Fingerprint construction through genotyping by sequencing for applied breeding in Brassica rapa

Abstract

This study evaluated the genotyping by sequencing (GBS) protocol for fingerprinting Brassica rapa, and the data derived were more reliable than the re-sequencing data of B. rapa. Of the 10 enzyme solutions used to analyze the numbers of genotypes and single-nucleotide polymorphisms (SNPs) in B. rapa, five solutions showed better results, namely, A (HaeIII, 450–500 bp), E (RsaI+HaeIII, 500–550 bp), F (RsaI+HaeIII, 500–600 bp), G (RsaI+HaeIII, ‘All’ fragment), and J (RsaI+EcoRV-HF®, ‘All’ fragment). The five enzyme solutions showed less than 40% similarity in different individuals from various samples, and 90% similarity between two individuals from one sample. The E enzyme solution was the most suitable for fingerprinting B. rapa, revealing well-distributed SNPs in the whole genome. Of the 82 highly inbred lines and 18 F1 lines of B. rapa sequenced by GBS in the E enzyme solution, known parents of 10 F1 lines were verified, and male parents were discovered for 8 F1 lines that had only known female parents. This study provides a valuable method for screening parents for F1 lines in B. rapa for the efficient evaluation of GBS with varied library construction strategies.