Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Wang, Shichen; Wong, Debbie; Forrest, Kerrie; Allen, Alexandra M.; Chao, Shiaoman; Huang, Bevan Emma; Maccaferri, Marco; Salvi, Silvio; Milner, Sara Giulia; Cattivelli, Luigi; Mastrangelo, Anna Maria; Whan, Alex; Stephen, Stuart; Barker, G. L.; Wieseke, Ralf; Plieske, Joerg; Lillemo, Morten; Mather, D. E.; Appels, R.; Dolferus, Rudy; Brown‐Guedira, Gina; Korol, Abraham B.; Akhunova, Alina; Feuillet, Catherine; Salse, Jérôme; Morgante, Michèle; Pozniak, Curtis; Luo, Ming‐Cheng; Dvořák, Jan; Morell, Matthew K.; Dubcovsky, Jorge; Ganal, Martin W.; Tuberosa, Roberto; Lawley, Cindy; Mikoulitch, Ivan; Cavanagh, Colin; Edwards, Keith J.; Hayden, Matthew; Akhunov, Eduard

doi:10.1111/pbi.12183

Cited by 1,529 publications

(1,987 citation statements)

References 41 publications

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“…It comprised 2575 markers spanning 5008.3 cM, with an average distance of 1.9 cM between adjacent markers. The B genome contained the maximum number of markers, followed by the A and D genomes, in accordance with earlier studies (Hao et al 2003;Xue et al 2008;Wang et al 2014;Wu et al 2015).…”

Section: Discussionsupporting

confidence: 91%

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Shi

Azam

et al. 2017

Euphytica

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Wheat (Triticum aestivum L.) yield is directly proportional to physio-morphological traits. A high-density genetic map consisting of 2575 markers was used for mapping QTL controlling stay-green and agronomic traits in wheat grown under four diverse water regimes. A total of 108 additive QTL were identified in target traits. Among them, 28 QTL for chlorophyll content (CC) were detected on 11 chromosomes, 43 for normalized difference vegetation index (NDVI) on all chromosomes except 5B, 5D, and 7D, five for spikes per plant (NSP) on different chromosomes, nine for plant height (PH) on four chromosomes, and 23 for thousand-kernel weight (TKW) on 11 chromosomes. Considering all traits, the phenotypic variation explained (PVE) ranged from 3.61 to 41.62%. A major QTL, QNDVI.cgb-5A.7, for NDVI with a maximum PVE of 20.21%, was located on chromosome 5A. A stable and major PH QTL was observed on chromosome 4D with a PVE close to 40%. Most distances between QTL and corresponding flanking markers were less than 1 cM, and approximately one-third of the QTL coincided with markers. Each of 16 QTL clusters on 10 chromosomes controlled more than one trait and therefore could be regarded as pleiotropic regions in response to different water regimes. Forty-one epistatic QTL were identified for all traits having PVE of 6.00 to 25.07%. Validated QTL closely linked to flanking markers will be beneficial for marker-assisted selection in improving drought-tolerance in wheat.

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Section: Discussionsupporting

confidence: 91%

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Shi

Azam

et al. 2017

Euphytica

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“…spelta, and 20 T. aestivum ssp. aestivum (10 spring and 10 winter) accessions obtained from the NSGC (SI Appendix, Table S6) were genotyped with the iSelect 90k SNP array (46). The population structure analysis was conducted using the program STRUCTURE version 2.3.4 (SI Appendix, Method S5).…”

Section: Methodsmentioning

confidence: 99%

“…sphaerococcum relative to the other subspecies. (46). The five subspecies were clustered into six groups, including two different groups for T. aestivum ssp.…”

Section: Vrn-d4mentioning

confidence: 99%

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

Kippes

Debernardi

Vasquez-Gross

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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106

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Wheat varieties with a winter growth habit require long exposures to low temperatures (vernalization) to accelerate flowering. Natural variation in four vernalization genes regulating this requirement has favored wheat adaptation to different environments. The first three genes (VRN1-VRN3) have been cloned and characterized before. Here we show that the fourth gene, VRN-D4, originated by the insertion of a ∼290-kb region from chromosome arm 5AL into the proximal region of chromosome arm 5DS. The inserted 5AL region includes a copy of VRN-A1 that carries distinctive mutations in its coding and regulatory regions. Three lines of evidence confirmed that this gene is VRN-D4: it cosegregated with VRN-D4 in a high-density mapping population; it was expressed earlier than other VRN1 genes in the absence of vernalization; and induced mutations in this gene resulted in delayed flowering. VRN-D4 was found in most accessions of the ancient subspecies Triticum aestivum ssp. sphaerococcum from South Asia. This subspecies showed a significant reduction of genetic diversity and increased genetic differentiation in the centromeric region of chromosome 5D, suggesting that VRN-D4 likely contributed to local adaptation and was favored by positive selection. Three adjacent SNPs in a regulatory region of the VRN-D4 first intron disrupt the binding of GLYCINE-RICH RNA-BINDING PROTEIN 2 (TaGRP2), a known repressor of VRN1 expression. The same SNPs were identified in VRN-A1 alleles previously associated with reduced vernalization requirement. These alleles can be used to modulate vernalization requirements and to develop wheat varieties better adapted to different or changing environments.wheat | flowering | vernalization | VRN1 | Triticum aestivum ssp. sphaerococcum

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“…As part of the Triticeae Coordinated Agricultural Project, the wheat cultivars and breeding lines selected by the project participants have been genotyped using the wheat iSelect single-nucleotide polymorphism (SNP) array containing 90,000 SNP (Wang et al 2014). The genotypic data were deposited and made available to the project members in the project database, The Triticeae Toolbox (http://triticeaetoolbox.org/wheat/).…”

Section: Methodsmentioning

confidence: 99%

Evaluation and Association Mapping of Resistance to Tan Spot and Stagonospora Nodorum Blotch in Adapted Winter Wheat Germplasm

et al. 2015

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Tan spot and Stagonospora nodorum blotch (SNB), often occurring together, are two economically significant diseases of wheat in the Northern Great Plains of the United States. They are caused by the fungi Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, both of which produce multiple necrotrophic effectors (NE) to cause disease. In this work, 120 hard red winter wheat (HRWW) cultivars or elite lines, mostly from the United States, were evaluated in the greenhouse for their reactions to the two diseases as well as NE produced by the two pathogens. One P. nodorum isolate (Sn4) and four Pyrenophora tritici-repentis isolates (Pti2, 331-9, DW5, and AR CrossB10) were used separately in the disease evaluations. NE sensitivity evaluation included ToxA, Ptr ToxB, SnTox1, and SnTox3. The numbers of lines that were rated highly resistant to individual isolates ranged from 11 (9%) to 30 (25%) but only six lines (5%) were highly resistant to all isolates, indicating limited sources of resistance to both diseases in the U.S. adapted HRWW germplasm. Sensitivity to ToxA was identified in 83 (69%) of the lines and significantly correlated with disease caused by Sn4 and Pti2, whereas sensitivity to other NE was present at much lower frequency and had no significant association with disease. As expected, association mapping located ToxA and SnTox3 sensitivity to chromosome arm 5BL and 5BS, respectively. A total of 24 potential quantitative trait loci was identified with −log (P value) > 3.0 on 12 chromosomes, some of which are novel. This work provides valuable information and tools for HRWW production and breeding in the Northern Great Plains.

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Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

Cited by 1,529 publications

References 41 publications

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

Evaluation and Association Mapping of Resistance to Tan Spot and Stagonospora Nodorum Blotch in Adapted Winter Wheat Germplasm

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