Title : Revealing allelic variations in candidate genes associated with grain yield under salinity stress between two contrasting rice genotypes
Abstract:
With the aim of assisting the breeding of salinity tolerant rice varieties by incorporating tolerance-associated candidate genes with desirable alleles, we previously re-sequenced the whole genome of two varieties, At354 (salinity tolerant) and Bg352 (salinity susceptible), using Illumina Hiseq 2000 platform. The sequence reads were mapped to the reference genomes, Oryza sativa japonica group cultivar Nipponbare IRGSP-1.0 (GenBank Assembly Accession: GCA_001433935.1). SNPs and InDels of At354 and Bg352 were deposited at the European Nucleotide Archive (ENA)
(https://www.ebi.ac.uk/ena/data/view/PRJEB35319). It was hypothesized that At354 possesses favorable alleles for yield under salinity stress as both the yield potential and salinity tolerance traits are higher in At354 than Bg352. This study aims at exploring the nucleotide variants between At354 and Bg352 for previously reported reproductive stage salinity tolerance QTLs and linked genes as an approach to reveal the candidate genes with specific desirable allelic architecture.
A comprehensive literature search was done to assemble QTLs reported on reproductive stage salinity tolerance. QTLs reported on different morphological parameters or related terminologies associated with grain yield were compiled for the annotation of the genes. All these QTLs were identified by screening at reproductive stages of progeny derived from the salinity tolerant and susceptible parental cross combinations. A total of 245 QTLs reported on reproductive stage salinity tolerance were compiled.
Genes linked to the QTLs were identified within 100 kb flanking the marker closest to the peak of the QTL using Nipponbare rice genome as the reference sequence. Sequence variations for the genes between the two genotypes were identified from SNPs and InDels data sheets. Non-synonymous SNPs causing amino acid changes were determined using SNPEf(https://pcingola.github.io/SnpEff/).
In total, 5000 genes linked to the 245 QTLs were analyzed for their allelic differences between At354 and Bg352. Of the 5000 genes, 139 genes were polymorphic with 184 SNPs between At354 and Bg352. However, only 41 SNPs were located either in exons or 3’UTR or 5’UTR, or Upstream or Downstream over 30 different genes. On the other hand, 406 genes covering 470 polymorphic InDels were identified between At354 and Bg352 of which 138 InDels were found in exons over 132 genes. From further investigations into the SNPs and InDels, we were able to identify five main categories of the candidate genes such as the genes associated with grain development, oxidative reduction and stress relieving, membrane transporter-based ionic adjustments, chlorophyll production, and plant defense and apoptosis were deciphered, which could play important roles contributing to the higher grain yield under salt stress environment.
Acknowledgements: Authors acknowledge NRC-16-16 research project (National Research Council, Sri Lanka) for providing the DNA sequences. Also authors acknowledge US-SL Fulbright Commission, Colombo for giving an opportunity to Dr. Nisha Kottearachchi to perform this collaborative research at the Louisiana State University, USA.
Keywords: Genes; Oryza sativa; QTLs; Salinity tolerance; Yield
