AUTHOR=Lachagari V. B. Reddy , Gupta Ravi , Lekkala Sivarama Prasad , Mahadevan Lakshmi , Kuriakose Boney , Chakravartty Navajeet , Mohan Katta A. V. S. K. , Santhosh Sam , Reddy Arjula R. , Thomas George 

TITLE=Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)

JOURNAL=Frontiers in Plant Science

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.00513

DOI=10.3389/fpls.2019.00513

ISSN=1664-462X

ABSTRACT=<p>Purpleputtu (<italic>Oryza sativa</italic> ssp. <italic>indica</italic> cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in <italic>Rc</italic> (<italic>Red colored</italic>, a transcription factor of <italic>bHLH</italic> class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in <italic>Rc</italic> gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of <italic>Rc</italic> locus revealed a distinct clade showing proximity to the progenitor species <italic>Oryza rufipogon</italic> and <italic>O. nivara.</italic> In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays.</p>