Genomic regions and candidate genes associated with feed efficiency traits in large yellow croaker (Larimichthys crocea) across different thermal environments

IF 3.9 1区农林科学 Q1 FISHERIES

Aquaculture Pub Date : 2025-09-25 DOI:10.1016/j.aquaculture.2025.743227

Pengxin Jiang , Miaosheng Feng , Yuxuan Liu , Junjia Zeng , Junzhu Xiao , Qiaozhen Ke , Longyu Chen , Jiaying Wang , Shuimu Hu , Zongbao Zhang , Yuxiang Zhang , Peng Xu

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引用次数: 0

Abstract

Understanding the biological mechanisms underlying feed efficiency (FE) traits is an important issue in addressing environmental challenges and improving farm economics. This study aimed to identify genomic regions and signaling pathways associated with two indicator traits of FE, feed conversion ratio (FCR) and residual feed intake (RFI), in large yellow croaker (Larimichthys crocea). In this study, we evaluated the FE phenotypes of the same group of fish under three different thermal environments (15 °C, 19 °C, and 24 °C). At 15 °C, 6 single nucleotide polymorphisms (SNPs) were associated with FCR_{15 °C}, 3 with RFI_{15 °C}, and 1 with both traits. A total of 31 genes, including slc12a7, slc45a4, apn, dgat1, far1, chka, pappa2, and neurod1, were identified as candidate genes that may affect FE traits through biological processes such as nutrient transport, lipid synthesis and metabolism, and insulin and insulin-like growth factor 1 (IGF-1) signaling pathway. At 19 °C, no SNPs were associated with FCR_{19 °C}, while 7 SNPs with RFI_{19 °C}. A total of 23 genes, including myc, slc25a29, wars, dio3, col2a1, and col5a2, were identified as candidate genes that may affect FE traits through biological processes such as amino acid metabolism, protein synthesis, and cellular proliferation and differentiation. At 24 °C, 7 SNPs were associated with FCR_{24 °C}, 6 with RFI_{24 °C}, and 5 with both traits. A total of 14 genes, including pqlc2, golim4, zbbx, kmt2d, alkbh8, che, aasdhppt, gucy1a2, and serpini1, were identified as candidate genes that may affect FE traits through biological processes such as amino acid and protein transport, DNA repair and transcription regulation, signal transduction and neural function. In addition, all of these candidate genes were enriched in several GO terms, including melanocyte-stimulating hormone receptor activity, transcription cis-regulatory region binding, and microtubule. This study provides valuable insights into the genetic basis of FE traits and identifies SNPs involved in marker-assisted breeding selection of FCR and RFI in large yellow croaker.

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不同热环境下大黄鱼饲料效率性状相关的基因组区域和候选基因

了解饲料效率（FE）性状的生物学机制是解决环境挑战和改善农业经济的重要问题。本研究旨在确定大黄鱼（Larimichthys crocea）饲料转化率（FCR）和剩余采食量（RFI）两个指标性状的基因组区域和信号通路。在本研究中，我们评估了同一组鱼在三种不同热环境（15°C， 19°C和24°C）下的FE表型。在15°C时，6个单核苷酸多态性（snp）与FCR15°C相关，3个与RFI15°C相关，1个与两个性状相关。共鉴定出31个候选基因，包括slc12a7、slc45a4、apn、dgat1、far1、chka、pappa2和neurod1，这些基因可能通过营养转运、脂质合成和代谢以及胰岛素和胰岛素样生长因子1 （IGF-1）信号通路等生物学过程影响FE性状。在19°C时，没有SNPs与FCR19°C相关，而7个SNPs与RFI19°C相关。共鉴定出23个候选基因，包括myc、slc25a29、wars、dio3、col2a1和col5a2，这些基因可能通过氨基酸代谢、蛋白质合成和细胞增殖分化等生物学过程影响FE性状。在24°C时，7个snp与FCR24°C相关，6个与RFI24°C相关，5个与两个性状相关。共鉴定出14个候选基因，包括pqlc2、golim4、zbbx、kmt2d、alkbh8、che、aasdhppt、gucy1a2和serini1，这些基因可能通过氨基酸和蛋白质转运、DNA修复和转录调控、信号转导和神经功能等生物学过程影响FE性状。此外，所有这些候选基因都在氧化石墨烯的几个方面富集，包括黑素细胞刺激激素受体活性、转录顺式调控区结合和微管。本研究为大黄鱼FE性状的遗传基础提供了有价值的见解，并确定了与FCR和RFI的标记辅助育种选择有关的snp。

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来源期刊

Aquaculture 农林科学-海洋与淡水生物学

CiteScore

8.60

自引率

17.80%

发文量

1246

审稿时长

56 days

期刊介绍： Aquaculture is an international journal for the exploration, improvement and management of all freshwater and marine food resources. It publishes novel and innovative research of world-wide interest on farming of aquatic organisms, which includes finfish, mollusks, crustaceans and aquatic plants for human consumption. Research on ornamentals is not a focus of the Journal. Aquaculture only publishes papers with a clear relevance to improving aquaculture practices or a potential application.