Abstract
Bovine mastitis is one of the most important economic and health issues in dairy farms. Data collection during routine recording procedures and access to large datasets have shed the light ...on the possibility to use trained machine learning algorithms to predict the udder health status of cows. In this study, we compared eight different machine learning methods (Linear Discriminant Analysis, Generalized Linear Model with logit link function, Naïve Bayes, Classification and Regression Trees, k-Nearest Neighbors, Support Vector Machines, Random Forest and Neural Network) to predict udder health status of cows based on somatic cell counts. Prediction accuracies of all methods were above 75%. According to different metrics, Neural Network, Random Forest and linear methods had the best performance in predicting udder health classes at a given test-day (healthy or mastitic according to somatic cell count below or above a predefined threshold of 200,000 cells/mL) based on the cow’s milk traits recorded at previous test-day. Our findings suggest machine learning algorithms as a promising tool to improve decision making for farmers. Machine learning analysis would improve the surveillance methods and help farmers to identify in advance those cows that would possibly have high somatic cell count in the subsequent test-day.
Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations ...of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.
The objective of this study was to estimate inbreeding coefficients in Holstein dairy cattle using imputed SNPs data. A data set of 95,540 Italian Holstein dairy cows from the routine genomic ...evaluations of the Italian National Association of Holstein, Brown, and Jersey Breeders were analyzed, with 84,445 imputed SNP. Ten widely used genomic inbreeding estimators were tested, including 4 PLINK v1.9 estimators (F, FHAT1, FHAT2, FHAT3), 3 genomic relationship matrix (GRM)-based methods VanRaden's first method with observed allele frequencies (FGRM) or with fixed frequencies at 0.5 (FGRM05), VanRaden's third method, allelic frequency free and pedigree regressed (FGRM2), runs of homozygosity (ROH)-based estimators in a complete (FROH) and simplified version (FROH2), and proportion of homozygous SNP (FPH). Pairwise comparisons among them were made, including the comparison with traditional pedigree-based inbreeding coefficients (FPED). Our results showed variability among the genomic inbreeding estimators. Coefficients of FGRM and FHAT3 were >1, meaning that more variability has been lost than the variability that existed in the base population. Regarding the remaining ones, FGRM05, FROH, FROH2, and FPH provided coefficients within the 0,1 space and are considered comparable to FPED. Not comparable to FPED, yet with an interpretable value, can be considered the coefficients of F, FHAT2, and FGRM2. Estimators based on ROH had the highest correlation with pedigree-based coefficients (0.59–0.66), among all estimators tested. In this study, Spearman correlations were shown to possibly provide a clearer estimation of the strength of the relationship between estimators. We hypothesize that imputation might cause extreme genomic inbreeding values that deserves further investigation.
Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population ...structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.
Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake.
The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.
Abstract
The main objective of this study was to assess the microbiota diversity in milk samples collected from Holstein cows with different estimated breeding values for predicted feed efficiency, ...milk coagulation, resilience to mastitis, and consequently, to study its effects on milk quality. One hundred and twenty milk samples were collected in two seasons (summer and winter) from different commercial dairy farms in the Nord-east of Italy. For each trait, 20 animals divided into two groups of the high (10 cows) and the low (10 cows) were selected to study the microbiota profile using 16S rRNA metabarcoding sequencing. The alpha and beta diversity analysis revealed significant differences between the high and the low groups for feed efficiency and resilience to mastitis, while no significant difference was detected for milk coagulation. Moreover, remarkable differences among the taxa were detected between the two seasons, where the winter was more diverse than summer when applied the Chao1 index. Lastly, the linear discriminant analysis (LDA) effect size (LEfSe) indicated
Aerococcus, Corynebacterium, Facklamia,
and
Psychrobacter
taxa with more abundance in the high group of feed efficiency, whereas, in resilience to mastitis, only two genera of
Mycoplana
and
Rhodococcus
were more abundant in the low group. In addition, LEfSe analysis between the seasons showed significant differences in the abundance of
Bacteroides
,
Lactobacillus
,
Corynebacterium
,
Escherichia
,
Citrobacter
,
Pantoea
,
Pseudomonas
, and
Stenotrophomonas
. These findings indicate that the different genetic predisposition for feed efficiency and resilience to mastitis could affect the raw milk microbiota and, consequently, its quality. Moreover, we found more abundance of mastitis-associated bacteria in the milk of dairy cows with a higher feed efficiency index.
DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized ...target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs.
The combined use of somatic cell count (SCC) and differential somatic cell count (DSCC), which is the ratio of neutrophils plus lymphocytes to total milk SCC, represents a novel approach to define ...cow’s udder health status, as it allows to identify healthy animals (those with low SCC and DSCC), cows susceptible to mastitis (those where an immune response has begun, so that there is an increase of neutrophils, i.e. DSCC, but not yet of total SCC), animals with a mastitic event in progress (those with high SCC and DSCC) and animals with possible chronic inflammation (those with high SCC and low DSCC, as macrophages prevail). We investigated the association of cow’s udder health status with milk yield, composition and coagulation properties in four cattle breeds. Results demonstrated that milk traits vary among cows with different udder health status, especially in terms of fat percentage, lactose percentage and coagulation ability. The most pronounced worsening in milk yield and coagulation ability was observed for animals with chronic inflammation. Our findings support the new approach based on the combined use of SCC and DSCC to screen for cow’s udder health, as it would allow to identify susceptible cows that will probably undergo a mastitic event and chronic cows that would possibly reduce the herd milk production and quality.HighlightsThe combined use of SCC and DSCC is a novel approach to screen for udder health status.Differences in milk yield, composition and coagulation exist among cows with different udder health status defined on the basis of combined SCC and DSCC.The information about udder health status may be used to develop mastitis pre-screening protocols.
Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the ...past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field.
Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In ...this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.
After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.
Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.
Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle ...breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds.
After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location.
This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.
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