Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines

Abstract

Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.

The Transcription Factor MYB37 Positively Regulates Photosynthetic Inhibition and Oxidative Damage in Arabidopsis Leaves Under Salt Stress

“…Tulay et al (2015) also found that salt stress increases the activity of chlorophyllase in Spergularia marina (Caryophyllaceae), decreases the content of Mg 2+ ions, accelerates the degradation of chlorophyll, inhibits the function of pigment protein complex, and the leaves become yellow or even fall off. Herein, MYB37 overexpression delayed chlorophyll degradation under salt stress and alleviated chlorophyll reduction effect, especially Chl a , similar to the results of Bundó et al (2022) . MYB37 overexpression can exhume or compartmentalize Na + in the cytoplasm into vacuoles, regulate the concentration of Na + in cells and maintain intracellular ion homeostasis by increasing the expression of Na + /H + antiporter NHX1 in the vacuolar membrane, thus delaying chlorophyll degradation and enhancing salt tolerance ( Zhao et al, 2019 ).…”

Integration of multi-omics technologies for crop improvement: Status and prospects

“…In recent years, dozens of powerful tools for quantitative trait loci (QTL) mapping have been developed based on deep sequencings, such as restriction-site associated DNA sequencing (RAD-seq), genotyping-by-sequencing (GBS), bulked segregant analysis sequencing (BSA-seq), and specific locus amplified fragment sequencing (SLAF-seq) ( Bundo et al, 2022 ). These mapping approaches used the genetic map or limited number of SNPs to seek the candidate genomic regions and genes for the traits.…”

Genome-wide and molecular characterization of the DNA replication helicase 2 (DNA2) gene family in rice under drought and salt stress

“…RNA seq data for drought and salt stresses were assessed from online data bases which are publically available with Bio-projects GSE145869 and GSE167342 ( Tarun et al, 2020 ; Bundó et al, 2022 ). In these studies, Nil-95 and Swarna genotypes were used as drought tolerant and sensitive, while IL22 and PL12 were used as a salt tolerant and sensitive rice genotype, respectively.…”