Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress

Prasanta K Subudhi,Rama Shankar,Mukesh Jain

doi:10.1038/s41598-020-78256-8

Abstract

Salinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

Highlights

Salinity is a major abiotic constraint for rice farming
Genetic engineering approaches using many genes associated with signaling pathways, ion transport, oxidative stress tolerance, and osmolyte accumulation have not led to commercialization of any salt tolerant rice variety
Together for all six combinations (IR64/Pokkali, IR64/Nona Bokra, Bengal/ Pokkali, Bengal/Nona Bokra, Cocodrie/Pokkali, and Cocodrie/Nona Bokra) (Supplementary Fig. S1), largest number of single nucleotide polymorphisms (SNPs) and InDels were identified in chromosome 1, whereas chromosome 9 harbored the least

Summary

Introduction

Salinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. A most significant undertaking in this regard involved sequencing of 3,010 diverse rice genotypes which revealed numerous novel protein coding genes and provided a comprehensive analysis of genetic diversity, population structure, and domestication process[11] These genomic resources have been exploited for developing markers for genome-wide association studies of agronomically important t raits[12] and for resolving the origin of cultivated rice[13]

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Results

Conclusion