Peanut (Arachis hypogaea L.) is an important source of oil and food around the world, and the testa color affects its appearance and commercial value. However, few studies focused on the mechanism of pigment formation in peanut testa. In this study, cultivars Shanhua 15 with pink testa and Zhonghua 12 with red testa were used as materials to perform the combined analysis of transcriptome and metabolome. A total of 198 flavonoid metabolites were detected, among which petunidin 3-O-glucoside and cyanidin O-acetylhexoside in Zhonghua12 were 15.23 and 14.72 times higher than those of Shanhua 15 at the R7 stage, revealing the anthocyanins underlying the red testa. Transcriptome analysis showed that there were 6059 and 3153 differentially expressed genes between Shanhua 15 and Zhonghua 12 in different growth periods, respectively. These differentially expressed genes were significantly enriched in the flavonoid biosynthesis, biosynthesis of secondary metabolites, and metabolic pathways. Integrated analysis of transcriptome and metabolome indicated CHS gene (arahy.CM90T6), F3H genes (arahy. 8F7PE4 and arahy. K8H9R8), and DFR genes (arahy. LDV9QN and arahy. X8EVF3) may be the key functional genes controlling the formation of pink and red testa in peanut. Transcription factors MYB (arahy.A2IWKV, arahy.US2SKM, arahy.SJGE27, arahy.H8DJRL, and arahy.PR7AYB), bHLH (arahy.26781N, arahy.HM1IVV, and arahy.MP3D3D), and WD40 (arahy.L6JJW9) in the biosynthetic pathway of anthocyanin were significantly upregulated in Zhonghua 12 which may be the key regulatory genes in testa pigment formation. This is a comprehensive analysis on flavonoid metabolites and related genes expression in peanut testa, providing reference for revealing the regulatory mechanism of pigment accumulation in peanut testa.

Auxin-responsive genes AUX/IAA are important during plant growth and development, but there are few relevant reports in peanut. In this study, 44 AhIAA genes were identified from cultivated peanut, of which 31 genes were expressed in seed at varying degrees. AhIAA-3A, AhIAA-16A and AhIAA-15B were up-regulated, while AhIAA-11A, AhIAA-5B and AhIAA-14B were down-regulated with seed development and maturation. The expression patterns of seven genes, AhIAA-1A, AhIAA-4A, AhIAA-10A, AhIAA-20A, AhIAA-1B, AhIAA-4B and AhIAA-19B, were consistent with the change trend of auxin, and expression in late-maturing variety LM was significantly higher than that in early-maturing EM. Furthermore, allelic polymorphism analysis of AhIAA-1A and AhIAA-1B, which were specifically expressed in seeds, showed that three SNP loci in 3′UTR of AhIAA-1A could effectively distinguish the EM- and LM- type germplasm, providing a basis for breeding markers development. Our results offered a comprehensive understanding of Aux/IAA genes in peanut and provided valuable clues for further investigation of the auxin signal transduction pathway and auxin regulation mechanism in peanut.