QTL Mapping of Kernel Traits and Validation of a Major QTL for Kernel Length-Width Ratio Using SNP and Bulked Segregant Analysis in Wheat

Fang, Xin; Zhu, Ting; Wei, Shuwei; Han, Yuyan; Zhao, Yue; Zhang, Dazhong; Ma, Lingjian; Ding, Qin

doi:10.1038/s41598-019-56979-7

Cited by 65 publications

(48 citation statements)

References 44 publications

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“…Those results are consistent with the significant correlation between them. The traits controlled by clusters might be explained by QTL with pleiotropy or a set of closely linked loci [ 36 , 37 ].…”

Section: Discussionmentioning

confidence: 99%

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Fan

Gao

et al. 2020

Plants

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Chrysanthemums (Chrysanthemum morifolium Ramat.) are famous ornamental crops with high medicinal and industrial values. The inflorescence and leaf traits are key factors that affect the yield and quality of chrysanthemum. However, the genetic improvement of those traits is slow within chrysanthemum because of its hexaploidy, high heterozygosity and enormous genome. To study the genetic control of the important traits and facilitate marker-assisted selection (MAS) in chrysanthemum, it is desirable to populate the genetic maps with an abundance of transferrable markers such as microsatellites (SSRs). A genetic map was constructed with expressed sequence tag–simple sequence repeat (EST-SSR) markers in an F1 progeny of 192 offspring. A total of 1000 alleles were generated from 223 EST-SSR primer pairs. The preliminary maternal and paternal maps consisted of 265 marker alleles arranged into 49 and 53 linkage groups (LGs), respectively. The recombined parental maps covered 906.3 and 970.1 cM of the genome, respectively. Finally, 264 polymorphic loci were allocated to nine LGs. The integrated map spanned 954.5 cM in length with an average genetic distance of 3.6 cM between two neighbouring loci. Quantitative trait loci (QTLs) analysis was performed using the integrated map for inflorescence diameter (ID), central disc flower diameter (CDFD), number of whorls of ray florets (NWRF), number of ray florets (NRF), number of disc florets (NDF), number of florets (NF), ray floret length (RFL), ray floret width (RFW), ray floret length/width (RFL/W), leaf length (LL), leaf width (LW) and leaf length/width (LL/W). Overall, 36 (21 major) QTLs were identified. The successful mapping of inflorescence and leaf traits QTL demonstrated the utility of the new integrated linkage map. This study is the first report of a genetic map based on EST-SSR markers in chrysanthemum. The EST-SSR markers, genetic map and QTLs reported here could be valuable resources in implementing MAS for chrysanthemums in breeding programs.

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Section: Discussionmentioning

confidence: 99%

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Fan

Gao

et al. 2020

Plants

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“…Most of the kernel weight and shape traits, including kernel diameter and kernel weight, exhibited moderate heritability under OP conditions, whereas high heritability under H and HD conditions was found (Table 1). Xin et al [35] found high heritability of kernel shape traits in four different environments. Traits with high heritability and genetic advances can be selected directly for crop improvement [36].…”

Section: Phenotypic Variation For Kernel Weight and Shape-related Tramentioning

confidence: 97%

Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses

Elhadi

Kamal

Gorafi

et al. 2021

IJMS

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Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat–drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin–protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.

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“…A threshold P value of 0.001 (−log10(P) ≥ 3.0) was used for QTL detection, P value frequently used for many agronomical important quantitative traits [56][57][58]; suggestive QTL were considered at the sub-threshold 2.5 < −log10(P) < 3.0 when declared at least in one year. A QTL was considered stable when detected at −log10(P) ≥ 3.0 in at least two years [41,[58][59][60]. The phenotypic variation (PVE = R 2 ) and additive effect were estimated for each detected QTL.…”

Section: Statistical Analysis and Qtl Detectionmentioning

confidence: 99%

Candidate Genes and Quantitative Trait Loci for Grain Yield and Seed Size in Durum Wheat

Mangini

Blanco

Nigro

et al. 2021

Plants

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Grain yield (YLD) is affected by thousand kernel weight (TKW) which reflects the combination of grain length (GL), grain width (GW) and grain area (AREA). Grain weight is also influenced by heading time (HT) and plant height (PH). To detect candidate genes and quantitative trait loci (QTL) of yield components, a durum wheat recombinant inbred line (RIL) population was evaluated in three field trials. The RIL was genotyped with a 90K single nucleotide polymorphism (SNP) array and a high-density genetic linkage map with 5134 markers was obtained. A total of 30 QTL were detected including 23 QTL grouped in clusters on 1B, 2A, 3A, 4B and 6B chromosomes. A QTL cluster on 2A chromosome included a major QTL for HT co-located with QTL for YLD, TKW, GL, GW and AREA, respectively. The photoperiod sensitivity (Ppd-A1) gene was found in the physical position of this cluster. Serine carboxypeptidase, Big grain 1 and β-fructofuranosidase candidate genes were mapped in clusters containing QTL for seed size. This study showed that yield components and phenological traits had higher inheritances than grain yield, allowing an accurate QTL cluster detection. This was a requisite to physically map QTL on durum genome and to identify candidate genes affecting grain yield.

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QTL Mapping of Kernel Traits and Validation of a Major QTL for Kernel Length-Width Ratio Using SNP and Bulked Segregant Analysis in Wheat

Cited by 65 publications

References 44 publications

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Chrysanthemum morifolium Ramat.)

Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses

Candidate Genes and Quantitative Trait Loci for Grain Yield and Seed Size in Durum Wheat

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