Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
Highlights
IntroductionLicensee MDPI, Basel, Switzerland.With a constant rise in the annual global rice consumption (about 504.3 million metric tons in the year 2020–2021), there is a need to increase its production to feed the rising world population, which is estimated to reach more than 9 billion by 2050 [1,2]
Licensee MDPI, Basel, Switzerland.With a constant rise in the annual global rice consumption, there is a need to increase its production to feed the rising world population, which is estimated to reach more than 9 billion by 2050 [1,2]
Number of Genes Encoding CBS domain containing proteins (CDCPs) Varies in Oryza Species
Summary
Licensee MDPI, Basel, Switzerland.With a constant rise in the annual global rice consumption (about 504.3 million metric tons in the year 2020–2021), there is a need to increase its production to feed the rising world population, which is estimated to reach more than 9 billion by 2050 [1,2]. The climate change, soil degradation, and sensitivity of rice crops to various biotic and abiotic stresses pose a major challenge to meet this demand. IR64 rice genotypes, and identified many genes which showed differential regulation under salt stress treatment. Among these are the genes encoding members of a protein family containing the conserved Cystathionine β-Synthase (CBS) domain [3]. Our lab carried out the genome-wide identification of the CBS domain containing proteins (CDCPs) in rice (Oryza sativa subsp. japonica) and Arabidopsis [4], and identified two CDCP members to impart tolerance to multiple abiotic stresses when overexpressed constitutively in tobacco [5,6]
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