A study of genetic diversity of Brassica rapa L. accessions from the VIR collection by analyzing DNA polymorphism in microsatellite loci

Abstract

The species Brassica rapa L. includes leafy and root crops grown in many countries of the world. Clarification of genetic relationships and population structure allows for a more accurate parental line selection for further breeding using genetically distinct forms. The B. rapa collection maintained at VIR contains 1750 accessions representing different subspecies and countries of origin, and it is a good tool for studying the diversity of cultivated forms using molecular genetic methods. The aim of the study was to investigate the genetic diversity and clarify the relationships within the B. rapa species using molecular markers. Molecular screening of 80 accessions using 16 microsatellite markers revealed alleles ranging in size from 85 to 460 bp with an average of 7.8 alleles per locus. The average polymorphic index content (PIC) was 0.278, and the expected heterozygosity (H) averaged was 0.35. Rare and unique alleles were identified for Beijing cabbage (k-63 and k-108), Japanese leafy vegetables (k-217 and k-335) and turnip (k-738) samples. Alleles of SSR loci BRMS-007 (123 bp) and BRMS-034 (136 bp) were identified, which are characteristic only of accessions of turnips, rapeseed and sarsons. In silico analysis of primer pairs was performed to clarify the sizes of expected fragments relative to the reference genome CAAS_Brap_v3.01 of Chinese cabbage line Chiifu-401-42. Phylogenetic analysis was performed using the STRUCTURE program and resulted in the distribution of accessions into four clusters according to botanical classification: Chinese cabbage; pakchoi, tatsoi; Japanese leafy vegetables, wutacai, tsoisum, mizuna and mibuna (kyona) and hybrid forms; turnip and rape accessions.