ArticleBMC genomics2014
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.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- Genome-wide identification and evolutionary analysis of disease resistance genes in Brassica carinata.The plant genome · 2025Article
- Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.Genomics, proteomics & bioinformatics · 2025Article
- Genome-Wide Identification, Expression, and Protein Analysis of CKX and IPT Gene Families in Radish (International journal of molecular sciences · 2024Article
- Genome-Wide Association Reveals Trait Loci for Seed Glucosinolate Accumulation in Indian Mustard (Plants (Basel, Switzerland) · 2022Article
- Article
- Exploring the gene pool of Brassica napus by genomics-based approaches.Plant biotechnology journal · 2021Review
- Challenges and prospects for a potential allohexaploid Brassica crop.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes.Plant biotechnology journal · 2021Article
- Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding.The plant genome · 2021Review
- Genetic Analysis of Heterosis for Yield Influencing Traits inFrontiers in plant science · 2021Article
- Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) inBiology · 2020Article
- A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes.BMC genomics · 2020Article
- Transcriptomic analysis reveals the mechanism of thermosensitive genic male sterility (TGMS) of Brassica napus under the high temperature inducement.BMC genomics · 2019Article
- Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa.BMC plant biology · 2019Article
- A Mapped Locus on LG A6 ofFrontiers in plant science · 2019Article
- Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities.3 Biotech · 2018Review
- Organization of the genome sequence of the polyploid crop species Brassica juncea.Nature genetics · 2018Article
- QTL Landscape for Oil Content inFrontiers in plant science · 2018Article
- Comparative Mapping Combined With Map-Based Cloning of theFrontiers in plant science · 2018Article
- De novo transcriptome reconstruction of a thermo-sensitive male sterility mutant in rapeseed (Applications in plant sciences · 2017Article
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6 authors.
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No grant is acknowledged in the PubMed record.
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.
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