IC4R005-GWAS-2015-25627243

Project Title

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

The Background of This Project

• Salinity tolerancein rice is highly desirable to sustainproduction inareasrenderedsaline duetovarious reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS).
• Rice, commonly known to be salt sensitive, 1 is greatly affected by soilsalinity. Salinity affects rice growth in varying degree at all stages starting from germination through maturation. 3–6 Excess salts adversely affect all major metabolic activities in rice, and cause overall decline in germination and seedling growth, leading ultimately to reduced growth and diminished grain yield. The reduction in major yield components including tiller numbers in plant and spikelet numbers per panicle has been reported to be the major cause of yield loss (27–50%) in rice cultivars during early reproductive panicle initiation stage under salinity stress. 5,8,9 Millions of hectares in the humid regions of South and Southeast Asia are technically suited for rice pro- duction but are left uncultivated or are grown with very low yields because of salinity and problem soils. Salt-affected soils in arid and semi-arid regionsof Asia, Africaand South Americacause considerable agronomic problems. In Asia, 12 million ha of land area is thought to be salinity affected with India having >50% salinity affected area. Considerable variation for different yield contributing agronomic traits has been observedindiverserice genotypes under salinitystress. 10,11 Therefore, to maximize productivity of rice under saline soils, there is an ur- gent need to look for discovery of genes imparting salt tolerance and their introduction in salt-sensitive rice cultivars.
• The dissectionof salt tolerance traits has beencarried out by quantitative trait loci (QTLs) mapping approach using bi-parental populations. These studies have led to identification of both majorand minor QTLs for various traits on different rice chromosomes. 13–22 For example, Koyama et al. 13 identified 11 QTLs for Na + and K + content related to salinity stress tolerance. Bonilla et al. mapped Saltol locus linked to major QTLs for Na + and K + uptake and Na + /K + ratio on chromosome 1 explaining 64.3% phenotypic variance. Lin et al. mapped QTLs for root and shoot Na + /K + concentration and transport on five rice chromosomes. Ammar et al. reported 25 QTLs for salt ion concentrations (Na + , K + and Cl − measured in the leaf tissues at the reproductive stage) on rice chromosomes 1, 2, 3 and 8. Pandit et al. reported eight QTLs for salt ion concentrations on rice chromosomes 1, 8 and 12, and Cheng et al. 23 reported 12 QTLs for salt ion concentrations on rice chromosomes 1, 2, 3, 4, 7 and 11, respectively.

Plant Culture & Treatment

• The experiment comprised of 220 rice accessions, which were obtained from various national and international institutes to assess the performance in normal and high saline stress conditions. These genotypes were evaluated in randomized complete block design with two replications under two environments, viz., normal (EC iw ∼1.0 dS/m) and high salinity stress (EC iw∼10 dS/m) in micro plots at the Central Soil Salinity Research Institute, Karnal, Haryana, India. This experimental site is situated at 29.43°N latitude and 76.58°N longitude and 245 m above the sea level. The 35-day-old seedlings from wet bed nurseries were transplanted using two seedlings per hill at a spacing of 15×20 cm. Basal fertilizers for the main crop were 120-60-60 kg of NPK/ha. The recommended agronomic practices were followed to get healthy and good crop. Twenty-one days after transplanting, salinity stress was imposed using 7 NaCl: 1Na 2 SO 4 :2 CaCl 2 onequivalent basis. Salinitywasrecorded onceina week and maintained at desired level (EC iw ∼10 dS/m) throughout the croppingseason.Randomlyfiveplantsweretaggedforeachgenotypein each replication, and phenotypic data were recorded for all traits. The response of the genotypes to salt stress was expressed using the stress susceptibility index (SSI) calculated according to Fischer and Maurer 39 using the following formula: SSI=(1−Ys/Yp)/D, where Ys=mean performance of a genotype under stress; Yp=mean performance of the same genotype without stress; D (stress intensity)=1−(mean Ys of all genotypes/mean Yp of all genotypes).

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Labs working on this Project

• National Research Centre on Plant Biotechnology, New Delhi 110012, India
• Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
• Indian Agricultural Statistics Research Institute, New Delhi 110012, India
• University of Delhi South Campus, New Delhi 110021, India
• Central Rice Research Institute, Cuttack, Odisha 753006, India

Corresponding Author

• Trilochan Mohapatra(tmnrcpb@gmail.com)