Pan-genomic, transcriptomic, and miRNA analyses to decipher genetic diversity and anthocyanin pathway genes among the traditional rice landraces

Black rice is famous for containing high anthocyanin while Joha rice is aromatic with low anthocyanin con-taining rice from the North-Eastern Region (NER) of India. However, there are limited reports on the anthocyanin biosynthesis in Manipur Black rice. Therefore, the present study was aimed to understand the origin, domesti-cation and anthocyanin biosynthesis pathways in Black rice using the next generation sequencing approaches. With the sequencing data, various analyses were carried out for differential expression and construction of a pan-genome. Protein coding RNA and small RNA sequencing analysis aided in determining 7415 and 131 differen-tially expressed transcripts and miRNAs, respectively in NER rice. This is the first extensive study on identifi-cation and expression analysis of miRNAs and their target genes in regulating anthocyanin biosynthesis in NER rice. This study will aid in better understanding for decoding the theory of high or low anthocyanin content in different rice genotypes.

Automated summary

This study aimed to understand the origin, domestication, and anthocyanin biosynthesis pathways in Black rice using next generation sequencing approaches. Various analyses were conducted for differential expression and construction of a pan-genome. The study identified and analyzed miRNAs and their target genes in regulating anthocyanin biosynthesis in NER rice for the first time, which will improve understanding of high or low anthocyanin content in different rice genotypes.