Two large inversions seriously suppress recombination and are essential for key genotype fixation in cabbage (Brassica oleracea L. var. capitata)

Abstract

Chromosomal inversion is an important structural variation that usually suppresses recombination and is critical for key genotype fixation. In a previous study, an 11.47 Mb recombination suppression region was identified in the yellow-green leaf locus BoYgl-1 on chromosome 1, but the cause of recombination suppression is still unclear. In this study, chlorophyll and carotenoid contents were found to be significantly decreased in the yellow-green leaf mutant YL-1. Genome assembly and comparative analysis revealed that two large inversions in YL-1 were responsible for the severe recombination suppression in the BoYgl-1 locus. Analyses with inversion-specific markers revealed that the inversions were present in 44 (including all wild cabbage; INV1 and INV2) of 195 cabbage inbred lines and 15 (INV1) ornamental kale inbred lines, indicating that these species with INV1 or INV2 may have evolved much earlier than other types of cabbage. Analyses with inversion-correlated markers revealed that the genotypes of CoINV1, CoINV2 and CoINV3 were highly correlated with INV1 and INV2, indicating that INVs could fix the key genotypes of the involved region. In addition, a 5.87 Mb assembly inversion was identified at the BoYgl-1 locus in the TO1000 genome by genome comparative analysis. This study provides new insight into the recombination suppression mechanism of chromosomal inversion and the application of genome fragment fixation in cabbage breeding.

Acknowledgments

This work was supported by a grant from the National Natural Science Foundation of China (31872948).

Author Contributions

Y.Z. conceived and designed the experiments. B.Z. performed the experiments and analyzed the data. B.Z. wrote the manuscript. Y.Z. revised the manuscript. Y.W. and S.L. conducted the evolutionary analysis. L.Y., M.Z., H.L., Y.W., J.J., and X.H. provided the valuable suggestions on the manuscript. All authors read and approved the manuscript.

Data Availability

All the data generated or analyzed in this study are included in this published article and its supplementary information files. All the sequence data of the present study have been deposited in the NCBI Sequence Read Archive (SRA) database under BioProject PRJNA949422. The reference genome ‘TO1000’ can be found from the website https://plants.ensembl.org/Brassica_oleracea/Info/Index. The genome assembly can be found through the NCBI Sequence Read Archive (SRA) database under BioProject PRJNA1060854.

Conflict of Interest statement

The authors declare that they have no competing interests.

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