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SUMMARY: Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome‐scale genome assembly of B. carinata accession HC20 using long‐read Oxford Nanopore 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 long‐read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide‐binding and leucine‐rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early‐generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species. Significance Statement: We report a highly contiguous genome assembly of allotetraploid mustard Brassica carinata HC20 (BBCC) which contains resistance to many diseases affecting the other extensively cultivated Brassica species of the U's triangle. Comparative analyses of the long‐read assemblies of the six Brassica species revealed high gene collinearity between the three diploid and their allotetraploid species. We tracked the early‐generation genomic interactions between the subgenomes of B. carinata (BBCC) and B. juncea (AABB) in their interspecific crosses using molecular karyotyping and proposed strategies to utilize this information for genomic introgressions. [ABSTRACT FROM AUTHOR]

The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea. [ABSTRACT FROM AUTHOR]

Sinapine is a major anti-nutritive compound that accumulates in the seeds of Brassica species. When ingested, sinapine imparts gritty flavuor in meat and milk of animals and fishy odor to eggs of brown egg layers, thereby compromising the potential use of the valuable protein rich seed meal. Sinapine content in Brassica juncea germplasm ranges from 6.7 to 15.1 mg/g of dry seed weight (DSW) which is significantly higher than the prescribed permissible level of 3.0 mg/g of DSW. Due to limited natural genetic variability, conventional plant breeding approach for reducing the sinapine content has largely been unsuccessful. Hence, transgenic approach for gene silencing was adopted by targeting two genes—SGT and SCT, encoding enzymes UDP- glucose: sinapate glucosyltransferase and sinapoylglucose: choline sinapoyltransferase, respectively, involved in the final two steps of sinapine biosynthetic pathway. These two genes were isolated from B. juncea and eight silencing constructs were developed using three different RNA silencing approaches viz. antisense RNA, RNAi and artificial microRNA. Transgenics in B. juncea were developed following Agrobacterium-mediated transformation. From a total of 1232 independent T0 transgenic events obtained using eight silencing constructs, 25 homozygous lines showing single gene inheritance were identified in the T2 generation. Reduction of seed sinapine content in these lines ranged from 15.8% to 67.2%; the line with maximum reduction had sinapine content of 3.79 mg/g of DSW. The study also revealed that RNAi method was more efficient than the other two methods used in this study. [ABSTRACT FROM AUTHOR]

Among the different types of methionine-derived aliphatic glucosinolates (GS), sinigrin (2-propenyl), the final product in 3C GS biosynthetic pathway is considered very important as it has many pharmacological and therapeutic properties. In Brassica species, the candidate gene regulating synthesis of 3C GS remains ambiguous. Earlier reports of GSL-PRO, an ortholog of Arabidopsis thaliana gene At1g18500 as a probable candidate gene responsible for 3C GS biosynthesis in B. napus and B. oleracea could not be validated in B. juncea through genetic analysis. In this communication, we report the isolation and characterization of the gene CYP79F1, an ortholog of A. thaliana gene At1g16410 that is involved in the first step of core GS biosynthesis. The gene CYP79F1 in B. juncea showed presence-absence polymorphism between lines Varuna that synthesizes sinigrin and Heera virtually free from sinigrin. Using this presence-absence polymorphism, CYP79F1 was mapped to the previously mapped 3C GS QTL region (J16Gsl4) in the LG B4 of B. juncea. In Heera, the gene was observed to be truncated due to an insertion of a ~4.7 kb TE like element leading to the loss of function of the gene. Functional validation of the gene was carried out through both genetic and transgenic approaches. An F2 population segregating only for the gene CYP79F1 and the sinigrin phenotype showed perfect co-segregation. Finally, genetic transformation of a B. juncea line (QTL-NIL J16Gsl4) having high seed GS but lacking sinigrin with the wild type CYP79F1 showed the synthesis of sinigrin validating the role of CYP79F1 in regulating the synthesis of 3C GS in B. juncea. [ABSTRACT FROM AUTHOR]

Abstract Analysis of the glucosinolate content and composition by high-pressure liquid chromatography indicated that varieties of Brassica juncea bred and grown in India have a high glucosinolate content characterized by the presence of 2-propenyl (allyl) and 3-butenyl as the major and 4-pentenyl as the minor fractions. In contrast, the B. juncea germplasm from other countries is characterized by the presence of 2-propenyl as the major glucosinolate fraction, trace amounts of 3-butenyl and a total lack of the 4-pentenyl types. In order to transfer the low glucosinolate trait to Indian B. juncea , the inheritance of total glucosinolates was investigated using doubled haploid (DH) populations derived from F1 (DH1 ) and BC1 (BC1 DH) of a cross between ‘Varuna’ (the most widely cultivated high glucosinolate variety of India) and ‘Heera’ (a non-allyl type low glucosinolate line). A total of 752 DH1 and 1263 BC1 DH gave rise to seven and 11 low glucosinolate (containing less than 18 µmol/g seed) individuals, respectively. On the basis of the frequency of the low glucosinolate individuals, the total glucosinolate was found to be under the control of seven genes. There was presence of both allyl and non-allyl types in DH1 and BC1 DH low-glucosinolate individuals and absence of 3-butenyl glucosinolate in some of the BC1 DH low glucosinolate individuals, indicating segregation for these fractions in the population. The size of the segregating DH population proved to be crucial for precise determination of the number of genes controlling the trait. Because of the large number of genes involved, incorporation of low glucosinolate trait in Indian B. juncea should be approached through doubled haploid (DH) breeding. [ABSTRACT FROM AUTHOR]

AFLP markers were employed to assess the genetic diversity amongst 21 established natural and nine synthetic varietes and lines of Brassica juncea originating from Asia, Australia, Canada, Eastern Europe and Russia. Six of the synthetics used for diversity studies have been developed recently. Twenty one EcoRI/MseI-based AFLP primer pairs generated a total of 1251 scorable fragments among the 30 genotypes studied, of which 778 bands were polymorphic with an average of 37 polymorphic bands per primer pair. On the basis of the similarity coefficients (F value), cluster analysis was performed using the UPGMA method. The 30 B. juncea lines could be grouped into three distinct clusters. All the Indian, Chinese and previously developed synthetics formed one cluster (cluster A), the recently developed synthetics formed a separate cluster (cluster B) and the lines from Australia, Canada, Eastern Europe and Russia formed the third cluster (cluster C). A majority of the lines were uniquely identified by one or more primer pairs due to the presence or absence of variety specific band(s). Four primer pairs were found to be most informative, since these uniquely identified all the genotypes assayed. These four primer pairs, could therefore be used as fingerprinting primers for varietal identification. [ABSTRACT FROM AUTHOR]

Chloroplast (cp) and mitochondrial (mt) DNA restriction profiles of a cytoplasmic male sterile (CMS) line of Brassica juncea and its maintainer line were compared and found to be markedly different. Comparison of cpDNA restriction profiles of fifty different species of genus Brassica and some allied genera showed that the cpDNA profiles of CMS lines were similar to that of B. tournefortii for twenty different restriction endonucleases. This CMS system is thus not of spontaneous origin as reported earlier, but is alloplasmic in nature. Comparison of restriction profiles of mtDNA of B. tournefortii and CMS lines revealed some differences which might either be due to changes in DNA pattern during the transfer, or, due to the cytoplasm coming from a B. tournefortii line different from the one used in this study. [ABSTRACT FROM AUTHOR]

• Seed-glucosinolate chemotypes of 641 Brassica juncea genotypes were analyzed. • PCA of glucosinolates data showed the distinctiveness of four populations used. • A comprehensive Vis-NIRS model developed using MPLS regression analysis. • The model has high predictability for 8 glucosinolates of B. juncea. • The Vis-NIRS model also facilitates cross-species glucosinolates quantification. The globally cultivated Brassica crops contain high deliverable concentrations of health-promoting glucosinolates. Development of a Visible-Near InfraRed Spectroscopy (Vis-NIRS) calibration to profile different glucosinolate components from 641 diverse Brassica juncea chemotypes was attempted in this study. Principal component analysis of HPLC-determined glucosinolates established the distinctiveness of four B. juncea populations used. Subsequently, modified partial least square regression based population-specific and combined Vis-NIRS models were developed, wherein the combined model exhibited higher coefficient of determination (R2; 0.81–0.97) for eight glucosinolates and higher ratio of prediction determination (RPD; 2.42–5.35) for seven glucosinolates in B. juncea populations. Furthermore, range error ratio (RER > 4) for twelve and RER > 10 for eight glucosinolates make the combined model acceptable for screening and quality control. The model also provided excellent prediction for aliphatic glucosinolates in four oilseed Brassica species. Overall, our work highlights the potential of Vis-NIR spectroscopy in estimating glucosinolate content in the economically important Brassica oilseeds. [ABSTRACT FROM AUTHOR]