Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

Abstract

Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN 1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.

Potential applications of the CRISPR/Cas technology for genetic improvement of yam (Dioscorea spp.)

“…However, the species is the least cultivated and consumed due to post‐harvest hardening, a phenomenon in which the tubers harden within 24 hours after harvest, rendering them unpalatable (Adebowale et al, 2013). A recent gene functional analysis attributed this occurrence to the upregulation of five genes, MYB transcription factor, chlorophyll a / b binding protein1 , 2 , 3 , 4 , xylan o ‐ acetyltransferase , and cellulose synthase A (Siadjeu et al, 2021). Thus, multiplex CRISPR‐mediated HDR could be done to replace the genes with the corresponding elite alleles from other yam species, such as D .…”

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…Meanwhile, with the help of short-, long-reads and chromosome conformation sequencing technologies, good-quality genomes were recently released in yams. These data enable the identification of genomic regions associated with agronomically important traits such as sex determination systems (Tamiru et al, 2017, Cormier et al, 2019, Sugihara et al, 2020), anthracnose resistance, tuber oxidative browning, tuber starch content (Bredeson et al, 2022), post-harvest hardening (Siadjeu et al, 2021).…”

Automatic identification and annotation of MYB gene family members in plants

“…AmMYB1 in amaranth was identified as best candidate gene to explain the seed coloration variation between accessions [ 38 ]. A MYB appears to be the underlying factor of post-harvest hardening that renders a specific yam accession inedible within a day [ 39 , 40 ]. MYB duplications between different apple cultivars appear responsible for differences in the red fruit flesh coloration [ 41 ].…”