Zhang Xuying, Jamwal Kokila, Distl Ottmar
Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
Sci Rep. 2022 Oct 27;12(1):18061. doi: 10.1038/s41598-022-22155-7.
Stray non-breeding cats (stray) represent the largest heterogeneous cat population subject to natural selection, while populations of the Siamese (SIAM) and Oriental Shorthair (OSH) breeds developed through intensive artificial selection for aesthetic traits. Runs of homozygosity (ROH) and demographic measures are useful tools to discover chromosomal regions of recent selection and to characterize genetic diversity in domestic cat populations. To achieve this, we genotyped 150 stray and 26 household non-breeding cats (household) on the Illumina feline 63 K SNP BeadChip and compared them to SIAM and OSH. The 50% decay value of squared correlation coefficients (r) in stray (0.23), household (0.25), OSH (0.24) and SIAM (0.25) corresponded to a mean marker distance of 1.12 Kb, 4.55 Kb, 62.50 Kb and 175.07 Kb, respectively. The effective population size (N) decreased in the current generation to 55 in stray, 11 in household, 9 in OSH and 7 in SIAM. In the recent generation, the increase in inbreeding per generation (ΔF) reached its maximum values of 0.0090, 0.0443, 0.0561 and 0.0710 in stray, household, OSH and SIAM, respectively. The genomic inbreeding coefficient (F) based on ROH was calculated for three length categories. The F was between 0.014 (F) and 0.020 (F) for stray, between 0.018 (F) and 0.024 (F) for household, between 0.048 (F) and 0.069 (F) for OSH and between 0.053 (F) and 0.073 (F) for SIAM. We identified nine unique selective regions for stray through genome-wide analyses for regions with reduced heterozygosity based on F statistics. Genes in these regions have previously been associated with reproduction (BUB1B), motor/neurological behavior (GPHN, GABRB3), cold-induced thermogenesis (DIO2, TSHR), immune system development (TSHR), viral carcinogenesis (GTF2A1), host immune response against bacteria, viruses, chemoattractant and cancer cells (PLCB2, BAHD1, TIGAR), and lifespan and aging (BUB1B, FGF23). In addition, we identified twelve unique selective regions for OSH containing candidate genes for a wide range of coat colors and patterns (ADAMTS20, KITLG, TYR, TYRO3-a MITF regulator, GPNMB, FGF7, RAB38) as well as congenital heart defects (PDE4D, PKP2) and gastrointestinal disorders (NLGN1, ALDH1B1). Genes in stray that represent unique selective events indicate, at least in part, natural selection for environmental adaptation and resistance to infectious disease, and should be the subject of future research. Stray cats represent an important genetic resource and have the potential to become a research model for disease resistance and longevity, which is why we recommend preserving semen before neutering.
流浪非繁殖猫（流浪猫）是受自然选择影响的最大的异质猫群体，而暹罗猫（SIAM）和东方短毛猫（OSH）品种的群体则是通过对美学特征的强化人工选择而发展起来的。纯合子片段（ROH）和群体统计指标是发现近期选择的染色体区域以及描述家猫群体遗传多样性的有用工具。为了实现这一目标，我们使用Illumina猫63K SNP芯片对150只流浪猫和26只家养非繁殖猫（家猫）进行了基因分型，并将它们与暹罗猫和东方短毛猫进行比较。流浪猫（0.23）、家猫（0.25）、东方短毛猫（0.24）和暹罗猫（0.25）的平方相关系数（r）的50%衰减值分别对应平均标记距离为1.12千碱基对、4.55千碱基对、62.50千碱基对和175.07千碱基对。有效种群大小（N）在当代有所下降，流浪猫为55，家猫为11，东方短毛猫为9，暹罗猫为7。在最近一代中，每代近交系数的增加（ΔF）在流浪猫、家猫、东方短毛猫和暹罗猫中分别达到最大值0.0090、0.0443、0.0561和0.0710。基于ROH计算了三个长度类别的基因组近交系数（F）。流浪猫的F在0.014（F）至0.020（F）之间，家猫在0.018（F）至0.024（F）之间，东方短毛猫在0.048（F）至0.069（F）之间，暹罗猫在0.053（F）至0.073（F）之间。通过基于F统计量对杂合度降低的区域进行全基因组分析，我们为流浪猫确定了9个独特的选择区域。这些区域中的基因以前与繁殖（BUB1B）、运动/神经行为（GPHN、GABRB3）、冷诱导产热（DIO2、TSHR）、免疫系统发育（TSHR）、病毒致癌作用（GTF2A1）、宿主对细菌、病毒、趋化因子和癌细胞的免疫反应（PLCB2、BAHD1、TIGAR）以及寿命和衰老（BUB1B、FGF23）有关。此外，我们为东方短毛猫确定了12个独特的选择区域，其中包含与多种毛色和花纹（ADAMTS20、KITLG、TYR、TYRO3-a MITF调节因子、GPNMB、FGF7、RAB38）以及先天性心脏缺陷（PDE4D、PKP2）和胃肠道疾病（NLGN1、ALDH1B1）相关的候选基因。流浪猫中代表独特选择事件的基因至少部分表明了对环境适应和对传染病抵抗力的自然选择，应该成为未来研究的主题。流浪猫是一种重要的遗传资源，有潜力成为抗病性和长寿的研究模型，这就是为什么我们建议在绝育前保存精液。
