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Brassica juncea L. is an important oilseed crop that yields edible oil and biofuel. Improving B. juncea seed traits is a primary breeding target, but these traits are genetically complex. MicroRNAs (miRNAs) regulate seed development by modulating gene expression at the post-transcriptional or translational level and are excellent candidates for improving seed traits. However, the roles of miRNAs in B. juncea seed development are yet to be investigated. Here, we report small RNA profiling and miRNA identification from developing seeds of two contrasting varieties of B. juncea, Early Heera2 (EH2) and Pusa Jaikisan (PJK). We identified 326 miRNAs, including 127 known and 199 novel miRNAs, of which 103 exhibited inter-varietal differential expression. Integrating miRNAome and our previous transcriptome data identified 13,683 putative miRNA-target modules. Segregation of differentially expressed miRNAs into different groups based on variety-wise upregulation, followed by comprehensive functional analysis of targets using pathway mapping, gene ontology, transcription factor mapping, and candidate gene analysis, revealed at least 11, 6, and 7 miRNAs as robust candidates for the regulation of seed size, seed coat color, and oil content, respectively. Further, co-localization with previously reported quantitative trait loci (QTL) proffered 29 and 15 miRNAs overlapping with seed weight and oil content QTLs, respectively. Our study is the first comprehensive report of miRNAome expression dynamics from developing seeds and provides candidate miRNAs and target genes for engineering seed traits in B. juncea.

Abstract Brassica juncea is an important oilseed crop, widely grown as a source of edible oil. Seed size is a pivotal agricultural trait in oilseed Brassicas. However, the regulatory mechanisms underlying seed size determination are poorly understood. To elucidate the transcriptional dynamics involved in the determination of seed size in B. juncea, we performed a comparative transcriptomic analysis using developing seeds of two varieties, small-seeded Early Heera2 (EH2) and bold-seeded Pusajaikisan (PJK), at three distinct stages (15, 30 and 45 days after pollination). We detected 112,550 transcripts, of which 27,186 and 19,522 were differentially expressed in the intra-variety comparisons and inter-variety comparisons, respectively. Functional analysis using pathway, gene ontology, and transcription factor enrichment revealed that cell cycle- and cell division-related transcripts stay upregulated during later stages of seed development in the bold-seeded variety but are downregulated at the same stage in the small-seeded variety, indicating that an extended period of cell proliferation in the later stages increased seed weight in PJK as compared to EH2. Further, k-means clustering and candidate genes-based analyses unravelled candidates for employing in seed size improvement of B. juncea. In addition, candidates involved in determining seed coat color, oil content, and other seed traits were also identified.

Abstract Sorghum is a self-pollinated crop with multiple economic uses as cereal, forage, and biofuel feedstock. Hybrid breeding is a cornerstone for sorghum improvement strategies that currently relies on cytoplasmic male sterile lines. To engineer genic male sterility, it is imperative to examine the genetic components regulating anther/pollen development in sorghum. To this end, we have performed transcriptomic analysis from three temporal stages of developing anthers that correspond to meiotic, microspore and mature pollen stages. A total of 5286 genes were differentially regulated among the three anther stages with 890 of them exhibiting anther-preferential expression. Differentially expressed genes could be clubbed into seven distinct developmental trajectories using K-means clustering. Pathway mapping revealed that genes involved in cell cycle, DNA repair, regulation of transcription, brassinosteroid and auxin biosynthesis/signalling exhibit peak expression in meiotic anthers, while those regulating abiotic stress, carbohydrate metabolism, and transport were enriched in microspore stage. Conversely, genes associated with protein degradation, post-translational modifications, cell wall biosynthesis/modifications, abscisic acid, ethylene, cytokinin and jasmonic acid biosynthesis/signalling were highly expressed in mature pollen stage. High concurrence in transcriptional dynamics and cis-regulatory elements of differentially expressed genes in rice and sorghum confirmed conserved developmental pathways regulating anther development across species. Comprehensive literature survey in conjunction with orthology analysis and anther-preferential accumulation enabled shortlisting of 21 prospective candidates for in-depth characterization and engineering male fertility in sorghum.