Investigating Salinity Tolerance in Rice Through Mapping QTLs for Reproductive-Stage Tolerance and Guide RNA Validation for Gene Editing of the HKT Family
Abstract
Salinity is the most extensive problem in coastal rice eco-systems and tolerance at reproductive stage of rice is crucial for higher grain yield. In this study, two salt-tolerant varieties, CSR28 and Hasawi, and a salt-sensitive variety, BRRI dhan28, were used as parents to develop two BC1F2mapping populations to identify QTLs for reproductive-stage salinity tolerance in rice. Salinity of EC 10 dS/m was applied at booting stage which was constantly maintained for 20 days after leaf pruning. Data on yield, yield components and important agronomic parameters were collected from reproductive stage screening. In addition, visual salinity scoring was done using Standard Evaluation System (SES) and Na+/K+ was analyzed to identify the tolerant and sensitive plants. Positive and significant correlations were observed between the grain yield and number of filled spikelets in both crosses and it is negatively correlated with SES, which implies that the SES score is an initial stress indicator to identify tolerant and sensitive genotypes. Grain yield of tolerant progenies from Hasawi x BRRI dhan28 was significantly higher than that from CSR28 x BRRI dhan28. A total of 15 and 35 QTLs under salinity stress were identified through inclusive composite interval mapping (ICIM) of the crosses, CSR28 x BRRI dhan28 and Hasawi x BRRI dhan28, respectively. The QTL analysis suggested that a genomic region on chromosome 10 affects salinity tolerance at reproductive stage by increasing in number of filled spikelets, percent filled spikelet and grain yield of CSR28 x BRRI dhan28 progenies. On the other hand, for Hasawi x BRRI dhan28, chromosome 3 affects salinity tolerance by increasing productive tillers, number of filled spikelets and grain yield. These loci are good targets for marker-assisted selection aimed at improving salinity tolerance. This study also focused on targeting seven gene members of the HKT gene family, which plays a central role in determining salinity tolerance mechanisms, via multiplex CRISPR/Cas9 based DNA free genome editing using CRISPR/Cas9 ribonucleoprotein (RNPs) and validating the gRNA designs using in vitro RNP assays. The results showed that cleavage activities of all genes were successful, which prepares the way for future gene editing to functionally characterize the HKT gene family.
Citation
Mondal, Sejuti (2020). Investigating Salinity Tolerance in Rice Through Mapping QTLs for Reproductive-Stage Tolerance and Guide RNA Validation for Gene Editing of the HKT Family. Doctoral dissertation, Texas A&M University. Available electronically from https : / /hdl .handle .net /1969 .1 /193038.