Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Abstract

BackgroundThere are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, ArAr; B. nigra, BniBni; B. oleracea, CoCo) and the derived allotetraploid species (i.e.: B. juncea, AjAjBjBj; B. napus, AnAnCnCn; B. carinata, BcBcCcCc). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).ResultsA dense genetic linkage map of B. juncea was constructed using an F2 population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing Aj-An than between An-Ar and Aj-Ar subgenome pairs.ConclusionsThe development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the Ar, and AnCn genomes allowed us to compare the A subgenome structure of B. juncea (Aj) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (Ar, An and Aj) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

“…We constructed a high-resolution genetic map with 5,333 bin markers and 18 pseudo-chromosomes (10A and 8B subgenomes; Supplementary Tables 5 and 6). We then integrated a published B. juncea genetic map 24 (Supplementary Table 7). Finally, we anchored 91.5% and 72.3% of A-and B-subgenome assembly sequences onto the 10 and the 8 pseudo-chromosomes, respectively (Supplementary Table 8a and Supplementary Fig.…”

“…3). This generated assembly v1.0 (Supplementary 24 to assess the genome assembly of B. juncea. The assembled genome of B. juncea was also validated by mapping 23,002 ESTs (length ≥ 500 bp) downloaded from NCBI.…”

Genome-Wide Identification, Localization, and Expression Analysis of Proanthocyanidin-Associated Genes in Brassica

“…The other BESs were mapped to other chromosomes or not detected in the B. rapa and B. napus reference genome. These findings indicate that although B. rapa, B. juncea , and B. napus have the common A-genome, the chromosomes of each of these species do not harbor the same structure (Zou et al, 2016). On the other hand, assembly of the present reference genomes of Brassica species need improving.…”

Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata

“…On the one hand, rich subgenomic variation exists within each of the Brassica A, B and C genomes as a result of speciation, domestication and geographic differentiation (Chalhoub et al, 2014;Liu et al, 2014;Wang et al, 2011). On the other hand, rich post-Neolithic variation exists between subgenomes as a result of hybridization, polyploidization, domestication and artificial selection for different human uses, such as between the A r /A j /A n subgenomes from B. rapa, B. juncea and B. napus Zou et al, 2016). Furthermore, early-modern variation exists within species (diverse lines), resulting from processes such as artificial selection and genetic improvement.…”