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SummaryBrassica carinata(BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes ofBrassica nigra(BB) andBrassica oleracea(CC). It is an oilseed crop endemic to the Northeastern regions of Africa. Although it is grown in a limited manner,B. carinatais of value as it is resistant/highly tolerant to most of the pathogens affecting cultivated Brassica species of the U’s triangle that are grown worldwide as oilseed and vegetable crops. We report a chromosome-scale genome assembly ofB. carinataaccession HC20 using long-read Oxford Nanopore and Illumina sequencing and BioNano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the available long-read genome assemblies of the six species of the U’s triangle and found a highly conserved gene number and collinearity suggesting thatB. juncea(AABB),B. napus(AACC), andB. carinataare strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire ofB. carinataresulting in the identification of 465 NLRs. We investigated the extent and nature of early generation genomic interactions between the subgenomes ofB. carinataandB. junceain interspecific crosses between the two species. We found that C chromosome additions are well tolerated, with homoeologous exchanges occurring between the A and C genomes. Based on the genomic interactions, we propose strategies to utilize the interspecific crosses for transferring disease resistance fromB. carinatatoB. junceaand other Brassica species.

Glucosinolate content in the Brassica oilseed crops has been reduced to the globally accepted Canola quality levels, making the seed meal useful as a protein-rich animal feed. However, the overall lower glucosinolate content in such plants renders them vulnerable to pests. We report CRISPR/Cas9-based editing of glucosinolate transporter (GTR) family genes to develop ideal oilseed mustard lines with the desired low levels of seed glucosinolates while maintaining high glucosinolate levels in leaves and pod walls, without affecting the seed yield and seed quality traits. The low-seed and high-leaf glucosinolate mustard lines with improved nutritional and defense traits will raise its international trade potential both as oilseed and feed crop.

Brassica juncea (AABB, 2n=36), commonly called mustard is an allopolyploid crop of recent origin but has considerable morphological and underlying genetic variation. An F1-derived doubled haploid (F1DH) population developed from a cross between a Indian oleiferous line, Varuna, and a Chinese stem type vegetable mustard, Tumida showed significant variability for some key plant architectural traits, including four stem strength-related traits, stem diameter, plant height, branch initiation height, number of primary branches (Pbr), and days to flowering (Df). Multi-environment QTL analysis identified twenty environmentally stable QTL for the nine plant architectural traits. Both Tumida and Varuna contain some positive QTL that can be used to breed superior ideotypes in mustard. A QTL cluster on LG A10 contained environmentally stable QTL for seven architectural traits. This region also contained overlapping environmentally stable major QTL (phenotypic variance ≥ 10%) for Df and Pbr, with Tumida contributing the trait enhancing alleles for both the traits. Since early flowering is critical for the cultivation of mustard in the Indian subcontinent, this QTL cannot be used for the improvement of Pbr in the Indian gene pool lines. Conditional QTL analysis for Pbr identified the QTL for improvement of Pbr without negative effects on Df. The environmentally stable QTL were projected on the genome assemblies of Tumida and Varuna for the identification of candidate genes. These findings provide insights into the genetics of plant architectural traits in two diverse gene pools of B. juncea and provide opportunities for improvement of the plant architecture through marker-assisted introgressions.Key MessageGenetic mapping of some key plant architectural traits in a vegetable type and an oleiferous B. juncea cross revealed environmentally stable QTL and candidate genes for breeding more productive ideotypes.

Brassica juncea (AABB; genome size ∼920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species – B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ∼100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.

White rust caused by oomycete pathogen Albugo candida is a significant disease of crucifer crops including Brassica juncea (mustard), a major oilseed crop of the Indian subcontinent. Earlier a resistance-conferring locus named AcB1-A5.1 was mapped in an east European gene pool line of B. juncea – Donskaja-IV. This line was tested along with some other lines of B. juncea (AABB), B. rapa (AA) and B. nigra (BB) for resistance to six isolates of A. candida collected from different mustard growing regions of India. Donskaja-IV was found to be completely resistant to all the tested isolates. Sequencing of a BAC spanning the locus AcB1-A5.1 showed the presence of a single CC-NB-LRR protein encoding R gene. The genomic sequence of the putative R gene with its native promoter and terminator was used for the genetic transformation of a susceptible Indian gene pool line Varuna and was found to confer complete resistance to all the isolates. This is the first white rust resistance-conferring gene described from Brassica species and has been named BjuWRR1. Allelic variants of the gene in B. juncea germplasm and orthologues in the Brassicaceae genomes were studied to understand the evolutionary dynamics of the BjuWRR1 gene.HighlightBjuWRR1, a CNL type R gene, was identified from an east European gene pool line of Brassica juncea and validated for conferring resistance to white rust by genetic transformation.