FINE MAPPING OF QTL FOR SALT TOLERANCE ON RICE CHROMOSOME 8
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Date
2019
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DIVISION OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI
Abstract
Rice is one of the major cereal crops grown across the world. Nearly half of the world
population is dependent on Rice (Oryza sativa L.) as a major staple food. Ninety percent
of total rice is consumed in Asian countries. In some Asian countries like India, Vietnam,
Bangladesh etc., per capita rice consumption exceeds 100kg/year. Abiotic stresses are often
known to create a barrier to the yield of many crops. As, thirty percent of the total rice
growing area worldwide has been affected soil salinity, it is one of the major abiotic stresses
that limit rice productivity. In India, 6.73 Mha land is salt affected, out of which 3.77 and
2.96 Mha are covered by sodic and saline soils, respectively. Identification of novel genes
in donors with different salt tolerance mechanisms is essential to pyramid them in high
yielding varieties to combat soil salinity. A number of salt tolerant rice varieties with
different mechanism in salt tolerance had been released by the Central Soil Salinity
Research Institute (CSSRI), Karnal, India, like CSR 10, CSR 11, CSR 27, CSR 36, and
CSR 30 etc. Though rice is relatively tolerant to salinity during germination stage, active
tillering stage and maturity but it is very susceptible during early seedling and reproductive
stage. In order to improve productivity in salt affected areas a lot of efforts have been given
to identify QTL related to salt tolerance related traits like plant survival, shoot and root
length, Na+ and K+ uptake, Na+/K+ ratio, grain yield, spikelet fertility, Stress
susceptibility index etc.. Though, hundreds of QTLs have been identified, most of them are
mapped within a bigger confidence interval. As a result, identification of genes within these
QTLs becomes very difficult. Most of the salt tolerance QTLs identified in rice confer
tolerance in seedling stage. ICAR-NIPB identified a consistent QTL, qSSISFH8.1 which
confer salt tolerance during reproductive stage. Initial mapping experiment limit this QTL
within an interval of 1.1 Mb. In this study, qSSISFH8.1 was narrowed down further to
identify candidate gene within this QTL. In order to fine map the QTL, a large F2 mapping
population consisting 4300 individuals was developed and homozygous recombinants were
identified. Homozygous recombinants were phenotyped during three years (2015 to 2017).
As fine mapping required additional markers within QTL region, 13 SNP markers were
developed by resequencing of parents. All homozygous recombinant lines were genotyped
with these 13 SNPs by using 13Plex SNP assay in Sequenom MassArray. Graphical
representation of 13 SNPs classified 146 homozygous recombinants into five genotypic
groups. Comparing phenotypic means of these genotypic groups narrowed down the QTL
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region within 600Kb interval. Gene model annotation revealed presence of 48 gene models
within the QTL region. Interestingly this region is enriched with transposons/retrosposons.
Apart from 48 gene models, this region also has 41 transposon genes. Among these 48
protein coding genes, 7 gene models were annotated as hypothetical protein and 20 gene
models were annotated as “expressed gene”. In order to identify candidate genes within
QTL region, differential gene expression was studied in response to salt stress. Five genes
were found to be differentially expressed in response to salt stress and these genes showed
different expression pattern in tolerant and susceptible parents. Hence these genes could be
strong candidate for the QTL, qSSISFH8.1. These five genes are taetraspanin, histone
acetyl transferase, prohibitin, BRI1 leucine-rich repeat receptor-like kinase, hydroxy
proline rich glycoproteins.
Key words: QTL- Quantitative Trait Loci, SNP-Single Nucleotide Polymorphism, SSISFStress Susceptibility Index for Spikelet Fertility
Description
T-10300