Department of Veterinary Medicine, Center for Agroveterinary Sciences, State University of Santa Catarina, 88520-000 Lages, Santa Catarina, Brazil.
Embrapa Pantanal, Brazilian Agricultural Research Company, 79320-900 Corumbá, Mato Grosso do Sul, Brazil.
Front Biosci (Schol Ed). 2024 Sep 29;16(3):18. doi: 10.31083/j.fbs1603018.
Sheep farming is growing substantially in Brazil, driven by the increasing demand for sheep meat. This rising demand has heightened the focus on sheep, making them the subject of numerous studies, including those centered on genetic analysis. A notable research area involves Pantaneiro sheep, which are indigenous to the Pantanal region of Mato Grosso do Sul and other locations. These sheep are of particular interest due to their adaptation to the unique environmental conditions of the Pantanal, a floodplain characterized by its distinctive climatic and ecological features. This study primarily aimed to conduct a comprehensive genomic analysis of Pantanal sheep subjected to natural selection within the Pantanal region and compare different sample herds using methodological approaches.
Genomic analysis was performed to examine genetic diversity and structure via GGP50K single nucleotide polymorphism (SNP) analysis. A sample of 192 adult sheep over 4 years old was categorized into seven populations based on location: Six populations comprised Pantaneiro sheep with one Texel sheep population. Outlier SNPs were assessed to pinpoint regions under natural selection, with comparisons between the Pantaneiro and the commercial Texel breeds. All data analyses were conducted using the R programming language, employing specialized genetic analysis packages. These outlier SNPs were detected using three methodologies, PCAdapt, OutFLANK, and FDIST2/fsthet, with false discovery rate (FDR) corrections applied to ensure result accuracy. Each method was evaluated, and the genes associated with the identified SNPs were cross-referenced with the most recent sheep genome database, focusing specifically on genes with known phenotypic traits.
Analysis of a sample comprising 192 adult individuals revealed greater genetic variability within the Pantaneiro breed than the Texel breed, highlighting the adaptation of the Pantaneiro breed to the unique Pantanal environment. Conversely, the Texel breed exhibited significantly higher levels of inbreeding, attributed to its controlled breeding practices. Outlier SNPs were detected with notable variation across different methodologies, underscoring the importance of FDR correction in ensuring the reliability and concentration of identified outliers. These outlier SNPs facilitated the identification of genes associated with key phenotypic traits, including hair growth, tissue regeneration, pigmentation regulation, and muscle capacity.
The integrated analysis of methodologies demonstrated significant efficiency in elucidating the genomic landscape of Pantanal sheep, highlighting the genetic richness inherent in sheep from the Pantanal region of Mato Grosso do Sul. The techniques employed effectively identified outlier SNPs associated with phenotypically relevant genes. These findings, which reveal greater genetic variability and adaptability, underscore the potential of these animals for future research and their significance within Brazilian sheep farming. The Texel breed served as a valuable comparative group, illustrating the limited genetic variability in highly controlled breeding environments.
巴西的绵羊养殖规模正在显著扩大，这主要是由于对羊肉的需求不断增加。这种需求的增长使得绵羊成为了众多研究的对象，包括以遗传分析为中心的研究。一个值得关注的研究领域是潘塔纳尔绵羊，它们原产于南马托格罗索州的潘塔纳尔地区和其他地区。这些绵羊之所以引起人们的兴趣，是因为它们适应了潘塔纳尔独特的环境条件，潘塔纳尔是一个具有独特气候和生态特征的泛滥平原。本研究主要旨在对潘塔纳尔地区自然选择下的潘塔纳尔绵羊进行全面的基因组分析，并使用方法学方法比较不同的样本群。
通过 GGP50K 单核苷酸多态性（SNP）分析进行基因组分析，以研究遗传多样性和结构。对 192 只 4 岁以上的成年绵羊进行了样本采集，并根据地点将其分为七个群体：六个群体由潘塔纳尔绵羊组成，一个群体由特克塞尔绵羊组成。评估了外显子 SNP，以确定受自然选择影响的区域，并比较了潘塔纳尔和商业特克塞尔品种之间的差异。所有数据分析均使用 R 编程语言和专门的遗传分析软件包进行。使用 PCAdapt、OutFLANK 和 FDIST2/fsthet 三种方法检测了外显子 SNP，并用错误发现率（FDR）校正来确保结果的准确性。对每种方法进行了评估，并将与鉴定出的 SNP 相关的基因与最新的绵羊基因组数据库进行了交叉引用，特别关注具有已知表型特征的基因。
对包括 192 只成年个体的样本进行的分析表明，潘塔纳尔品种的遗传多样性大于特克塞尔品种，这突出了潘塔纳尔品种对潘塔纳尔独特环境的适应性。相反，特克塞尔品种的近交程度显著较高，这归因于其受控的繁殖实践。使用不同的方法检测到了明显的外显子 SNP 变异，这突出了 FDR 校正对于确保鉴定出的外显子的可靠性和集中性的重要性。这些外显子 SNP 有助于确定与关键表型特征相关的基因，包括毛发生长、组织再生、色素沉着调节和肌肉容量。
综合使用多种方法进行分析，显著提高了对潘塔纳尔绵羊基因组景观的解析效率，突出了马托格罗索州潘塔纳尔地区绵羊所具有的遗传丰富性。所采用的技术有效地鉴定了与表型相关基因相关的外显子 SNP。这些发现表明，这些动物具有更大的遗传变异性和适应性，突显了它们在未来研究中的潜力及其在巴西绵羊养殖中的重要性。特克塞尔品种作为一个有价值的对照组，说明了在高度受控的繁殖环境中遗传变异性有限。
