Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis–next generation sequencing and virus-induced gene silencing strategies

Zhu, Jiankun; Chen, Jiedan; Gao, Fengkai; Xu, Chenyu; Wu, Huaitong; Chen, Kun; Si, Zhanfeng; Hu, Yan; Zhang, Tianzhen

doi:10.1093/jxb/erx240

Cited by 48 publications

(43 citation statements)

References 61 publications

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“…S4 ); however, due to the low polymorphism between T582 and TM-1 ( Kohel and Lewis, 1984 ) in the near-isogenic background, it was difficult to fine-map cl 1 . Therefore, the bulked segregant analysis method was integrated with next generation sequencing techniques to delimit the cl 1 locus to between 13.87 and 18.38 Mb on chr.D07 of the TM-1 reference genome ( Zhang et al , 2015 ; Zhu et al , 2017 ). Within this region, 66 indel markers were further developed ( Supplementary Table S2 ).…”

Section: Resultsmentioning

confidence: 99%

“…We extracted DNAs from 28 cluster boll individuals from (T582×TM-1)BC 1 progeny and bulked these in an equal ratio to generate a ‘mutant type’ pool to conduct whole-genome resequencing with T582 parents. A total of 221.6 Gb of short (101-bp) paired-end reads was generated, including 94.7 Gb reads (37.9-fold genome coverage) for T582 and an average of 25.4 Gb, ranging from ~17.9 to 34.4 Gb (~7.2- to 13.8-fold genome coverage) for five bulks for different mutant traits (virescent-1 (v 1 ), cup leaf (cu), glandless-1 (gl 1 ), frego bract (fg) and cluster-1 (cl 1 )) ( Zhu et al , 2017 ). These reads were trimmed with Sickle software and then aligned to the TM-1 reference genome ( Zhang et al , 2015 ).…”

Section: Methodsmentioning

confidence: 99%

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Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture

Liu

Zhu

et al. 2018

Journal of Experimental Botany

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture

Liu

Zhu

et al. 2018

Journal of Experimental Botany

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“…We hypothesized that the different phenotype of the virescent-1 mutant in T582 compared with normal plant in 3-79 is probably due to the promoter difference between them (Zhu et al 2017;Mao et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)

et al. 2018

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Background: Virescence, as a recognizable phenotype in the early development stage of cotton, is not only available for research on chloroplast development and photosynthesis but also for heterosis exploitation in cotton. Methods: In current study, for fine mapping of virescent-1 (v 1 ) in cotton, three populations with a total of 5 678 individuals were constructed using T582 which has the virescent trait. Tobacco rattle virus, TRV1 and TRV2 (pYL156), were used as vectors for the virus-induced gene silencing (VIGS) assay. Results:The v 1 gene was fine-mapped to a 20 kb interval on chromosome 20 of tetraploid cotton. We identified only one candidate gene with four single nucleotide polymorphisms between parents, among which the single nucleotide polymorphism at the position of 1 082 base pair caused the change of amino acid residue from Arg (3-79) to Lys (T582). The relative expression of the candidate gene in virescent plants was extensively lower than that in normal plants. Nullification of the gene by VIGS significantly turned the green leaf of normal cotton plants into yellow. We named this candidate gene as GhRVL. Conclusions: This study will facilitate the further research on virescent formation, and will be useful for breeding of hybrid cottons.

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“…Next-generation sequencing (NGS)-based bulked segregant analysis (BSA) is a powerful tool for mapping disease resistance gene/genes that has been applied to Arabidopsis , rice ( Oryza sativa ), sorghum ( Sorghum bicolor ), soybean ( Gycin emax ), wheat ( Triticum turgidum ), and cotton ( Gossypium ; Trick et al, 2012 ; Yang et al, 2013 ; Uchida et al, 2014 ; Han et al, 2015 ; Song et al, 2017 ; Zhu et al, 2017 ). In the present study, we found the Chinese cabbage inbred line “85-74,” which exhibited resistance to the local pathogen “LAB-19” (race 4) and was distinct from CR germplasms harboring CRa , Crr1 , and Crr3 .…”

Section: Introductionmentioning

confidence: 99%

Identification and Mapping of the Clubroot Resistance Gene CRd in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Pang

et al. 2018

Front. Plant Sci.

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The rapid spread of clubroot disease, which is caused by Plasmodiophora brassicae, threatens Brassicaceae crop production worldwide. Breeding plants that have broad-spectrum disease resistance is one of the best ways to prevent clubroot. In the present study, eight Chinese cabbage germplasms were screened using published clubroot-resistant (CR) loci-/gene-linked markers. A CR gene Crr3 potential carrier “85-74” was detected which linked to marker BRSTS61; however, “85-74” shows different responses to local pathogens “LAB-19,” “LNND-2,” and “LAB-10” from “CR-73” which harbors Crr3. We used a next-generation sequencing-based bulked segregant analysis approach combined with genetic mapping to detect CR genes in an F2 segregant population generated from a cross between the Chinese cabbage inbred lines “85-74” (CR) and “BJN3-1” (clubroot susceptible). The “85-74” line showed resistance to a local pathogen “LAB-19” which was identified as race 4; a genetic analysis revealed that the resistance was conferred by a single dominant gene. The CR gene which we named CRd was mapped to a 60 kb (1 cM) region between markers yau389 and yau376 on chromosome A03. CRd is located upstream of Crr3 which was confirmed based on the physical positions of Crr3 linked markers. The identification of CRd linked markers can be applied to marker-assisted selection in the breeding of new CR cultivars of Chinese cabbage and other Brassica crops.

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Rapid mapping and cloning of the virescent-1 gene in cotton by bulked segregant analysis–next generation sequencing and virus-induced gene silencing strategies

Abstract: An improved method of rapid gene mapping and identification was successfully used to map and identify the causal gene at the virescent-1 locus of upland cotton.

Cited by 48 publications

References 61 publications

Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture

Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)

Identification and Mapping of the Clubroot Resistance Gene CRd in Chinese Cabbage (Brassica rapa ssp. pekinensis)

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