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Michel Georges and colleagues report fine mapping and functional characterization of a quantitative trait locus with a large effect on bovine stature. They show that the likely causal variants at this locus modulate expression of a chromosomal domain encompassing PLAG1 and several other genes. We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ∼780-kb interval using a Hidden Markov Model–based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ∼780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.

Domestication of wild cattle, sheep, and pigs began a process of body size diminution. In most of Western Europe this process continued across prehistory and was not reversed until the Roman period. However, in Italy, an increase in livestock body size occurred during the Iron Age, earlier than the Western provinces. In order to better understand the nature and timing of this early increase in animal size, this paper presents a detailed regional study of taxonomic abundance and biometric data from zooarchaeological assemblages recovered from the Po and Venetian-Friulian Plains in northern Italy. Our results demonstrate a high level of regionality in the choice of species exploited, with husbandry systems focused on different domesticates, as well as regional differences in animal size. However, despite significant variation in species frequencies, settlement structure, and epigraphic tradition, all areas with sufficient data demonstrate similar significant changes in livestock body size. Cattle and sheep increased incrementally in size prior to the Roman conquest in all regions considered; surprisingly, pigs continued to decrease in size throughout later prehistory. The incremental pace and pan-regional character of the size change in cattle and sheep suggests an internally motivated phenomenon rather than herd replacement with a new larger population, as might follow colonisation or conquest. The divergence in size trends for bovids and suids suggests a noteworthy change in cattle and sheep herding practices during the Iron Age or final centuries of the Bronze Age, in contrast with greater continuity in pig management. Our analysis provides a thorough zooarchaeological synthesis for northern Italy and, for the first time, demonstrates that both cattle and sheep increased in size outside of Roman territory well before the conquest of this area. This study offers a basis for future chemical analyses (DNA, isotopes), which will further investigate the cause(s) of livestock size changes in northern Italy.

Given that complex behavior evolved multiple times independently in different lineages, a crucial question is whether these independent evolutionary events coincided with modifications to common neural systems. To test this question in mammals, we investigate the lateral cerebellum, a neurobiological system that is novel to mammals, and is associated with higher cognitive functions. We map the evolutionary diversification of the mammalian cerebellum and find that relative volumetric changes of the lateral cerebellar hemispheres (independent of cerebellar size) are correlated with measures of domain-general cognition in primates, and are characterized by a combination of parallel and convergent shifts towards similar levels of expansion in distantly related mammalian lineages. Results suggest that multiple independent evolutionary occurrences of increased behavioral complexity in mammals may at least partly be explained by selection on a common neural system, the cerebellum, which may have been subject to multiple independent neurodevelopmental remodeling events during mammalian evolution. The brains of mammals consist of the same basic structures, but each of these structures varies from one species to the next. A given structure may be larger in one species than another, for example. It may contain different numbers or sizes of cells. It may even have different connections to other brain regions. By comparing individual brain structures between species, we can map how the mammalian brain has evolved. Smaers et al. have now done this for the cerebellum, a structure at the back of the brain. The mammalian cerebellum consists of three main areas: the vermis, paravermis, and the lateral hemispheres. Smaers et al. show that in apes, dolphins and seals, the lateral hemispheres are unusually large relative to the cerebellum as a whole. This could indicate that these three groups of animals share a common ancestor with enlarged lateral hemispheres. Yet, genetic studies suggest that this is not the case. Another possibility is that apes, dolphins and seals independently evolved enlarged lateral hemispheres. This may have given rise to a trait that proved beneficial for each of them. But what might this be? Studies in people suggest that the lateral hemispheres help to support some forms of learning. Apes, dolphins and seals are among only a few species of mammal with the ability to learn new calls and vocalizations. The expansion of the lateral cerebellum may therefore have contributed to the evolution of vocal learning, and this may have occurred independently on at least three separate occasions. Future work should extend this analysis to other cognitive skills, as well as to other species. Bats, for example, would be of particular interest because of their ability to echolocate. Finally, the lateral hemispheres consist of several subregions that play different roles in learning and information processing. Further experiments should explore whether different subregions have increased in size in different species.

The body dimension measurement of large animals plays a significant role in quality improvement and genetic breeding, and the non-contact measurements by computer vision-based remote sensing could represent great progress in the case of dangerous stress responses and time-costing manual measurements. This paper presents a novel approach for three-dimensional digital modeling of live adult Qinchuan cattle for body size measurement. On the basis of capturing the original point data series of live cattle by a Light Detection and Ranging (LiDAR) sensor, the conditional, statistical outliers and voxel grid filtering methods are fused to cancel the background and outliers. After the segmentation of K-means clustering extraction and the RANdom SAmple Consensus (RANSAC) algorithm, the Fast Point Feature Histogram (FPFH) is put forward to get the cattle data automatically. The cattle surface is reconstructed to get the 3D cattle model using fast Iterative Closest Point (ICP) matching with Bi-directional Random K-D Trees and a Greedy Projection Triangulation (GPT) reconstruction method by which the feature points of cattle silhouettes could be clicked and calculated. Finally, the five body parameters (withers height, chest depth, back height, body length, and waist height) are measured in the field and verified within an accuracy of 2 mm and an error close to 2%. The experimental results show that this approach could be considered as a new feasible method towards the non-contact body measurement for large physique livestock.

In actual farms, individual livestock identification technology relies on large models with slow recognition speeds, which seriously restricts its practical application. In this study, we use deep learning to recognize the features of individual cows. Alexnet is used as a skeleton network for a lightweight convolutional neural network that can recognise individual cows in images with complex backgrounds. The model is improved for multiple multiscale convolutions of Alexnet using the short-circuit connected BasicBlock to fit the desired values and avoid gradient disappearance or explosion. An improved inception module and attention mechanism are added to extract features at multiple scales to enhance the detection of feature points. In experiments, side-view images of 13 cows were collected. The proposed method achieved 97.95% accuracy in cow identification with a single training time of only 6 s, which is one-sixth that of the original Alexnet. To verify the validity of the model, the dataset and experimental parameters were kept constant and compared with the results of Vgg16, Resnet50, Mobilnet V2 and GoogLenet. The proposed model ensured high accuracy while having the smallest parameter size of 6.51 MB, which is 1.3 times less than that of the Mobilnet V2 network, which is famous for its light weight. This method overcomes the defects of traditional methods, which require artificial extraction of features, are often not robust enough, have slow recognition speeds, and require large numbers of parameters in the recognition model. The proposed method works with images with complex backgrounds, making it suitable for actual farming environments. It also provides a reference for the identification of individual cows in images with complex backgrounds.

Abstract Body size plays a key role in production, health, selection, and environmental adaptation of animals, but the genetic basis of body size variation is not clearly understood. Here, we conducted genome-wide association studies (GWAS) of 15 body size traits using autosomal single nucleotide polymorphisms (SNPs) derived from whole-genome sequences of 31 Brahman cattle and 131 Yunling cattle and identified 20 significant loci, which implicated 18 candidate genes. For ischium width, the most significant SNP was assigned to LCORL, a famous gene controlling body size. For chest width, the most significant SNP was located upstream of BMP5, a secreted ligand of transformation growth factor-beta superfamily of proteins involved in bone and cartilage development. Subsequently, we detected selective sweeps in Brahman cattle using integrated Haplotype Score, composite likelihood ratio, and nucleotide diversity. The results showed CNTNAP5 locus associated with hip cross height and LIMCH1 locus associated with forehead size were in selective signals, which were consistent with higher hip cross height and higher forehead size in Brahman cattle compared with Yunling cattle. Our findings provide genetic insights into variation and selection of body size using GWAS and selective signals and will accelerate future efforts aimed at cattle improvement.

Savannas worldwide are vital for both socioeconomic and biodiversity values. In these ecosystems, management decisions are based on the perception that wildlife and livestock compete for food, yet there are virtually no experimental data to support this assumption. We examined the effects of wild African ungulates on cattle performance, food intake, and diet quality. Wild ungulates depressed cattle food intake and performance during the dry season (competition) but enhanced cattle diet quality and performance during the wet season (facilitation). These results extend our understanding of the context-dependent—competition-facilitation balance, in general, and are critical for better understanding and managing wildlife-livestock coexistence in human-occupied savanna landscapes.

We assessed dairy cows' body postures while they were performing different stationary activities in a loose housing system and then used the variation within and between individuals to identify potential connections between specific postures and the valence and arousal dimensions of emotion. We observed 72 individuals within a single milking herd focusing on their ear, neck and tail positions while they were: feeding from individual roughage bins, being brushed by a mechanical rotating brush and queuing to enter a single automatic milking system. Cows showed different ear, neck and tail postures depending on the situation. When combined, their body posture during feeding was ears back up and neck down, with tail wags directed towards the body, during queuing their ears were mainly axial and forward, their neck below the horizontal and the tail hanging stationary, and during brushing their ears were backwards and asymmetric, the neck horizontal and the tail wagging vigorously. We then placed these findings about cow body posture during routine activities into an arousal/valence framework used in animal emotion research (dimensional model of core affect). In this way we generate a priori predictions of how the positions of the ears, neck and tail of cows may change in other situations, previously demonstrated to vary in valence and arousal. We propose that this new methodology, with its different steps of integration, could contribute to the identification and validation of behavioural (postural) indicators of how positively or negatively cows experience other activities, or situations, and how calm or aroused they are. Although developed here on dairy cattle, by focusing on relevant postures, this approach could be easily adapted to other species.

The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent 14 C dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years. The domestication of cattle took place during the early Holocene, independently in the Near East and in southern Asia. Here, Zhang et al. provide evidence for management of taurine cattle in northern China, an area not previously considered as an independent domestication centre.

Intramuscular fat (IMF) in cattle is an important component of traits that influence meat quality. We measured carcass characteristics and gene expression in Korean steers to clarify the molecular mechanism(s) underlying IMF deposition in LM tissue by determining the correlation between IMF content and gene expression abundance and by developing models to predict IMF content using gene expression abundance. The deposition of IMF is determined by a balance between fat deposition and fat removal in the LM. We measured mRNA abundance of lipid metabolic genes including lipogenesis [acetyl CoA carboxylase (ACC), fatty acid synthase (FASN)], fatty lipid uptake [lipoprotein lipase (LPL), fatty acid translocase (CD36), fatty acid transport protein 1 (FATP1)], fatty acid esterification [glycerol-3-phosphate acyltransferase 1 (GPAT1), acylglycerol phosphate acyltransferase 1 (AGPAT1), diacylglycerol acyltransferase 1 (DGAT1), DGAT2], lipolysis [adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), monoglyceride lipase (MGL)], and fatty acid oxidation [carnitine palmitoyl transferase 1B, very long-chain acyl-CoA dehydrogenase (VLCAD), medium-chain acyl-CoA dehydrogenase (MCAD)] in the LM. The mRNA abundance of the GPAT1 gene showed the greatest correlation (r = 0.74; P < 0.001) with IMF content among 9 fat deposition genes. The gene expression abundance of other fat deposition genes including ACC, FASN, LPL, CD36, FATP1, AGPAT1, DGAT1, and DGAT2 also exhibited significant positive correlations (P < 0.05) with IMF content in the LM. Conversely, ATGL mRNA abundance showed the greatest negative correlation (r = –0.68; P < 0.001) with IMF content in the LM among 6 fat removal genes. The expression of other fat removal genes including MGL, VLCAD, and MCAD showed significant negative correlations (P < 0.05) with IMF content. Our findings show that the combined effects of increases in lipogenesis, fatty acid uptake, fatty acid esterification, and of decreases in lipolysis and fatty acid oxidation contribute to increasing IMF deposition in Korean steers. The multiple regression analysis revealed that the mRNA abundance of the GPAT1 gene in the LM was the first major variable predicting IMF content (54%) among 15 lipid metabolic genes. The second was mRNA abundance of ATGL (11%). In conclusion, these results suggest that GPAT1 and ATGL genes could be used as genetic markers to predict IMF deposition in the LM.