PhD Research Scholar, International Rice Research Institute
QTL mapping will be an approach for developing salt tolerant rice variety through MAS
Rice is currently the model crop cereal as half of the world population depends on rice. To meet the projected demand for rice, it has been estimated that global annual rice production needs to be increased to 850 million tons by 2025. But unfavorable environmental conditions pose a huge threat for the future food security of the rice world. Among them, salinity is the second most serious threat to the increased rice production as the seedling and reproductive stages are the most sensitive growth stages against salinity stress due to very poor association, suggesting that they are regulated by different processes and sets of genes/QTLs (Quantitative Trait Loci). The reproductive stage is most crucial as it determines grain yield. Millions of hectares in the humid regions of South and Southeast Asia are technically suited for rice production but are left uncultivated or are grown with very low yields because of salinity and problem soils. So, the development of salt tolerant varieties has been considered as an important effort to increase rice production under saline conditions to feed the people living in such adverse environments. I have identified major genes/QTLs which are responsible for salt tolerance at reproductive stage and these will be helpful for understanding the further molecular interaction. Recently, the plant breeding methods have considerably advanced with the introduction of molecular techniques. DNA based molecular markers are used extensively to assess the genetic diversity in most crop species. It has enormous potential to improve efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). Molecular markers are now using to tag QTLs and evaluate their contributions to the phenotype by selecting for favorable alleles (genes) at these loci in MAS scheme that aims to accelerate genetic advancement in rice. In this study, high throughput DNA marker was used to identify potential marker(s) associated with salinity tolerance. The mapping of QTLs for salinity tolerance at the reproductive stage of rice can aid in the identification of genetic control of salinity tolerance leading to development of varieties with improved tolerance by precisely transferring QTLs into adapted varieties.
Abstract: Breeding for salt tolerance is the most promising approach to enhance the productivity of saline prone areas. However, polygenic inheritance of salt tolerance in rice acts as a bottleneck in conventional breeding for salt tolerance. Hence, we set our goals to construct a single nucleotide polymorphism (SNP)-based molecular map employing high-throughput SNP marker technology and to investigate salinity tolerant QTLs with closest flanking markers using an elite rice background. Seedling stage salinity responses were assessed in a population of 281 recombinant inbred lines (RILs) derived from the cross between At354 (salt tolerant) and Bg352 (salt susceptible), by 11 morpho-physiological indices under a hydroponic system. Selected extreme 94 RILs were genotyped using Illumina Infinium rice 6K SNP array and densely saturated molecular map spanning 1460.81 cM of the rice genome with an average interval of 1.29 cM between marker loci was constructed using 1135 polymorphic SNP markers. The results revealed 83 significant QTLs for 11 salt responsive traits explaining 12.5-46.7 % of phenotypic variation in respective traits. Of them, 72 QTLs responsible for 10 traits were co-localized together forming 14 QTL hotspots at 14 different genomic regions. The all QTL hotspots were flanked less than 1 Mb intervals and therefore the SNP loci associated with these QTL hotspots would be important in candidate gene discovery for salt tolerance.
Pub.: 19 Aug '16, Pinned: 29 Jun '18
Abstract: Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line 'Pokkali' developed in a susceptible high yielding rice cultivar 'Bengal' background was evaluated for several morphological and physiological traits under salt stress. Both SSR and genotyping-by-sequencing (GBS) derived SNP markers were utilized to characterize the ILs and identify QTLs for traits related to salinity tolerance. A total of eighteen and thirty-two QTLs were detected using SSR and SNP markers, respectively. At least fourteen QTLs detected in the RIL population developed from the same cross were validated in IL population. Analysis of phenotypic responses, genomic composition, and QTLs present in the tolerant ILs suggested that the mechanisms of tolerance could be Na+ dilution in leaves, vacuolar Na+ compartmentation, and possibly synthesis of compatible solutes. Our results emphasize the use of salt injury score (SIS) QTLs in marker-assisted breeding to improve salinity tolerance. The tolerant lines identified in this study will serve as improved breeding materials for transferring salinity tolerance without the undesirable traits of Pokkali. Additionally, the lines will be useful for fine mapping and map-based cloning of genes responsible for salinity tolerance.
Pub.: 08 Apr '17, Pinned: 29 Jun '18