Nerated according to Euclidean distance utilizing package `dendextend’ version 1.13.four in R version three.six.3. four.six. DNA Isolation and SNP Genotyping Total genomic DNA was isolated from young leaves employing Cetyl Trimethyl Ammonium Bromide (CTAB) process . The DNA was quantified utilizing a nano-drop spectrophotometer (NanoDropTM 2000/2000 c, Thermo Fisher Scientific, DE, United states of america). Higher throughput genotyping was FGFR Accession carried out employing a “OsSNPnks” 50 K genic Affymetrix chip containing a total of 50,051 high-quality SNPs. The chip was determined by single copy genes, covering all 12 rice chromosomes . DNA amplification, fragmentation, chip hybridization, single-base extension via DNA ligation, and signal amplification was carried out utilizing the system recommended by Singh et al. . 4.7. Population Structure Evaluation The application STRUCTURE 2.three.4  was utilized to establish the population structure of 96 genotypes employing a Bayesian model of ADMIXTURE , wherein ten independent runs with 50,000 burn-ins and Markov Chain Monte Carlo (MCMC) period set to 50,000 was carried out for each K. Moreover, STRUCTURE HARVESTER  was employed to estimate the optimum number of sub-populations . 4.8. Genome-Wide Association Study Association mapping panel of 96 germplasm lines had been genotyped employing 50 K SNP chip. SNP ALK2 Formulation Information was filtered for minor allele frequency (MAF) 0.05 and maximum missing internet sites per SNP was fixed to 20 . Just after filtering, a total of 26,108 SNPs were used to detect MTAs. MTAs have been identified making use of Multilevel marketing and FarmCPU [94,95] implemented in GAPIT (genomic association and prediction integrated tool). five. Conclusions Morphological and physiological characterization of rice germplasm lines identified 11 genotypes tolerant to salinity anxiety. These lines might be utilized as donors within a breeding system for creating salt tolerant rice varieties. In addition, GWAS identified a total of 23 MTAs for traits associated with seedling stage salinity tolerance, of which two are novel.Supplementary Materials: The following are readily available on line at https://www.mdpi.com/2223-774 7/10/3/559/s1, Figure S1: Correlation between the traits for seedling stage salinity tolerant. Table S1: Morpho-physiological traits and biochemical information of the rice genotypes evaluated for seedling stage salinity tolerance. Table S2: Information of germplasm used within the existing study; Table S3: The chemical composition of modified Yoshida nutrient remedy utilised within the study. Author Contributions: Conceptualization and methodology, A.K.S.; Validation, A.K.Y. and N.G.; Formal evaluation, H.B., R.K.E., plus a.K.Y.; Investigation, K.K.V., A.K.Y., N.G., P.K.B., R.K.E., and H.B.; Resources, A.K.S., S.G.K., H.B., and M.N.; Information curation, K.K.V., A.K.Y.; Writing–original draft preparation, A.K.Y., and R.K.E.; Writing–review and editing, R.K.E.; Supervision, A.K.S., S.G.K., in addition to a.K.; Project administration, A.K.S.; Funding acquisition, A.K.S. All authors have read and agreed for the published version of the manuscript. Funding: This study was funded by Indian Council of Agricultural Investigation (ICAR) funded network project on “Incentivizing in Agricultural Research” plus the National Agricultural HigherPlants 2021, ten,14 ofEducation Project (NAHEP)-Centre for Advanced Agricultural Science and Technologies (CAAST) project on “Genomics Assisted Breeding for Crop Improvement”, in the World Bank and ICAR. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Information Ava.