Genome-wide association and genomic selection studies on feed efficiency with fishmeal-free feed in large yellow croaker (Larimichthys crocea)

IF 3.9 1区农林科学 Q1 FISHERIES

Aquaculture Pub Date : 2025-04-29 DOI:10.1016/j.aquaculture.2025.742632

Gongsi Wang , Yingbo Yuan , Xiaotong Li , Ranxin Fu , Xingcheng Zhu , Zhenye Zhao , Yuhan Jin , Sen Zhang , Peng Ren , Lining Zhang , Qinghui Ai , Ming Fang , Zhiyong Wang

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引用次数: 0

Abstract

Large yellow croaker (Larimichthys crocea) is one of the most economically important marine fish and the largest consumer of fishmeal in China. To address the challenges of fishmeal shortages and eutrophication in the culture sea area, it is crucial to breed strains that can adapt to fishmeal-free (FMF) feed while maintaining high feed efficiency (FE). To achieve this, we conducted 28-day indoor feeding experiments using FMF formula feed, during which the feeding behavior was monitored through video recordings. We evaluated individual feed intake (FI) and FE, finding significant variations among individuals. Whole genome sequencing of 534 experimental individuals identified over 6 million single nucleotide polymorphisms (SNPs). We estimated the heritabilities of feed efficiency ratio, residual feed intake and weight gain rate as 0.162, 0.087 and 0.288, respectively. The genomewide association study (GWAS) identified 11 significant SNPs on 9 chromosomes associated with FE. Within these GWAS loci, several candidate genes, such as cadm3, galnt9, cmoat2 and gef28, which are involved in nutrient-sensing, inflammatory response and immune response. We also evaluated the predictive ability of breeding values for feed efficiency ratio, residual feed intake and weight growth rate. The predictive abilities were 0.150, 0.061 and 0.233 with GBLUP, and 0.158, 0.081 and 0.261 with BayesB, respectively. This study provides a crucial foundation for implementing genomic selection to enhance the adaptability and FE of L. crocea to FMF feed and to analyze the underlying genetic mechanisms.

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大黄鱼（Larimichthys crocea）无鱼粉饲料饲料效率全基因组关联与基因组选择研究

大黄鱼（Larimichthys crocea）是中国经济上最重要的海鱼之一，也是中国最大的鱼粉消费者。为了解决养殖海域鱼粉短缺和富营养化的挑战，培育适应无鱼粉饲料（FMF）同时保持高饲料效率（FE）的品系至关重要。为此，我们采用FMF配方饲料进行了为期28天的室内饲养实验，并通过录像监控饲养过程中的摄食行为。我们评估了个体采食量（FI）和FE，发现个体之间存在显著差异。534个实验个体的全基因组测序鉴定出超过600万个单核苷酸多态性（snp）。饲料效率、剩余采食量和增重率的遗传力分别为0.162、0.087和0.288。全基因组关联研究（GWAS）鉴定出与FE相关的9条染色体上的11个显著snp。在这些GWAS基因座中，有几个候选基因，如cadm3、galnt9、cmoat2和gef28，它们参与营养感知、炎症反应和免疫反应。并对饲料效率比、剩余采食量和体重生长率的预测能力进行了评价。GBLUP的预测能力分别为0.150、0.061和0.233，BayesB的预测能力分别为0.158、0.081和0.261。本研究为实施基因组选择提高荷兰花对FMF饲料的适应性和生长率以及分析其遗传机制提供了重要依据。

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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.