ArticlePlant cell reports2016
Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm.
Article in Plant cell reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 32 citations in OpenAlex.
- Superior haplotypes for transforming crop breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Rice Adaptation to Abiotic Stresses Caused by Soil Inorganic Elements.International journal of molecular sciences · 2025Review
- Restructuring plant types for developing tailor-made crops.Plant biotechnology journal · 2023Review
- Genome-Wide Identification ofPlants (Basel, Switzerland) · 2022Article
- Unlocking Allelic Diversity for Sustainable Development of Salinity Stress Tolerance in Rice.Current genomics · 2021Review
- Salinity tolerance mechanisms and their breeding implications.Journal, genetic engineering & biotechnology · 2021Review
- Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2021Article
- Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants.Frontiers in plant science · 2021Review
- Identification of QTN and candidate genes for Salinity Tolerance at the Germination and Seedling Stages in Rice by Genome-Wide Association Analyses.Scientific reports · 2018Article
- Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild RiceFrontiers in plant science · 2018Article
- Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes.Frontiers in plant science · 2017Review
- Improvement of Salt Tolerance Using Wild Rice Genes.Frontiers in plant science · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageThe association of natural genetic variations of salt-responsive candidate genes belonging to different gene families with salt-tolerance phenotype and their haplotype variation in different geographic regions. Soil salinity covers a large part of the arable land of the world and is a major factor for yield losses in salt-sensitive crops, such as rice. Different gene families that respond to salinity have been identified in rice, but limited success has been achieved in developing salt-tolerant cultivars. Therefore, 21 salt stress-responsive candidate genes belonging to different gene families were re-sequenced to analyse their genetic variation and association with salt tolerance. The average single nucleotide polymorphism (SNP) density was 16 SNPs per kbp amongst these genes. The identified nucleotide and haplotype diversity showed comparatively higher genetic variation in the transporter family genes. Linkage disequilibrium (LD) analysis showed significant associations of SNPs in BADH2, HsfC1B, MIPS1, MIPS2, MYB2, NHX1, NHX2, NHX3, P5CS1, P5CS2, PIP1, SIK1, SOS1, and SOS2 genes with the salt-tolerant phenotype. A combined analysis of SNPs in the 21 candidate genes and eight other HKT transporter genes produced two separate clusters of tolerant genotypes, carrying unique SNPs in the ion transporter and osmoticum-related genes. Haplotype network analysis showed all the major and few minor alleles distributed over distant geographic regions. Minor haplotypes may be recently evolved alleles which migrated to distant geographic regions and may represent recent expansion of Indian wild rice. The analysis of genetic variation in different gene families identified the relationship between adaptive variations and functional significance of the genes. Introgression of the identified alleles from wild relatives may enhance the salt tolerance and consequently rice production in the salinity-affected areas.
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