Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation

Abstract

Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as “peanut seed coat crack and brown color mutant line (pscb).” The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.

Fine-Mapping the Branching Habit Trait in Cultivated Peanut by Combining Bulked Segregant Analysis and High-Throughput Sequencing

“…Samples were taken of each of the ground tissues (400 mg each) and were used for RNA extraction using the hot-borate method, as described by Brand and Hovav (2010). The total RNA was used to prepare two RNA-Seq libraries, using TruSeq RNA Sample Preparation Kit v2 (Illumina) following the manufacturer's protocol as described previously (Gupta et al, 2016). Libraries were validated using DNA Screen Tape D1000 and the Tapestation 2200 (Agilent).…”

Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant

“…Flavonoid components determine the color of the peanut testa [21][22][23]. Flavonoid biosynthesis pathway genes were searched based on their KO identifications within the KEGG database as well as synonyms identified in combined with functional annotations, this enabled the identification of 433 DEGs in flavonoid metabolic pathways ( Table 1).…”

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

“…Mannose‐1‐phosphate guanylyltransferase that was flanked by the STA (Affx‐152041326) plays a vital role in plant development and cell‐wall architecture as it mediates N‐linked glycosylation for cellulose biosynthesis (Wolfgang et al , ). Cellulose is important component of peanut seed coat and pod shells (Wan et al , ); hence, the mannose‐1‐phosphate guanylyltransferase might be involved in the regulation of PW and seed coat of seed. Nodulin was identified on chromosome (A05) flanked by STA (Affx‐152042939) reported to be expressed in root nodules and seed as well as pods (Clevenger et al , ).…”