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家畜重要性状QTL组的探索与富集分析

Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species.

作者信息

Jahuey-Martínez Francisco J, Martínez-Quintana José A, Rodríguez-Almeida Felipe A, Parra-Bracamonte Gaspar M

机构信息

Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31453, Mexico.

Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico.

出版信息

Genes (Basel). 2024 Nov 26;15(12):1513. doi: 10.3390/genes15121513.

DOI:10.3390/genes15121513
PMID:39766781
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11675464/
Abstract

Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species' genomes is crucial for animal genetics research. This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994-2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species ( < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows ( < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs.

摘要

数量性状基因座（QTL）是影响家畜重要性状的基因组区域。了解跨物种基因组的QTL分布和密度对于动物遗传学研究至关重要。本研究通过分析QTL分布并评估QTL、基因密度和染色体大小之间的相关性，探索了牛、猪、羊和鸡的QTL组，旨在识别富含QTL的基因组区域。方法：从AnimalQTLdb中检索了211,715个QTL（1994 - 2021年）的数据，并使用R软件v4.2.1进行分析。确定了独特的QTL注释，并去除了冗余或不一致的数据。统计分析包括Pearson相关性分析以及二项式、超几何和基于Bootstrap的富集检验。牛、猪、羊和鸡基因组每兆碱基的QTL密度分别为10、4、1和3。对染色体上QTL分布的分析揭示了不均匀的模式，某些区域富含QTL。相关性分析表明，所有物种的QTL与基因密度/染色体大小之间均存在强正相关（<0.05）。富集分析确定了多效性区域，其中QTL影响多个性状，通常与已知的候选基因和主要基因一致。检测到显著富含QTL的窗口（<0.05），牛、猪、羊和鸡分别有699（187）、355（68）、50（15）和38（17）个基因组窗口与总体性状（和特定表型类别）相关。本研究为QTL分布及其与基因密度的相关性提供了关键见解，为推进家畜物种的遗传研究提供了有价值的数据。富含QTL区域的识别也突出了性状改良计划未来探索的关键领域。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/47a22f761e1e/genes-15-01513-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/6b0ff3106f35/genes-15-01513-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/691b40432720/genes-15-01513-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/9b91893b922d/genes-15-01513-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/d6bd2e135994/genes-15-01513-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/b93ba1f0ce51/genes-15-01513-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/c8d92b2c9b2d/genes-15-01513-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/6cdf470ff4c5/genes-15-01513-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/e635c28e0c06/genes-15-01513-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/47a22f761e1e/genes-15-01513-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/6b0ff3106f35/genes-15-01513-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/691b40432720/genes-15-01513-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/9b91893b922d/genes-15-01513-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/d6bd2e135994/genes-15-01513-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/b93ba1f0ce51/genes-15-01513-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/c8d92b2c9b2d/genes-15-01513-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/6cdf470ff4c5/genes-15-01513-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/e635c28e0c06/genes-15-01513-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/be31/11675464/47a22f761e1e/genes-15-01513-g009.jpg

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