Genomic selection and genetic architecture of agronomic traits during modern flowering Chinese cabbage breeding

Abstract

Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired traits during a short-term artificial selection process. Here, we investigate the genetic variation, population structure, and diversity of a diverse germplasm collection of 403 flowering Chinese cabbage accessions. Our investigation seeks to elucidate the genomic basis that guides the selection of adaptability, yield, and pivotal agronomic traits. We further investigated breeding improvement associated with stem development by integrating transcriptome data. Genome-wide association analysis identified 642 loci and corresponding candidate genes associated with 11 essential agronomic traits, including plant architecture and yield. Furthermore, we uncovered a significant disparity in the allele frequency distribution of nonsynonymous mutations in these candidate genes throughout the improvement stages. Our results shed light on the genetic basis of improvement and crucial agronomic traits in flowering Chinese cabbage, offering invaluable resources for upcoming genomics-assisted breeding endeavors.

Acknowledgements

This work was funded by the Key-Area Research and Development Program of Guangdong Province (2022B0202080001), the Science and Technology Program of Guangzhou (202206010173, 2023B03J1270), the Seed Industry Revitalization Project of Guangdong Province Rural Revitalization Strategy Special Fund in 2022 (2024-NPY-03-001), the Guangdong Province Seed Industry Revitalization Project (2022-NJS-03-001), and the Guangzhou Agricultural Support Fund Project (Sui Cai Bian [2023] No. 1).

Author contributions

C.M.C., Y.L., and Y.S.Z. designed the experiments; Y.H.Z., G.G.L., D.J., and Z.S.Z. performed experiments; Y.H.Z., Y.L., J.T.W., K.X.Z., and M.X.C. analyzed data; Y.H.Z. Y.L., and C.M.C. wrote the manuscript and substantively revised the manuscript; Y. L. and M.H. reviewed the manuscript. The final manuscript has been read and approved by all authors.

Data availability

The transcriptome and reference genome data used in this study are derived from previously published research. Specifically, the transcriptome data of stalks and leaves were obtained from the publicly accessible National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/) under the accession numbers PRJNA390062 and PRJNA778186 [33,34]. The reference genome sequence and the raw genome resequencing data used in this study are available in CNGBdb under Bioproject number CNP0006162 [24].

Conflict of interest statement

None declared.

Supplementary data

Supplementary data are available at Horticulture Research online.

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