Ancient Mitogenomes Reveal the Domestication and Distribution of Cattle During the Longshan Culture Period in North China

Cattle, as an important tool for agricultural production in ancient China, have a complex history of domestication and distribution in China. Although it is generally accepted that ancient Chinese taurine cattle originated from the Near East, the explanation regarding their spread through China and whether or not this spread was associated with native aurochs during ancient times are still unclear. In this study, we obtained three nearly complete mitochondrial genomes (mitogenomes) from bovine remains dating back ca. 4,000 years at the Taosi and Guchengzhai sites in North China. For the first time at the mitogenome level, phylogenetic analyses confirmed the approximately 4,000-year-old bovines from North China as taurine cattle. All ancient cattle from both sites belonged to the T3 haplogroup, suggesting their origin from the Near East. The high affinity between ancient samples and southern Chinese taurine cattle indicated that ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. A rapid decrease in the female effective population size ca. 4.65 thousand years ago (kya) and a steep increase ca. 1.99 kya occurred in Chinese taurine cattle. Overall, these results provide increasing evidence of the origin of cattle in the middle Yellow River region of China.

Deleterious protein-coding variants in diverse cattle breeds of the world

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

Yak Domestication: A Review of Linguistic, Archaeological, and Genetic Evidence

Yak, a species of bovid uniquely adapted to high-altitude environments, plays a critical role in the life of the inhabitants of the Tibetan Plateau and neighboring areas. There is currently no consensus on when these animals may have been domesticated. In this paper, we review the archaeological, genetic, and linguistic evidence relevant to this question, and suggest that the domestication took place following hybridization with taurine cattle from the end of the fourth millennium BCE. This study also shows that the original domesticators of yaks included not only the ancestors of the Tibetans, but also Rgyalrongic speaking people from Eastern Tibet.

Values and Beliefs That Shape Cattle Breeding in Southwestern Burkina Faso

Cattle production in southwestern Burkina Faso is under pressure because of resource scarcity, changing climate, and cattle diseases. Well-adapted local breeds, such as Lobi taurine cattle, are increasingly replaced by more productive exotic breeds. Community-based breeding programs (CBBPs) could be a viable option for preserving the breed and improving its productivity. Presuming that CBBPs would succeed only if they align with producers’ beliefs and values, we relied on a combination of conceptual frameworks (theory of basic values, rural livelihood transitions) to explore the values and beliefs of cattle producers. Security was the respondents’ dominant value in their aim to mitigate threats to livelihood, and it was closely linked to achievement in terms of harvest and animal quantity. Livestock-oriented respondents particularly valued conformity with accepted social roles, while achievement and power were more pronounced among crop-oriented respondents. We conclude that CBBPs, to be successful, will need to reduce threats to participants’ livelihood and make benefits of participation immediately visible. We consider the emergence of trusted leadership from the community to be pivotal for creating momentum for novel arrangements in cattle keeping and feeding.

Population Structure Assessed Using Microsatellite and SNP Data: An Empirical Comparison in West African Cattle

A sample of 185 West African cattle belonging to nine different taurine, sanga, and zebu populations was typed using a set of 33 microsatellites and the BovineHD BeadChip of Illumina. The information provided by each type of marker was summarized via clustering methods and principal component analyses (PCA). The aim was to assess differences in performance between both marker types for the identification of population structure and the projection of genetic variability on geographical maps. In general, both microsatellites and Single Nucleotide Polymorphism (SNP) allowed us to differentiate taurine cattle from zebu and sanga cattle, which, in turn, would form a single population. Pearson and Spearman correlation coefficients computed among the admixture coefficients (fitting K = 2) and the eigenvectors corresponding to the first two factors identified using PCA on both microsatellite and SNP data were statistically significant (most of them having p < 0.0001) and high. However, SNP data allowed for a better fine-scale identification of population structure within taurine cattle: Lagunaire cattle from Benin were separated from two different N’Dama cattle samples. Furthermore, when clustering analyses assumed the existence of two parental populations only (K = 2), the SNPs could differentiate a different genetic background in Lagunaire and N’Dama cattle. Although the two N’Dama cattle populations had very different breeding histories, the microsatellite set could not separate the two N’Dama cattle populations. Classic bidimensional dispersion plots constructed using factors identified via PCA gave different shapes for microsatellites and SNPs: plots constructed using microsatellite polymorphism would suggest the existence of weakly differentiated, highly intermingled, subpopulations. However, the projection of the factors identified on synthetic maps gave comparable images. This would suggest that results on population structuring must be interpreted with caution. The geographic projection of genetic variation on synthetic maps avoids interpretations that go beyond the results obtained, particularly when previous information on the analyzed populations is scant. Factors influencing the performance of the projection of genetic parameters on geographic maps, together with restrictions that may affect the election of a given type of markers, are discussed.

Novel functional sequences uncovered through a bovine multi-assembly graph

Linear reference genomes are typically assembled from single individuals. They are unable to reflect the genetic diversity of populations and lack millions of bases. To overcome such limitations and make non-reference sequences amenable to genetic investigations, we build a multi-assembly graph from six reference-quality assemblies from taurine cattle and their close relatives. We uncover 70,329,827 bases that are missing in the bovine linear reference genome. The missing sequences encode novel transcripts that are differentially expressed between individual animals. Reads which were previously poorly or unmapped against the bovine reference genome now align accurately to the non-reference sequences. We show that the non-reference sequences contain polymorphic sites that segregate within and between breeds of cattle. Our efforts to uncover novel functional sequences from a multi-assembly graph pave the way towards the transition to a more representative bovine reference genome.

Temporal variation in body measurements in three Taurine cattle populations of Burkina Faso supports introgression of Zebu genes into West African Taurine cattle

A total of 769 adult females belonging to 3 taurine and one zebu cattle populations sampled in 3 provinces of Burkina Faso were assessed for 19 body measurements during two different years (2014 and 2018). The aim of this research was to identify temporal morphological variation in cattle bred in the humid southern zones to obtain empirical evidence supporting a possible introgression of zebu cattle genes into Gourounsi and Lobi taurine cattle breeds. Zebu cattle samples were used as out-group for both 2014 and 2018 subsets. Least square means of body measurements allowed to classify Burkina Faso taurine cattle into three subgroups according to body size (Gourounsi–Sanguié –GourS-, Gourounsi-Nahouri –GourN- and Lobi from the tallest to the smallest respectively). Principal Component Analysis suggested that in 2014, taurine populations were structured. Dispersion map constructed using the two first factors informed that the GourS population was well separated from both the Lobi and the GourN, which, in turn, overlapped. However, in 2018 a strong signal of homogenization was identified, with GourN partially overlapping the other two populations. Linear Discriminant Analysis suggested that about 20% of both GourS and GourN individuals were reciprocally misclassified. Clues for such increase have been pointed out by MANOVA analysis. Although on 2014, Lobi cattle was clearly smaller than Gourounsi and both GourS and GourN populations showed clear differences on body traits, on 2018 it could be assessed an increase in size in Lobi cattle and a strong homogenization signal within Gourounsi cattle. Zebu cattle gene flow southwards in Burkina Faso is likely to have caused these changes, suggesting a fast erosion of taurine cattle genetic background. Keywords: Body traits, quantitative traits, Gourounsi cattle, Lobi, Burkina Faso.

Whole genome re-sequencing reveals adaptation prior to the divergence of buffalo subspecies

The application of high throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran and Khuzestan provinces, were re-sequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2X per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20 and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using re-sequencing data from other five bovine species as well as the Axiom® Buffalo Genotyping Array 90 K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.