High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in <i>Capsicum frutescens</i>

Yangmin Zhong; Yuan Cheng; Meiying Ruan; Qingjing Ye; Rongqing Wang; Zhuping Yao; Guozhi Zhou; Jia Liu; Jiahong Yu; Hongjian Wan

doi:10.3390/horticulturae7070187

Horticulturae (Jul 2021)

High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in <i>Capsicum frutescens</i>

Yangmin Zhong,
Yuan Cheng,
Meiying Ruan,
Qingjing Ye,
Rongqing Wang,
Zhuping Yao,
Guozhi Zhou,
Jia Liu,
Jiahong Yu,
Hongjian Wan

Affiliations

Yangmin Zhong: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Yuan Cheng: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Meiying Ruan: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Qingjing Ye: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Rongqing Wang: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Zhuping Yao: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Guozhi Zhou: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Jia Liu: Wulanchabu Academy of Agricultural and Husbandry Sciences, Wulanchabu 012000, China
Jiahong Yu: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Hongjian Wan: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

DOI: https://doi.org/10.3390/horticulturae7070187
Journal volume & issue: Vol. 7, no. 7
p. 187

Abstract

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Capsicum frutescens, one of the domesticated species of pepper grown worldwide, is thought to be highly advantageous due to its strong resistance against plant pathogenesis, high productivity, and intense aroma. However, a shortage of molecular markers limits the efficiency and accuracy of genetic breeding for pepper. With the newly developed next-generation sequencing technology, genome sequences of C. frutescens can be generated, which are now available for identifying SSR markers via data mining. In this study, a total of 278,425 SSRs were detected from the pepper genome using MISA software. It was observed that trinucleotides were the dominant repeat motif. This was followed by dinucleotides, tetranucleotides, pentanucleotides, and the hexanucleotides repeat types. (AT)n (TTG)n (AAAT)n (AAATA)n (TATAGA)n is known to be the most common repeat motifs corresponding to dinucleotide to hexanucleotide repeats, respectively. In addition, a total of 240 SSR primers evenly distributed over all 12 chromosomes were designed and screened against 8 C. frutescens cultivars. Of these, 33 SSR markers that have high polymorphism, have been scrutinized for 147 accessions from 25 countries. The dendrogram constructed clustered these accessions into seven major groups. The groups were found to be consistent with their origins. The results obtained in this study provided resources of SSR molecular markers and insight into genetic diversity of the C. frutescens.

Published in Horticulturae

ISSN: 2311-7524 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Agriculture: Plant culture
Website: http://www.mdpi.com/journal/horticulturae

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