Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.)

Abstract

Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.

A near‐complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program

“…To measure flower initiation, the date of the appearance of the first flower was recorded for each line. To measure SPM, 10 plants of each line were harvested eight times at weekly intervals between 26 Aug. and 14 Oct. 2016, and the sum of the two highest grain yields from two consecutive weeks was divided by the total yield (Ha et al, 2020a). Theoretically, a SPM value of 1 indicates that all pods mature at the same time.…”

“…Although determinate growth habit has been characterized in mungbean (Li et al, 2018), the genetic basis of SPM remains unresolved. Synchronous pod maturity (SPM) is a complex trait affected by multiple factors, such as flowering time, maturity time, inflorescence structure, and plant architecture (Ha et al, 2020a(Ha et al, , 2020b. Quantitative trait locus analyses of these factors in mungbean are limited, especially those that Core Ideas…”

Multi-location evaluation of mungbean (Vigna radiata L.) in Indian climates: Ecophenological dynamics, yield relation, and characterization of locations

“…The negative association between the reproductive period and ambient temperature suggests either forced maturity under high-temperature environments or an extended grain-filling period in relatively cooler regions, such as the northern hill and southern zones. Non-synchronous maturity is a common phenomenon in rainy season legumes like mungbean, urdbean ( Vigna mungo L.), and cowpea ( Vigna unguiculata L.) owing to indeterminate growth habit, particularly if the moisture conditions are favorable at the later growth stages (Ha et al, 2020 ). Often, favorable conditions during the reproductive period result in the second flush of flowers, their subsequent fertilization, and seed/pod set, which extends the maturity duration (Marwiyah et al, 2021 ).…”

Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops

“…The authors of [137] determined differentially methylated profiles between high and low synchronous pod maturity (SPM) groups in a mungbean recombinant inbred line (RIL) population. The differentially methylated regions (DMRs) were independent of genetic variation and significantly affected the expression of nearby genes.…”