QTLs in salt rice variety CSR10 reveals salinity tolerance at reproductive stage

Devi, A. Nithya; Krishnamurthy, S. L.; Sharma, Parbodh Chander; Vinaykumar, N. M.

doi:10.1007/s11738-020-03183-0

Cited by 27 publications

(16 citation statements)

References 62 publications

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“…This QTL, designated qSTGF2, was confined to a 2.3 Mb region between RM13928 and Indel 31.98. The region of qSTGY2.2 coincides with a QTL region for GY, which was detected recently under salt stress conditions [54]. However, when it comes to qSTPN2 and qSTGF2, QTLs detected previously are in regions distinct from those of our QTLs [55].…”

Section: Validation and Fine Mapping Of Detected Qtlssupporting

confidence: 70%

Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies

et al. 2021

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Unraveling the complex genetic bases and mechanisms underlying salt tolerance is of great importance for developing salt-tolerant varieties. In this study, we evaluated 42 chromosome segment substitution lines (CSSLs) carrying chromosome segments from IR64 on the genetic background of Koshihikari under salt stress. Two CSSLs, SL2007 and SL2038, produced higher plant dry weight and grain yield than did Koshihikari under the stress condition. These CSSLs also showed lower Na+ and Cl− accumulation in the leaf and whole plant at the full heading stage, which might be related to the higher grain yield and yield components. To understand the genetic control of its grain yield and yield components, a SL2007/Koshihikari F2 population was generated for quantitative trait locus (QTL) analysis. Six QTLs for grain yield and yield-related traits were detected on chromosome 2. Using near-isogenic lines (NILs) from a SL2007/Koshihikari F5 population, qSTGY2.2 was delimited to a 2.5 Mb region and novel qSTPN2 was delimited to a 0.6 Mb region. We also detected a novel QTL, qSTGF2, for grain filling, which was considered an important contributor to grain yield under salt stress in this CSSL. Our results provide insights into mechanisms conferring grain yield under salinity stress and new genetic resources for cloning and breeding.

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Section: Validation and Fine Mapping Of Detected Qtlssupporting

confidence: 70%

Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies

et al. 2021

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“…Salinity is one of the signi cant abiotic stress that affects the rice production. Large tracts of agricultural lands are left unproductive because of the lack of suitable salt-tolerant rice varieties (Pundir et al 2021). To increase rice production in these barren areas, it is essential to identify novel alleles and genes that control complex quantitative salt tolerance traits in diverse rice germplasm (Kumar et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of DNA polymorphism in salt-tolerant and sensitive rice genotypes using double digest RADseq

Tariq

Arif

Zhang

et al. 2022

Preprint

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Salt-tolerant rice varietal development is necessary and the best approach to enhance crop productivity in areas with high salinity. To identify the genetic variation in stress-related genes in salt-tolerant genotypes, we carried out genotyping by sequencing (GBS) of seven rice lines with contrasting responses to salinity stress, including FL478 as a tolerant variety and IR64 as a sensitive check. The GBS reduces genomic complexity and enables us to obtain many SNP markers in the genome. A total of 7,980,092 high-quality single-end reads of 94 bp each were generated, and approximately 83% of the reads mapped to the rice reference genome (Nipponbare). We identified a total of 80,159 SNPs and 6,403 InDels among the seven rice genotypes. Forty-two percent of these SNPs were identified from the genic regions, and further, 27% were observed in the coding areas out of these genic SNPs. We used bioinformatics analysis to identify functional SNPs in the genes that changed the functions of proteins. We found variations between tolerant and sensitive genotypes by comparing the identified SNPs in coding regions. We found that 566 of the SNPs identified in the coding regions were non-synonymous (nsSNPs), affecting proteins. We identified 116 abiotic stress-related genes that contained 138 nsSNPs (between FL478 and IR64) in coding regions, thus directly affecting the proteins. Analysis indicated that these genes might contribute to the salt stress phenotype in rice varieties and the identified nsSNP markers that were useful to distinguish tolerant and sensitive genotypes. Our results revealed that the identified SNPs could be used as an essential source of genomic variability for improving and developing saline tolerant genotypes.

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“…The MTA qSDW12.1 was identified in the genomic region reported to be associated with initial and final standard evaluation system (SES) score, seedling survival and leaf chlorophyll content (qSES12, qSUR12, and qCHL12: RM27933-RM17) [24]. A large amount of truncated proteins derived from the candidate gene OsCMO (29.34 Mb on chromosome 6) located near the MTA qRDW6 (AX-95956901-29.72 Mb) was reported to induce in response to salinity stress [45].The MTA qRDW7 was located in the vicinity of genomic region reported to be associated with root K + concentration and stress evaluation score (qSES7.1; qRK7.1: HvSSR 07-25-HvSSR 07-37) at reproductive stage salt stress [46]. The MTAs qRNC2.1 and qRNC2.2 were located in the genomic region reported to be associated with root K + concentration (qRKC2: RM13197-RM6318) [24] and germination percentage in 10 days (qGP2:RM8254-RM5804) [41].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

Yadav

Kumar

Grover

et al. 2021

Plants

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Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker–trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.

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QTLs in salt rice variety CSR10 reveals salinity tolerance at reproductive stage

Cited by 27 publications

References 62 publications

Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies

Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies

Genome-wide identification of DNA polymorphism in salt-tolerant and sensitive rice genotypes using double digest RADseq

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

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