Identification and characterization of chromosomal variations in chromosome 9 of Oryza sativa varieties Nipponbare, Ir8, Zs97, N22, Mh63, & R498

Abstract

The development of high-yielding stress-tolerant varieties helps in decreasing the demand for food brought about by poverty. Comparative genomics enables the development of these varieties by identifying the preferred DNA polymorphisms and stress tolerance genes present in selected varieties and transferring them to a desired target specimen. In this study, the whole chromosome 9 sequences and that of selected stress tolerance genes of the rice reference genome Nipponbare were aligned against the corresponding ones in Zhengshan97, Minghui63, Shuhui498, N22, and IR8 varieties using MUMmer software. Stress tolerance gene comparison showed that Zhengshan97 shared the highest identity, as it had three out of five genes that were 100% identical to the reference sequence. N22 was found to not possess the zinc finger AN1 domaincontaining stress-associated protein 17-like (SAP17) gene for salt, cold, and drought tolerance. Indel comparison showed that Minghui63, Shuhui498, Zhengshan97, and IR8 had similar gaps and indel patterns with the reference, while N22 was the most different. ZS97 was found to bear the closest sequence to Nipponbare while N22 had the least similarity. Analysis for sequence repeats using RepeatMasker, showed that interspersed repeats were present in all varieties in the genes for dehydration-responsive element-binding protein 1A-like (DREB1A), dehydration-responsive element-binding protein 1B-like (DREB1B), and NAC domain-containing protein 17 (NAC42). All the interspersed repeats that were detected were transposons from the MULE-MuDR and CMC-EnSpm family. All selected varieties had no satellite tandem repeats in the genes considered, but had varying lengths of simple repeats. Only the H/ACA ribonucleoprotein complex subunit GAR1 (ALBA7) gene had a low complexity repeat. The gene level haplotype analysis performed via the SNP-Seek genotype query indicate the presence of commonly occurring haplotypes in Zhengshan97, Minghui63, N22 and Nipponbare. Haplotype comparison within and across subpopulations revealed that some haplotypes were only present within their subpopulation.