Map-based cloning and functional characterization reveal CDF3 as the causal gene for the flowering time phenotype in Brassica rapa and Brassica napus

Abstract

Spring-type Brassicarapa L.isavaluablegeneticresourceforbreedingearly-maturingcrops,offeringadvantagessuchasearly flowering and rapid maturation. However, the genetic mechanisms governing flowering time in spring-type B. rapa remain insufficiently understood. In this study, we investigated the flowering-time trait of an extremely early-maturing landrace, ‘Haoyou 11’, originating from the Qinghai-Tibetan Plateau. Initial mapping was conducted using an F₂ population derived from the cross between Haoyou 11 and Dahuang (a late-flowering spring-type landrace of B. rapa). A major quantitative trait locus for flowering time, designated qFTA06, was identified within a 1.7-Mb interval on chromosome A06 using genotyping-by-sequencing and bulked segregant analysis sequencing (BSA-seq). The locus qFTA06 was subsequently fine-mapped to a 75.16-kb region with a set of near-isogenic lines (NILs), and BrCDF3, a gene encoding a Dof transcription factor, was identified as the causal gene underlying qFTA06. Virus-induced gene silencing experiments revealed that BrCDF3 acts as a negative regulator of flowering time under long-day conditions, with sequence variation contributing to the early-flowering phenotype in Haoyou 11. Phenotypic analysis of NILs showed that NIL-E, carrying the BrCDF3 allele from Haoyou 11, flowered ∼7 days earlier than NIL-L, which harbors the BrCDF3 allele from Dahuang. By employing CRISPR/Cas9 technology, we further validated that the homologous gene BnCDF3 also functions as a negative regulator of flowering time in Brassica napus L., and analyzed natural variations in the CDF3 gene across natural populations. This study provides new insights into the genetic basis of flowering time in spring-type B. rapa, advancing early-maturity breeding efforts in crops.

Acknowledgements

This study was supported by the National Natural Science Foun-dation of China (U24A20398), the Qinghai Provincial High-level Scientist Responsibility System Project (2022-NK-170), and the Earmarked Fund for China Agriculture Research System (CRAS-12).

Author contributions

L.X. (Lu Xiao) and D.D. were responsible for the experimental design. Q.M. carried out the experiments. L.X. (Lu Xiao) and Q.M. wrote and revised the manuscript. K.L. helped with the experimental design. Z.Z., G.T., and L.X. (Liang Xu) provided experimental materials. Y.Q. investigated the phenotypes of natural populations. H.L., L.W., H.Z., and D.P. aided in performing the experiments.

Data availability

Supporting data for this work are included in the manuscript and its supplementary files. The BSA and GBS datasets can be found in the NCBI database under SRA accession numbers PRJNA1214907 and PRJNA1214908.

Conflicts of interest statement

The authors declare no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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