Haplotype, molecular marker and phenotype effects associated with mineral nutrient and grain size traits of TaGS1a in wheat

Guo, Ying; Sun, Jin-jie; Zhang, Guizhi; Wang, Yingying; Kong, Fanmei; Zhao, Yan; Li, Sishen

doi:10.1016/j.fcr.2013.07.012

Cited by 68 publications

(40 citation statements)

References 44 publications

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“…However, a significant positive correlation has also been reported between GPS and TKW in Chinese modern cultivars (Zhang et al 2012a ). Several causal genes for grain traits including TKW and grain number have been cloned and their functional markers (FMs) have been developed including TaSnRK2.3 - 1A/1B (Miao et al 2017 ), TaSnRK2.10 - 4A (Zhang et al 2017 ), TaFlo2 - A1 (Sajjad et al 2017 ), TaTGW6 - A1 (Hanif et al 2016 ), TaGS5 - 3A (Ma et al 2016 ), TaCwi - A1 (Ma et al 2012 ), TaSus2 - 2B (Jiang et al 2011 ), TaGW2 (Su et al 2011 ), TaCKX6 - D1 (Zhang et al 2012b ), TaSAP1 - A1 (Chang et al 2013 ), TaGS1a (Guo et al 2013 ), TaGS - D1 (Zhang et al 2014 ) and TaGASR7 - A1 (Dong et al 2014 ).…”

Section: Introductionmentioning

confidence: 99%

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits

et al. 2018

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Key message We developed breeder-friendly high-throughput and cost-effective KASP marker for marker-assisted selection for grain yield related traits in wheat. Abstract Plant-specific protein kinase, SnRK2s, is a major family of signaling genes associated with metabolic regulations, nutrient utilization and response to external stimuli. In the present study, three copies of TaSnRK2.9 were isolated from chromosomes 5A, 5B and 5D of wheat ( Triticum aestivum L.). The coding regions of TaSnRK2.9 -5A, TaSnRK2.9 -5B and promoter region of TaSnRK2.9 -5D were investigated for sequence polymorphism. Single nucleotide polymorphisms (SNPs) were identified for TaSnRK2.9 -5A, while no polymorphism was identified in TaSnRK2.9 -5B and TaSnRK2.9 -5D. The nucleotide sequence of TaSnRK2.9 -5A consisted of 2180 bp having eight introns and nine exons. Three SNPs were identified at 308 nt, 698 nt and 1700 nt. For high-throughput genotyping, two kompetitive allele-specific PCR (KASP) markers were developed. Four haplotypes Hap -5A-1, Hap -5A-2, Hap -5A-3 and Hap -5A-4 were detected in wheat populations collected from China, Europe and Pakistan. Association analysis was performed with mixed linear model in TASSEL (v 5.0). The results indicated that Hap -5A-1/2 of TaSnRK2.9 -5A were significantly associated with high thousand kernel weight, while Hap -5A-4 with high grains per spike. Overexpressing transgenic rice also showed higher grains per spike which is in accordance with association analysis results. Geographic distribution and allelic frequency indicted that the favored haplotypes were positively selected in Chinese ( Hap -5A-1/2), Pakistani ( Hap -5A-1), east European ( Hap -5A-1) and west European ( Hap -5A-4) wheat breeding. The results suggest that the developed KASP markers can be utilized in yield improvement by marker-assisted selection in wheat breeding. Electronic supplementary material The online version of this article (10.1007/s00122-018-3247-7) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits

et al. 2018

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“…Up to date, no gene/QTL associated with grain shape and size has been cloned in wheat via a map-based cloning approach. However, some QTLs for grain size and weight in wheat were associated with the orthologs of rice grain traits QTLs, including TaCwi-1A [ 14 ], TaSus2–2B [ 15 ], TaGw2–6A [ 6 ], TaCKX6-D1 [ 16 ], TaSap1-A1 [ 17 ], TaGS1–6D [ 18 ] and TaLsu1 [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

et al. 2015

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High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010–2014 by inclusive composite interval mapping (ICIM) (LOD≥2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82–23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.

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“…Out of the seven grain-size related genes segregating in the EA wheat population, only TaCKX-D1 showed a significant effect on TKW. It is important to note that the polymorphism reported in these genes were only shown to be associated with, but were not validated as being causal of the natural variation in TKW (Zhang et al 2012;Guo et al 2013;Hou et al 2014;Zheng et al 2014;Jiang et al 2015;Wang et al 2016). It is, therefore, possible that the lack of phenotypic effect in our study might be due to difference in the haplotype structure between the EA wheat population and the original study population used to identify these markers.…”

Section: Importance Of Validating Population-specific Effect Of Benefmentioning

confidence: 80%

Allelic diversity study of functional genes in East Africa bread wheat highlights opportunities for genetic improvement

Wamalwa

Tadesse

Muthui

et al. 2020

Preprint

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Wheat (Triticum aestivum L.) is a major staple crop in East Africa (EA) providing 9% and 10% of daily calories and protein intake, respectively. However, EA countries depend on import to meet 55% of their domestic wheat supplies due to increasing demands and low domestic yields. To determine the beneficial gene pool currently exploited for wheat improvement in EA, we examined the allelic diversity of 42 genes of breeding importance in a collection of 239 wheat cultivars and breeding lines from Kenya and Ethiopia using KASP markers. The assayed genes have been shown to control variations in plant height, thousand kernel weight (TKW), grain protein content, pre-harvest sprouting (PHS), disease resistance and flowering time. We observed the beneficial alleles of some major genes including Rht-D1, Gpc-B1, Yr5, Yr15, Sr26, and Fhb1 to be missing or present at low frequencies in this population. Furthermore, we validated the effects of the major Rht-1 alleles and TaCKX-6A in controlling variation in plant height and thousand kernel weight, respectively, under EA conditions. Our results uncover hitherto unexploited allelic diversity that can be used to improve the genetic potential of EA wheat germplasm. This will inform strategies to rapidly mobilize these beneficial alleles for wheat improvement in EA.

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Haplotype, molecular marker and phenotype effects associated with mineral nutrient and grain size traits of TaGS1a in wheat

Cited by 68 publications

References 44 publications

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits

High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

Allelic diversity study of functional genes in East Africa bread wheat highlights opportunities for genetic improvement

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