Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines (original) (raw)
Related papers
2020
Using 14 ISSR primers for molecular profiling in relation to salinity tolerance of 18 landraces and varieties of rice, altogether 483 allelic variants including 236 shared and 247 unique alleles were generated with an average of 34.50 alleles per primer, revealing ample genetic differentiation and divergence amongst the entries under evaluation. Every primer generated polymorphic amplified products, but only 12 out of 14 primers yielded unique products. The primers having (AG)8YT, (CT)8A, (AG)8YA, (GA)8YT, (GA)8YC, (CT)8G, (TC)8C, (GATA)4 and (GA)8YG repeat motifs recorded relatively higher polymorphism per cent expressed in terms of the percentage of unique alleles in descending order of magnitude. Polymorphism information content of the primers varied from 0.612 to 0.992 for the primers (GACA)4 and (AG)8YA, respectively, with an average of 0.919 across the primers. Comparatively higher numerical values were obtained in respect of the primers (GA)8C, (CT)8A, (CT)8G, (TC)8C, (TC)8G,...
Research Square (Research Square), 2024
In the present investigation of genetic diversity related to salinity tolerance in rice at the early seedling stage, ten salt stress responsive candidate genes were employed to screen a collection of eighteen rice varieties with two tolerant (Pokkali, CSR-36) and two sensitive (IR-29, IR-64) as checks. The microsatellite repeat motifs found in the six salt stress responsive candidate genes (OsHKT1;5, SNAC1, CDMK, CCC, SHMT1, SHMT2) revealed a comparatively higher alleles number per locus, ranged from 3 (OsHKT1;5) to 12 (SHMT1). The remaining four salt stress responsive candidate genes (OsHKT1;1, OsHKT1;3, OsHKT2;3, OsHKT2;4) produced a signi cantly smaller number of alleles because they lacked microsatellite. The polymorphism percentage was found to be lowest in the cases of OsHKT1;5 and CDMK (00.00%) and highest in the case of SHMT1 (75.00%). Ampli cation pro les dependent similarity indices, together with hierarchical classi cation and spatial distribution patterns, clearly distinguished 18 varieties according to their tolerance to salt stress. The results of the hierarchical classi cation of the varieties were fully supported by principal coordinate analysis. Microsatellite including six salt stress responsive candidate gene (OsHKT1;5, SNAC1, CDMK, CCC, SHMT1, SHMT2) as well as microsatellite lacking four salt stress responsive candidate gene (OsHKT1;1, OsHKT1;3, OsHKT2;3, OsHKT2;4) speci c markers based genetic pro ling facilitated clear discrimination between salt stress sensitive and tolerant varieties, validating their utility for differentiation. The identi ed salt tolerant varieties, along with validated markers, can be in uential in developing salt tolerant rice varieties through targeted breeding programs.
2016
The present study investigated eight rice lines (Rupsal, Nagalmutha, Polai, Ravana, Marishal, Talmugra, Kamini and Raspanjar) collected from coastal region of eastern India for salinity tolerance through phenotypic and genotypic screening. Among these, three rice lines as highly tolerant (Talmugra, Marishal and Kamini), three tolerant (Rupsal, Polai and Raspanjar) and two moderately tolerant (Ravana and Nagalmutha) to salt stress were identified in phenotypic screening. Pokkali was categorized as tolerant under salinity condition (12 EC dS m-1). In PCR screening using microsatellite (SSR) markers located within Saltol locus, we documented new allelic pattern in selected highly tolerant and tolerant genotypes with RM8094 marker as compared to Pokkali. Besides, another marker RM10694 was found to associate with selection of salinity tolerant genotypes similar to Pokkali. In gene expression, no significant difference linked with abscisic acid (ABA), calcium-dependent proteins kinase (C...
Two different DNA-based techniques viz, simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers were used to estimate genetic diversity among 20 rice genotypes possessing different physiological mechanisms contributing to salt tolerance. A total of 11 clear and repeatable bands were amplified from ten selected SSR primers pairs and 43 fragments were detected from nine ISSR primers. The level of polymorphism was 1.1% with SSR compared to 90.7% with ISSRs. Mean genetic similarity of 0.88 based on SSRs and 0.85 using ISSRs was observed. A total of 43 (39 polymorphic) and 11 bands were detected using 9 ISSR primers and 10 well distributed mapped SSR markers, respectively. Estimates of genetic similarity of ISSRs based on the 39 polymorphic markers between 20 rice cultivars ranged from 0.55 for PR108/CSR19 to 0.94 for Pokkali/CSR20 with an average of 0.81. The estimates revealed by the 11 polymorphic SSR bands showed the average value (0.94) and also the range of genetic similarity (from 0.86 to 1.00 for CSR22/CSR18 and CSR24/CSR20, respectively) reflecting their hyper variability and their high resolution power. The findings are likely to expedite breeding new salt tolerant cultivars by involving parents from diverse molecular clusters.
Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice
Rice
Background Rice is one of the most salt sensitive crops at seedling, early vegetative and reproductive stages. Varieties with salinity tolerance at seedling stage promote an efficient growth at early stages in salt affected soils, leading to healthy vegetative growth that protects crop yield. Saltol major QTL confers capacity to young rice plants growing under salt condition by maintaining a low Na+/K+ molar ratio in the shoots. Results Marker-assisted backcross (MABC) procedure was adopted to transfer Saltol locus conferring salt tolerance at seedling stage from donor indica IR64-Saltol to two temperate japonica varieties, Vialone Nano and Onice. Forward and background selections were accomplished using polymorphic KASP markers and a final evaluation of genetic background recovery of the selected lines was conducted using 15,580 SNP markers obtained from Genotyping by Sequencing. Three MABC generations followed by two selfing, allowed the identification of introgression lines achie...
Salt stress response in rice: genetics, molecular biology, and comparative genomics
Functional & Integrative Genomics, 2006
Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers. Salt-tolerant transgenic rice plants have been produced using a host of different genes and transcript profiling by micro-and macroarraybased methods has opened the gates for the discovery of novel salt stress mechanisms in rice, and comparative genomics is turning out to be a critical input in this respect. In this paper, we present a comprehensive review of the genetic, molecular biology, and comparative genomics effort towards the generation of salt-tolerant rice. From the data on comprehensive transcript expression profiling of clones representing salt-stress-associated genes of rice, it is shown that transcriptional and translational machineries are important determinants in controlling salt stress response, and gene expression response in tolerant and susceptible rice plants differs mainly in quantitative terms.
Genes
'KDML105' rice, known as jasmine rice, is grown in northeast Thailand. The soil there has high salinity, which leads to low productivity. Chromosome substitution lines (CSSLs) with the 'KDML105' rice genetic background were evaluated for salt tolerance. CSSL18 showed the highest salt tolerance among the four lines tested. Based on a comparison between the CSSL18 and 'KDML105' transcriptomes, more than 27,000 genes were mapped onto the rice genome. Gene ontology enrichment of the significantly differentially expressed genes (DEGs) revealed that different mechanisms were involved in the salt stress responses between these lines. Biological process and molecular function enrichment analysis of the DEGs from both lines revealed differences in the two-component signal transduction system, involving LOC_Os04g23890, which encodes phototropin 2 (PHOT2), and LOC_Os07g44330, which encodes pyruvate dehydrogenase kinase (PDK), the enzyme that inhibits pyruvate dehydrogenase in respiration. OsPHOT2 expression was maintained in CSSL18 under salt stress, whereas it was significantly decreased in 'KDML105', suggesting OsPHOT2 signaling may be involved in salt tolerance in CSSL18. PDK expression was induced only in 'KDML105'. These results suggested respiration was more inhibited in 'KDML105' than in CSSL18, and this may contribute to the higher salt susceptibility of 'KDML105' rice. Moreover, the DEGs between 'KDML105' and CSSL18 revealed the enrichment in transcription factors and signaling proteins located on salt-tolerant quantitative trait loci (QTLs) on chromosome 1. Two of them, OsIRO2 and OsMSR2, showed the potential to be involved in salt stress response, especially, OsMSR2, whose orthologous genes in Arabidopsis had the potential role in photosynthesis adaptation under salt stress.
Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice
Agriculture
Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(P) threshold of ≥3.66. The QTL of qSIS2, showed −log10(P) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4, showed −log10(P) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10(P) = 3.78 and the lead SNP explained 7.83% of tota...
Molecular Genetics and Genomics, 2010
IdentiWcation of genes for quantitative traits is diYcult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome proWling was used to narrow down the number of diVerentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and saltsensitive variety MI 48 was used to map QTL for salt ion concentrations in diVerent tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight signiWcant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was colocated in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it diYcult to pinpoint the genes responsible for the functional diVerences for the traits. Similarly, transcriptome proWling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 diVerentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of diVerentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate markerassisted breeding.
International Journal of Molecular Sciences, 2019
Salinity critically limits rice metabolism, growth, and productivity worldwide. Improvement of the salt resistance of locally grown high-yielding cultivars is a slow process. The objective of this study was to develop a new salt-tolerant rice germplasm using speed-breeding. Here, we precisely introgressed the hst1 gene, transferring salinity tolerance from “Kaijin” into high-yielding “Yukinko-mai” (WT) rice through single nucleotide polymorphism (SNP) marker-assisted selection. Using a biotron speed-breeding technique, we developed a BC3F3 population, named “YNU31-2-4”, in six generations and 17 months. High-resolution genotyping by whole-genome sequencing revealed that the BC3F2 genome had 93.5% similarity to the WT and fixed only 2.7% of donor parent alleles. Functional annotation of BC3F2 variants along with field assessment data indicated that “YNU31-2-4” plants carrying the hst1 gene had similar agronomic traits to the WT under normal growth condition. “YNU31-2-4” seedlings sub...