What's happening at IRRI

Thursday Seminar

Thursday, October 20, 2016, 01:15pm - 02:15pm


Whole-genome sequencing and comparative genomic analysis reveal novel allelic variations unique to a purple-colored rice landrace (Oryza sativa ssp.indica cv. Purpleputtu)

V.B. Reddy Lachagari
Chief Scientific Officer-Plant Genomics
AgriGenome Labs Pvt Ltd
A subsidiary of SciGenom Labs

Nutraceutical foods containing anthocyanins, which confer red, purple, and black colour to seed and other plants, and other flavonoids (conferring hues of yellow), are increasingly being considered to be beneficial for human health. Though wild progenitor rice such as O.rufipogon is colored, most, if not all, of the present-day high-yielding modern rice cultivars are completely devoid of anthocyanins in seed and plants. In a comparative genomic approach, we have analysed allelic variations in Purpleputtu (Oryza sativa, ssp indica var Purpleputtu), which is a unique rice landrace/cultivar that exhibits purple color in all parts of the plant, except the inter-nodes and pollen, and accumulates anthocyanins in seed and plant parts. Nextgen sequencing and comparative genomic analysis was carried out between Purpleputtu and colored and colorless rice lines belonging to both indica and japonica types, in addition to that of wild progenitors. Variant prediction confirms that the Purpleputtu genome is marked by the absence of a 14-bp deletion within the Rc gene, a key regulatory gene of the anthocyanin biosynthetic pathway, in contrast to its ubiquitous presence in white pericarp rice lines. All the four major anthocyanin biosynthetic pathway genes were found to have several novel variants unique to Purpleputtu. Furthermore, the Purpleputtu genome also showed a well conserved 4.5-Mbp region on Chromosome 5. This region harbors several loci associated with domestication of rice. Phylogenetic analysis, with other majorly anthocyanin-producing species and genera, indicates a distinct clade and close proximity to progenitor species rufipogon and nivara. Comparison with 3,023 lines of rice SNP-Seek database shows 1,633,845 SNPs in Purpleputtu that could be utilized in forward breeding approaches such as GWAS and genomic prediction. The results may help in understanding the genomic changes caused in target gene loci during the long history of domestication/non-domestication, selection, and modern breeding processes in rice. The details along with other initiatives of the SciGenom group for Plant Genomics will be discussed


Havener Auditorium, International Rice Research Institute, Los Baños, 4030 Laguna, Philippines