Mapping of powdery mildew resistance genes in melon ( Cucumis melo L.) by bulked segregant analysis

Li, Bing; Zhao, Yulong; Zhu, Qianglong; Zhang, Zhipeng; Fan, Chao; Amanullah, Sikandar; Luan, Feishi

doi:10.1016/j.scienta.2017.04.001

Cited by 61 publications

(38 citation statements)

References 39 publications

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“…The strategy of bulked segregant analysis (BSA) proposed by Michelmore et al [ 23 ], provides a simple and more effective approach to rapidly identify candidate genomic regions that underlie the target genes based on whole genome resequencing of bulked populations and both parents [ 24 ]. Bulked-segregant analysis coupled with global sequencing (BSA-seq) has been successfully applied to clone genes in plants, including rice [ 24 , 25 , 26 , 27 , 28 ], melon [ 29 ], soybean [ 30 , 31 ], tomato [ 32 ], chickpea [ 33 , 34 ], cucumber [ 35 ], maize [ 36 ], Brassica rapa [ 37 ], and strawberry [ 38 ]. Four sets of chromosomes in autotetraploid and neo-tetraploid rice made it difficult to map genes associated with fertility.…”

Section: Introductionmentioning

confidence: 99%

Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice

Kamara

Jiao

et al. 2021

IJMS

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Neo-tetraploid rice with high fertility is a useful germplasm for polyploid rice breeding, which was developed from the crossing of different autotetraploid rice lines. However, little information is available on the molecular mechanism underlying the fertility of neo-tetraploid rice. Here, two contrasting populations of tetraploid rice, including one with high fertility (hereafter referred to as JG) and another with low fertility (hereafter referred to as JD), were generated by crossing Huaduo 3 (H3), a high fertility neo-tetraploid rice that was developed by crossing Jackson-4x with 96025-4x, and Huajingxian74-4x (T452), a low fertility autotetraploid rice parent. Cytological, global genome sequencing-based bulked-segregant (BSA-seq) and CRISPR/Cas9 technology were employed to study the genes associated with pollen fertility in neo-tetraploid rice. The embryo sacs of JG and JD lines were normal; however, pollen fertility was low in JD, which led to scarce fertilization and low seed setting. Cytological observations displayed low pollen fertility (25.1%) and approximately 31.3 and 27.2% chromosome lagging at metaphase I and II, and 28.8 and 24.8% chromosome straggling at anaphase I and II in JD, respectively. BSA-seq of F2–3 generations and RNA-seq of F4 generation detected a common fragment, i.e., 18,915,234–19,500,000, at chromosome 7, which was comprised of 78 genes associated with fertility. Among 78 genes, 9 genes had been known to be involved in meiosis and pollen development. Two mutants ny1 (LOC_Os07g32406) and ny2 (LOC_Os07g32040) were generated by CRISPR/Cas9 knockout in neo-tetraploid rice, and which exhibited low pollen fertility and abnormal chromosome behavior. Our study revealed that two unknown genes, LOC_Os07g32406 (NY1) and LOC_Os07g32040 (NY2) play an important role in pollen development of neo-tetraploid rice and provides a new perspective about the genetic mechanisms of fertility in polyploid rice.

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Section: Introductionmentioning

confidence: 99%

Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice

Kamara

Jiao

et al. 2021

IJMS

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“…Fourteen RpsZS18 allelic haplotypes sequence of soybean genotypes were reconstructed by substituting the bases with confident variant calls in the reference genome. Identification of varients in gene region including promoter, UTR, extron or intron region is an effective way of discovering candidate genes, and this approach has been used to identify candidate genes for multiple plant diseases in recent years (Silva et al, 2012 ; Sudheesh et al, 2015 ; Singh et al, 2016a , b ; Li B. et al, 2017 ; Li W. et al, 2017 ; Pandey et al, 2017 ). Allele haplotype sequences containing the respective SNPs and InDels are aligned with each other.…”

Section: Discussionmentioning

confidence: 99%

Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean

et al. 2018

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Phytophthora root rot (PRR) caused by Phytophthora sojae is a major soybean disease that causes severe economic losses worldwide. Using soybean cultivars carrying a Rps resistance gene is the most effective strategy for controlling this disease. We previously detected a novel Phytophthora resistance gene, RpsZS18, on chromosome 2 of the soybean cultivar Zaoshu18. The aim of the present study was to identify and finely map RpsZS18. We used 232 F2:3 families generated from a cross between Zaoshu18 (resistant) and Williams (susceptible) as the mapping population. Simple sequence repeat (SSR) markers distributed on chromosome 2 were used to map RpsZS18. First, 12 SSR markers linked with RpsZS18 were identified by linkage analyses, including two newly developed SSR markers, ZCSSR33 and ZCSSR46, that flanked the gene at distances of 0.9 and 0.5 cM, respectively. Second, PCR-based InDel markers were developed based on sequence differences between the two parents and used to further narrow down the mapping region of RpsZS18 to 71.3 kb. Third, haplotype analyses were carried out in the RpsZS18 region using 14 soybean genotypes with whole-genome resequencing. We detected six genes with unique haplotype sequences in Zaoshu18. Finally, quantitative real-time PCR assays of the six genes revealed an EF-hand calcium-binding domain containing protein encoding gene (Glyma.02g245700), a pfkB carbohydrate kinase encoding gene (Glyma.02g245800), and a gene with no functional annotation (Glyma.02g246300), are putative candidate PRR resistance genes. This study provides useful information for breeding P. sojae-resistant soybean cultivars.

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“…It is a convenient and rapid method for identifying genes by generating two DNA bulks with contrast target trait (Michelmore, Paran, & Kesseli, ). With the release of sequenced genomes, the combined application of BSA and next‐generation sequencing technology represents a new approach to accelerate the identification of candidate genes to regulate important agronomic traits in various crops (Li et al, ; Lu et al, ; Sushma et al, ; Takagi et al, ; Zheng et al, ).…”

Section: Introductionmentioning

confidence: 99%

Identification of loci for single/double flower trait by combining genome‐wide association analysis and bulked segregant analysis in peach (Prunus persica)

Zhu

Fang

et al. 2019

Plant Breeding

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Background Peach is a typical perennial fruit crop that can be categorized both as an ornamental and edible crop. Double flower is an important appearance trait, in which breeders are pursuing in high‐quality ornamental peach breeding. The single/double flower character in peach is controlled by one gene, Dl, and the underlying genetic mechanism is unknown. Objective In this study, we explored the genetic basis of single/double flower trait in peach in a genome‐wide association study using 1 042 687 SNPs characterized in 201 accessions. Methodology Four loci were identified to be significantly associated with the trait on chromosomes (Chr.) 1, 2 and 6. Besides, the bulked segregant analysis (BSA) was performed with two DNA bulks (single and double flower pool) from the F1 population plants of a cross 'Juhuatao' × 'Honggengansutao'. Results We found a genomic region on Chr. 2 by the BSA, which overlapped the association peak on Chr. 2 in the GWAS—denoted as a region harbouring Dl. Finally, a candidate gene was identified by expression analysis of different plant tissues. Conclusion Our results provide insights into the genetic basis of flower shape and might facilitate marker‐assisted selection breeding for ornamental peach.

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Mapping of powdery mildew resistance genes in melon ( Cucumis melo L.) by bulked segregant analysis

Cited by 61 publications

References 39 publications

Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice

Cytological Observations and Bulked-Segregant Analysis Coupled Global Genome Sequencing Reveal Two Genes Associated with Pollen Fertility in Tetraploid Rice

Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean

Identification of loci for single/double flower trait by combining genome‐wide association analysis and bulked segregant analysis in peach (Prunus persica)

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