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

Abstract

Purpleputtu (Oryza sativa ssp. indica 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 dedomestication 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 Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. 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.

The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain

“…Several authors have attempted to correlate sequence variants of a number of regulatory genes, e.g., C1 and OSB2, with phenotypic variation in rice grain pigmentation (Sakulsingharoj et al, 2016;Rachasima et al, 2017;Sun et al, 2018). Lachagari et al (2019) conducted comparative genomics in 108 rice lines and identified novel allelic variants in a number of genes belonging to the flavonoid pathway, cytokinins glucoside, and betanidin degradation biosynthesis that were associated with purple pigmentation. Although a number of genes responsible for grain pigmentation have already been identified ( Table 2), there is still a possibility that additional genes and variants thereof, remain to be discovered.…”

The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)

“…HTS systems offer extremely cost-effective sequencing generation for large amounts of data. Therefore, HTS systems are already used in genotyping projects that employ different strategies to find polymorphisms, such as genotyping by sequencing [ 54 ], capturing strategies [ 55 , 56 , 57 ], or the shotgun sequencing of entire genomes [ 58 ]. Microsatellites are multiallelic markers, which makes them ideal for the management of plant germplasm.…”

Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

“…The development of NGS technology can compensate for these deficiencies and promote the development of plant molecular breeding [31,32,33,34]. BSA mixed population separation analysis is often used in whole-genome resequencing, and two groups with extreme traits are mainly sequenced by mixed pool.…”