Natural variation in growth and physiology under salt stress in rice: QTL mapping in aHorkuch×IR29mapping population at seedling and reproductive stages

Abstract

3 1 severe due to recent climate changes. To cope with this increased soil salinity, we need to 3 2 develop salt tolerant rice varieties that can maintaining higher yield. Rice landraces indigenous to 3 3 the coastal region of Bangladesh can be a great resource to study the genetic basis of salt 3 4 adaptation. In this study, we developed a reciprocal mapping population between a salt tolerant 3 5landrace Horkuch and a high yielding rice variety IR29. We applied a QTL analysis framework 3 6to identify genetic loci that contributes to salt adaptive responses for two different developmental 3 7 stages of salinity treatment. We identified 14 QTL for 9 traits and found most QTL are unique to 3 8 the specific developmental stage. Moreover, we discovered a significant effect of the 3 9 cytoplasmic genome on the QTL model for some important traits such as leaf total potassium 4 0 and filled grain number. This underscores the importance of considering cytoplasm-nuclear 4 1interaction for breeding programs. Along with that, we detected QTL co-localization for multiple 4 2 traits that highlights the constraint of multiple QTL selection for breeding program. Overall, in 4 3 this study we identified multiple QTL for different physiological and yield related traits for 4 4 salinity treatment for two different developmental stages of the rice plant. We detected a 4 5 significant contribution of cytoplasm-nuclear genome interaction for many traits. This study also 4 6 suggests the selection constraint of donor alleles due to the presence of QTL co-localization. 4 7

Genome-Wide Association Analysis for Salt–Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages

“…To mitigate the adverse effects of salinity on rice, a prospective practice is to breed varieties with salt tolerance at both sensitive stages and develop new rice varieties with enhanced resilience in salt stress environments. However, only a few attempts have been made to discover loci associated with ST across developmental stages and, especially, at the reproductive stage ( Ganie et al, 2019 ; Haque et al, 2020 ). This is mainly due to the fact that it is so difficult to obtain precise phenotypes at this stage, especially for natural varieties, because they vary largely on the time entering into reproductive stage ( Zeng et al, 2002 ).…”

Genome-wide association analysis for rice salt tolerance at seedling and reproductive stages

“…Considerable efforts have been devoted to the identi cation of ST QTLs/genes at each sensitive stage independently, such as the characterization of the Salto at the seedling stage (Thomson et al, 2010;Zeng et al, 2002;Mohammadi et al, 2013;Bimpong et al, 2014;Hossain et al, 2015). However, only a few attempts have been made to discover loci associated with ST across developmental stages and especially at the reproductive stage (Ganie et al, 2019;Haque et al, 2020).…”

Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding Approach

“…The molecular dissection of salt tolerance has considerably enhanced using the molecular platforms for identifying quantitative trait loci (QTL) controlling related genetic variation in crops including rice [1,2,8,60,[66][67][68][69][70][71][72].…”

“…Moreover, several QTLs related with physiological, agronomic traits conferring salinity tolerance at seedling and reproductive stage have been reported [1,8,71,73,74] including major QTLs for salinity tolerance such as SKC1 [75] (a sodium transporter OsHKT1; 5 in the SKC1 locus [76] and Saltol [71,77] (Table 2). Recently unraveled molecular basis of various rice landraces such as Pokkali [71,77], Nona Bokra [76], Hasawi [1], Capsule [2], Changmaogu [74] and Horkuch [72] can withstand different levels of salt-stress at various sensitive growth stages of rice.…”