Publications of NIPGR Scientists

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    Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes
    (Elsevier B.V., 2025) Soundararajan, Prabhakaran; Vivek, AT; Suresh, Gokul Babu; Shukla, Bhavya; Singh, Kanchan B.M.; Kumar, Shailesh; Manivannan, Abinaya
    WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.
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    miR394 enhances WUSCHEL-induced somatic embryogenesis in Arabidopsis thaliana
    (John Wiley & Sons, 2023) Lu, Lu; Holt, Anna; Chen, Xinying; Liu, Yang; Knauer, Steffen; Tucker, Elise J.; Sarkar, Ananda K.; Hao, Zhaodong; Roodbarkelari, Farshad; Shi, Jisen; Chen, Jinhui; Laux, Thomas
    Many plant species can give rise to embryos from somatic cells after a simple hormone treatment, illustrating the remarkable developmental plasticity of differentiated plant cells. However, many species are recalcitrant to somatic embryo formation for unknown reasons, which poses a significant challenge to agriculture, where somatic embryogenesis is an important tool to propagate desired genotypes. The micro RNA394 (miR394) promotes shoot meristem maintenance in Arabidopsis thaliana, but the underlying mechanisms have remained elusive. We analyzed whether miR394 affects indirect somatic embryogenesis and determined the transcriptome of embryogenic callus upon miR394-enhanced somatic embryogenesis. We show that ectopic miR394 expression enhances somatic embryogenesis in the recalcitrant Ler accession when co-expressed with the transcription factor WUSCHEL (WUS) and that miR394 acts in this process through silencing the target LEAF CURLING RESPONSIVENESS (LCR). Furthermore, we show that higher endogenous miR394 levels are required for the elevated embryogenic potential of the Columbia accession compared to Ler, providing a mechanistic explanation for this natural variation. Our transcriptional analysis provides a framework for miR394 function in regulating pluripotency by expanding WUS-mediated direct transcriptional repression.