EPIDERMAL PATTERNING FACTOR 2-like (McEPFL2) gene is a putative candidate for the continuous ridge (cr) fruit skin locus in bitter gourd (Momordica charantia L.)

Authors: YANG, JING - Huazhong Agricultural University; Weng, Yiqun; LI, HUIHONG - Huazhong Agricultural University; KONG, QIUSHENG - Huazhong Agricultural University; WANG, WEILAN - Huazhong Agricultural University; YAN, CHENGHUAN - Huazhong Agricultural University; WANG, LIPING - Huazhong Agricultural University

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2022
Publication Date: 6/25/2022
Citation: Yang, J., Weng, Y., Li, H., Kong, Q., Wang, W., Yan, C., Wang, L. 2022. EPIDERMAL PATTERNING FACTOR 2-like (McEPFL2) gene is a putative candidate for the continuous ridge (cr) fruit skin locus in bitter gourd (Momordica charantia L.). Genes. 2022, 13(7), 1148. https://doi.org/10.3390/genes13071148.
DOI: https://doi.org/10.3390/genes13071148

Interpretive Summary: Background: Bitter gourd or bitter melon is a popular vegetable crop and medicinal plants in many regions of the world. Little has been done in understanding the genetic basis of horticulturally important traits in bitter gourd. It is consumed primarily for young immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. Major findings: In the present study, we conducted molecular mapping of a gene that controls fruit ridge continuity. A genetic mapping population was developed from the crosses between two bitter gourd inbred lines Y1 with continuous ridges (CR) and Z14 with discontinuous ridges (DCR). Genetic analysis suggested that CR was controlled by a recessive gene which is named cr. High throughput genome sequencing of CR and DCR pooled leaf samples in conjunction with genetic mapping with molecular marker in an F2 population placed the cr locus in a DNA region that was 108 kilobases in size and contains 16 predicted gene. Sequence variation and gene expression analyses supported the epidermal patterning factor 2-like or McEPFL2 as the best candidate of the Cr locus. Comparison of DNA sequences between Z-1-4 and Y1 identified a 1-bp deletion inside the coding region McEPFL2 in Y1 that may cause difference of fruit ridge continuity between the two parental lines. The same association between the 1-bp deletion and continuous ridge was further supported by comparing of this DNA region among 31 bitter gourd varieties. Why it matters: This work provides a foundation for understanding the genetic control of fruit ridge morphogenesis, and facilitates marker-assisted selection in bitter melon breeding.

Technical Abstract: Bitter gourd (Momordica charantia L.) is an economically important vegetable crop in many regions of the world. Little has been done in understanding the genetic basis of horticulturally important traits in bitter gourd. It is consumed primarily for young immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. In the present study, we conducted molecular mapping of a locus underlying fruit ridge continuity. Genetic analysis in segregating populations derived from the crosses between two inbred lines Y1 with continuous ridges (CR) and Z-1-4 with discontinuous ridges (DCR) suggested that CR was controlled by a recessive gene (cr). High throughput genome sequencing of CR and DCR bulks combined with high-resolution genetic mapping in an F2 population placed the cr locus in a 108kb region containing 16 predicted gene. Sequence variation analysis and expression profiling based on RNA-Seq data of the 16 genes supported the EPIDERMAL PATTERNING FACTOR 2-like (McEPFL2) gene as the best candidate of the Cr locus. Cloning of genomic and cDNA sequences from Z-1-4 and Y1 revealed a 1-bp deletion in the first exon of McEPFL2 in Y1 that may be the causal polymorphism for the phenotypic difference between the two parental lines. The association of this 1-bp deletion with continuous ridge was further supported by cloning and comparing of the target region among 31 bitter gourd accessions. This work provides a foundation for understanding the genetic control of fruit ridge morphogenesis, and facilitates marker-assisted selection in bitter melon breeding.