Kar Dibyasha, Ganguly Indrajit, Singh Sanjeev, Bhatia Avnish Kumar, Dixit S P
Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India.
Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India.
3 Biotech. 2024 Mar;14(3):81. doi: 10.1007/s13205-024-03921-y. Epub 2024 Feb 17.
The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat () breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (AL) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding () was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations.
The online version contains supplementary material available at 10.1007/s13205-024-03921-y.
本研究使用全基因组测序分析了11个不同印度山羊品种的102只动物中的纯合性连续片段（ROH）和共有ROH区域。共鉴定出51705个ROH和21271个共有区域。每只动物的ROH平均数量在肉用品种焦达讷格布尔黑山羊中最高（2693个），在克什米尔山羊绒山羊品种中最低（60个）。ROH的平均长度（AL）在卡尼亚杜山羊中最长（974.11千碱基），在特利切里山羊中最短（146.98千碱基）。长ROH通常与更近的近亲繁殖相关，而短ROH与更古老的近亲繁殖有关。在所有品种中，基于ROH的全基因组近亲繁殖系数（FROH）在焦达讷格布尔黑山羊中最高（0.602），其次是卡尼亚杜山羊（0.120）和桑加姆内里山羊（0.108）。在ROH长度类别达到5兆碱基时，焦达讷格布尔黑山羊的FROH高于卡尼亚杜山羊。然而，在ROH长度类别大于20兆碱基时，卡尼亚杜山羊（0.98）的FROH显著高于焦达讷格布尔黑山羊（0.46）。这意味着卡尼亚杜山羊比焦达讷格布尔黑山羊有更高水平的近期近亲繁殖。尽管如此，由于同时存在近期和古老的近亲繁殖，焦达讷格布尔黑山羊的总体FROH仍高于卡尼亚杜山羊。ROH模式显示兼用型（肉用和乳用）和克什米尔山羊绒山羊品种的血缘关系较低，而近期近亲繁殖在肉用品种中很明显。对ROH共有区域的分析确定了肉用品种中控制肌内脂肪沉积、肉嫩化、瘦肉生产和胴体重量的关键基因（CDK4、ALOX15、CASP9、PRDM16、DVL1）中的选择信号；兼用型（肉用和乳用）品种中乳脂百分比和乳腺发育（POLD1、NOTCH2、ARHGAP35）的选择信号；而在克什米尔山羊绒山羊品种中是冷适应和毛囊发育（APOBEC1、DNAJC3、F2RL1、FGF9）的选择信号。还确定了与克什米尔山羊绒山羊毛囊形态发生相关的心丝虫病、RAS、骨形态发生蛋白和Wnt信号通路。基于ROH共有区域的主成分分析表明，肉用品种比其他山羊品种/群体更多样化。
在线版本包含可在10.1007/s13205-024-03921-y获取的补充材料。
