Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars

Abstract

Background Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency.

Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9

“…Raw reads were subjected to Trimmomatic software (v0.40) to remove adapters, poly-N-containing reads, and low-quality reads, Q20, Q30, and GC contents of clean data were calculated. The genome of Arachis hypogaea (GenBank accession number GCF_003086295.2_arahy.Tifrunner.gnml.KYV3) was used as a reference sequence [ 15 ], and the clean data were mapped against the reference genome using the software Hisat2 (v2.0.1). Sequences with total mapped reads or fragments larger than 70% of the data were selected for subsequent analysis.…”

Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut (Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency

“…As an important economic and oil crop grown worldwide, peanuts often suffer from abiotic stress, such as drought, salt, and low temperatures [31]. In addition, it is important to note that peanut is a calcium-addicted crop, and calcium (Ca) deficiency can significantly impact the growth and development of the plant, resulting in various physiological changes [32,33]. Previous transcriptomic studies have indicated that Ca 2+ deficiency in soil can lead to the abortion of peanut embryos or prevent kernel expansion, ultimately resulting in reduced peanut yields [34][35][36].…”