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

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.

Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (Juglans regia L.) in Middle Asia

“…The Ho and He of non-heading Chinese cabbage were 0.530 and 0.726, respectively. Both of them were higher than the present study, however they were artificially selected plant species [64,65]. Genetic diversity is influenced by many factors, including reproductive systems, natural selection, bottleneck effect, evolution, life history, habitat fragmentation, anthropogenic disturbance, and many others [60].…”

Establishment of novel SSR markers from transcriptome data of Chimonanthus praecox and application in the variety identification

“…SSRs also known as microsatellites are one of the most important marker systems for plant genetic analysis, gene mapping, quantitative trait locus (QTL) mapping, and marker-assisted selection (MAS) breeding based on their high rates of mutation, universal distribution and high density in a multitude of genomes [38,39]. Due to their homology among related species in DNA coding regions and adequate polymorphisms provide large variations in DNA non-coding regions [38,40], SSR markers have been speci cally applied in a variety of identi cation procedures that includes the cultivars of a number of plants, such as Prunus persica [41], Morella rubra [42], Punica granatum [43], sympodial bamboo [44] and so more. Traditional SSR development method is a di cult, costly and labour intensively process, but the next-generation sequencing technology can effectively identify a large number of SSRs at a small cost and effort compared to traditional methods.…”

Morphological variation and expressed sequence tags-simple sequence repeats-based genetic diversity of Aspergillus cristatus in Chinese dark tea

“…Although the clustering tree topology of EST-SSR markers and morphological markers were not completely consistent, the traits of species are usually determined by multiple genes, and the detected EST-SSR loci are not necessarily associated with the traits. The integration of EST-SSR markers and morphological markers enhances the elucidation of the genetic diversity present within a species ( Yin et al, 2023b ).…”