ArticleBMC plant biology2015
Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.).
Article in BMC plant biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Integrative Physiological and Transcriptomic Analysis Reveals Metabolic Adaptation and Cold-Tolerance Marker Development in Winter Rye Under Low-Temperature Stress.Plants (Basel, Switzerland) · 2025Article
- Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways.Frontiers in plant science · 2024Article
- Molecular switch to regulate salt tolerance in rice.The Plant cell · 2023Article
- Understanding natural genetic variation for grain phytic acid content and functional marker development for phytic acid-related genes in rice.BMC plant biology · 2022Article
- DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials.Rice (New York, N.Y.) · 2022Article
- Identification and Characterization of DNA Demethylase Genes and Their Association With Thermal Stress in Wheat (Frontiers in genetics · 2022Article
- Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice.Plants (Basel, Switzerland) · 2021Article
- Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding.Molecular biology reports · 2021Article
- Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS.Scientific reports · 2020Article
- Single-nucleotide editing foraBIOTECH · 2020Article
- Diversity analysis of selected rice landraces from West Bengal and their linked molecular markers for salinity tolerance.Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers inGenes · 2020Article
- Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective.Rice (New York, N.Y.) · 2019Review
- Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study.Rice (New York, N.Y.) · 2019Article
- Advances in understanding salt tolerance in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation.BMC plant biology · 2019Article
- Meta-Analysis of Salt Stress Transcriptome Responses in Different Rice Genotypes at the Seedling Stage.Plants (Basel, Switzerland) · 2019Article
- Seedling stage salt stress response specific characterization of genetic polymorphism and validation of SSR markers in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2019Article
- Novel screening protocol for precise phenotyping of salt-tolerance at reproductive stage in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2018Article
- Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat.BMC plant biology · 2018Article
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Abstract
backgroundMajority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice.
resultsIn the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5'UTR (26%), intron (21.6%) and 3'UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes.
conclusionThe present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
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