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Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

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Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement.

Abstract

Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

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References

  • Abeysekara NS, Friesen TL, Liu ZH, McClean PE, Faris JD (2010) Marker development and saturation mapping of the tan spot PtrToxB sensitivity locus Tsc2 in hexaploid wheat. Plant Genome 3:179–189

    Article  CAS  Google Scholar 

  • Blake NK, Lehfeldt BR, Lavin M, Talbert LE (1999) Phylogenetic reconstruction based on low copy DNA sequence data in an alloploid: the B genome of wheat. Genome 42:351–360

    Article  PubMed  CAS  Google Scholar 

  • Blanco A, Bellomo MP, Cenci A, De Giovanni C, D’Ovidio R, Iacono E, Laddomada B, Pagnotta MA, Porceddu E, Sciancalepore A, Simeone R, Tanzarella OA (1998) A genetic linkage map of durum wheat. 97:721–728

    CAS  Google Scholar 

  • Borner A, Schumann E, Furste A, Coster H, Leithold B, Roder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936

    Article  PubMed  Google Scholar 

  • Buerstmayr M, Huber K, Heckmann J, Steiner B, Nelson JC, Buerstmayr H (2012) Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum × Triticum durum. Theor Appl Genet 125:1751–1765

    Article  PubMed  PubMed Central  Google Scholar 

  • Cavanagh C, Chao S, Huang BE, Wang S, Stephen S, Forrest K, Kiani S, Saintenac C, Brown-Guedira G, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson J, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell P, Dubcovsky J, Morell M, Sorrells M, Hayden M, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landrace and cultivars. Proc Natl Acad Sci USA 110:8057–8062

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Chalupska D, Lee HY, Faris JD, Evrard A, Chalhoub B, Haselkorn R, Gornicki P (2008) Acchomoeoloci and the evolution of the wheat genomes. Proc Natl Acad Sci USA 105:9691–9696

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Chu C-G, Chao S, Friesen TL, Faris JD, Zhong S, Xu SS (2010) Identification of novel tan spot resistance QTLs using an SSR-based linkage map of tetraploid wheat. Mol Breeding 25:327–338

    Article  CAS  Google Scholar 

  • Colasuonno P, Mastrangelo AM, Blanco A, Gadaleta A (2013) Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes. BMC Genet 14:114

    Article  PubMed  PubMed Central  Google Scholar 

  • Cuthbert JL, Somers DJ, Brule-Babel AL, Brown PD, Crow GH (2008) Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor Appl Genet 117:595–608

    Article  PubMed  CAS  Google Scholar 

  • Dvorak J, Zhang HB (1990) Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc Natl Acad Sci USA 87:9640–9644

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Dvorak J, di Terlizzi P, Zhang H-B, Resta P (1993) The evolution of polyploid wheats: identification of the A genome donor species. Genome 36:21–31

    Article  PubMed  CAS  Google Scholar 

  • Dvorak J, Deal KR, Luo M-C, You FM, von Borstel K, Dehghani H (2012) The origin of spelt and free-threshing hexaploid wheat. J Hered 103:426–441

    Article  PubMed  CAS  Google Scholar 

  • 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 moister regimes. Theor Appl Genet 127:791–807

    Article  PubMed  CAS  Google Scholar 

  • Elias EM, Miller JD (1998) Registration of ‘Ben’durum wheat. Crop Sci 38:895

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Faris JD (2014) Wheat domestication: Key to agricultural revolutions past and future. In: Tuberosa R, Graner A, Frison E (ed) Genomics of plant genetic resources, vol. 1 Managing, sequensing and mining genetic resources. Springer, pp 439–464

  • Faris JD, Gill BS (2002) Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 45:706–718

    Article  PubMed  CAS  Google Scholar 

  • Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311–321

    PubMed  CAS  PubMed Central  Google Scholar 

  • Faris JD, Simons KJ, Zhang Z, Gill BS (2005) The wheat super domestication gene Q. Wheat Info Serv 100:129–148

    Google Scholar 

  • Faris JD, Zhang Z, Chao S (2014a) Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication. Gene 542:198–208

    Article  PubMed  CAS  Google Scholar 

  • Faris JD, Zhang Z, Garvin DF, Xu SS (2014b) Molecular and comparative mapping of genes governing spike compactness from wild emmer wheat. Mol Genet Genomics 289:641–651

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez-Hernandez JL, Elias EM, Kianian SF (2004) Mapping genes for grain protein concentration and grain yield on chromosome 5B of Triticum turgidum (L.) var. dicoccoides. Euphytica 139:217–225

    Article  CAS  Google Scholar 

  • Graziani M, Maccaferri M, Royo C, Salvatorelli F, Tuberosa R (2014) QTL dissection of yield components and morpho-physiological traits in a durum wheat elite population tested in contrasting thermo-pluviometric conditions. Crop Pasture Sci 65:80–95

    Google Scholar 

  • Groos C, Robert N, Bervas E, Charmet G (2003) Genetic analysis of grain protein-content, grain yield and thousand-kernel weight in bread wheat. Theor Appl Genet 106:1032–1040

    PubMed  CAS  Google Scholar 

  • Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99:8133–8138

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Jantasuriyarat C, Vales MI, Watson CJW, Riera-Lizarazu O (2004) Identification and mapping of genetic loci affecting free-threshing habit and spike compactness in wheat (Triticum aestivum L.). Theor Appl Genet 108:261–273

    Article  PubMed  CAS  Google Scholar 

  • Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789

    Article  PubMed  CAS  Google Scholar 

  • Kamran A, Iqbal M, Spaner D (2014) Flowering time in wheat (Triticum aestivum L.): a key factor for global adaptability. Euphytica 197:1–26

    Article  CAS  Google Scholar 

  • Kato K, Miura H, Sawada S (1999) QTL mapping of genes controlling ear emergence time and plant height on chromosome 5A of wheat. Theor Appl Genet 98:472–476

    Article  CAS  Google Scholar 

  • Kato K, Sonokawa R, Miura H, Sawada S (2003) Dwarfing effect associated with the threshability gene Q on wheat chromosome 5A. Plant Breed 122:489–492

    Article  CAS  Google Scholar 

  • Kerber ER, Dyck PL (1969) Inheritance in hexaploid wheat of leaf rust resistance and other characters derived from Aegilops squarossa. Can J Genet Cytol 11:639–647

    Google Scholar 

  • Kerber ER, Rowland GG (1974) Origin of the free threshing character in hexaploid wheat. Can J Genet Cytol 16:145–154

    Google Scholar 

  • Kihara H (1944) Discovery of the DD-analyzer, one of the ancestors of Triticum vulgare. Agric Hortic (Tokyo) 19:13–14

    Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Kumar S, Gill BS, Faris JD (2007) Identification and characterization of segregation distortion loci along chromosome 5B in tetraploid wheat. Mol Genet Genomics 278:187–196

    Article  PubMed  CAS  Google Scholar 

  • Li WL, Gill BS (2006) Multiple pathways for seed shattering in the grasses. Funct Integr Genomics 6:300–309

    Article  PubMed  CAS  Google Scholar 

  • Lin F, Xue SL, Tian DG, Li CJ, Cao Y, Zhang ZZ, Zhang CQ, Ma ZQ (2008) Mapping chromosomal regions affecting flowering time in a spring wheat RIL population. Euphytica 164:769–777

    Article  Google Scholar 

  • Lorieux M (2012) MapDisto: fast and efficient computation of genetic linkage maps. Mol Breeding 30:1231–1235

    Article  CAS  Google Scholar 

  • Ma Z, Zhao D, Zhang C, Zhang Z, Xue S, Lin F, Kong Z, Tian D, Luo Q (2007) Molecular genetic analysis of five spike-related traits in wheat using RIL and immortalized F2 populations. Mol Genet Genomics 277:31–42

    Article  PubMed  CAS  Google Scholar 

  • Mantovani P, Maccaferri M, Sanguineti MC, Tuberosa R, Catizone I, Wenzl P, Thomson B, Carling J, Huttner E, DeAmbrogio E, Kilian A (2008) An integrated DArT-SSR linkage map of durum wheat. Mol Breed 22:629–648

    Article  CAS  Google Scholar 

  • Marone D, Laido G, Gadaleta A, Colusuonno P, Ficco DBM, Giancaspro A, Giove S, Panio G, Russo MA, De Vita P, Cattivelli L, Papa R, Blanco A, Mastrangelo AM (2012) A high-density consensus map of A and B wheat genomes. Theor Appl Genet 125:1619–1638

    Article  PubMed  PubMed Central  Google Scholar 

  • Marza F, Bai G-H, Carver BF, Zhou W-C (2005) Quantitative trait loci for yield and related traits in the wheat population Ning7840 × Clark. Theor Appl Genet 112:688–698

    Article  PubMed  Google Scholar 

  • Matsuoka Y (2011) Evolution of polyploid Triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification. Plant Cell Physiol 52:750–764

    Article  PubMed  CAS  Google Scholar 

  • Matsuoka Y, Nasuda S (2004) Durum wheat as a candidate for the unknown female progenitor of bread wheat: an empirical study with a highly fertile F1 hybrid with Aegilopstauschii Coss. Theor Appl Genet 109:1710–1717

    Article  PubMed  Google Scholar 

  • McFadden ES, Sears ER (1946) The origin of Triticum spelta and its free-threshing hexaploid relatives. J Hered 37(81–89):107–116

    Google Scholar 

  • Mohler V, Lukman R, Ortiz-Islas S, William M, Worland AJ, Van Beem J, Wenzel G (2004) Genetic and physical mapping of photoperiod insensitive gene Ppd-B1 in common wheat. Euphytica 138:33–40

    Article  CAS  Google Scholar 

  • Muramatsu M (1963) Dosage effect of the spelta gene q of hexaploid wheat. Genetics 48:469–482

    PubMed  CAS  PubMed Central  Google Scholar 

  • Muramatsu M (1979) Presence of the vulgare gene, Q, in a dense-spike variety of Triticum dicoccum Schübl. Report of the Plant Germ-Plasm Institute, Kyoto Univ 4:39–41

    Google Scholar 

  • Muramatsu M (1985) Spike type in two cultivars of Triticum dicoccum with the spelta gene q compared with the Q-bearing variety liguliforme. Jpn J Breed 35:255–267

    Article  Google Scholar 

  • Muramatsu M (1986) The vulgare super gene, Q: its universality in durum wheat and its phenotypic effects in tetraploid and hexaploid wheats. Can J Genet Cytol 28:30–41

    Google Scholar 

  • Nalam VJ, Vales MI, Watson CJW, Kianian SF, Riera-Lizarazu O (2006) Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.). Theor Appl Genet 112:373–381

    Article  PubMed  CAS  Google Scholar 

  • Nalam VJ, Vales MI, Watson CJW, Johnson EB, Riera-Lizarazu O (2007) Map-based analysis of genetic loci on chromosome 2D that affect glume tenacity and threshability components of free-threshing habit in common wheat (Triticum aestivum L.). Theor Appl Genet 116:135–145

    Article  PubMed  Google Scholar 

  • Nesbitt M, Samuel D (1996) From staple crop to extinction? The archaeology and history of hulled wheats. In: Padulosi S, Hammer K, Heller J (eds) Hulled wheats, Promoting the conservation and use of underutilized and neglected crops 4: Proceedings of the first international workshop on hulled wheats. Castelvecchio Pascoli, Tuscany, Italy, pp 41–100

    Google Scholar 

  • Peleg Z, Fahima T, Korol AB, Abbo S, Saranga Y (2011) Genetic analysis of wheat domestication and evolution under domestication. J Exp Botany 62:5051–5061

    Article  CAS  Google Scholar 

  • Peng JH, Ronin Y, Fahima T, Roder MS, Li YC, Nevo E, Korol A (2003) Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489–2494

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Pestsova E, Ganal MW, Röder MS (2000) Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43:689–697

    Article  PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    Google Scholar 

  • Salse J, Chague V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A, Segurens B, Charles M, Ravel C, Samain S, Charmet G, Boudet N, Chalhoub B (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genom 9:555

    Article  Google Scholar 

  • SAS Institute (2011) SAS/STAT 9.3 User’s Guide. SAS Institute Inc., Cary, NC

  • Sears ER (1956) The systematics, cytology and genetics of wheat. Handb Pflanzenzücht, vol. 2, 2nd edn, pp 164–187

  • Simonetti MC, Bellomo MP, Laghetti G, Perrino P, Simeone R, Blanco A (1999) Quantitative trait loci influencing free-threshing habit in tetraploid wheats. Genet Res Crop Evol 46:267–271

    Article  Google Scholar 

  • Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Trticum aestivum L.). Theor Appl Genet 109:1105–1114

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560

    Article  PubMed  CAS  Google Scholar 

  • Sood S, Kuraparthy V, Bai GH, Gill BS (2009) The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci. Theor Appl Genet 119:341–351

    Article  PubMed  Google Scholar 

  • Sourdille P, Cadalen T, Guyomarc’h H, Snape JW, Perretant MR, Charmet G, Boeuf C, Bernard S, Bernard M (2003) An update of the Courtot x Chinese Spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat. Theor Appl Genet 106:530–538

    PubMed  CAS  Google Scholar 

  • Sourdille P, Singh S, Cadalen T, Brown-Guedira GL, Gay G, Qi L, Gill BS, Dufour P, Murigneux A, Bernard M (2004) Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.). Funct Integr Genomics 4:12–25

    Article  PubMed  CAS  Google Scholar 

  • Thanh PT, Vladutu CI, Kianian SF, Thanh PT, Ishii T, Nitta M, Nasuda S, Mori N (2013) Molecular genetic analysis of domestication traits in emmer wheat. I: map construction and QTL analysis using an F2 population. Biotechnology 27:3627–3637

    Google Scholar 

  • Trebbi D, Maccaferri M, de Heer P, Sorensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen AG, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123:555–569

    Article  PubMed  Google Scholar 

  • Tzarfati R, Saranga Y, Barak V, Gopher A, Korol AB, Abbo S (2013) Threshing efficiency as an incentive for rapid domestication of emmer wheat. Ann Bot 112:829–837

    Article  PubMed  PubMed Central  Google Scholar 

  • vanPoecke RMP, Maccaferri M, Tang J, Truong HT, Janssen A, van Orsouw NJ, Salvi S, Sanguineti MC, Tuberosa R, van der Vossen EAG (2013) Sequence-based SNP genotyping in durum wheat. Plant Biotechnol J 11:809–817

    Article  CAS  Google Scholar 

  • Wang J, Liao X, Li Y, Zhou R, Yang X, Gao L, Jia J (2010) Fine mapping a domestication-related QTL for spike-related traits in a synthetic wheat. Genome 53:798–804

    Article  PubMed  CAS  Google Scholar 

  • Watanabe N, Ikebata N (2000) The effects of homoeologous group 3 chromosomes on grain colour dependent seed dormancy and brittle rachis in tetraploid wheat. Euphytica 115:215–220

    Article  Google Scholar 

  • Watkins AE (1940) The inheritance of glume shape in Triticum. J Genet 39:249–264

    Article  Google Scholar 

  • Zhang ZC, Belcram H, Gornicki P, Charles M, Just J, Huneau C, Magdelenat G, Couloux A, Samain S, Gill BS, Rasmussen JB, Barbe V, Faris JD, Chalhoub B (2011) Duplication and partitioning in evolution and function of homoeologousQ loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108:18737–18742

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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Acknowledgments

The authors thank Ms. Breanna Oldenburg and Ms. Megan Stoley for technical assistance. This research was supported by USDA-ARS CRIS project 5442-22000-037-00D.

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The authors declare no conflict of interest.

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Authors and Affiliations

  1. USDA-Agricultural Research Service, Cereal Crops Research Unit, Red River Valley Agricultural Research Unit, Fargo, ND, 58102, USA

    Justin D. Faris, Shiaoman Chao, Zengcui Zhang & Steven S. Xu

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Qijun Zhang

  3. USDA-ARS, NCSL, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA

    Justin D. Faris

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  1. Justin D. Faris
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Correspondence to Justin D. Faris.

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Communicated by Takao Komatsuda.

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122_2014_2380_MOESM1_ESM.pdf

Online Resource 1: Spreadsheet containing the BP025 genetic linkage mapping information including chromosome designations, markers, genetic positions, and segregation distortion information. SSR markers are highlighted in yellow and EST-STS markers are highlighted in purple (PDF 294 kb)

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Faris, J.D., Zhang, Q., Chao, S. et al. Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map. Theor Appl Genet 127, 2333–2348 (2014). https://doi.org/10.1007/s00122-014-2380-1

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