Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
11 09 2020
11 09 2020
Historique:
received:
04
07
2019
accepted:
16
08
2020
entrez:
12
9
2020
pubmed:
13
9
2020
medline:
29
9
2020
Statut:
epublish
Résumé
Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseq
Identifiants
pubmed: 32917907
doi: 10.1038/s41467-020-18404-w
pii: 10.1038/s41467-020-18404-w
pmc: PMC7486412
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4572Subventions
Organisme : Biotechnology and Biological Sciences Research Council
Pays : United Kingdom
Références
Goel, S., Yadav, M., Singh, K., Jaat, R. S. & Singh, N. K. Exploring diverse wheat germplasm for novel alleles in HMW-GS for bread quality improvement. J. Food Sci. Technol. 55, 3257–3262 (2018).
pubmed: 30065437
pmcid: 6046000
Velu, G., Singh, R. P., Huerta, J. & Guzmán, C. Genetic impact of Rht dwarfing genes on grain micronutrients concentration in wheat. F. Crop. Res. 214, 373–377 (2017).
Heuzé, V., Tran, G., Renaudeau, D., Lessire, M. & Lebas, F. Wheat Grain. Feedipedia, a Programme by INRA, CIRAD, AFZ and FAO https://www.feedipedia.org/node/223 (2015).
Talebnia, F., Karakashev, D. & Angelidaki, I. Production of bioethanol from wheat straw: an overview on pretreatment, hydrolysis and fermentation. Bioresour. Technol. 101, 4744–4753 (2010).
pubmed: 20031394
Swain, M. & Mohanty, S. Bioethanol Production From Corn and Wheat: Food, Fuel, and Future 1st edn, 45–59 (Academic, 2018).
Peng, J. H., Sun, D. & Nevo, E. Domestication evolution, genetics and genomics in wheat. Mol. Breed. 28, 281–301 (2011).
Kilian, B., Martin, W. & Salamini, F. in Evolution in Action: Case studies in Adaptive Radiation, Speciation and the Origin of Biodiversity (ed Glaubrecht, M.) 137–166 (Springer, Berlin Heidelberg, 2010).
Kilian, B., Özkan, H., Pozzi, C. & Salamini, F. in Plant Genetics and Genomics: Crops and Models 7 (eds Feuillet, C. & Muehlbauer, G. J.) 81–119 (Springer Science+Business Media, New York, 2009).
Kantar, M. B., Nashoba, A. R., Anderson, J. E., Blackman, B. K. & Rieseberg, L. H. The Genetics and Genomics of Plant Domestication. Bioscience 67, 971–982 (2017).
Maccaferri, M. et al. Durum wheat genome reveals past domestication signatures and future improvement targets. Nat. Genet. 51, 885–895 (2019).
Wang, S. et al. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol. J. 12, 787–796 (2014).
pubmed: 24646323
pmcid: 4265271
Tanksley, S. D. & McCouch, S. R. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063–1066 (1997).
pubmed: 9262467
Cox, T. S. Deepening the wheat gene pool. J. Crop Prod. 1, 1–25 (1997).
Reif, J. C. et al. Wheat genetic diversity trends during domestication and breeding. Theor. Appl. Genet. 110, 859–864 (2005).
pubmed: 15690175
McCouch, S. et al. Agriculture: feeding the future. Nature 499, 23–24 (2013).
pubmed: 23823779
Bhatta, M., Morgounov, A., Belamkar, V., Poland, J. & Baenziger, P. S. Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat. BMC Genomics 19, 591 (2018).
pubmed: 30081829
pmcid: 6090860
Milner, S. G. et al. Genebank genomics highlights the diversity of a global barley collection. Nat. Genet. 51, 319–326 (2019).
pubmed: 30420647
Hajjar, R. & Hodgkin, T. The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156, 1–13 (2007).
Maxted, N., Kell, S., Ford-Lloyd, B., Dulloo, M. & Toledo, Á. Toward the systematic conservation of global crop wild relative diversity. Crop Sci. 52, 774–785 (2012).
Dempewolf, H. et al. Past and future use of wild relatives in crop breeding. Crop Sci. 57, 1070–1082 (2017).
Müller, T. et al. Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt. Theor. Appl. Genet. 131, 407–416 (2018).
pubmed: 29103142
Langridge, P. & Waugh, R. Harnessing the potential of germplasm collections. Nat. Genet. 51, 200–201 (2019).
pubmed: 30664746
Pixley, K. V. et al. Genome editing, gene drives, and synthetic biology: will they contribute to disease-resistant crops, and who will benefit? Annu. Rev. Phytopathol. 57, 165–188 (2019).
pubmed: 31150590
Brown, A. Core collections: a practical approach to genetic resource management. Genome 31, 818–824 (1989).
Vikram, P. et al. Unlocking the genetic diversity of Creole wheats. Sci. Rep. 6, 23092 (2016).
pubmed: 26976656
pmcid: 4791556
Takenaka, S., Nitta, M. & Nasuda, S. Population structure and association analyses of the core collection of hexaploid accessions conserved ex situ in the Japanese gene bank NBRP-Wheat. Genes Genet. Syst. 93, 237–254 (2019).
Romay, M. C. et al. Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol. 14, R55 (2013).
pubmed: 23759205
pmcid: 3707059
Singh, S. et al. Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security. Sci. Rep. 8, 12527 (2018).
pubmed: 30131572
pmcid: 6104032
Pixley, K. et al. CIMMYT’s seeds of discovery initiative: harnessing biodiversity for food security and sustainable development. Indian J. Plant Genet. Resour. 31, 1 (2018).
Sehgal, D. et al. Exploring and mobilizing the gene bank biodiversity for wheat improvement. PLoS ONE 10, 1–18 (2015).
Crossa, J. et al. Genomic prediction of gene bank wheat landraces. G3 6, 1819–1834 (2016).
pubmed: 27172218
Saint Pierre, C. et al. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones. Sci. Rep. 6, 1–11 (2016).
Sansaloni, C. et al. 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 (2011).
pmcid: 3240076
Appels, R. et al. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361, eaar7191 (2018).
Dreisigacker, S. et al. SSR and pedigree analyses of genetic diversity among CIMMYT wheat lines targeted to different megaenvironments. Crop Sci. 44, 381–388 (2004).
Dreisigacker, S. et al. Genetic structures of the CIMMYT international yield trial targeted to irrigated environments. Mol. Breed. 29, 529–541 (2012).
Villareal, R. L., Rajaram, S., Mujeeb-Kazi, A. & Toro, E. The effect of Chromosome 1B/1R translocation on the yield potential of certain spring wheats (Triticum aestivum L.). Plant Breed. 106, 77–81 (2006).
Harlan, J. R. Ethiopia: a center of diversity. Econ. Bot. 23, 309–314 (1969).
Kilian, B. et al. in Wild Crop Relatives: Genomic and Breeding Resources: Temperate Fruits (ed Kole, C.) 1–76 (Springer, Berlin, Heidelberg, 2011).
Keilwagen, J. et al. Separating the wheat from the chaff – a strategy to utilize plant genetic resources from ex situ genebanks. Sci. Rep. 4, 14–18 (2014).
Dorofeev, V., Filatenko, A., Migushova, E., Udaczin, R. & Jakubziner, M. Flora of cultivated plants of the USSR (Kolos, Leningrad, 1979).
van Slageren, M. W. & International Center For Agricoltural Research In the Dry Areas. Wild Wheats: a Monograph of Aegilops L. and Amblyopyrum (Jaub. & Spach) Eig (Poaceae), Vol. 9 (Wageningen Agricultural University Papers, 1994).
Nakamura, S. et al. A wheat homolog of MOTHER of FT and TFL1 acts in the regulation of germination. Plant Cell 23, 3129–3215 (2011).
Kumar, A. et al. Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross. PLoS ONE 14, e0221826 (2019).
Kumar, J. et al. Genetics of Fe, Zn, β-carotene, GPC and yield traits in bread wheat (Triticum aestivum L.) using multi-locus and multi-traits GWAS. Euphytica 214, 219 (2018).
Wrigley, C., Bekes, F. & Bushuk, W. in Gliadin and Glutenin the Unique Balance of Wheat Quality (eds Wrigley, C., Bekes, F. & Bushuk, W.) 3–32 (2006).
Sehgal, D. et al. Identification of genomic regions for grain yield and yield stability and their epistatic interactions. Sci. Rep. 7, 1–12 (2017).
Holbrook, C. C., Anderson, W. F. & Pittman, R. N. Selection of a core collection from the U.S. germplasm collection of peanut. Crop Sci. 33 859–861 (1993).
Upadhyaya, H., Laxmipathi Gowda, C. & Dvssr, S. Plant genetic resources management: collection, characterization, conservation and utilization. J. SAT Agric. Res. 6, 1–12 (2007).
Xu, Y. in Molecular Plant Breeding, 151–194 (CAB International, Cambridge, 2010).
Khazaei, H., Street, K., Bari, A., Mackay, M. & Stoddard, F. L. The FIGS (Focused Identification of Germplasm Strategy) approach identifies traits related to drought adaptation in vicia faba genetic resources. PLoS ONE 8, e63107 (2013).
pubmed: 23667581
pmcid: 3648475
Romero Navarro, J. A. et al. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat. Genet. 49, 476–480 (2017).
pubmed: 28166212
Gates, D. J. et al. Single-gene resolution of locally adaptive genetic variation in Mexican maize. bioRxiv 706739. https://doi.org/10.1101/706739 (2019).
Hoisington, D., Khairallah, M. & Gonzalez-de-Leon, D. CIMMYT Applied Molecular Genetics Laboratory (CIMMYT, México, 1994).
Wittenberg, A. H. J. et al. Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol. Genet. Genomics 274, 30–39 (2005).
pubmed: 15937704
Alam, M., Neal, J., O’Connor, K., Kilian, A. & Topp, B. Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia. PLoS ONE 13, e0203465 (2018).
pubmed: 30169500
pmcid: 6118395
Gruber, B., Unmack, P., Berry, O. & Georges, A. in Beginning DAX with Power BI, Ch. 1, 1–25 (Apress, 2019).
Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328 (2012).
pubmed: 23060615
pmcid: 3519454
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
pubmed: 3322381
pmcid: 3322381
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943
pmcid: 19505943
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012).
pubmed: 22728672
pmcid: 3679285
Berg, E. E. & Hamrick, J. L. Fine-scale genetic structure of a turkey oak forest. Evolution 49, 110–120 (1995).
pubmed: 28593662
Weir, B. S. Genetic Data Analysis II: Methods for Discrete Population Genetic Data, 150–156 (Sinauer Associates, Sunderland, MA, 1996).
Mardia, K. V, Kent, J. T. & Bibby, J. M. Multivariate Analysis (Academic, New York, 1979).
Dryden, I. L. & Mardia, K. V. Statistical Shape Analysis: With Applications in R (Wiley, 2016).
De Leeuw, J. & Mair, P. Multidimensional scaling using majorization: SMACOF in R. J. Stat. Softw. 31, 1–30 (2009).
Harabasz, J. A dendrite method for cluster analysis AU - Caliński, T. Commun. Stat. 3, 1–27 (1974).
Weir, B. S. & Cockerham, C. C. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).
pubmed: 28563791
Franco, J., Crossa, J., Taba, S. & Shands, H. A sampling strategy for conserving genetic diversity when forming core subsets. Crop Sci. 45, 1035–1044 (2005).
Franco, J., Crossa, J., Warburton, M. L. & Taba, S. Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Sci. 46, 854–864 (2006).
Ward, J. H. J. Hierarchical grouping to optimize an objective function AU - ward. Joe H. J. Am. Stat. Assoc. 58, 236–244 (1963).
Nei, M. Analysis of Gene Diversity in Subdivided Populations. Proc. Natl Acad. Sci. USA 70, 3321–3323 (1973).
pubmed: 4519626
Berg, E. E. & Hamrick, J. L. Quantification of genetic diversity at allozyme loci. Can. J. For. Res. 27, 415–424 (1997).
Liu, X., Huang, M., Fan, B., Buckler, E. S. & Zhang, Z. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLOS Genet. 12, e1005767 (2016).
pubmed: 26828793
pmcid: 4734661