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Identification and fine mapping of a major locus controlling branching in Brassica napus

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Abstract

Key message

A candidate branching-controlling gene for qDBA09 was identified after delimiting a Brassica napus recessive locus within a 270-kb interval on chromosome A09.

Abstract

Although branching is an important trait associated with the adaptation and yield potential of rapeseed (Brassica napus), the genetic mechanisms underlining branching in this crop remain poorly understood. In this study, we characterized a naturally occurring rapeseed mutant, db1, which showed an ultrahigh branching density phenotype. By combining bulked segregant analysis (BSA) and the Brassica 60K SNP BeadChip Array, we identified two major quantitative trait loci (QTLs), qDBA09 and qDBC06, which were subsequently confirmed using the traditional QTL-mapping approach. Analysis of 208 individuals from a BC1F3 population indicated that the qDBA09 locus is a single Mendelian factor and that the dense branching phenotype is controlled by a single recessive gene. Furthermore, QTL analysis confirmed that qDBA09 explained between 9.5 and 70.5% of the variation in branching-related traits. Using 7785 individuals from the BC1F3 population, we mapped qDBA09 to a DNA fragment of approximately 270 kb in length that contained 27 predicted genes, three of which were identified as potentially involved in the control of the dense branching trait. Based on the reported function of these genes, together with sequence comparisons and co-segregation analysis, we identified a potential candidate gene for the qDBA09 locus. The present findings lay the foundations for further in-depth research on the branching mechanisms of B. napus.

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Acknowledgments

This work was financed by the National Key Research and Development Program of China (Grant Number 2016YFD0100305).

Author information

BL performed the experiments and prepared the manuscript. JG and JC helped with the experiments. ZW and WS helped analyze the data. JW, BY, CM, and TF gave advises to the experimental design. JT conceived the project and revised the manuscript.

Correspondence to Jinxing Tu.

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Electronic supplementary material

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Supplementary Fig. S1. Additional branching phenotypes associated the db1 alleles. Fasciated inflorescence of db1 (a). Primary inflorescence of T109 (b) and db1 (c). Bar = 5 cm (TIF 15944 kb)

Supplementary Fig. S2. Alignment of the amino acid sequences of candidate genes that are polymorphic between T109 and db1. (TIF 11602 kb)

Supplementary Fig. S3. Relative expressions of the candidate genes that exhibited a higher expression in the SAM of TT plants. Asterisks indicate significant differences between plants homozygous for db1 (DD) and T109 (TT). (TIF 947 kb)

Supplementary Fig. S4. Alignment of the gDNA sequences of db1 and T109. BnaA09.ELP6, T109, and db1 denote the sequences of Darmor-bzh, T109, and db1, respectively. (TIF 20100 kb)

Supplementary Table S1. Molecular markers developed in this study. IP, intron polymorphism; SSR, simple sequence repeat. (XLSX 10 kb)

Supplementary Table S2. Primers designed for gene cloning, vector construction and expression analysis. (XLSX 13 kb)

Supplementary Table S3. Single-nucleotide polymorphisms between “dense branching” bulks and “normal branching” bulks. (XLSX 33 kb)

Supplementary Table S4. Co-segregation analysis using 176 recombinants from the BC1F3 population. aPhenotype of the plants: DD, dense branching; TT, normal branching; INTER, intermediate. bGenotype of maker P12: DD, homozygous for the db1 allele; TT, homozygous for the T109 allele; and H, heterozygous. cThree classes were identified for the qDBA09 genotype [homozygous for db1 (DD) and T109 (TT) and heterozygote (H)] using a progeny test. (XLSX 50 kb)

Supplementary Table S5. Predicted Brassica napus genes in the candidate region of the qDBA09 locus, and the best hits for these genes among Arabidopsis thaliana proteins using BLAST. (XLSX 11 kb)

Supplementary Table S6. Co-segregation analysis using 208 plants from the BC1F3 population. Three classes were identified for the qDBA09 genotype [homozygous for db1 (DD) and T109 (TT) and heterozygote (H)] using a progeny test. (XLSX 16 kb)

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Li, B., Gao, J., Chen, J. et al. Identification and fine mapping of a major locus controlling branching in Brassica napus. Theor Appl Genet 133, 771–783 (2020). https://doi.org/10.1007/s00122-019-03506-x

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