近日，中国农业科学院研究生院埃塞俄比亚籍留学生Haile Berihulay在中国农业科学院北京畜牧兽医研究所马月辉研究员的指导下，在中科院JCR生物大类2区期刊Frontiers in Genetics(Impact factor=3.819)在线发表了题为“Whole genome re-sequencing reveals selection signatures associated with important traits in Ethiopian indigenous goat populations”的原创性文章，Haile同学为本文的第一作者，北京畜牧兽医研究所马月辉研究员和蒋琳研究员为本文的共同通讯作者。该文首次对埃塞俄比亚5种不同地方山羊品种种质资源特性进行挖掘和鉴定，为保种和育种策略的制定、品种的评估和利用提供了重要的遗传信息。

Recently, a GSCAAS PhD student Haile under the guidance of Professor Yuehui Ma at Institute of Animal Sciences, CAAS, Beijing, published an on-line research article entitled “Whole genome re-sequencing reveals selection signatures associated with important traits in Ethiopian indigenous goat populations” in the Frontiers in Genetics journal (CAS-Q2, Impact factor=3.52). Haile is the first author, Prof. Yuehui Ma and Prof.  Lin Jiang are the corresponding authors of this paper. This study is the first time whole genome re-sequencing to characterize genomic polymorphisms among the indigenous goat populations in Ethiopian.

埃塞俄比亚位于非洲之角的中心，境内多山地高原，经济上以农牧业为主，现存3020万只山羊。这些山羊可以划分为7个遗传特征群体和14个表型特征群体，长期的选择和进化使它们在形态、体型、毛色、繁殖性状以及适应能力上具有不同的特性。此外，这些山羊的动物产品（如羊肉、羊奶、粪便等）是当地民众重要的生活资料和收入来源，因此，运用先进的基因组学分析方法对埃塞俄比亚地方山羊进行遗传评估和鉴定至关重要。

Ethiopia is located in the center of the horn of Africa, which mainly consist of mountains and plateaus, and its economy is dominated by agriculture and animal husbandry. Ethiopia is a home for 30.2 million goats, with seven genetically characterized groups and 14 local phenotypically classified populations which are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other production traits, this implies that natural selection has most probably played a key role in the adaptation of these populations under the diverse range of environments. Moreover, the indigenous goats are primarily used as a source of income, milk, meat, manure and many other sociocultural functions. Hence, genomic characterization of these indigenous goat breed using modern genomic tools is paramount important to ensure breeding of these hardy goat populations.

该研究收集了来自埃塞俄比亚5个地方山羊品种的44份样品（Abergelle, Afar, Begait, Central Highland 和Meafure），通过对其进行重测序数据分析，共发现了1600万个SNP位点和123577个插入缺失，在5个绵羊群体中分别发现11137576, 10760581, 10833847, 12229657 ，10749996个SNP位点。然后基于群体分化指数（FST）和杂合度（HP）两种方法对这些SNP位点和Indel进行选择信号分析，筛选重要候选基因。最终发现CAMK2D, KANK4 NIN, RSPH6A 和UGT2A2基因与繁殖性状相关；SCN9A, GIGYF2 和PPP1R1A基因与体重相关；TMEM117基因与脂肪酸代谢相关；PPP4R3B 和PNPT1基因与疾病相关。本研究为保种方案的设计、优秀品种的管理、山羊地方品种的遗传改良提供了重要的理论参考，进一步加深了对埃塞俄比亚优良地方品种的认识。该研究得到了国家自然科学基因（31601910和U1603232）的支持

The investigation focused on the whole-genome re-sequencing of 44 goats from 5 Ethiopian indigenous goat populations. This work identified about 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. We also detected 11,137,576, 10,760,581, 10,833,847, 12,229,657 and 10,749,996 putative SNPs in Abergelle, Afar, Begait, Central Highland and Meafure goat populations, respectively. Further, we used population differentiation (FST) and pooled heterozygosity (HP) based approaches to perform selection signatures analysis and screen important genes. Several of the candidate genes are involved in the reproduction (CAMK2D, KANK4 NIN, RSPH6A and UGT2A2), body weight (SCN9A, GIGYF2 and PPP1R1A), fatty acids (TMEM117), and disease related (PPP4R3B and PNPT1) genes. Our investigation contributes to deliver valuable genetic information and paves the way to design conservation strategy, breed management, genetic improvement, and utilization programs. The genomic resources generated in the study will offer an opportunity for further investigations. This work was financial supported by the National Natural Science Foundation of China (31601910 and U1603232).

Figure1. Geographic distribution and sample collection site of the five indigenous goat populations

Figure 2. Genome-wide distributions of selection signals between Begait and Abergelle (A), between Begait and Central Highland (B) goat populations

原文链接Original link:

https://www.frontiersin.org/articles/10.3389/fgene.2019.01190/full

该文第一作者Haile是我院埃塞俄比亚籍动物遗传育种与繁殖专业博士研究生，2016年9月加入中国农业科学院北京畜牧兽医研究所马月辉研究员畜禽种质资源保护与利用科技创新团队，2019年毕业并获得我院优秀毕业生荣誉，以第一作者发表学术论文4篇，发表文章及期刊如下：

The first author Haile Berihulay from Ethiopia is a PhD student with the major Animal Breeding, Genetics and Reproduction, specialty Animal germplasm resources at the Institute of Animal Science, Beijing. He joined the Animal germplasm resources group Professor Yuehui Ma at IAS-CAAS as a fully funded scholarship by China Scholarship Council in September 2016 and won the 2019 Outstanding Graduate Student Award. Haile has published 4 publications as the first author in the international journals as follows:

Dr. Berihulay’s Publications

https://www.researchgate.net/profile/Haile_Berihulay/research

Prof. Yuehui Ma’s Publications

https://www.researchgate.net/profile/Yuehui_Ma

His homepage

http://ias.caas.cn/en/scientists/faculty/29036.htm

Institute of Animal Sciences, CAAS

http://ias.caas.cn/en/index.htm