Identification and fine mapping of qSB.A09, a major QTL that controls shoot branching in Brassica rapa ssp. chinensis Makino
QTL mapping plus bulked segregant analysis revealed a major QTL for shoot branching in non-heading Chinese cabbage. The candidate gene was then identified using sequence alignment and expression analysis.
Shoot branching is a complex quantitative trait that contributes to plant architecture and ultimately yield. Although many studies have examined branching in grain crops, the genetic control of shoot branching in vegetable crops such as Brassica rapa L. ssp. chinensis remains poorly understood. In this study, we used bulked segregant analysis (BSA) of an F2 population to detect a major quantitative trait locus (QTL) for shoot branching, designated shoot branching 9 (qSB.A09) on the long arm of chromosome A09 in Brassica rapa L. ssp. chinensis. In addition, traditional QTL mapping of the F2 population revealed six QTLs in different regions. Of these, the mapping region on chromosome A09 was consistent with the results of BSA-seq analysis, as well as being stable over the 2-year study period, explaining 19.37% and 22.18% of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants, qSB.A09 was further delimited to a 127-kb genomic region harboring 28 annotated genes. We subsequently identified the GRAS transcription factor gene Bra007056 as a potential candidate gene; Bra007056 is an ortholog of MONOCULM 1 (MOC1), the key gene that controls tillering in rice. Quantitative RT-PCR further revealed that expression of Bra007056 was positively correlated with the shoot branching phenotype. Furthermore, an insertion/deletion marker specific to Bra007056 co-segregated with the shoot branching trait in the F2 populations. Overall, these results provide the basis for elucidating the molecular mechanism of shoot branching in Brassica rapa ssp. chinensis Makino.
This research was financially supported by the National Natural Science Foundation of China (No. 31801873), the Outstanding Scientists Training Program, BAAFS (JKZX201906), the Beijing Academy of Agricultural and Forestry Sciences (KJCX20180204), the China Postdoctoral Science Foundation (2019T120066), the Beijing Postdoctoral Research Foundation (2017-ZZ-085) and the Earmarked Fund for China Agriculture Research System (CARS-23-A-05).
Author contribution statement
SY, TS, PL, and FZ designed the experiments. PL, TS, BZ, XX, WW, YY, and DZ carried out the experiments. PL, SY, and TS performed data analysis and wrote the paper. TS, SY, and XZ provided guidance for phenotypic assays, SY, TS, and PRL assisted in genetic analysis. All authors discussed the results and commented on the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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