Validation of a set of informative simple sequence repeats markers for variety identification in Pak‐choi (Brassica rapa L. ssp. chinensis var. communis)

Abstract

A core set of 21 simple sequence repeats (SSR) markers was developed for Pak‐choi (Brassica rapa ssp. chinensis var. communis) variety identification. We initially selected 74 SSR markers which exhibited high polymorphism and reproducibility in SSR detection from 2129 SSRs. Using the 74 SSR‐based dendrogram for 45 inbred lines as calibration, 21 core SSRs were selected out. The utility of this core set SSRs was firstly tested in 45 inbred lines and finally verified in 102 commercial varieties. We also constructed a molecular ladder for each core SSR as a reference standard. Diversity analysis of this core SSR panel in 102 varieties demonstrated that each marker generates 2–3 alleles (averaged 2.33), with polymorphism information content values ranging from 0.01 to 0.56 (averaged 0.31). The averaged values of Shannon information index, observed heterozygosity, expected heterozygosity and Wright's fixation index were 0.59, 0.43, 0.38 and −0.09, respectively. Furthermore, the 21 SSR‐based classifications for 102 varieties were consistent with traditional classification based on morphology. This core SSR panel represents an effective tool for genetic variation analysis in Pak‐choi.

Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

“…Furthermore, the PIC of SSR markers in Pak‐choi (0.31) was lower than that of core SNP markers in non‐heading Chinese cabbage (0.34). The reason for this higher value may be that the materials used in our paper were more diverse than those in the previous study (Su et al, ). We would also like to stress that the molecular information provided in this paper can easily be adapted and exploited on alternative technological platforms for SNP detection.…”

“…In previous studies, SSR markers were detected within morphotypes represented by multiple accessions, with mean reported PIC values of 0.50 (Brussels sprouts), 0.54 (broccoli), 0.57 (cauliflower) and 0.65 (cabbage) (Iniguez‐Luy, Voort, & Osborn, ; Su et al, ). We note that the PIC of biallelic markers, such as SNPs, ranges from 0 to 0.5, whereas PIC values of multiallelic markers, such as SSRs, can exceed 0.5 and even approach 1.…”

“…Single‐nucleotide polymorphism marker technology has been applied in genetic diversity analyses, genetic map construction, association map analyses and marker‐assisted selection breeding of many different crop species (Semagn, Babu, Hearne, & Olsen, ; Sindhu et al, ; Tian et al, ; Varshney et al, ). In non‐heading Chinese cabbage, however, RAPD, AFLP and SSR markers have primarily been used (Guo, Zhou, Ma, & Cao, ; Han, Hou, Hai‐Ming, Shi, & Wang, ; Su et al, ). Single‐nucleotide polymorphism markers have recently been developed and adapted for use with cost‐effective genotyping platforms such as KASP and BeadXpress assays (Allen et al, ; Cortés et al, ; Hiremath et al, ).…”

“…To identify high‐quality core SNP markers, principal component analysis (PCA) was performed using Tassel 4.0 (Bradbury et al, ), and SNP markers with suitable eigenvector values were taken into account (Su et al, ; van Heerwaarden, Odong, & van Eeuwijk, ). Polymorphic information content (PIC) and gene diversity values for the SNP markers in this study were calculated using PowerMarker (https://brcwebportal.cos.ncsu.edu/powermarker/).…”