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.
Highlights
Rice (Oryza sativa L.) is one of the most important cereal crops in the world and serves as a staple food for more than half of the world’s population
Several marker-assisted approaches were used for selection of progenies through the backcrossing process, which involved the use of Saltol SSR marker SKC10 by PCR (Thomson et al, 2010) and Kompetitive allele specific PCR (KASPar) markers coupled to the Light Cycler 480 system and the Fluidigm technology (Roche) (Supplementary Figure 2 and Supplementary Table 1)
The 30 BC3F4 lines derived from four different BC3F1 plants, which resulted in four different introgression patterns in the introgression line (IL) at the BC3F3 generation
Summary
Rice (Oryza sativa L.) is one of the most important cereal crops in the world and serves as a staple food for more than half of the world’s population. Rice is considered a salt-sensitive crop, at the seedling and reproductive stages (Zeng and Shannon, 2000). The extent and severity of salt-affected agricultural land is predicted to worsen as a result of inadequate drainage of irrigated land, entry of sea water in coastal rice fields, and global warming. Tolerance to salt stress in plants is a complex trait governed by a multitude of physiological and molecular mechanisms (Van Zelm et al, 2020). The transcriptional reprogramming of plant leaves during adaptation to salt stress has deserved less attention. More sensitive to salt stress than roots
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