Identification of SNPs in the 5′-flanking region and 3′-UTR of theMIHgene and their association with precocity of the Chinese mitten crabEriocheir sinensis

Abstract

Moult-inhibiting hormone (MIH), an important regulator of steroidogenesis, inhibits the synthesis of ecdysteroid in Y-organ (YO) and plays a significant role in the regulation of moulting and postembryonic development of crustacean. Because unsuccessful moulting have been widely observed in precocious crabs, we investigated whether genetic variants in the 5 0 -flanking region and 3 0 -untranslated region (3 0 -UTR) of the MIH gene are associated with precocity of the Chinese mitten crab. Thirty individual DNA samples were sequenced to search for SNPs in the 5 0 -flanking region and 3 0 -UTR of the MIH gene. Five SNPs (g.196 T>A, g.230 C>T, g.305 T>C, g.323 C>A and g.372 C>T) in the 5 0 -flanking region and 6 SNPs (g.2677 C>T, g.2759 T>A, g.2807 T>C, g.3042 A>G, g.3088 T>G and g.3295 T>G) in the 3 0 -UTR of the MIH gene were selected for the individual genotyping in a two-stage association study. We found that a SNP g.3088 T>G in the 3 0 -UTR of MIH gene was consistently associated with precocity of the Chinese mitten crab in stage 1 and stage 2, with a per-allele OR (Odds Ratio) of 1.469 (95% CI: 1.169-1.844) after two stages combined (P = 0.001). However, no significant associations were observed between the other 10 SNPs and precocity of the Chinese mitten crab. To our best knowledge, this is the first association study between various SNP genotypes and phenotype attributes in Chinese mitten crab. Our findings suggest that the SNP g.3088 T>G may be a candidate marker for effective marker-assisted selection to decrease the precocity of the Chinese mitten crab in future studies.

Identification SNPs in vitellogenin gene and their association with ovarian development and growth of Macrobrachium nipponense

“…The average Ne of 31SNPs were 1.8094, which indicated these SNP loci were evenly distributed. The average (Buaklin et al, 2016;He et al, 2008;Xu et al, 2016). The results of this study further elucidate the relationship between gonad development and growth in M.…”

“…At present, SNP researches in aquatic economic species are mainly focused on screening more loci associated with growth traits (Chi et al, 2020; Du et al, 2021; Thanh et al, 2010). There were a few reports on screening more loci in reproduction related genes which associated with reproductive traits, such as SNPs of CYP19a gene associated with GSI in Paralichthys olivaceus , SNPs of MIH gene associated with precocity in Eriocheir sinensis and SNPs of catechol O‐methyltransferase gene associated with GSI in Penaeus monodon (Buaklin et al, 2016; He et al, 2008; Xu et al, 2016). The results of this study further elucidate the relationship between gonad development and growth in M. nipponense and further identify SNP loci related to ovarian development and growth in Mn‐Vg gene.…”

Development of coding single nucleotide polymorphic markers in the pearl oyster Pinctada fucata based on next-generation sequencing and high-resolution melting analysis

“…The post-transcriptional regulation of gene expression is crucial for many physiological processes. SNPs within UTRs may have consequences for gene splicing, expression, and regulation (Malodobra-Mazur et al, 2016;Xu et al, 2016). SNPs developed from functional genes may be used in association studies, which could genetically improve species.…”

Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White Shrimp Litopenaeus vannamei by Target Sequencing Approach

“…Single nucleotide polymorphisms (SNPs) are a type of widely used markers for MAS due to its high polymorphism and abundance in the genome. It has already been used in aquatic species to facilitate selection breeding and speed up the discovery of genes related to the economic trait, such as high growth (Lv et al, 2015; Tsai et al, 2015), disease resistance (Yue et al, 2012), precocity (Xu et al, 2016), and body conformation (Geng et al, 2017).…”