Genome wide association study of MAGIC population reveals a novel QTL for salinity and sodicity tolerance in rice

Abstract

The present study was conducted to identify the novel QTLs controlling salinity and sodicity tolerance using indica MAGIC rice population. Phenotyping was carried out in salinity (EC ~ 10 dS/m) and sodicity (pH ~ 9.8) at the seedling stage. Among 391 lines, 43 and 98 lines were found tolerant and moderately tolerant to salinity. For sodicity condition, 2 and 45 lines were showed tolerance and moderately tolerance at seedling stage. MAGIC population was genotyped with the help of genotyping by sequencing (GBS) and filtered 27041SNPs were used for genome wide marker trait association studies. With respect to salinity tolerance, 25 SNPs were distributed on chromosomes 1, 5, 11 and 12, whereas 18 SNPs were mapped on chromosomes 6, 4 and 11 with LOD value of > 3.25 to sodicity tolerance in rice. The candidate gene analysis detected twelve causal genes including SKC1 gene at Saltol region for salinity and six associated genes for sodic stress tolerance. The significant haplotypes responsible for core histone protein coding gene (LOC_Os12g25120) and three uncharacterized protein coding genes (LOC_Os01g20710, LOC_Os01g20870 and LOC_Os12g22020) were identified under saline stress. Likewise, five significant haplotypes coding for ribose 5-phosphate isomerise (LOC_Os04g24140), aspartyl protease (LOC_Os06g15760), aluminum-activated malate transporter (LOC_Os06g15779), OsFBX421-Fbox domain containing protein (LOC_Os11g32940) and one uncharacterized protein (LOC_Os11g32930) were detected for sodic stress tolerance. The identified novel SNPs could be the potential candidates for functional characterization. These candidate genes aid to further understanding of genetic mechanism on salinity and sodicity stress tolerance in rice. The tolerant line could be used in future breeding programme to enhance the salinity and sodicity tolerance in rice.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-022-01174-8.

Keywords: GBS; GWAS; MAGIC; Rice; Salinity; Sodicity.

Fig. 1

a Genome wide distribution of SNPs presented in Manhattan plot for salt injury score (vigour score) for salinity stress through MLM model, b The expected and observed -log₁₀ probability distribution of SNPs presented in Q-Q plot for salt injury score (vigour score) for salinity stress through MLM model. Saltol region, a known QTL responsible for salinity tolerance at seedling stage on chromosome 1 was highlighted

Fig. 2

Boxplots indicating phenotypic responses for salinity vigor score among indica MAGIC rice lines with alternative haplotypes for candidate genes determined from significantly associated SNPs by GWAS analysis (X-axis = Haplotypes; Y-axis = Vigor score). a LOC_Os01g20160; b LOC_Os01g20710; c LOC_Os01g20720; d LOC_Os01g20830; e LOC_Os01g20870; f LOC_Os01g22590; g LOC_Os05g03900; h LOC_Os11g35870; i LOC_Os12g22020; j LOC_Os12g25120

Fig. 3

a Genome wide distribution of SNPs presented in Manhattan plot for sodic injury score (vigour score) under sodic stress through MLM model b The expected and observed -log₁₀ probability distribution of SNPs presented in Q-Q plot for sodic injury score (vigour score) under sodic stress through MLM model

Fig. 4

Boxplots indicating phenotypic responses for sodic vigor score among indica MAGIC rice lines with alternative haplotypes for candidate genes determined from significantly associated SNPs by GWAS analysis (X-axis = Haplotypes; Y-axis = Vigor score). a LOC_Os04g24140; b LOC_Os06g15730; c LOC_Os06g15760; d LOC_Os06g15779; e LOC_Os11g32930; f LOC_Os11g32940