Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

Abstract

Fragrance of rice is an important trait that confers a large economic benefit to the farmers who cultivate aromatic rice varieties. Several aromatic rice varieties have limited geographic distribution, and are endowed with variety-specific unique fragrances. BADH2 was identified as a fragrance gene in 2005, and it is essential to identify the fragrance alleles from diverse geographical locations and genetic backgrounds. Seeragasamba is a short-grain aromatic rice variety of the indica type, which is cultivated in a limited area in India. Whole genome sequencing of this variety identified a new badh2 allele (badh2-p) with an 8 bp insertion in the promoter region of the BADH2 gene. When the whole genome sequences of 76 aromatic varieties in the 3000 rice genome project were analyzed, the badh2-p allele was present in 13 varieties (approximately 17%) of both indica and japonica types. In addition, the badh2-p allele was present in 17 varieties that already had the loss-of-function allele, badh2-E7. Taken together, the frequency of badh2-p allele (approximately 40%) was found to be greater than that of the badh2-E7 allele (approximately 34%) among the aromatic rice varieties. Therefore, it is suggested to include badh2-p as a predominant allele when screening for fragrance alleles in aromatic rice varieties.

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

“…The mapped genome of PP revealed a clear bias toward transitions (almost twice that of transversions) deviating from the expected ratio of 0.5. Higher Ts/Tv ratios were reported in rice, maize, otus, medicago, diploid wheat, Triticum monococcum and barley (Batley et al, 2003a; Vitte and Bennetzen, 2006; Subbaiyan et al, 2012; Bindusree et al, 2017). Due to wobble effect, transitions manifest mostly into silent mutations that do not alter the amino acid and thus conserves the amino acid chain (Wakeley, 1996).…”

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

“…The mapped genome of PP revealed a clear bias towards transitions (almost twice that of transversions) deviating from the expected ratio of 0.5. Higher Ts/Tv ratios were reported in rice, maize, otus, medicago, diploid wheat, Triticum monococcum and barley (Bindusree et al , 2017; Subbaiyan et al , 2012; Batley et al , 2003; Vitte et al , 2006). Due to wobble effect, transitions manifest mostly into silent mutations that do not alter the amino acid and thus conserves the amino acid chain (Wakeley, 1996).…”

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

“…The recent rapid development of NGS has boosted the number of genomic sequences for hundreds to thousands of rice varieties [24]. Evolutionary research on rice has been performed previously (Khush 1997) and various strategies, such as whole-genome resequencing [25] or sequencing [26,27], natural or artificial selection [12], and genotyping-by-sequencing [16], have been explored by breeders to broaden the genetic diversity of crops by examining sequence variations and either evolutionary relationships between or among populations using NGS data. Genetic variations (alleles) have been detected using various selection methods and have been increasing in number due to their distinctive patterns or signatures due to selection or other confounding effects, such as bottlenecks, expansions, or subdivided populations [28].…”