Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice.

Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm-1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs. Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm-1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Mono-oxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.

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

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.

Introgressed Saltol QTL Lines Improves the Salinity Tolerance in Rice at Seedling Stage.

Rice is a staple food crop in Asia and plays a crucial role in the economy of this region. However, production of rice and its cultivating areas are under constant threat of soil salinity. A major QTL, Saltol, responsible for salinity tolerance at seedling stage has been mapped on chromosome 1 using Pokkali/IR29 Recombinant Inbred Lines (RIL) population. The present study was aimed to incorporate Saltol Quantitative Trait Loci (QTL) in two high yielding mega rice varieties i.e. Pusa44 and Sarjoo52 through Marker Assisted Backcross Breeding (MABB). To improve the seedling stage salinity tolerance in these cultivars, we introgressed the Saltol QTL from donor parent FL478 a derivative of Pokkali. A total of three backcrosses (BC3) followed by selfing have led to successful introgression of Saltol QTL. Foreground selection at each breeding cycle was done using micro-satellite markers RM3412 and AP3206 to confirm Saltol QTL. The precise transfer of Saltol region was established using recombinant selection through flanking markers RM493 and G11a. Finally, 10 Saltol near isogenic lines (NILs) of Pusa44 and eight NILs of Sarjoo52 were successfully developed. These NILs (BC3F4) were evaluated for seedling stage salinity under hydroponic system. The NILs PU99, PU176, PU200, PU215, PU229, PU240, PU241, PU244, PU252, PU263 of Pusa44 and SAR17, SAR23, SAR35, SAR39, SAR77, SAR87, SAR123, SAR136 NILs of Sarjoo52 confirmed tolerance to salinity with low salt injury score of 3 or 5. Ratio of Na+/K+ content of Saltol NILs ranged from 1.26 to 1.85 in Pusa44 and 1.08 to 1.69 in Sarjoo52. The successfully developed NILs were further phenotyped stringently for morphological traits to estimate Phenotypic Recovery. Background selection of NILs along with parents was carried out with 50K SNP chip and recovered 94.83-98.38% in Pusa44 NILs and 94.51 to 98.31% in Sarjoo52 NILs of recurrent genome. The present study of MAB has accelerated the development of salt tolerant lines in the genetic background of Pusa44 and Sarjoo52. These NILs could be used for commercial cultivation in saline affected area.