RNA-seq based SNPs for mapping in Brassica juncea (AABB): synteny analysis between the two constituent genomes A (from B. rapa) and B (from B. nigra) shows highly divergent gene block arrangement and unique block fragmentation patterns

Abstract

BackgroundBrassica juncea (AABB) is an allotetraploid species containing genomes of B. rapa (AA) and B. nigra (BB). It is a major oilseed crop in South Asia, and grown on approximately 6–7 million hectares of land in India during the winter season under dryland conditions. B. juncea has two well defined gene pools – Indian and east European. Hybrids between the two gene pools are heterotic for yield. A large number of qualitative and quantitative traits need to be introgressed from one gene pool into the other. This study explores the availability of SNPs in RNA-seq generated contigs, and their use for general mapping, fine mapping of selected regions, and comparative arrangement of gene blocks on B. juncea A and B genomes.ResultsRNA isolated from two lines of B. juncea – Varuna (Indian type) and Heera (east European type) – was sequenced using Illumina paired end sequencing technology, and assembled using the Velvet de novo programme. A and B genome specific contigs were identified in two steps. First, by aligning contigs against the B. rapa protein database (available at BRAD), and second by comparing percentage identity at the nucleotide level with B. rapa CDS and B. nigra transcriptome. 135,693 SNPs were recorded in the assembled partial gene models of Varuna and Heera, 85,473 in the A genome and 50,236 in the B. Using KASpar technology, 999 markers were added to an earlier intron polymorphism marker based map of a B. juncea Varuna x Heera DH population. Many new gene blocks were identified in the B genome. A number of SNP markers covered single copy homoeologues of the A and B genomes, and these were used to identify homoeologous blocks between the two genomes. Comparison of the block architecture of A and B genomes revealed extensive differences in gene block associations and block fragmentation patterns.ConclusionsSufficient SNP markers are available for general and specific -region fine mapping of crosses between lines of two diverse B. juncea gene pools. Comparative gene block arrangement and block fragmentation patterns between A and B genomes support the hypothesis that the two genomes evolved from independent hexaploidy events.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-396) contains supplementary material, which is available to authorized users.

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

“…This analysis could validate around 93% of the predicted genes. Predicted genes were also confirmed by the Isoseq transcriptome analysis and short-read RNA-seq data generated for B. juncea in some other studies 17,19,20 (Supplementary File 1). A total of 82,008 genes were found to express in one or the other study -38,232 (~79%), 43,776 (~76%) in the A and B genome, respectively.…”

“…Gene block associations have been extensively studied in the selected taxa of the family Brassicaceae by in situ hybridizations 27 , genetic mapping 17,28,29 and genome sequencing 30 to understand the evolutionary processes. These studies have been summarized as -'presence and absence of ancestral genomic block associations in 35 species belonging to different tribes recognized in the family Brassicaceae' 30 ( Supplementary Table 19).…”

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea

“…Previously published transcriptome of Brassica juncea [GSE624286; GBEQ0187 and GSE7320188] and 2. In case of no targets identified in Brassica juncea , targets were identified using Brassica rapa as a reference genome.…”

A Mapped Locus on LG A6 of Brassica juncea Line Tumida Conferring Resistance to White Rust Contains a CNL Type R Gene

“…Genetic mapping was carried out using IP (Intron Polymorphism), genic SSR (simple sequence repeats) and genic SNP (assayed by KASP technology, USA) markers developed earlier for different B. juncea mapping populations in the laboratory (Panjabi et al, 2008;Paritosh et al, 2014;Dhaka et al, 2017). Further, GBS based markers described recently (Paritosh et al, 2019) were added to the map.…”