Identification of new QTL for salt tolerance from rice variety Pokkali

Abstract

Salt stress is an ever‐present threat to rice production worldwide. Rice salinity tolerance is complex, both genetically and physiologically. The success and effectiveness in selecting salt‐tolerant rice variety require the identification of QTL for the tolerance and closely linked molecular markers. In the present study, a RIL population consisting of 148 lines, derived from a cross between IR29 (salt‐sensitive) and Pokkali (salt‐tolerant), was used to identify new QTL for salt tolerance and investigate the relationships between salt stress caused injury and the changes in different physiological and morphological traits at the seedling stage. 14,470 high‐quality SNP markers generated by the Rice 56K SNP array were converted to 1,467 bin markers for linkage mapping. A high‐density genetic linkage map covering 1,680.9 cM was constructed, with the physical to genetic distance ratio being 222 Kb/cM. In total, 23 QTL for different salt tolerance indices were identified, including the previously reported Saltol which is currently used in breeding programmes. Three QTL for salt injury score (SIS) were located on chromosomes 1, 4 and 12, all being closely related to the long‐distant Na+ transport from roots to shoots. These QTL showed additive effects, thus can be effectively used in breeding programme to pyramid various tolerance genes.

Phenotypic response of farmer‐selected CWR‐derived rice lines to salt stress in the Mekong Delta

“…However, new donors, especially from CWRs, are becoming increasingly important (Ahmad Ganie, Molla, Henry, Bhat, & Mondal, 2019; Solis et al., 2020). Several presumably beneficial QTL for salinity tolerance have been identified in rice at the seedling stage (Chen et al., 2020; L. Cheng et al., 2012; Jahan et al., 2020) and with beneficial alleles coming from CWRs (Tian, Tan, Liu, Cai, & Sun, 2011, Wang et al., 2017; Quan et al., 2018, Yichie, Brien, Berger, Roberts, & Atwell, 2018). These loci need to be genetically and physiologically characterized and their effects validated before molecular markers can be developed for more effective salinity screening and efficient development of salt‐tolerant varieties.…”

“…However, new donors, especially from CWRs, are becoming increasingly important (Ahmad Ganie, Molla, Henry, Bhat, & Mondal, 2019;Solis et al, 2020). Several presumably beneficial QTL for salinity tolerance have been identified in rice at the seedling stage (Chen et al, 2020;L. Cheng et al, 2012;Jahan et al, 2020) and with beneficial alleles coming from CWRs (Tian, Tan, Liu, Cai, & Sun, 2011, Wang et al, 2017Quan et al, 2018, Yichie, Brien, Berger, Roberts, & Atwell, 2018.…”

Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat

“…A visual symptom scoring at seedling or reproductive stage is a widely used method for screening a large number of plants (Darko et al 2017;Hura et al 2017). The damage score, based on the combination of leaf chlorosis and wilting, has been used extensively to assess biotic and abiotic stress tolerance in many cereals (Chen et al 2020;Choudhury et al 2019;Fan et al 2016;Kang et al 2020;Xu et al 2012a). In the present study, visual scoring was used to assess salinity tolerance in wheat.…”

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

“…Therefore, Na + , K + , and Na + /K + in shoot are used as an effective criterion in determining salt stress tolerance in rice [ 14 , 18 ]. Furthermore, QTL mapping approach has been successful in identifying genomic regions governing salinity tolerance in rice [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 ]. Several QTLs have been identified, of which Saltol a major QTL for seedling stage salinity tolerance from landrace Pokkali was identified on chromosome 1 which regulates shoot Na + /K + under salt stress [ 17 , 20 , 24 ].…”