SSR marker based analysis for identification and of genetic diversity of non-heading Chinese cabbage varieties

Jiwei Yin; Hong Zhao; Xingting Wu; Yingxue Ma; Jingli Zhang; Ying Li; Guirong Shao; Hairong Chen; Ruixi Han; Zhenjiang Xu

doi:10.3389/fpls.2023.1112748

SSR marker based analysis for identification and of genetic diversity of non-heading Chinese cabbage varieties

Front Plant Sci. 2023 Feb 6:14:1112748. doi: 10.3389/fpls.2023.1112748. eCollection 2023.

Authors

Jiwei Yin¹, Hong Zhao², Xingting Wu³, Yingxue Ma³, Jingli Zhang², Ying Li⁴, Guirong Shao⁵, Hairong Chen², Ruixi Han³, Zhenjiang Xu¹

Affiliations

¹ College of Agriculture, South China Agricultural University, Guangzhou, China.
² Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China.
³ Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China.
⁴ State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
⁵ Research and development center, Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou, China.

Abstract

As a widely cultivated vegetable in China and Southeast Asia, the breeding of non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) is widespread; more than 400 varieties have been granted new plant variety rights (PVRs) in China. Distinctness is one of the key requirements for the granting of PVRs, and molecular markers are widely used as a robust supplementary method for similar variety selection in the distinctness test. Although many genome-wide molecular markers have been developed, they have not all been well used in variety identification and tests of distinctness of non-heading Chinese cabbage. In this study, by using 423 non-heading Chinese cabbage varieties collected from different regions of China, 287 simple sequence repeat (SSR) markers were screened for polymorphisms, and 23 core markers were finally selected. The polymorphic information content (PIC) values of the 23 SSR markers ranged from 0.555 to 0.911, with an average of 0.693, and the average number of alleles per marker was 13.65. Using these 23 SSR markers, 418 out of 423 varieties could be distinguished, with a discrimination rate of 99.994%. Field tests indicated that those undistinguished varieties were very similar and could be further distinguished by a few morphological characteristics. According to the clustering results, the 423 varieties could be divided into three groups: pak-choi, caitai, and tacai. The similarity coefficient between the SSR markers and morphological characteristics was moderate (0.53), and the efficiency of variety identification was significantly improved by using a combination of SSR markers and morphological characteristics.

Keywords: DUS test; SSR; genetic diversity; non-heading Chinese cabbage; variety identification.

Grants and funding

The study was co-financed by the National Species Resources Protection Project (h20210472) and the Construction of Agricultural Products Quality and Safety Standards System (2130109).