Genome-wide association study on dairy goat milk production traits using three models.

IF 2.8 3区生物学 Q2 GENETICS & HEREDITY

Frontiers in Genetics Pub Date : 2025-08-22 eCollection Date: 2025-01-01 DOI:10.3389/fgene.2025.1650836

Zhengang Huang, Yuanping Tang, Jianyu Zhou, Dongliang Xu, Xiaokun Lin, Ming Cheng, Jianguang Wang, Qinan Zhao, Jianning He, Xiaoxiao Gao, Jinshan Zhao, Hegang Li

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引用次数: 0

Abstract

Introduction: Identifying genetic markers associated with economically important traits in dairy goats helps enhance breeding efficiency, thereby increasing industry value. However, the potential genetic structure of key economic traits in dairy goats is still largely unknown.

Methods: This study used three genome-wide association study (GWAS) models (GLM, MLM, FarmCPU) to analyze dairy goat milk production traits (milk yield, fat percentage, protein percentage, lactose percentage, ash percentage, total dry matter, and somatic cell count). The goal was to identify SNPs and positional and functional candidate genes significantly associated with these traits.

Results: The GWAS analysis results identified a total of 242 significant SNPs. Among these, 45 SNPs exhibited genome-wide significance, while 197 SNPs demonstrated suggestive associations, corresponding to 99 positional candidate genes within a 50 kb upstream and downstream range. 15 significant SNP loci were consistently identified across all three models, corresponding to 18 candidate genes.The integrated analysis of three models detected 2, 19, 17, 4, 115, 23, and 62 significant SNPs associated with milk yield, ash percentage, protein percentage, lactose percentage, somatic cell count, fat percentage, and total dry matter percentage, respectively. Correspondingly, 6, 24, 9, 12, 37, 14, and 30 candidate genes were identified for these traits. Additionally, several new candidate genes related to milk production traits were proposed (LCORL, TNFRSF1A, VWF, SPATA6, MAN1C1, MASP1, BRCA2).

Discussion: In summary, the results of this study provide an important reference for further exploration of the genetic mechanisms underlying dairy goat milk production traits and the development of molecular breeding markers.

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基于三种模型的奶山羊产奶性状全基因组关联研究

导读：鉴定与奶山羊经济性状相关的遗传标记有助于提高育种效率，从而增加产业价值。然而，奶山羊关键经济性状的潜在遗传结构在很大程度上仍然未知。方法：采用三种全基因组关联研究（GWAS）模型（GLM、MLM、FarmCPU）对奶山羊产奶性状（产奶量、脂肪率、蛋白质率、乳糖率、灰分率、总干物质和体细胞计数）进行分析。目的是鉴定snp以及与这些性状显著相关的位置和功能候选基因。结果：GWAS分析结果共鉴定出242个显著snp。其中，45个snp表现出全基因组的显著性，197个snp表现出暗示的相关性，对应于上游和下游50 kb范围内的99个位置候选基因。在所有三种模型中一致鉴定出15个显著SNP位点，对应于18个候选基因。综合分析3个模型，分别检测到产奶量、灰分率、蛋白质率、乳糖率、体细胞数、脂肪率和总干物质率相关的显著snp有2个、19个、17个、4个、115个、23个和62个。相应的，这些性状的候选基因有6、24、9、12、37、14和30个。此外，还提出了几个与产奶性状相关的新候选基因（LCORL、TNFRSF1A、VWF、SPATA6、MAN1C1、MASP1、BRCA2）。综上所述，本研究结果为进一步探索奶山羊产奶性状的遗传机制和开发分子育种标记提供了重要参考。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Frontiers in Genetics Biochemistry, Genetics and Molecular Biology-Molecular Medicine

CiteScore

5.50

自引率

8.10%

发文量

3491

审稿时长

14 weeks

期刊介绍： Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public. The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.