Genomic signatures of vegetable and oilseed allopolyploid Brassica juncea and genetic loci controlling the accumulation of glucosinolates.

Sheng Chen,Tongyun Sha,Zhesi He,Lili Zhang,Zaiyun Li,Yuanguo Gu,Xiaolong Lyu,Jinghua Yang,Zhongyuan Hu,Hongju He,Mingfang Zhang,Xuming Li,Ian Bancroft,Jing Wang,Zhangping Li

doi:10.1111/pbi.13687

Abstract

SummaryAllopolyploid Brassica juncea crops in Brassicaceae are becoming increasingly revitalized as vegetables and oilseeds owing to wide adaptability and significant economic values. However, the genomic differentiation of diversified vegetables and oilseed B. juncea and the genetic basis underlying glucosinolates accumulation have yet to be elucidated. To address this knowledge gap, we report the sequencing of pairwise genomes of vegetable and oilseed B. juncea at chromosome scale. Comparative genomics analysis unveils panoramic structural variation footprints, particularly the genetic loci of HSP20 and TGA1 associated with abiotic and biotic stresses responses between oilseed and vegetable subgroups. We anchored two major loci of MYB28 (HAG1) orthologues caused by copy number variations on A02 and A09 chromosomes using scored genomic SNPs‐based GWAS that are responsible for seed oil quality‐determining glucosinolates biosynthesis. These findings will provide valuable repertories of polyploidy genomic information enabling polyploidy genome evolution studies and precise genomic selections for crucial traits like functional components of glucosinolates in B. juncea crops and beyond.

Highlights

A single reference genome does not represent the gene content of a species due to gene presence/absence variation (PAV) between individuals
Neofunctionalization of duplicated genes has been observed in cotton (Adams et al, 2003; Rong et al, 2010; Yang et al, 2017), while in Brassica napus, homoeologous exchange (HE) between chromosomes is associated with gene loss (Hurgobin et al, 2018) and with the generation of novel chimeric genes (Zhang et al, 2020)
The number of genes is similar to the 101 040 genes in the Darmorbzh v4 annotation (Chalhoub et al, 2014) and 94 586 to 100 919 genes in eight high-quality B. napus genomes (Song et al, 2020)

Summary

Introduction

A single reference genome does not represent the gene content of a species due to gene presence/absence variation (PAV) between individuals. Genome duplication through polyploidization provides an opportunity for differential gene loss and subsequent presence/absence variation between individuals, and species that have experienced relatively recent polyploidy often host a relatively high proportion of dispensable genes. Several studies have examined gene conservation and loss following polyploidization. Differential fractionation of genomes has been observed following ancient triplication in the diploid Brassica species B. rapa and B. oleracea (Cheng et al, 2014), while in octoploid strawberry (Fragaria ananassa), the diploid F. vesca subgenome dominates the other three subgenomes, having lost the fewest genes (Edger et al, 2019). (2021) Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.

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Conclusion