Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus

Zhang, Kaijing; Wang, Xing; Zhu, Wenwei; Qin, Xiaodong; Xu, Jian; Cheng, Chunyan; Lou, Qunfeng; Li, Ji

doi:10.1007/s00122-018-3150-2

Cited by 61 publications

(47 citation statements)

References 60 publications

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“…Previous studies showed that most of the QTLs for PM resistance in cucumber are recessively inherited [6,7,34], indicating that the resistance is governed by impaired susceptibility (S) genes [12,13] mapped cucumber genes that are homolog to know plant S genes for PM and downy mildew (DM) resistance.…”

Section: Discussionmentioning

confidence: 99%

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Identification of novel loci and candidate genes for resistance to cucumber powdery mildew using GWAS

Li¹,

Lu²,

Liu³

et al. 2020

Preprint

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Background Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been detected in previous studies, however, none of these studies used the approach of genome-wide association analysis (GWAS). In this study, a cucumber core germplasm (CG) consisting of 109 resequenced lines was evaluated for PM resistance in three seasons. Results twelve loci (pmG1.1, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1 and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7 using GWAS. Among these loci, pmG2.1, pmG4.1 and pmG6.1 were the novel ones that have not been reported in previous studies. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in three seasons, for which three candidate genes Csa2G022790, Csa5G484620 and Csa5G604330 were respectively predicted using pairwise LD correlation and qRT-PCR analysis. Further, Csa4G022270 in pmG4.1, Csa6G022350 and Csa6G022370 in pmG6.1 might be the candidate genes based on the annotation of homologous genes in Arabidopsis. Conclusion Twelve Loci related to powdery mildew resistance in cucumber were detected by genome-wide association analysis, three of which namely pmG2.1, pmG4.1 and pmG6.1 are novel. Three candidate genes within the genomic region of locus pmG2.1, pmG5.2 and pmG5.3 were identified, respectively. These results provide targets for gene cloning and genetic breeding of PM resistance in cucumber.

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Section: Discussionmentioning

confidence: 99%

“…For example, The MLO-like gene CsaMLO8 [13] located nearby pmG5.4 [15]. A DMR and PMR candidate gene Csa5M622830 (Chr.5: 24735193… 24738505) was also nearby the pmG5.4 [34]. The candidate gene Csa5G604340 for pmG5.3 is a homology of AtPMR6 [13].…”

Section: Discussionmentioning

confidence: 99%

Identification of novel loci and candidate genes for resistance to cucumber powdery mildew using GWAS

Li¹,

Lu²,

Liu³

et al. 2020

Preprint

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“…One hundred and forty-five F 2 populations (B/S population) were generated from the cross between 'EC1' and '8419s-1' [15]. One hundred and fifty-five RILs population (O/S population) were derived from the cross of 'CCMC' and 'IL52' [16]. 'EC1' is an inbred line derived from a European type 'Delta star' [15], which bear blunt round fruit tip with fruit tip index in range of 2.873±0.110 and fruit tip angel in range of 151°±7° ( Fig.…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

“…IL52 is an introgression line derived from interspecific hybridization between cucumber and the wild relative species Cucumis hystrix Chakr. [16,[42][43][44], which bear oval round fruit tip with fruit tip index in range of 2.441±0.047 and fruit tip angel in range of 127°±4° (Fig. 2B, Additional file 1: Table S1).…”

Section: Plant Materials and Growth Conditionsmentioning

confidence: 99%

Diversity of cucumber fruit tip is attributed to the epistatic QTL pairs Ft4.1 and Ft6.1

Zhu¹,

Zhang²,

Liang³

et al. 2020

Preprint

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BackgroundThe shape of fruit tip is critical to appearance quality and commodity value of cucumber (Cucumis sativus L.). Although diversity of cucumber fruit tip is rich, the genetic basis and molecular mechanism were poorly understood. In this study, the morphological and histological features of fruit tip were investigated to accurately evaluate the diversity in cucumber germplasm. QTLs of fruit tip were genetically mapped by using F 2 and RILs populations. Candidate genes of major-effect QTLs were predicted. ResultsThe appearance of cucumber fruit tip was generally divided into sharp, oval-round and blunt-round categories, but morphological measurement showed that the angle of fruit tip was continuously distribute in range of 99~173° and the fruit tip index (the ratio of diameter and length of tips) was in range of 1.4~3.5. Histological analysis suggested that the different structures of fruit tips were owed to the different distribution of cell number in vertical and horizontal direction, rather than difference in cell size. In total, thirty fruit tip related QTLs were identified from two mapping populations including a F 2 population derived from EC1 (blunt round tip) × 8419s-1 (sharp tip) and a RILs population derived from IL52 (oval round tip) × CCMC (sharp tip). Two major-effect QTLs were detected, of which Ft4.

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“…one bulk has more allele A while the other bulk has more allele a. BSA was primarily used to develop genetic markers for detecting gene-trait association at its early stage (1,2). Application of the next generation sequencing (NGS) technology to BSA eliminated the time-consuming and labor-intensive marker development and genetic mapping steps, and dramatically sped up the detection of gene-trait associations (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). This technique was termed either QTL-seq or BSA-Seq in different publications (5,6,19), we adapted the latter here because it can be applied to study both qualitative and quantitative traits.…”

Section: Introductionmentioning

confidence: 99%

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

Zhang

Panthee

2019

Preprint

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Bulked segregant analysis (BSA), coupled with next generation sequencing (NGS), allows the rapid identification of both qualitative and quantitative trait loci (QTL), and this technique is referred to as BSA-Seq here. The current SNP index method and G-statistic method for BSA-Seq data analysis require relatively high sequencing coverage to detect major single nucleotide polymorphism (SNP)-trait associations, which leads to high sequencing cost. Here we developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python, the program was named PyBSASeq. Using PyBSASeq, the likely trait-associated SNPs (ltaSNPs) were identified via Fisher's exact test and then the ratio of the ltaSNPs to total SNPs in a chromosomal interval was used to identify the genomic regions that condition the trait of interest. The results obtained this way are similar to those generated by the current methods, but with more than five times higher sensitivity, which can reduce the sequencing cost by~80% and makes BSA-Seq more applicable for the species with a large genome.

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Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus

Cited by 61 publications

References 60 publications

Identification of novel loci and candidate genes for resistance to cucumber powdery mildew using GWAS

Identification of novel loci and candidate genes for resistance to cucumber powdery mildew using GWAS

Diversity of cucumber fruit tip is attributed to the epistatic QTL pairs Ft4.1 and Ft6.1

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

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