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

Abstract

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 different cultivars, we treated a large-seed (sensitive) and a small-seed (tolerant) cultivar with different calcium levels. The transcriptome analyses identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups, and these DEGs were entirely covered by gene modules in each respective group via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analyses have shown 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 enriched in lipid metabolism such as glycerolipid and glycerophospholipid metabolisms. A total of eight hub-DEGs were finally identified from two gene modules, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities, 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 study as well as breeding efforts to improve peanut survivability under calcium deficiency.