Genetic Studies on Salt Tolerance in Rice (O. Sativa) Using Conventional and Molecular Methods

Abstract

Niger’s rice production has not been able to match growth in demand. The slow growth in domestic rice production has been attributed to salinity, non-adapted germplasm, and low farmer adoption of improved varieties. This study was carried out to: determine farmers’ perception on influence of salinity in rice production and their preference for rice varieties in salt affected areas; identify potential sources of genes for salt tolerance from local and exotic rice germplasm; determine genetic control of salt tolerance in rice; and evaluate yield performance of early segregating generations of rice from crossing diverse parental genotypes. Participatory rural appraisal (PRA) was conducted in three regions of Niger involving 197 farmers from 11 villages. The results showed that rice is the most preferred crop. Farmers identified lack of fertilizer, diseases, salinity, and lack of good varieties as the main production constraints. Ninety (90) percent of the farmers were aware of salinity problem and use manure and/or ashes, straw, and the avoidance of urea as coping strategies. The farmers preferred high yielding rice varieties with tolerance to diseases and salinity, medium height and high tillering ability. Laboratory analyses were carried out on soils from irrigated and non-irrigated fields as well as irrigation water. Most of the irrigated rice fields were clayey (40 to 50% clay). The non-irrigated ones were mostly sandy (50 to 90% of sand). The irrigated soils were characterized by pH which varied from 3.2 to 6.8, an electrical conductivity (EC) above 4, a sodium adsorption ratio (SAR) below 13 and an exchangeable sodium percentage (ESP) below 15. The water analysis indicated the sodium adsorption ration (SAR), the potassium adsorption ration (PAR) the total dissolved solids (TDS), and sodium content of irrigation water varied from site to site. The total sodium quantity estimated to be deposited per hectare per year varied from 87 kg/ha/year to 218 kg/ha/year. Fifteen exotic and five local varieties were evaluated in a greenhouse under four salt levels and a control without salt. Significant genotype by salt concentration effect was observed. Significant variability among varieties (probability level of 0.001) across and within salt levels was present for all the traits measured. Four salt tolerant genotypes with high selection index were identified. One hundred and twenty F3 families derived from a diallel cross of 4 parents were evaluated in salt affected farmer’s fields in two sites. High heritability was observed for almost all the traits. Additive effects for tiller number, panicle number, and panicle weight, additive maternal effects, and partial dominance effects for height and duration were observed. Yield potential varied significantly (Probability level of 0.001) among F3 families ranging from 2.52 to 4.17 t/ha. Correlation analysis among traits showed that yield was significantly and positively associated with height, tiller and panicle number, and panicle weight. Leaf samples of the four parents used in the diallel were genotyped by LGC genomics, (United Kingdom) using 1896 SNPs. The results indicated that all the parents were homozygote and genetically differed from each other in terms of substitution pattern, sequences disparity and divergence and base composition. Two hundred SNPs were polymorphic and were selected for early generations screening for salt tolerance.