Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat

Dong, Caixia; Zhang, Lichao; Chen, Zhongxu; Xia, Chuan; Gu, Yong–Qiang; Wang, Jirui; Li, Danping; Xie, Zhencheng; Zhang, Qiang; Zhang, Xueying; Gui, Lixuan; Liu, Xu; Kong, Xiuying

doi:10.3389/fpls.2020.01249

Cited by 35 publications

(21 citation statements)

References 62 publications

(76 reference statements)

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“…The result was a main peak in a 6.69 Mb interval (from 518.43 to 525.12 Mb) on chromosome 5AL (Fig. 1), which con rmed the effectiveness of mixing pools constructed with representative samples of extreme phenotypes in a RIL population (Martinez et al 2020;Dong et al 2020). BSE-Seq led to a reduction in the data analyzed and in the cost related to sequencing a large genome, especially in wheat.…”

Section: Discussionmentioning

confidence: 67%

“…As an effective method, BSE-Seq has been successfully used for mapping and gene identi cation in wheat. However, the traits identi ed by BSE-Seq to date are mainly controlled by a single gene, and few results have been reported for complex traits in RIL populations (Martinez et al 2020;Dong et al 2020;Breseghello and Sorrells 2006;Harrington et al 2019). To determine the usefulness of BSE-Seq data in complex trait gene mapping, SL throughout an RIL population was analyzed.…”

Section: Discussionmentioning

confidence: 99%

“…Due to the large size of the wheat genome (~ 16 Gb in hexaploid wheat) (Bennett and Smith 1976) and highly repetitive content (Lukaszewski et al 2014), whole-genome DNA resequencing for BSA is still costly (Martinez et al 2020). Exons constitute approximately 0.95% of the wheat genome and code primary protein components that play essential roles in plant growth and development (Dong et al 2020). Therefore, exome capture can effectively capture the protein-coding regions of the wheat genome to discover SNPs (Allen et al 2013;Win eld et al 2012) and catalog induced mutations (Henry et al 2014;King et al 2015).…”

Section: Introductionmentioning

confidence: 99%

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Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

Fan

et al. 2021

Mol Breeding

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Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a cross between 13F10 and Chuanmai 42 (CM42) were evaluated for spike length in six environments. Sixty RILs consisting of 30 high and 30 low SLs were genotyped using the bulked segregant analysis exome sequencing (BSE-Seq) analysis for preliminary quantitative trait locus (QTL) mapping. A 6.69 12 Mb) region on chromosome 5AL was found to have a signi cant effect on the SL trait. Fifteen kompetitive allele speci c PCR (KASP) markers were successfully converted from the single nucleotide polymorphisms (SNPs) in the SL target region. Combined with four novel simple sequence repeat (SSR) markers, a genetic linkage map spanning 21.159 cM was constructed. The mapping result con rmed the identity of a major and stable QTL named QSl.cib-5A in the targeted region that explained 7.88-26.60% of the phenotypic variation in SL. QSl.cib-5A was narrowed to a region of 4.84 cM interval corresponding to a 4.67 Mb (516.60-521.27 Mb) physical region in the Chinese Spring RefSeq v2.0 containing 17 high-con dence genes with 25 transcripts. In addition, this QTL exhibited pleiotropic effects on spikelet density (SD), with the phenotypic variances proportion ranging from 11.34-19.92%. This study provides a foundational step for cloning the QSl.cib-5A, which is involved in the regulation of spike morphology in common wheat.

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Section: Discussionmentioning

confidence: 67%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

Fan

et al. 2021

Mol Breeding

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“…Genomic DNA of the resistant parent GX was sequenced using the wheat exome capture sequencing protocol described by Dong et al (2020) . The raw sequence data have been submitted to GenBank under Bioproject no.…”

Section: Methodsmentioning

confidence: 99%

Molecular Mapping and Analysis of an Excellent Quantitative Trait Loci Conferring Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landrace Gaoxianguangtoumai

et al. 2021

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The Chinese wheat landrace “Gaoxianguangtoumai” (GX) has exhibited a high level of adult-plant resistance (APR) to stripe rust in the field for more than a decade. To reveal the genetic background for APR to stripe rust in GX, a set of 249 F6:8 (F6, F7, and F8) recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar “Taichung 29.” The parents and RILs were evaluated for disease severity at the adult-plant stage in the field by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers finally. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS in GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 11.5–13.5% of the total phenotypic variation, respectively. Compared with published Yr genes and QTL, QYr.GX-7DS and Yr18 may be the same, whereas QYr.GX-2AS is likely to be novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which presents in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a heterogeneous inbred family (HIF) population from a residual heterozygous plant in an F8 generation of RIL, QYr.GX-2AS was further flanked by KP2A_36.85 and KP2A_38.22 with a physical distance of about 1.37Mb and co-segregated with the KP2A_37.09. Furthermore, three tightly linked Kompetitive allele-specific PCR (KASP) markers were highly polymorphic among 109 Chinese wheat cultivars. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

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“…Genotyping, linkage map construction, and QTL analysis Genomic DNA was extracted from a single plant for each line of the wheat materials using the cetyltrimethylammonium bromide method (Stewart and Via 1993) Exome capture sequencing, development of KASP markers, and genetic mapping Genomic DNA of the parents, GX and TC 29, was sequenced using the wheat exome capture sequencing protocol described by Dong et al (2020). The sequence variants were identi ed using the variant calling pipeline GATK4 (Heldenbrand et al 2019).…”

Section: Evaluation Of Resistance To Stripe Rustmentioning

confidence: 99%

Mendelization and Molecular Mapping of a Large-effect QTL Conferring Durable Adult-plant Resistance to Stripe Rust in a Chinese Wheat Landrace ‘Gaoxianguangtoumai’

Wang¹,

Liang²,

Guan³

et al. 2021

Preprint

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The Chinese wheat landrace ‘Gaoxianguangtoumai’ (GX) has exhibited a high degree of adult-plant resistance (APR) to stripe rust in field environments for more than a decade. To reveal the genetic basis for APR to stripe rust in GX, a set of 249 F6:8 recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar ‘Taichung 29’. The parents and RILs were evaluated for disease severity at the adult-plant stage in field environments by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons, and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS from GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 9.6–15.6% of the total phenotypic variation, respectively. Compared with published genes and QTL, QYr.GX-7DS is likely Yr18, whereas QYr.GX-2AS is probably novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which present in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a near-isogenic line population, QYr.GX-2AS was further mapped to an interval with a physical distance of about 1.37 Mb and co-segregated with a Kompetitive allele-specific PCR (KASP) marker. Furthermore, three tightly linked KASP markers were highly polymorphic among 109 Chinese wheat cultivars. The short physical interval and tightly linked KASP markers developed in this study will facilitate marker-assisted selection and map-based cloning of QYr.GX-2AS.

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Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat

Cited by 35 publications

References 62 publications

Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

Molecular Mapping and Analysis of an Excellent Quantitative Trait Loci Conferring Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landrace Gaoxianguangtoumai

Mendelization and Molecular Mapping of a Large-effect QTL Conferring Durable Adult-plant Resistance to Stripe Rust in a Chinese Wheat Landrace ‘Gaoxianguangtoumai’

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