文献类型： 外文期刊

作者： Ayalew, Wondossen ¹ ; Wu, Xiaoyun ¹ ; Tarekegn, Getinet Mekuriaw ³ ; Tessema, Tesfaye Sisay ³ ; Chu, Min ¹ ; Liang, Chunnian ¹ ; Naboulsi, Rakan ⁶ ; Van Damme, Renaud ⁷ ; Bongcam-Rudloff, Erik ⁷ ; Ping, Yan ¹ ;

作者机构： 1.Minist Agr & Rural Affairs, Key Lab Anim Genet & Breeding Tibetan Plateau, Lanzhou 30050, Peoples R China

2.Chinese Acad Agr Sci, Lanzhou Inst Husb & Pharmaceut Sci, Key Lab Yak Breeding Engn, Lanzhou 730050, Peoples R China

3.Addis Ababa Univ, Inst Biotechnol, POB 1176, Addis Ababa, Ethiopia

4.South China Agr Univ, State Key Lab Swine & Poultry Breeding Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breedi, Natl Engn Res Ctr Breeding Swine Ind,Coll Anim Sci, Guangzhou 510642, Peoples R China

5.Univ Edinburgh, Scotlands Rural Coll SRUC, Roslin Inst Bldg, Edinburgh EH25 9RG, Scotland

6.Karolinska Inst, Dept Womens & Childrens Hlth, Childhood Canc Res Unit, Tomtebodavagen 18A, S-17177 Stockholm, Sweden

7.Swedish Univ Agr Sci, Dept Anim Biosci, S-75007 Uppsala, Sweden

8.Chinese Acad Agr Sci, Inst Western Agr, Changji 831100, Peoples R China

关键词： Adaptation; Copy number variation; Ethiopian cattle; Whole-genome sequencing

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundGenomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds-Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations.ResultsWe identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (VST) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits.ConclusionsOur comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.