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Archile Paguem, Babette Abanda, Mbunkah Daniel Achukwi, Praveen Baskaran, Stefan Czemmel, Alfons Renz, Albert Eisenbarth
Department of Biological Science, Faculty of Science, University of Ngaoundéré, Ngaoundéré, Cameroon.
Department of Comparative Zoology, Institute for Evolution and Ecology, University of Tübingen, Tübingen, Germany.
BMC Genet. 2020 Jun 22;21(1):64. doi: 10.1186/s12863-020-00869-9.
African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs, husbandry practices, limited feed resources, disease burden and lack of sustained breeding for trait improvement. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi, an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.
Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~ 99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~ 64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N'Dama breeds. A total of ~ 100 million (M) SNPs were identified and 7.7 M of those were breed-specific. An approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic signatures and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N'Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome.
The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.
非洲本地的瘤牛表现出独特的适应性特征，这些特征是由饲养管理、地区气候和暴露于地方病原体塑造的。它们的牛奶和肉类产量较低，这与体型小、传统观念、饲养方式、饲料资源有限、疾病负担以及缺乏持续的性状改良育种有关。这导致它们的种群数量严重减少，使其面临灭绝的危险。楠奇瘤牛品种被称为[楠奇（Doayo）]，表现出对锥虫感染和蜱虫侵袭的抗性特征。尽管如此，历史上后来引入的瘤牛品种是当今非洲的主要牛种，尽管它们更容易受到当地流行病原体的影响。通过使用全基因组测序方法，我们首次对来自喀麦隆的五个牛品种进行了深度测序，为未来的非洲牛种改良提供了有价值的遗传资源：楠奇，一种濒临灭绝的抗锥虫耐受瘤牛品种；卡普斯基，一种土著的易感染锥虫的瘤牛品种；以及三种瘤牛（Bos indicus indicus）品种：恩贾代尔·古达利、白富拉尼和红富拉尼。
每个品种产生了约 167 吉字节的原始测序数据，并映射到牛参考基因组 ARS-UCD1.2 和 UMD3.1 上。当将读数与 ARS-UCD1.2 对齐时，覆盖率为 103 到 140 倍，平均映射率约为 99%；当与 UMD3.1 对齐时，覆盖率为 22 到 30 倍，平均映射率约为 64%。使用基因组 ARS-UCD1.2 进行分析获得的单核苷酸多态性（SNP）与欧洲荷斯坦牛 Bos taurus、亚洲印度瘤牛 Bos indicus Brahman 和非洲抗锥虫 N'Dama 品种的参考基因组进行了比较。总共鉴定出了约 1 亿（M）个 SNP，其中 770 万个是品种特异性的。大约 1110 万个 SNP 是由小的插入和缺失组成的。通过仅使用品种特异性的非同义变异，我们确定了一些基因作为遗传特征，并确定了与特定牛种表型相关的基因本体论（GO）术语，这些表型特征可以解释某些牛种的特性，如楠奇品种对锥虫寄生虫的耐受性增加和卡普斯基品种的耐热性。系统发育分析将卡普斯基、恩贾代尔·古达利、N'Dama 和荷斯坦瘤牛品种归为一组，而白富拉尼和红富拉尼、古达利和印度瘤牛品种则归为另一组。楠奇的结果有些偏离，表明所选动物的杂交状态，最近有瘤牛基因的渗入到其基因组中。
这些发现提供了喀麦隆最重要的牛种的全基因组变异数据的首个全面数据集。基因组数据将构成品种改良的基础，同时利用可遗传的性状，并支持濒危地方牛种的保护工作。
