Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace ‘Pokkali’

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.

A quantitative trait locus,qSE3, promotes seed germination and seedling establishment under salinity stress in rice

“…In rice, many quantitative trait loci (QTLs) for seed germination and seedling growth under salinity stress have been identified. Of these QTLs, QTLs conferring salinity tolerance have been identified primarily at the seedling stage (Prasad et al ., ; Koyama et al ., ; Lin et al ., ; Ren et al ., ; Lee et al ., ; Cheng et al ., ; Wang et al ., ,b; De Leon et al ., , ; Puram et al ., ; Yu et al ., ), with a few reports of such QTLs at the seed germination stage (Wang et al ., ). At the seedling stage, the characteristics of Na + and K + concentrations and the Na + /K + ratio are used to evaluate salinity tolerance.…”

Identification of new QTL for salt tolerance from rice variety Pokkali

“…For instance, qRSKC1.1 , qSNaC1.1 , qSKNa1 , qRNaC1 and qRKNa1 were located within the Saltol segment (11.0 Mb‒12.2 Mb) on chromosome 1 (Thomson et al, ), and the nearest bin marker Bin1_11.35‐11.50 harboured the SKC1 gene (11.46 Mb) (Ren et al, ). Furthermore, qSIS1 , qRSKC1.2 and qSNaC1.2 on chromosome 1 were co‐localized with qSIS1.39 (39.5 Mb) detected in a set of introgression lines of Pokkali as donor (De Leon et al, ) and qST1.1 (40.3 Mb) from a salt‐tolerant Dongxiang wild rice (Quan et al, ). This region is also close to OsHAK5 (40.8 Mb), OsHAK6 (40.9 Mb) and OsHAK2 (41.1 Mb) which encode high‐affinity potassium transporters mediating K + uptake (Banuelos, Garciadeblas, Cubero, & Rodriguez‐Navarro, ; Horie et al, ).…”

“…Pokkali is a landrace rice variety. Due to its unique saline tolerance, Pokkali has been widely used in QTL mapping for salt tolerance (Alam et al, 2011;Bonilla et al, 2002;De Leon et al, 2016;De Leon, Linscombe, & Subudhi, 2017;Gregorio, 1997a;Thomson et al, 2010). However, the Saltol identified from Pokkali does not provide a high degree of salt tolerance based on overall visual performances at seedling stage (Alam et al, 2011;Thomson et al, 2010), indicating that additional salt-responsive QTL derived from Pokkali exist.…”

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice

“…However, due to the genetic complexity of the trait, development of resilient varieties against salinity stress cannot be achieved by a single step strategy. Due to the polygenic nature of the trait, many Quantitative Trait Loci (QTLs) and Quantitative Trait Nucleotides (QTNs) have been reported linking either with salinity tolerance or susceptibility traits distributed throughout the genome in many rice lines [8][9][10][11][12][13].Although rice is sensitive to salt, especially at the seedling stage and reproductive stage, vast diversity for this trait across the rice varieties offers a promising tool for improving salt tolerance in rice. Pokkali and Nona bokra are popular traditional salt-tolerant indica rice varieties that tolerate up to 80 mM NaCl at the seedling stage and serve as donors for rice salt tolerance [14].…”

“…This approach helps to shortlist promising candidate genes of the trait by analyzing SNPs, InDels and structural variations which can later be validated by expression studies and promoter analysis. Instead of costly conventional fine mapping done with large inbred populations that need significant labor and time, QTLs and QTNs targeted annotation of the NGS derived sequences has revealed many candidate genes in various disciplines of plants [2,8,10,28,29].…”