Saleh Medhat S, Landi Vincenzo, Derks Martijn F L, Centoducati Gerardo, Groenen Martien A M, De Palo Pasquale, Ciani Elena, Strillacci Maria G, Bagnato Alessandro, Pugliese Nicola, Circella Elena, Camarda Antonio
Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy; Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, Wageningen, 6700 AH, the Netherlands; Department of Animal Production, Faculty of Agriculture, Benha University, Benha 13736, Egypt.
Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy.
Poult Sci. 2025 Jan;104(1):104543. doi: 10.1016/j.psj.2024.104543. Epub 2024 Nov 20.
Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. We used new data from 73 WGS samples (12X) representing five turkey populations, together with previous data from 107 birds genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array from 11 populations. The PCA and Admixture show a relatively strong isolation effect between the populations. Moreover, the values of genomic inbreeding based on ROH (F) showed marked differences among populations and ranged from 0.096 to 0.643. Selective sweeps were identified using the integrated haplotype score (iHS) within the local group, the commercial line, and the Narragansett breed, resulting in the identification of 20, 19, and 27 regions with a total of 73, 48, and 90 candidate genes, respectively. Some of these genes such as FAM107B, MSTN, PDZRN4, HSF2 and GJA1 are associated with heat stress, growth, and carcass traits. We conclude that our results improve our understanding of the genomic architecture of the Italian turkey populations. The findings of iHS suggest that selection can play a significant role in shaping selection signatures in local turkey populations and could provide a basis for identifying gene mutations that may be beneficial in adaptation to climate change. Our results will be useful in developing and implementing conservation and selection plans for Italian turkey populations.
意大利本地火鸡种群是遗传多样性的重要来源，应通过活体保存方法加以保护。全基因组测序（WGS）和基因分型数据集用于评估种群内部和种群之间的遗传变异性，对种群进行全基因组比较分析，并识别意大利火鸡种群中的选择信号。我们使用了来自代表五个火鸡种群的73个WGS样本（12倍覆盖度）的新数据，以及之前来自11个种群的107只使用Affymetrix 600K单核苷酸多态性（SNP）火鸡芯片进行基因分型的鸟类数据。主成分分析（PCA）和混合分析显示种群之间存在相对较强的隔离效应。此外，基于连续纯合片段（ROH）的基因组近亲繁殖值（F）在种群之间显示出显著差异，范围从0.096到0.643。在本地种群、商业品系和纳拉甘西特品种中，使用综合单倍型评分（iHS）识别选择清除，分别鉴定出20、19和27个区域，共有73、48和90个候选基因。其中一些基因，如FAM107B、MSTN、PDZRN4、HSF2和GJA1，与热应激、生长和胴体性状相关。我们得出结论，我们的结果增进了我们对意大利火鸡种群基因组结构的理解。iHS的结果表明，选择在塑造本地火鸡种群的选择信号中可能发挥重要作用，并可为识别可能有利于适应气候变化的基因突变提供基础。我们的结果将有助于制定和实施意大利火鸡种群的保护和选择计划。
