Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs)

Shi Jun Ma; Kyu Jin Sa; Tak-Ki Hong; Ju Kyong Lee

doi:10.1007/s13258-018-0756-3

Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs)

Genes Genomics. 2019 Mar;41(3):267-281. doi: 10.1007/s13258-018-0756-3. Epub 2018 Nov 14.

Authors

Shi Jun Ma^{1

2}, Kyu Jin Sa¹, Tak-Ki Hong¹, Ju Kyong Lee³

Affiliations

¹ Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, South Korea.
² School of Life Sciences, Shandong University, No.72 Binhai Road, Jimo District, Qingdao, 266237, P.R. China.
³ Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, South Korea. jukyonglee@kangwon.ac.kr.

PMID: 30426456
DOI: 10.1007/s13258-018-0756-3

Abstract

Introduction: Identification of genetic variation is an essential ability for the long-term success of breeding programs and maximizes the use of germplasm resources. In East Asia, China has a long history of the cultivation of Perilla crop, but there has been little research on the genetic diversity and genetic relationships among accessions of Perilla crop and their weedy types.

Objectives: To better understand the genetic variations of the cultivated and weedy types of Perilla crop in China, the 91 accessions were evaluated for genetic diversity by 21 simple sequence repeat (SSR) markers.

Methods: SSR amplifications were conducted in a total volume of 20 µL, consisting of 20 ng genomic DNA, 1X PCR buffer, 0.5 µM forward and reverse primers, 0.2 mM dNTPs, and 1 U Taq polymerase. Power Marker version 3.25 was applied to obtain the information on the number of alleles, allele frequency, major allele frequency, gene diversity (GD), and polymorphic information content (PIC). The similarity matrix was used to construct an unweighted pair group method with arithmetic mean dendrogram by the application of SAHN-Clustering from NTSYS-pc.V.2.1.

Results: A total of 147 alleles were identified with an average of 7 alleles per locus. The average values of PIC and GD were 0.577 and 0.537, respectively. The genetic diversity level of accessions from Northern China was lower than accessions from Southern China. The genetic diversity level and PIC values for accessions of var. crispa were the highest. For accessions of cultivated var. frutescens, genetic diversity in Southern China was higher than that in Northern China.

Conclusion: Most cultivated Perilla accessions were clearly separated from weedy Perilla accessions, but there was no clear geographic structure between cultivated Perilla crop and weedy types based on their regional distribution. This study demonstrated the utility of SSR analysis for performing genetic and population analysis of cultivated and weedy types of Perilla accessions in China.

Keywords: Genetic similarity; Geographical location; Perilla frutescens; Polymorphic information content; Population structure; SSR marker.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Microsatellite Repeats*
Perilla / genetics*
Polymorphism, Genetic*