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Molecular characterization of winter durum wheat (Triticum durum) based on a genotyping-by-sequencing approach

Published online by Cambridge University Press:  05 August 2015

Alisa-Naomi Sieber ,
C. Friedrich H. Longin  and
Tobias Würschum
Alisa-Naomi Sieber
Affiliation:
State Plant Breeding Institute, University of Hohenheim, 70593Stuttgart, Germany
C. Friedrich H. Longin
Affiliation:
State Plant Breeding Institute, University of Hohenheim, 70593Stuttgart, Germany
Tobias Würschum*
Affiliation:
State Plant Breeding Institute, University of Hohenheim, 70593Stuttgart, Germany
*
*Corresponding author. E-mail: [email protected]
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Abstract

Durum wheat (Triticum durum) is predominantly grown as spring type and depending on the production area autumn or spring sowing is used. For the durum production in Austria and Germany, autumn sowing has several advantages, such as yield increase and stability, but this requires the selection for winter hardiness including a good frost tolerance. The aim of this study was to support breeding of winter durum and to facilitate genomic approaches by molecularly characterizing a panel of 170 diverse winter and 14 spring durum lines employing a genotyping-by-sequencing approach. We obtained an unprecedentedly high number of 30,611 polymorphic markers covering the entire genome. The principal coordinate analysis and the cluster analysis revealed the absence of a major population structure but a tendency of lines to group according to their country of origin. Linkage disequilibrium was found to decay within a short distance of approximately 2–5 cM and also showed variable patterns along chromosomes. In summary, our results can assist breeding of durum wheat and pave the way for genomic approaches towards knowledge-based winter durum breeding.

Keywords

allelic diversitygenetic diversitygenotyping-by-sequencinglinkage disequilibriumpopulation structureTriticum durumwinter durum
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 1 , February 2017 , pp. 36 - 44
Copyright
Copyright © NIAB 2015 

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References

Akhunov, ED, Akhunova, AR, Anderson, OD, Anderson, JA, Blake, N, Clegg, MT, Coleman-Derr, D, Conley, EJ, Crossman, CC, Deal, KR, Dubcovsky, J, Gill, BS, Gu, YQ, Hadam, J, Heo, H, Huo, N, Lazo, GR, Luo, M-C, Ma, YQ, Matthews, DE, McGuire, PE, Morrell, PL, Qualset, CO, Renfro, J, Tabanao, D, Talbert, LE, Tian, C, Toleno, DM, Warburton, ML, You, FM, Zhang, W and Dvorak, J (2010) Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 11: 702.Google Scholar
Alheit, KV, Maurer, HP, Reif, JC, Tucker, MR, Hahn, V, Weissmann, EA and Würschum, T (2012) Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale ( ×  Triticosecale Wittmack). BMC Genomics 13: 235–244.Google Scholar
Badea, A, Eudes, F, Salmon, D, Tuvesson, S, Vrolijk, A, Larsson, C-T, Caig, V, Huttner, E, Kilian, A and Laroche, A (2011) Development and assessment of DArT markers in triticale. Theoretical and Applied Genetics 122: 1547–1560.Google Scholar
Breseghello, F and Sorrells, ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165–1177.CrossRefGoogle ScholarPubMed
Chao, S, Dubcovsky, J, Dvorak, J, Luo, M-C, Baenziger, 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 and Akhunov, ED (2010) Population-and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 11: 727.CrossRefGoogle ScholarPubMed
Elias, EM (1995) Durum wheat products. Durum Wheat Improvement in the Mediterranean Region: New Challenges Serie A: Séminaires Méditerranéennes 40: 23–31.Google Scholar
Gower, JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53: 325–338.Google Scholar
Hahn, V and Würschum, T (2014) Molecular genetic characterization of Central European soybean breeding germplasm. Plant Breeding 133: 748–755.Google Scholar
Laidò, G, Mangini, G, Taranto, F, Gadaleta, A, Blanco, A, Cattivelli, L, Marone, D, Mastrangelo, AM, Papa, R and De Vita, P (2013) Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) estimated by SSR, DArT and pedigree data. PLoS ONE 8: e67280.CrossRefGoogle ScholarPubMed
Longin, CFH, Mühleisen, J, Maurer, HP, Zhang, H, Gowda, M and Reif, JC (2012) Hybrid breeding in autogamous cereals. Theoretical and Applied Genetics 125: 1087–1096.CrossRefGoogle ScholarPubMed
Maccaferri, M, Sanguineti, MC, Noli, E and Tuberosa, R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Molecular Breeding 15: 271–290.Google Scholar
Maccaferri, M, Sanguineti, MC, Natoli, V, Ortega, JLA, Salem, MB, Bort, J, Chenenaoui, C, De Ambrogio, E, del Moral, LG, De Montis, A, El-Ahmed, A, Maalouf, F, Machlab, H, Moragues, M, Motawaj, J, Nachit, M, Nserallah, N, Ouabbou, H, Royo, C and Tuberosa, R (2006) A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies. Plant Genetic Resources: Characterization and Utilization 4: 79–85.Google Scholar
Maurer, HP, Melchinger, AE and Frisch, M (2008) Population genetic simulation and data analysis with Plabsoft. Euphytica 161: 133–139.Google Scholar
Mondini, L, Farina, A, Porceddu, E and Pagnotta, MA (2010) Analysis of durum wheat germplasm adapted to different climatic conditions. Annals of Applied Biology 156: 211–219.CrossRefGoogle Scholar
Myles, S, Peiffer, J, Brown, PJ, Ersoz, ES, Zhang, Z, Costich, DE and Buckler, ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. The Plant Cell Online 21: 2194–2202.CrossRefGoogle ScholarPubMed
Nielsen, NH, Backes, G, Stougaard, J, Andersen, SU and Jahoor, A (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties. PLoS ONE 9: e94000.Google Scholar
Palamarchuk, A (2005) Selection strategies for traits relevant for winter and facultative durum wheat. In: Royo, C, Nachit, M, Di Fonzo, N and Araus, J (eds) Durum Wheat Breeding: Current Approaches and Future Strategies, vol. 2. New York: The Haworth Press, Inc., pp. 599–644.Google Scholar
R Development Core Team(2011) R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.Google Scholar
Ren, E, Sun, D, Chen, L, You, FM, Wang, J, Peng, Y, Nevo, E, Sun, D, Luo, M-C and Peng, J (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. International Journal of Molecular Sciences 14: 7061–7088.CrossRefGoogle Scholar
Royo, C, Elias, EM and Manthey, FA (2009) Durum wheat breeding. In: Carena, MJ (ed) Cereals (Handbook of Plant Breeding). New York: Springer, pp. 199–226.Google Scholar
Ruiz, M, Giraldo, P, Royo, C and Carrillo, JM (2013) Creation and validation of the Spanish durum wheat core collection. Crop Science 53: 2530–2537.Google Scholar
Sieber, A-N, Würschum, T and Longin, CFH (2014) Evaluation of a semi-controlled test as a selection tool for frost tolerance in durum wheat (Triticum durum). Plant Breeding 133: 465–469.CrossRefGoogle Scholar
Somers, DJ, Banks, T, DePauw, R, Fox, S, Clarke, J, Pozniak, C and McCartney, C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50: 557–567.CrossRefGoogle ScholarPubMed
Sorrells, ME, Barbosa, J, Nachit, MM, Ketata, H and Autrique, E (1995) Relationships among 81 durum genotypes based on RFLPs, gliadins, parentage and quality traits. Options Mediterraneenes, Serie A, Seminaires Mediterraneens 22: 249–262.Google Scholar
van Poecke, RMP, Maccaferri, M, Tang, J, Truong, HT, Janssen, A, Orsouw, NJ, Salvi, S, Sanguineti, MC, Tuberosa, R and van der Vossen, EAG (2013) Sequence-based SNP genotyping in durum wheat. Plant Biotechnology Journal 11: 809–817.Google Scholar
Walther, F (1978) Breeding problems in winter durum wheat, Triticum durum Desf. Z. Pflanzenzüchtung 80: 11–23.Google Scholar
Weir, BS and Cockerham, CC (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, MA: Sinauer Assoc. Inc.Google Scholar
Wenzl, P, Carling, J, Kudrna, D, Jaccoud, D, Huttner, E, Kleinhofs, A and Kilian, A (2004) Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proceedings of the National Academy of Sciences of the United States of America 101: 9915–9920.Google Scholar
Wright, S (1978) Evolution and Genetics of Populations, Variability within and among Natural Populations, vol. 4. Chicago: The University of Chicago Press.Google Scholar
Würschum, T (2012) Mapping QTL for agronomic traits in breeding populations. Theoretical and Applied Genetics 125: 201–210.Google Scholar
Würschum, T, Maurer, HP, Kraft, T, Janssen, G, Nilsson, C and Reif, JC (2011) Genome-wide association mapping of agronomic traits in sugar beet. Theoretical and Applied Genetics 123: 1121–1131.Google Scholar
Würschum, T, Langer, SM, Longin, CFH, Korzun, V, Akhunov, E, Ebmeyer, E, Schachschneider, R, Schacht, J, Kazman, E and Reif, JC (2013) Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theoretical and Applied Genetics 126: 1477–1486.CrossRefGoogle ScholarPubMed
Würschum, T, Langer, SM and Longin, CFH (2015) Genetic control of plant height in European winter wheat cultivars. Theoretical and Applied Genetics 128: 865–874.Google Scholar
Zhang, LY, Marchand, S, Tinker, NA and Belzile, F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theoretical and Applied Genetics 119: 43–52.Google Scholar
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