High-resolution mapping of quantitative trait loci controlling main floral stalk length in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

BACKGROUND: For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have been studied extensively, the main flower stalk length (MFSL) have been rarely investigated. Two inbred lines, 06–247 and He102, have significant differences in the MFSL. In this study, these two materials were selected as parental lines for the construction of a recombinant inbred line (RIL) mapping population. High-density mapping of QTL for the MFSL was performed based on the deep resequencing of parental lines and specific locus-amplified fragment sequencing (SLAF-Seq) of individual recombination inbred lines. RESULTS: An F(7) population consisting of 150 lines was developed. Deep resequencing of parental lines produced 21.08 gigabases, whereas SLAF-Seq produced an average of 428.35 million bases for each progeny. The total aligned data from the parental lines identified 1,082,885 high-quality single nucleotide polymorphisms (SNPs) between parental lines. Out of these, 5392 SNP markers with a segregation type of aa×bb and average integrity of > 99% were suitable for the genetic linkage map construction. The final map contained 10 linkage groups (LGs) was 1687.82 cM in length with an average distance of 0.32 cM between adjacent markers. Based on the high-density map, nine QTLs for MFSL were found to be distributed on seven chromosomes, and two major-effect QTLs were identified for the first time. The physical distance between adjacent markers of two major-effect QTLs was 44.37 kbp and 121.91 kbp, respectively. Approximately 2056 and 6769 SNP markers within confidence intervals were identified according to the results of parental line resequencing, which involved 24 and 199 mutant genes. CONCLUSIONS: The linkage map constructed in this study has the highest density in Chinese cabbage to date. Two major-effect QTLs for MFSL in Chinese cabbage were also identified. Among these, a novel QTL associated with bolting mapped on LG A04 was identified based on MFSL. The results of this study provide an important platform for gene/QTL mapping and marker-assisted selection (MAS) breeding for bolting-resistant Chinese cabbage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5810-2) contains supplementary material, which is available to authorized users.