de Carvalho Felipe E, Ferraz José Bento S, Pedrosa Victor B, Matos Elisangela C, Eler Joanir P, Silva Marcio R, Guimarães José D, Bussiman Fernando, Silva Barbara C A, Mulim Henrique A, Rocha Artur Oliveira, Araujo Andre C, Wen Hui, Campos Gabriel S, Brito Luiz F
Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil.
Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA.
BMC Genomics. 2025 Jan 10;26(1):26. doi: 10.1186/s12864-024-11193-2.
The profitability of the beef industry is directly influenced by the fertility rate and reproductive performance of both males and females, which can be improved through selective breeding. When performing genomic analyses, genetic markers located on the X chromosome have been commonly ignored despite the X chromosome being one of the largest chromosomes in the cattle genome. Therefore, the primary objectives of this study were to: (1) estimate variance components and genetic parameters for eighteen male and five female fertility and reproductive traits in Nellore cattle including X chromosome markers in the analyses; and (2) perform genome-wide association studies and functional genomic analyses to better understand the genetic background of male and female fertility and reproductive performance traits in Nellore cattle.
The percentage of the total direct heritability (h) explained by the X chromosome markers (h) ranged from 3 to 32% (average: 16.4%) and from 9 to 67% (average: 25.61%) for female reproductive performance and male fertility traits, respectively. Among the traits related to breeding soundness evaluation, the overall bull and semen evaluation and semen quality traits accounted for the highest proportion of h relative to h with an average of 39.5% and 38.75%, respectively. The total number of significant genomic markers per trait ranged from 7 (seminal vesicle width) to 43 (total major defects). The number of significant markers located on the X chromosome ranged from zero to five. A total of 683, 252, 694, 382, 61, and 77 genes overlapped with the genomic regions identified for traits related to female reproductive performance, semen quality, semen morphology, semen defects, overall bulls' fertility evaluation, and overall semen evaluation traits, respectively. The key candidate genes located on the X chromosome are PRR32, STK26, TMSB4X, TLR7, PRPS2, SMS, SMARCA1, UTP14A, and BCORL1. The main gene ontology terms identified are "Oocyte Meiosis", "Progesterone Mediated Oocyte Maturation", "Thermogenesis", "Sperm Flagellum", and "Innate Immune Response".
Our findings indicate the key role of genes located on the X chromosome on the phenotypic variability of male and female reproduction and fertility traits in Nellore cattle. Breeding programs aiming to improve these traits should consider adding the information from X chromosome markers in their genomic analyses.
肉牛产业的盈利能力直接受到公母畜生育率和繁殖性能的影响，而通过选择性育种可以提高这些性能。在进行基因组分析时，尽管X染色体是牛基因组中最大的染色体之一，但位于X染色体上的遗传标记通常被忽略。因此，本研究的主要目的是：（1）估计内洛尔牛18个雄性和5个雌性生育力及繁殖性状的方差成分和遗传参数，分析中包括X染色体标记；（2）进行全基因组关联研究和功能基因组分析，以更好地了解内洛尔牛雄性和雌性生育力及繁殖性能性状的遗传背景。
X染色体标记解释的总直接遗传力（h）百分比，雌性繁殖性能性状为3%至32%（平均：16.4%），雄性生育力性状为9%至67%（平均：25.61%）。在与繁殖健全性评估相关的性状中，总体公牛和精液评估以及精液质量性状相对于h占h的比例最高，平均分别为39.5%和38.75%。每个性状的显著基因组标记总数从7个（精囊宽度）到43个（总主要缺陷）不等。位于X染色体上的显著标记数量从零到五个不等。分别有683、252、694、382、61和77个基因与为雌性繁殖性能、精液质量、精液形态、精液缺陷、总体公牛生育力评估和总体精液评估性状鉴定的基因组区域重叠。位于X染色体上的关键候选基因是PRR32、STK26、TMSB4X、TLR7、PRPS2、SMS、SMARCA1、UTP14A和BCORL1。确定的主要基因本体术语是“卵母细胞减数分裂”、“孕酮介导的卵母细胞成熟”、“产热”、“精子鞭毛”和“先天免疫反应”。
我们的研究结果表明，位于X染色体上的基因对内洛尔牛雄性和雌性繁殖及生育性状的表型变异起着关键作用。旨在改善这些性状的育种计划应考虑在其基因组分析中加入来自X染色体标记的信息。
