Genome-wide characterization of the PP2C gene family in peanut (Arachis hypogaea L.) and the identification of candidate genes involved in salinity-stress response

Abstract

Plant protein phosphatase 2C (PP2C) play important roles in response to salt stress by influencing metabolic processes, hormone levels, growth factors, etc. Members of the PP2C family have been identified in many plant species. However, they are rarely reported in peanut. In this study, 178 PP2C genes were identified in peanut, which were unevenly distributed across the 20 chromosomes, with segmental duplication in 78 gene pairs. AhPP2Cs could be divided into 10 clades (A-J) by phylogenetic analysis. AhPP2Cs had experienced segmental duplications and strong purifying selection pressure. 22 miRNAs from 14 different families were identified, targeting 57 AhPP2C genes. Gene structures and motifs analysis exhibited PP2Cs in subclades AI and AII had high structural and functional similarities. Phosphorylation sites of AhPP2C45/59/134/150/35/121 were predicted in motifs 2 and 4, which located within the catalytic site at the C-terminus. We discovered multiple MYB binding factors and ABA response elements in the promoter regions of the six genes (AhPP2C45/59/134/150/35/121) by cis-elements analysis. GO and KEGG enrichment analysis confirmed AhPP2C-A genes in protein binding, signal transduction, protein modification process response to abiotic stimulus through environmental information processing. Based on RNA-Seq data of 22 peanut tissues, clade A AhPP2Cs showed a varying degree of tissue specificity, of which, AhPP2C35 and AhPP2C121 specifically expressed in seeds, while AhPP2C45/59/134/150 expressed in leaves and roots. qRT-PCR indicated that AhPP2C45 and AhPP2C134 displayed significantly up-regulated expression in response to salt stress. These results indicated that AhPP2C45 and AhPP2C134 could be candidate PP2Cs conferring salt tolerance. These results provide further insights into the peanut PP2C gene family and indicate PP2Cs potentially involved in the response to salt stress, which can now be further investigated in peanut breeding efforts to obtain cultivars with improved salt tolerance.

Functional screening of the Arabidopsis 2C protein phosphatases family identifies PP2C15 as a negative regulator of plant immunity by targeting BRI1‐associated receptor kinase 1

“…PP2Cs represent more than 60% of the total phosphatase repertoire, with 80, 90, 91, and 88 genes identified in Arabidopsis , rice, tomato, and hot pepper genomes, respectively (Singh et al., 2016 ). Sequence and gene structure analyses of the PP2C family members in different plant species support their conservation in higher plants (Guo, Shi, et al., 2023 ; Wu et al., 2023 ). Similar to that observed in earlier studies (Ayatollahi et al., 2022 ; Couto et al., 2016 ; Sidonskaya et al., 2016 ), although mutant plants showed a more prominent response to immune signals, no autoimmunity was detected in pp2c5 and pp2c15 mutant plants (Figures 1 , 2 , 3 , 4 , 5 ).…”

Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut

“…In our study, two genes ( arahy.SJ8MZN and arahy.CRLU4M ) encode mitogen-activated protein kinase kinase kinase 3 (MAPKKK), which plays an essential role in MAPK signal perception, transduction, and amplification [ 38 ]. Additionally, phosphatase 2C 51 (encoded by arahy.8GI8KI ), a component of ABA signal transduction, is known to directly participate in plant salt stress regulation [ 59 , 60 ]. Furthermore, the hub gene arahy.ID0B6N encodes peroxidase 3, which plays a significant role in antioxidant responses and stress tolerance in plants, contributing to salt tolerance in soybean as well [ 61 ].…”

Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses

“…Previous studies on motif distribution in Arabidopsis [ 10 ], rice [ 10 ], and cucumber [ 56 ] PP2C genes demonstrated that motifs were particular to only one or more subgroups which support our findings. Notably, the number of identified conserved motifs in HanPP2C (20 motifs) is higher than cucumber (10 motifs) [ 56 ], tomato (10 motifs) [ 31 ], peanut (10 motifs) [ 92 ], Arabidopsis (11 motifs) [ 10 ], and Medicago truncatula (15 motifs) [ 9 ].…”

“…This study revealed that all 53 pairs of duplicated HanPP2c genes predominantly evolved through purifying selection. Previous investigation on tomato [ 31 ] and peanut [ 92 ] PP2C genes showed that all duplicated SIPP2C and AhPP2C genes have evolved from purifying selection. However, both purifying and positive selection were identified in the duplicated PP2C genes of woodland strawberries and pineapple strawberries [ 80 ].…”