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    Genome-wide association studies of salinity tolerance in local aman rice
    (C M B Assoc, 2024) Jahan, Nusrat; Raihan, Mohammad Sharif; Islam, M. Moshiul; Era, Farzana Mustafa; Alalawy, Adel I.; Omran, Awatif M. E.; Alanazi, Yasmene F.
    The present study aimed to identify and characterize new sources of salt tolerance among 94 rice genotypes from varied geographic origins. The genotypes were divided into five groups based on their morphological characteristics at both vegetative and reproductive stages using salinity scores from the Standard Evaluation System (SES). The experiment was designed as per CRD (Completely Randomized Design) with two sets of salinity treatments for 8 dS/meter and 12 dS/meter, respectively compared with one non-salinized control set. Using a Soil Plant Analysis Development (SPAD) meter, assessments of the apparent chlorophyll content (greenness) of the genotypes were done to comprehend the mechanism underlying their salt tolerance. To evaluate molecular genetic diversity, a panel of 1 K RiCA SNP markers was employed. Utilizing TASSEL 5.0 software, 598 filtered SNPs were used for molecular analysis. Whole-genome association studies (GWAS) were also used to investigate panicle number per plant (pn, tiller number per plant (till), SPAD value (spad), sterility (percent) (str), plant height (ph) and panicle length (pl). It is noteworthy that these characteristics oversee conveying the visible signs of salt damage in rice. Based on genotype data, diversity analysis divided the germplasm groups into four distinct clusters (I, II, III and IV). For the traits studied, thirteen significant marker -trait associations were discovered. According to the phenotypic screening, seven genotypes namely Koijuri, Asha, Kajal, Kaliboro, Hanumanjata, Akundi and Dular, are highly tolerant to salinity stress. The greenness of these genotypes was found to be more stable over time, indicating that these genotypes are more resistant to stress. Regarding their tolerance levels, the GWAS analysis produced comparable results, supporting that salinity -tolerant genotypes having minor alleles in significant SNP positions showed more greenness during the stress period. The Manhattan plot demonstrated that at the designated significant SNP position, the highly tolerant genotypes shared common alleles. These genotypes could therefore be seen as important genomic resources for accelerating the development and release of rice varieties that are tolerant to salinity.
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    Öğe
    Identification of significant SNPs for yield-related salt tolerant traits in rice through genome-wide association analysis.
    (Cell Mol Biol, 2025-01-12) Era, Farzana Mustafa; Raihan, Mohammad Sharif; Jahan, Nusrat; Pandey, Saurabh; Alalawy, Adel I; Al-Duais, Mohammed Ali; Alharbi, Basmah M; Alqurashi, Mohammed; Erden, Zeki; Toprak, Çağdaş Can; Islam, A K M Aminul
    Rice salt tolerance is highly anticipated to meet global demand in response to decreasing farmland and soil salinization. Therefore, dissecting the genetic loci controlling salt tolerance in rice for improving productivity is of utmost importance. Here, we evaluated six salt-tolerance-related traits of a biparental mapping population comprising 280 F2 rice individuals (Oryza sativa L.) at the seedling and reproductive stages. We performed a genome-wide association study (GWAS) to identify marker-trait associations under artificially induced salt stress using the 1K RICA chip (Agriplex Genomics, Cedar Avenue, Suite 250, Cleveland, 011444106, USA). We have identified 8 single nucleotide polymorphisms (SNPs) representing eight genomic regions on chromosomes 5, 8, 9, and 10. These were significantly associated with the six salt-tolerance-related traits, no. of tillers per plant (TPP), effective tillers per plant (ETP), spikelet fertility percentage (SFP), field grain number (FGN), grain length breadth ratio (LBR) and thousand-grain weight (TGW).  FGN has two significant SNPs (SNP0758 and SNP0759) on Chromosome 9, whereas SFP on chromosomes 8 and 12 (SNP1127 and SNP0966, respectively). Similarly, for TPP (SNP0796), a significant SNP was detected on chromosome 10, and for ETP (SNP0414) on chromosome 5.  Two significant SNPs were found in chromosome 12 for LBR (SNP0920) and TGW (SNP0976). Based on all loci, we screened 3 possible candidate genes in chromosomes 8, 9, and 12 between the genomic region of SNP0920 and SNP1127 under salt stress. Interestingly, these genes were involved in protein coding, none of which was previously reported as being involved in plant salt tolerance. Further, the genetic relationship between the mapping population and population structure was classified by STRUCTURE v 2.3. Genotypes with ≥ 80% of shared ancestry were explained into two major clusters (I and II), and < 80% of shared ancestry were categorized as admixtures. An unrooted alpha was developed by TASSEL 5.0, dividing the genotypes into three major groups where 97 individuals were in Cluster 1, cluster 2 consisted of 93 individuals, and the remaining Cluster 3 included 90 individuals. A kinship matrix developed from 860 SNPs indicated group formation and more substantial relatedness among the genotypes with a red zone. Our findings provide valuable information for enhancing the understanding of complicated salt tolerance mechanisms in rice seedlings and the identified candidates potentially used for breeding salt-tolerant genotypes.