article  Google Scholar 

  • Liu S, Assanga SO, Dhakal S, Gu X, Tan CT, Yang Y, Rudd J, Hays D, Ibrahim AMH, Xue Q, Chao S, Devkota R, Shachter S, Huggins T, Mohammed S, Fuentealba MP (2016) Validation of chromosomal locations of 90K array single nucleotide polymorphisms in US wheat. Crop Sci 56:364–373

    Article  CAS  Google Scholar 

  • Liu Z, El-Basyoni I, Kariyawasam G, Zhang G, Fritz A, Hansen J, Marais F, Friskop A, Chao S, Akhunov E, Baenziger PS (2015) Evaluation and association mapping of resistance to tan spot and stagonospora nodorum blotch in adapted winter wheat germplasm. Plant Dis 99:1333–1341

    Article  CAS  Google Scholar 

  • Mackay TFC (2001) The genetic architecture of quantitative traits. Annu Rev Genet, pp 303–339

  • McCallum BD, DePauw RM (2008) A review of wheat cultivars grown in the Canadian prairies. Can J Plant Sci 88:649–677

    Article  Google Scholar 

  • McCartney CA, Somers DJ, Lukow O, Ames N, Noll J, Cloutier S, Humphreys DG, McCallum BD (2006) QTL analysis of quality traits in the spring wheat cross RL4452 x ‘AC domain’. Plant Breed 125:565–575

    Article  CAS  Google Scholar 

  • Mengistu N, Baenziger PS, Eskridge KM, Dweikat I, Wegulo SN, Gill KS, Mujeeb-Kazi A (2012) Validation of QTL for grain yield-related traits on wheat chromosome 3A using recombinant inbred chromosome lines. Crop Sci 52:1622–1632

    Article  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 Breed 29:963–972

    Article  Google Scholar 

  • Miura H, Worland AJ (1994) Genetic control of vernalization, day-length response, and earliness per se by homoeologous group-3 chromosomes in wheat. Plant Breed 113:160–169

    Article  Google Scholar 

  • Mwadzingeni L, Shimelis H, Rees DJG, Tsilo TJ (2017) Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions. PLoS One 12:e0171692

    Article  PubMed  PubMed Central  Google Scholar 

  • Narasimhamoorthy B, Gill BS, Fritz AK, Nelson JC, Brown-Guedira GL (2006) Advanced backcross QTL analysis of a hard winter wheat x synthetic wheat population. Theor Appl Genet 112:787–796

    Article  CAS  PubMed  Google Scholar 

  • Oury F-X, Godin C (2007) Yield and grain protein concentration in bread wheat: how to use the negative relationship between the two characters to identify favourable genotypes? Euphytica 157:45–57

    Article  CAS  Google Scholar 

  • Pánková K, Milec Z, Simmonds J, Leverington-Waite M, Fish L, Snape JW (2008) Genetic mapping of a new flowering time gene on chromosome 3B of wheat. Euphytica 164:779–787

    Article  Google Scholar 

  • Perez-Lara E, Semagn K, Chen H, Iqbal M, N’Diaye A, Kamran A, Navabi A, Pozniak C, Spaner D (2016) QTLs associated with agronomic traits in the Cutler × AC Barrie spring wheat mapping population using single nucleotide polymorphic markers. PLoS One 11:e0160623

    Article  PubMed  PubMed Central  Google Scholar 

  • Perez-Lara E, Semagn K, Chen H, Tran AN, Ciechanowska I, Iqbal M, N’Diaye A, Pozniak C, Strelkov SE, Hucl PJ, Graf RJ, Randhawa H, Spaner D (2017a) Allelic variation and effects of 16 candidate genes on disease resistance in western Canadian spring wheat cultivars. Mol Breed 37:23

    Article  Google Scholar 

  • Perez-Lara E, Semagn K, Tran AN, Ciechanowska I, Chen H, Iqbal M, N’Diaye A, Pozniak C, Strelkov SE, Hucl PJ, Graf RJ, Randhawa H, Spaner D (2017b) Population structure and genomewide association analysis of resistance to disease and insensitivity to Ptr toxins in Canadian spring wheat using 90K SNP array. Crop Sci 57:1522–1539

    Article  Google Scholar 

  • Plessis A, Ravel C, Bordes J, Fc B, Martre P (2013) Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. J Exp Bot 64:3627–3644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poland J, Endelman J, Dawson J, Rutkoski J, Wu SY, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells M, Jannink JL (2012) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113

    Article  CAS  Google Scholar 

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81

  • Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusić D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti MC, Hollington PA, Aragués R, Royo A, Dodig D (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring x SQ1 and its use to compare QTLs for grain yield across a range of environments. Theor Appl Genet 110:865–880

    Article  CAS  PubMed  Google Scholar 

  • Racedo J, Gutiérrez L, Perera MF, Ostengo S, Pardo EM, Cuenya MI, Welin B, Castagnaro AP (2016) Genome-wide association mapping of quantitative traits in a breeding population of sugarcane. BMC Plant Biol 16:1–16

    Article  Google Scholar 

  • Ramya P, Chaubal a KK, Gupta L, Kadoo N, Dhaliwal HS, Chhuneja P, Lagu M, Gupta V (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 

  • Randhawa HS, Asif M, Pozniak C, Clarke JM, Graf RJ, Fox SL, Humphreys DG, Knox RE, DePauw RM, Singh AK, Cuthbert RD, Hucl P, Spaner D (2013) Application of molecular markers to wheat breeding in Canada. Plant Breed 132:458–471

    CAS  Google Scholar 

  • Rehman Arif MA, Nagel M, Neumann K, Kobiljski B, Lohwasser U, Börner A (2012a) Genetic studies of seed longevity in hexaploid wheat using segregation and association mapping approaches. Euphytica 186:1–13

    Article  Google Scholar 

  • Rehman Arif MA, Neumann K, Nagel M, Kobiljski B, Lohwasser U, Börner A (2012b) An association mapping analysis of dormancy and pre-harvest sprouting in wheat. Euphytica 188:409–417

    Article  CAS  Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517

    Article  CAS  PubMed  Google Scholar 

  • Rousset M, Bonnin I, Remoué C, Falque M, Rhoné B, Veyrieras JB, Madur D, Murigneux A, Balfourier F, Le Gouis J, Santoni S, Goldringer I (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

    Article  PubMed  Google Scholar 

  • Rustgi S, Shafqat MN, Kumar N, Baenziger PS, Ali ML, Dweikat I, Campbell BT, Gill KS (2013) Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes. PLoS One 8:e70526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sajjad M, Khan SH, Ahmad MQ, Rasheed A, Mujeeb-Kazi A, Khan IA (2014) Association mapping identifies QTLS on wheat chromosome 3A for yield related traits. Cereal Res Commun 42:177–188

    Article  CAS  Google Scholar 

  • Sansaloni C, Petroli C, Jaccoud D, Carling J, Detering F, Grattapaglia D, Kilian A (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5:P54

    Article  PubMed Central  Google Scholar 

  • Scarth R, Law CN (1983) The location of the photoperiod gene, Ppd-B1 and an additional genetic factor for ear-emergence time on chromosome 2B of wheat. Heredity 51:607–619

    Article  Google Scholar 

  • Semagn K, Bjornstad A, Xu Y (2010) The genetic dissection of quantitative traits in crops. Electron J Biotechnol 13. https://doi.org/10.2225/vol2213-issue2225-fulltext-2214

  • Shewry PR, Halford NG, Tatham AS (1992) High molecular weight subunits of wheat glutenin. J Cereal Sci 15:105–120

    Article  CAS  Google Scholar 

  • Sobrino B, Brion M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194

    Article  CAS  PubMed  Google Scholar 

  • Sukumaran S, Dreisigacker S, Lopes M, Chavez P, Reynolds MP (2015) 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

    Article  CAS  PubMed  Google Scholar 

  • Syvanen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Rev Genet 2:930–942

    Article  CAS  PubMed  Google Scholar 

  • Tadesse W, Ogbonnaya FC, Jighly A, Sanchez-Garcia M, Sohail Q, Rajaram S, Baum M (2015) Genome-wide association mapping of yield and grain quality traits in winter wheat genotypes. PLoS One 10:e0141339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian J, Deng Z, Zhang K, Yu H, Jiang X, Li C (2015) Genetic analyses of wheat and molecular marker-assisted breeding. Science Press, Springer, Bejing

    Book  Google Scholar 

  • Vazquez JF, Ruiz M, Nieto-Taladriz MT, Albuquerque MM (1996) Effects on gluten strength of low Mr glutenin subunits coded by alleles at Glu-A3 and Glu-B3 loci in durum wheat. J Cereal Sci 24:125–130

    Article  CAS  Google Scholar 

  • Wang S, Dvorkin D, Da Y (2012) SNPEVG: a graphical tool for GWAS graphing with mouse clicks. BMC Bioinformatics 13:1–6

    Article  Google Scholar 

  • Wang S, 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, Brown-Guedira G, 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 90,000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilhelm EP, Turner AS, Laurie DA (2009) Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.) Theor Appl Genet 118:285–294

    Article  CAS  PubMed  Google Scholar 

  • Wu X, Chang X, Jing R (2012) Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS One 7:e31249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci 103:19581–19586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A 100:6263–6268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoshida T, Nishida H, Zhu J, Nitcher R, Distelfeld A, Akashi Y, Kato K, Dubcovsky J (2010) Vrn-D4 is a vernalization gene located on the centromeric region of chromosome 5D in hexaploid wheat. Theor Appl Genet 120:543–552

    Article  CAS  PubMed  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

    Article  PubMed  PubMed Central  Google Scholar 

  • Zanke CD, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Neumann K, Ganal MW, Röder MS (2014) Whole genome association mapping of plant height in winter wheat (Triticum aestivum L). PLoS One 9:e113287

    Article  PubMed  PubMed Central  Google Scholar 

  • Zegeye H, Rasheed A, Makdis F, Badebo A, Ogbonnaya FC (2014) Genome-wide association mapping for seedling and adult plant resistance to stripe rust in synthetic hexaploid wheat. PLoS One 9:e105593

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Mao X, Zhang J, Chang X, Wang C, Jing R (2011) Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat. Genetica 139:743–753

    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

  • Zou J, Semagn K, Iqbal M, N’Diaye A, Chen H, Asif M, Navabi A, Perez-Lara E, Pozniak C, Yang RC, Randhawa H, Spaner D (2017a) Mapping QTLs controlling agronomic traits in the Attila x CDC Go spring wheat population under organic management using 90K SNP array. Crop Sci 365–377

  • Zou J, Semagn K, Iqbal M, N’Diaye A, Chen H, Asif M, Navabi A, Perez-Lara E, Pozniak C, Yang RC, Randhawa H, Spaner D (2017b) QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management. PLoS One 12:e0171528

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors would like to thank Klaus Strenzke and all other research technicians in Wheat Breeding group at the University of Alberta and University of Saskachewan for evaluating the population over multiple years.

Funding

This research was supported by grants to the University of Alberta wheat breeding program from the Alberta Crop Industry Development Fund, Alberta Wheat Commission, Agriculture and Agri-Food Canada, Western Grains Research Foundation Endowment Fund and Core Program check-off funds to D. Spaner. This work was conducted in part within the project “Canadian Triticum Advancement Through Genomics (CTAG).” We would like to acknowledge CTAG funding provided by the Saskatchewan Ministry of Agriculture, Western Grains Research Foundation, Agriculture and Agri-Food Canada, Genome Canada, Genome Prairie, Genome Alberta and Alberta Innovates. The study was also supported by the Chinese Government Scholarship to Hua Chen.

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Authors and Affiliations

  1. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada

    Hua Chen, Kassa Semagn, Muhammad Iqbal, Neshat Pazooki Moakhar & Dean Spaner

  2. National Agricultural Research Centre, National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan

    Muhammad Iqbal

  3. Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada

    Teketel Haile, Amidou N’Diaye, Pierre Hucl & Curtis Pozniak

  4. Alberta Agriculture and Rural Development, Edmonton, Canada

    Rong-Cai Yang

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  1. Hua Chen
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  8. Pierre Hucl
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  9. Curtis Pozniak
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  10. Dean Spaner
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Correspondence to Dean Spaner.

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Chen, H., Semagn, K., Iqbal, M. et al. Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat. Mol Breeding 37, 141 (2017). https://doi.org/10.1007/s11032-017-0741-6

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  • DOI: https://doi.org/10.1007/s11032-017-0741-6

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