Dataset Information

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F₅ Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

ABSTRACT: Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F₅ population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP markers were utilized for the construction of genetic linkage map and QTL analysis. Overall read mapping percentage of 87.29% was achieved in this study with the total length of mapped region ranging from 2,956,730 to 25,537,525 bp. A total of 41,111 polymorphic SNPs were identified, and a final of 1,841 SNPs were filtered for the construction of a linkage map. A total of 12 linkage groups were constructed corresponding to each chromosome with 1,308 SNP markers with the map length of 2506.8 cM. Further, two QTLs such as Pm-2.1 and Pm-5.1 were identified in chromosomes 2 and 5, respectively, for the PM resistance. Overall, the outcomes of the present endeavor can be utilized for the marker-assisted selection of pepper with powdery mildew-resistant trait.

SUBMITTER: Manivannan A

PROVIDER: S-EPMC7987414 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F<sub>5</sub> Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Manivannan Abinaya A Choi Sena S Jun Tae-Hwan TH Yang Eun-Young EY Kim Jin-Hee JH Lee Eun-Su ES Lee Hye-Eun HE Kim Do-Sun DS Ahn Yul-Kyun YK

BioMed research international 20210315

Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F<sub>5</sub> population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP mar ...[more]

PMID: 33816626

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Project description:BackgroundCucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL).ResultsWe herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.ConclusionOur results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.

Dataset Information

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F₅ Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Publications

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F<sub>5</sub> Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

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Dataset Information

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Publications

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F<sub>5</sub> Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F₅ Population of Pepper with Contrasting Powdery Mildew Resistance Trait.