AUTHOR=Fatima Kinza , Sadaqat Muhammad , Azeem Farrukh , Rao Muhammad Junaid , Albekairi Norah A. , Alshammari Abdulrahman , Tahir ul Qamar Muhammad 

TITLE=Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses

JOURNAL=Frontiers in Genetics

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1252020

DOI=10.3389/fgene.2023.1252020

ISSN=1664-8021

ABSTRACT=<p><italic>Arachis hypogaea</italic> (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in <italic>Arachis hypogaea</italic> and its progenitors. This study conducts a pangenome-wide investigation of <italic>A. hypogaea</italic> and its two progenitors, <italic>A. duranensis</italic> and <italic>A. ipaensis CRK</italic> genes (<italic>AhCRKs</italic>, <italic>AdCRKs</italic>, and <italic>AiCRKs</italic>). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter <italic>cis</italic>-elements, protein–protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut <italic>CRK</italic> genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the <italic>AhCRK</italic> genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that <italic>AhCRKs</italic> have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the <italic>AhCRK</italic> genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of <italic>AhCRKs</italic> were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the <italic>CRK</italic> gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.</p>