Cattle are central to the lives and diverse cultures of African people. It has played a crucial role in providing valuable protein for billions of households and sources of income and employment for producers and other actors in the livestock value chains. The long-term natural selection of African cattle typically signals signatures in the genome, contributes to high genetic differentiations across breeds. This has enabled them to develop unique adaptive traits to cope with inadequate feed supply, high temperatures, high internal and external parasites, and diseases. However, these unique cattle genetic resources are threatened by indiscriminate cross-breeding, breed replacements with exotic cosmopolitan breeds, and climate change pressures. Although there are no functional genomics studies, recent advancements in genotyping and sequencing technologies have identified and annotated limited functional genes and causal variants associated with unique adaptive and economical traits of African cattle populations. These genome-wide variants serve as candidates for breed improvement and support conservation efforts for endangered cattle breeds against future climate changes. Therefore, this review plans to collate comprehensive information on the identified selection footprints to support genomic studies in African cattle to confirm the validity of the results and provide a framework for further genetic association and QTL fine mapping studies.

【背景】牦牛骨骼肌的生长发育决定其产肉量，进而影响经济收入。因此提高牦牛的产肉性能是发展牦牛产业的重要任务。骨骼肌发育过程受许多基因的调控，包括一些非编码RNA的调控，如miRNA。然而牦牛出生前后骨骼肌中miRNA的转录调控机制并不清楚。【目的】通过小RNA测序挖掘与牦牛骨骼肌生长发育有关的miRNA，并通过C2C12细胞对候选miRNA进行功能研究，为牦牛骨骼肌发育机制解析提供基础。【方法】对出生前后牦牛背最长肌（3个胎牛和3个成年牛）进行miRNA转录本测序，基于（log2 (差异倍数) |>1，P值≤0.05）筛选差异miRNAs，并通过Miranda和TargetScan算法预测差异miRNAs靶基因并求交集，对差异miRNA靶基因进行GO和KEGG富集分析。在C2C12细胞中通过干扰和过表达实验对候选miRNA进行功能分析，通过双荧光素酶实验验证候选miRNA的靶基因。【结果】本研究在胎牛和成年牦牛背最长肌中共鉴定到264个miRNAs。264个差异miRNAs共预测到5183个靶基因。GO和KEGG结果显示，差异miRNA的靶基因主要富集在能量平衡，蛋白激酶结合，ATP结合等GO条目，及一些与肌肉发育有关的信号通路，如MAPK，PI3K-Akt，Hippo等信号通路。其中候选miR-652在胎牛背最长肌中上调表达。通过在C2C12细胞中转染miR-652发现，miR-652可促进C2C12细胞的增殖和分化（P≤0.05），同时抑制C2C12细胞晚期凋亡（P≤0.001）。细胞周期实验结果显示，miR-652可导致C2C12细胞百分比在G1期下降（P≤0.001），S期和G2期上升（P≤0.01）。双荧光素酶实验结果提示ISL1是miR-652的一个靶基因。【结论】牦牛在出生前后骨骼肌中存在大量差异表达的miRNA，表明miRNA参与牦牛骨骼肌发育，miR-652可能通过靶向ISL1基因调控牦牛骨骼肌生长发育。

本研究利用已公布的4165个来自于全世界196个品种的山羊线粒体D_Loop序列，进行核苷酸多样性、单倍型构建、单倍型多样性、群体系统发育学研究、中性检验及群体遗传距离等一系列遗传参数进行评估。在全部个体的401 bp片段长度的D_Loop区域内共鉴定得到301个多态位点，总体核苷酸多样性为0.03471；构建获得并构建2409个D_Loop单倍型，单倍型平均多样性为0.9983。系统发育分析表明，98.92%的单倍型被聚类为已知的6个山羊线粒体D_loop单倍型簇，其中单倍型A所占比例最大(86%)，D_Loop单倍型B簇在中国山羊中出现频率最高。中国西南地区山羊群体中发现了两个未知的D_Loop单倍型簇(Unknown I和Unknown II)。分子方差分析(AMOVA)和群体间成对差异(PiXY)研究结果表明，不同品种家养山羊间群体变异较小，群体遗传分化与地理分布不完全一致，表明群体间广泛存在遗传物质交流。中性检验(Tajima‘D和Fu’Fs检验)和错配分布研究结果表明，单倍型簇B、C和G存在群体扩张历史。较其他野羊，Capra aegagrus与家养山羊系统发育关系最为密切，并可能贡献于山羊A、B、C和F单倍群簇的驯化起源。本研究表明线粒体D_Loop单倍型B簇可能起源于中国或在山羊驯化早期已迁至中国，在中国西南地区山羊群体中两个未知的D_Loop单倍型簇的发现表明中国西南地区可能具有独特的山羊母系背景或驯化历史；Capra aegagrus是最可能的家养山羊野生祖先，并可能贡献于山羊A、B、C和F单倍群簇的驯化起源。本研究利用大样本量全世界山羊线粒体D_Loop序列数据集分析有助于更好的理解世界范围内山羊母系驯化起源及基因流动的历史变化，为进一步明确世界山羊群体迁徙的演变历史及种群系统发育定位提供了宝贵的理论依据。

Endothelial PAS domain protein 1 gene (EPAS1) is a key transcription factor that activates the expression of oxygen-regulated genes. In this study, in order to better understand the effects of EPAS1 gene on hematologic parameters in yak, we firstly quantified the tissue expression patterns for EPAS1 mRNA of yak, identified polymorphism in this gene and evaluated its association with hematologic parameters. Expression of EPAS1 mRNA was detected in all eight tissues (heart, liver, lung, spleen, pancreas, kidney, muscles and ovary). The expressions of EPAS1 in lung and pancreas were extremely higher than other tissues examined. Three novel single nucleotide polymorphisms (SNPs) (g.83052 C>T, g.83065 G>A and g.83067 C>A) within the EPAS1 were identified and genotyped in Pali (PL), Gannan (GN) and Tianzhu White (TZW) yak breeds. Significant higher frequencies of the AA and GA genotypes and A allele of the g.83065 G>A were observed in the PL and GN breeds than that in the TZW breed (P<0.01). Association analysis of the PL breed indicated that the g.83065 G>A polymorphism was significantly associated with hemoglobin (HGB) concentration in yaks (P<0.05). Individuals with genotype AA had significantly higher HGB concentration (P<0.05) than those with genotype GA and GG. All these results will help our further understanding of biological functional of yak EPAS1 gene in responding to hypoxia and also indicate EPAS1 might contribute to the hypoxia adaptation of the yak.

In the present study we studied the genetic structure of five Chinese sheep populations of Hu sheep, Tong sheep, SmalltailedHan sheep, Tan sheep, and Wadi (WD) sheep using 15 microsatellite loci. The results showed that the FIT, FST, andFIS statistics computed for the complete dataset had the following values, 0.523±0.140, 0.363±0.131 and 0.263±0.092,respectively. All loci were significantly contributed to the genetic differentiation among population (P<0.001). There is norelationship between the scatter of pairwise FST geographical distance points as geographical distance increases betweenthe five populations. Membership probabilities and genetic structure of sheep populations were estimated when K=2, thepopulations were classified into Hu, Tong, Han and WD, and Tan sheep group. However, when K=3, the populations wereclassified into Hu and Tong, Han and WD, and Tan sheep group. The findings supported the previous literatures thatthese populations are originated on different time stages from the primogenitor population and communicated geneticallywith each other by natural and artificial selection in different ecological environment.

Research on the identity of genes and their relationship with traits of economic importance in farm animals could assist in the selection of livestock. In this study, the polymorphisms of insulin-like growth factor 1 (IGF1) gene in 561 goats of ten breeds were detected by polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) and their association with litter size and birth weight in three breeds were investigated. The effects of IGF1 polymorphisms on the breeding value for litter size and birth weight were examined using least square methods. Two deletions (CA) were detected in the microsatellite and two mutations (A1637G, T1640C) were found in 5´-flanking regulatory region. No significant association between the polymorphisms in 5´-flanking region of IGF1 and birth weight was found in the three breeds of goats. In Gulin Ma goats, two polymorphisms were found to affect litter size traits. In Chuandong White goats and Guizhou White goats, no significant difference (P<0.05) in litter size between goats carrying different genotypes was observed. Further evaluation and confirmation studies in more goat populations with larger sample sizes are necessary.