Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds

Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle. A major difficulty during this transition period is the need of SNP data for parents and offspring, which in most cases is not yet feasible due to the genotyping cost. To overcome the unavailability of same genotyping platform during the transition period, in this study we aimed to assess the feasibility of a MS imputation pipeline from SNPs in four native sheep dairy breeds: Comisana (N = 331), Massese (N = 210), Delle Langhe (N = 59) and Sarda (N = 1003). Those sheep were genotyped for 11 MS and with the Ovine SNP50 Bead Chip. Prior to imputation, a quality control (QC) was performed, and SNPs located within a window of 2 Mb from each MS were selected. The core of the developed pipeline was made up of three steps: (a) storing of both MS and SNP data in a Variant Call Format file, (b) masking MS information in a random sample of individuals (10%), (c) imputing masked MS based on non-missing individuals (90%) using an imputation program. The feasability of the proposed methodology was assessed also among different training - testing split ratio, population size, number of flanking SNPs as well as within and among breeds. The accuracy of the MS imputation was assessed based on the genotype concordance as well as at parentage verification level in a subset of animals in which assigned parents' MS were available. A total of 8 MS passed the QC, and 505 SNPs were located within the ±2 Mb window from each MS, with an average of 63 SNPs per MS. The results were encouraging since when excluding the worst imputed MS (OARAE129), and regardless on the analyses performed (within and across breeds) for all breeds, we achieved an overall concordance rate over 94%. In addition, on average, the imputed offspring MS resulted in equivalent parentage outcome in 94% of the cases when compared to verification using original MS, highlighting both the feasibility and the eventual practical advantage of using this imputation pipeline.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

Exploratory Study on Individual Locomotor Activity in Local Dual-Purpose and Commercial Breeder Pullets

Improving animal welfare is a prerequisite for the societal acceptance of poultry production. Support for improvements requires practical tools to quantify animal welfare and identify predispositions at the individual level, where possible. In this study, the activities and behavior of dual-purpose chickens (N = 245) and commercial breeders (N = 224) were analyzed. The general locomotor activity (GLA) data were collected using an RFID system over five days with 9-to-14-week-old animals. The results show that the animals of comparable age and stocking density differed from each other in their activity (p ≤ 0.001) according to breed, but no sex differences were observed (p = 0.159). No correlations were found between GLA and plumage condition (p > 0.05). The individual variations within the breeds are presented and discussed on an animal-by-animal level, providing new insights into the individual behavioral variability of chickens. The RFID systems can reliably generate GLA data that help to understand the potential interplay between behavior and animal welfare. The technology is also suitable for creating individual (personality) profiles that can be used for breeding. With a better understanding of the role of activity, husbandry and management practices can be adapted to improve animal welfare.

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

Y-Chromosome Haplotype Report among Eight Italian Horse Breeds

Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies.

Avoidance-related behavioral and blood-based physiological responses of Nguni and Boran cattle subjected to routine handling activities post relocation

Introduction

This study aimed to investigate the avoidance-related behavioral and blood-based physiological responses of Nguni and Boran cattle during routine handling activities post-relocation, with a particular focus on the effect of breed, week, and waiting time.

Methods

A total of 20 animals, 10 from each breed, were subjected to handling activities at fortnight intervals post-relocation. The animals were observed for entry time (ES), chute score (CS), kicking score (KS), blood sampling time, cortisol, and glucose concentrations. The data were analyzed using ANOVA and regression analysis.

Results and Discussion

Results showed that breed had a significant effect on avoidance-related behavioral responses (ES: p = 0.0032; CS: p = 0.0071; and EX: p = 0.0320), with Nguni cattle displaying more active avoidance behaviors compared to Boran cattle. Additionally, breed differences were observed in physiological responses, with Nguni cattle exhibiting higher cortisol and glucose levels compared to Boran cattle. Waiting time in the race had a greater impact on chute score (CS: p = 0.0037) and cortisol release (p = 0.0375) in the two breeds. Regression analysis revealed that the amount of time spent in the handling facility prior to sampling and the duration of blood collection significantly increased from week 3 to 15. Steers that waited in the race for more than 10 min had higher cortisol levels (p = 0.0031). These findings suggest that breed-specific management practices may be necessary to reduce stress-related responses and improve animal welfare during routine handling activities post-relocation. Overall, this study highlights the importance of considering the effects of breed, week, and waiting time when evaluating the avoidance-related behavioral and blood-based physiological responses of cattle during routine handling activities. These factors play a significant role in understanding and addressing the stress and welfare concerns associated with handling procedures, particularly after relocation.

The use of a genomic relationship matrix for breed assignment of cattle breeds: comparison and combination with a machine learning method

To develop a breed assignment model, three main steps are generally followed: 1) The selection of breed informative SNP; 2) The training of a model, based on a reference population, that allows to classify animals to their breed of origin; and 3) The validation of the developed model on external animals i.e., that were not used in previous steps. However, there is no consensus in the literature about which methodology to follow for the first step, nor about the number of SNP to be selected. This can raise many questions when developing the model and lead to the use of sophisticated methodologies for selecting SNP (e.g., with iterative algorithms, partitions of SNP or combination of several methods). Therefore, it may be of interest to avoid the first step by the use of all the available SNP. For this purpose, we propose the use of a genomic relationship matrix (GRM), combined or not with a machine learning method, for breed assignment. We compared it with a previously developed model based on selected informative SNP. Four methodologies were investigated: 1) The PLS_NSC methodology: selection of SNP based on a partial least square-discriminant analysis (PLS-DA) and breed assignment by classification based on the nearest shrunken centroids (NSC) method; 2) Breed assignment based on the highest mean relatedness of an animal to the reference populations of each breed (referred to mean_GRM); 3) Breed assignment based on the highest SD of the relatedness of an animal to the reference populations of each breed (referred to SD_GRM) and 4) The GRM_SVM methodology: the use of means and SD of the relatedness defined in mean_GRM and SD_GRM methodologies combined with the linear support vector machine (SVM), a machine learning method used for classification. Regarding mean global accuracies, results showed that the use of mean_GRM or GRM_SVM was not significantly different (Bonferroni corrected P > 0.0083) than the model based on a reduced SNP panel (PLS_NSC). Moreover, the mean_GRM and GRM_SVM methodology were more efficient than PLS_NSC as it was faster to compute. Therefore, it is possible to bypass the selection of SNP and, by the use of a GRM, to develop an efficient breed assignment model. In routine, we recommend the use of GRM_SVM over mean_GRM as it gave a slightly increased global accuracy, which can help endangered breeds to be maintained. The script to execute the different methodologies can be accessed on: https : //github.com/hwilmot675/Breed_assignment.

Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle (Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers

Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.

RNAseq reveals modulation of genes involved in fatty acid biosynthesis in chicken liver according to genetic background, sex, and diet

Increases in chicken production are mainly due to specialised breeds. However, local breeds are of increasing importance, known for ability to adapt to the environment and unique products. Conventional poultry products contain lower levels of n-3 fatty acids (FAs) compared to those obtained from local breeds, therefore the aim of this study was to evaluate the modulation of expression of genes involved in long-chain polyunsaturated FA (PUFA) biosynthesis pathways according to genetic background, diet conditions, and sex. Animals from two local breeds and a commercial line were fed different diets: control and experimental diet (10% linseed supplementation). For each breed and diet group, both sexes were reared. The RNA was extracted from 36 liver samples and sequenced by RNAseq method. Bioinformatic analysis was carried out to find differentially expressed genes from comparisons between experimental groups. Results showed low impact of diet on differentially expressed genes related to FA biosynthesis, but linseed diet increased percentage of n-3 FAs of liver. Sex and genetic background determined the differential expression of genes related to long-chain PUFA biosynthesis. Specifically, females of local breeds shared 23 up-regulated genes when compared to their respective commercial line groups. Some of the shared genes had a role in de novo triglyceride biosynthesis (MTTPL and GPAM), and in de novo FA biosynthesis (ACACA and SCD) was detected. In conclusion, local breeds are able to better adapt to a diet rich in PUFA, by triggering certain transcriptomic shifts in the liver that allow birds to process the high PUFA content provided by diet.

Ram Semen Cryopreservation for Portuguese Native Breeds: Season and Breed Effects on Semen Quality Variation

The semen quality is one of the determinant factors of ram semen cryopreservation. The present retrospective study aimed to characterize the seasonal ram pattern during the year for ten Portuguese local sheep breeds, hypothesizing that the breed and season had low effects on the main spermatozoa traits. A total of 1471 ejaculates were used and evaluated (fresh semen) from 85 rams between 2004 and 2020 and re-evaluated after thawing (thawed semen). The effect of breed, season, and sperm cryopreservation on nine semen traits were evaluated. The volume per ejaculate, spermatozoa (SPZ) concentration, and total number of SPZ per ejaculate, were affected by breed (p < 0.001) but not by season (p > 0.05). As expected, the semen processing was the most significant (p < 0.001) factor of variation on seminal parameters. Moreover, breed and interactions between breed × semen processing, modulated the response of alive SPZ, abnormal morphology, head, and intermediate piece defects. In fresh semen, season only affected the intermediate piece defects due to the highest percentage observed between February and April period in some breeds. Overall, and despite the mentioned particularities, there were similarities among the ten local breeds. We also concluded that the seasonal effect on ejaculate and SPZ traits is not significant in our region. These local ram breeds have low seasonality and can be employed in natural mating as well as semen donors for cryopreservation and assisted reproductive biotechnologies during the whole year at our latitude.

Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.

Exploring the Italian equine gene pool via high-throughput genotyping

Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.

Genetic Diversity of Montenegrin Local Sheep Breeds Based on Microsatellite Markers

The Montenegrin sheep population mostly consists of local breeds and their crossbreeds that are very valuable from their genome preservation point of view. The aim of this study was the investigation of the genetic diversity of seven Montenegrin sheep breeds (Jezeropivska-JP, Sora-SOR, Zetska zuja-ZZ, Bardoka-BAR, Sjenička-SJ, Ljaba-Lj, and Piperska zuja-PIP) using 18 microsatellite sets of markers. The genotyping was done for 291 samples from seven populations using the multiplex amplification of sequences with polymerase chain reaction (PCR). The parameters of genetic diversity were estimated using several software tools. In total, 243 alleles were found, with a range of 6 to 25 by locus. The mean observed heterozygosity (Ho), polymorphism information content (PIC), and Fis values (fixation index) per marker were 0.728, 0.781, and -0.007, respectively. The mean number of alleles per breed varied from 4.889 in ZZ to 10.056 in JP. The highest Ho was estimated for JP (0.763) and the lowest for ZZ (0.640). The genetic structure showed close relations between SOR and JP, and both of them with SJ, while ZZ, LJ, and PIP were more distanced. This study provides useful indicators for the development of further in-depth studies and the creation of appropriate conservation programs.

Carcass and Meat Quality Traits of Males and Females of the "Branca" Portuguese Autochthonous Chicken Breed

Simple Summary

Local breeds play a crucial role in the rural economies of many countries, as a considerable valuable genetic resource and, well adapted to the environment, their production can reduce the negative impact of intensive production systems. Portuguese chicken breeds are almost extinct, with the “Branca” population presenting the most worrying situation. Bred as a dual-purpose breed, the characterization of meat quality is fundamental to the conservation and promotion of this population., by increasing the value on these small-scale farms production. The carcass characteristics and meat quality of the “Branca” breed were evaluated, showing an interesting physicochemical profile, with good proportion of minerals, essential fatty acids (EFA) and n-3-PUFAs (docosapentanoic (C22:5n-3, DPA), and docosahexaenoic (C22:6n-3, DHA) acids), ensuring that consumers receive a highly nutritional and differentiated product.

Abstract

The “Branca” breed is a dual-purpose Portuguese autochthonous chicken breed, produced in extensive systems and in small flocks, especially in the Entre Douro and Minho regions. A total of 40 birds (n = 20/sex) were slaughtered between 38 and 42 weeks (males) and 110 and 120 weeks (females), and carcass and meat quality parameters were evaluated. The results showed significantly higher weights and differences for males between sexes and pieces (p ≤ 0.05) in the meat physicochemical composition. Water holding capacity (WRC), moisture and ash contents were influenced by sex. They were higher in males in the breast and drumstick and lightness (L*) and lipid content were higher in females (p ≤ 0.05). The breast meat presented greater lightness, moisture, ash and protein contents, while the drumstick showed a higher pH value, redness (a*) and lipid content, in both sexes (p ≤ 0.05). Regarding the nutritional properties, “Branca” meat revealed a good proportion of minerals and the female meat showed, in both pieces (p ≤ 0.05), significantly lower values for total saturated fatty acids (SFAs) and higher values for monounsaturated fatty acids (MUFAs). Breast meat was richer in n-3-PUFAs (C22:5n-3 and C22:6n-3) in both sexes (p ≤ 0.05). Considering the results obtained, it can be concluded that “Branca” breed meat is a healthy food characterized by a good general nutritional profile.

Carrageenophyte Kappaphycus malesianus Inhibits Microglia-Mediated Neuroinflammation via Suppression of AKT/NF-κB and ERK Signaling Pathways

Neuroinflammation is an inflammatory response in any part of the central nervous system triggered by the activation of microglia and astrocytes to produce proinflammatory cytokines in the brain. However, overproduction of proinflammatory cytokines further contributes to the development of neurodegenerative disorders. Red seaweed, Kappaphycus malesianus, is a predominant carrageenophyte commercially cultivated in Semporna, Sabah, Malaysia. It is an important source of raw material for kappa-carrageenan productions in the food, pharmaceutical and cosmetics industries. However, no studies have been conducted focusing on the antineuroinflammatory effects of K. malesianus. The aim of the present study was to investigate the effect of the antineuroinflammatory activity of K. malesianus extracts (ethyl acetate, ethanol and methanol) on lipopolysaccharide-stimulated BV2 microglia and the underlying mechanisms involved in the regulation of neuroinflammatory pathways. Extract with the most promising antineuroinflammatory activity was analyzed using liquid chromatography-mass spectrometry (LC-MS). Our results show that methanol extract has a convincing antineuroinflammatory effect by suppressing both AKT/NF-κB and ERK signaling pathways to inhibit the expression of all proinflammatory cytokines without causing a cytotoxicity effect. LC-MS analysis of methanol extract revealed two compounds: prosopinine and eplerenone. Our findings indicated that metabolites of K. malesianus are potent antineuroinflammatory agents with respect to prevention of neurological disorders.

Variability of Meat and Carcass Quality from Worldwide Native Chicken Breeds

The present research aimed to determine the differential clustering patterns of carcass and meat quality traits in local chicken breeds from around the world and to develop a method to productively characterize minority bird populations. For this, a comprehensive meta-analysis of 91 research documents that dealt with the study of chicken local breeds through the last 20 years was performed. Thirty-nine traits were sorted into the following clusters: weight-related traits, histological properties, pH, color traits, water-holding capacity, texture-related traits, flavor content-related nucleotides, and gross nutrients. Multicollinearity problems reported for pH 72 h post mortem, L* meat 72 h post mortem, a* meat 72 h post mortem, sex, firmness, and chewiness, were thus discarded from further analyses (VIF < 5). Data-mining cross-validation and chi-squared automatic interaction detection (CHAID) decision tree development allowed us to detect similarities across genotypes. Easily collectable trait, such as shear force, muscle fiber diameter, carcass/pieces weight, and pH, presented high explanatory potential of breed variability. Hence, the aforementioned variables must be considered in the experimental methodology of characterization of carcass and meat from native genotypes. This research enables the characterization of local chicken populations to satisfy the needs of specific commercial niches for poultry meat consumers.

Genomic Uniqueness of Local Sheep Breeds From Morocco

Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

The Meat Quality Characteristics of Holstein Calves: The Story of Israeli 'Dairy Beef'

Global animal production systems are often criticized for their lack of sustainability and insufficient resilience to ensure food security. The ‘farm-to-fork’ approach aims at orienting food systems towards the creation of a positive environmental impact, nutritious, healthy, safe and sufficient foods, and fairer economic returns for primary producers. Many countries rely on an imported supply of live animals to fulfill their needs for fresh meat. In Israel, ~60% of the sources of fresh beef come from the import of live animals. In order to encourage sustainable beef production in Israel, the proportion of local beef should be raised at the expense of imported animals. However, for this to be achieved, the superior performance of local beef should be justified. The current study was conducted to compare between the meat quality characteristics of local (Israeli Holstein; N = 205) vs. imported (Australian; N = 169) animals. Generally, while the imported calves presented a higher dressing percentage (p < 0.0001), the local animals were characterized by tenderer meat (p < 0.0001), longer sarcomeres (p < 0.0001), higher a* color attributes and pH (p < 0.001), superior cooking (p = 0.002) and thawing loss (p < 0.0001), higher intra-muscular fat (IMF) content, and a higher PUFA proportion (p < 0.01 and p < 0.0001, respectively) and PUFA:SFA ratio. The findings shown herein may provide sound arguments for stakeholders and policy makers to facilitate sustainable local beef production in Israel.

SNPs in Sheep: Characterization of Lithuanian Sheep Populations

In Lithuania, there are two recognised native sheep breeds: old native Lithuanian Coarsewooled and Lithuanian Blackface. In addition, in 2005, primitive Heidschnucke-type Skudde sheep were imported to Lithuania and were argued to possibly represent a lost Lithuanian sheep type. The aim of the study was to investigate the genetic variation in the two Lithuanian native sheep breeds, compare them with the imported Skudde sheep and establish the historical patterns of admixture and the genetic relatedness of Lithuanian sheep to British, Central European and Nordic sheep breeds included in the SheepHapMap study. In total, 72 individuals, representing two Lithuanian native and imported Skudde sheep breeds, were genotyped using a Neogen 12K Illumina Infinium chip. The population analysis was carried out by model-based clustering, principal component analysis and neighbour net analysis, and showed similar patterns for the Lithuanian sheep populations. Lithuanian Coarsewooled and Skudde in Lithuania have unique divergence and possibly some shared ancestry, while the Lithuanian Blackface conforms to a modern synthetic breed. The study clearly showed that the Coarsewooled and the Skudde breeds are distinct from each other. Historical data strongly suggest that the Coarsewooled breed represents a local breed, while the Skudde origin is less directly linked to the geographical area of modern-day Lithuania. Within the modern-day Lithuanian context, the Lithuanian Coarsewooled sheep is very important historical sheep type for conservation.

Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed-informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross-validation, 14 models had a global cross-validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares-discriminant analysis (PLS-DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS-DA method when selecting breed-informative SNPs.

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats

Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.

Discriminant Canonical Tool for Differential Biometric Characterization of Multivariety Endangered Hen Breeds

Simple Summary

Breed undefinition boosts the risk of irreversible breed loss due to its substitution by dominant breeds. Breed loss results detrimental for the fraction of the genetic pool which is linked to the value of livestock as perfectly adapted elements of domestic ecosystems among other desirable features. In turn, this ensures and maximizes population sustainability. The present study aimed to design a biometric characterization tool in autochthonous avian breeds and their varieties in Andalusia (south of Spain): Utrerana and Sureña breeds. For this, different quantitative and qualitative measurements were collected in 473 females and 135 roosters belonging to these breeds. Even though both genotypes belong to a common original trunk, discriminant canonical analysis (DCA) revealed clear differences between both breeds and within the varieties that they comprise. In particular, certain variables such as ocular ratio and phaneroptic characteristics, which may be intrinsically related to the capacity of the breeds to adapt to the environmental conditions in which they thrive, could allow breeders to develop breeding programs focused on the enhancement productive potential of individuals.

Abstract

This study aimed to develop a tool to perform the morphological characterization of Sureña and Utrerana breeds, two endangered autochthonous breeds ascribed to the Mediterranean trunk of Spanish autochthonous hens and their varieties (n = 608; 473 females and 135 males). Kruskal–Wallis H test reported sex dimorphism pieces of evidence (p < 0.05 at least). Multicollinearity analysis reported (variance inflation factor (VIF) >5 variables were discarded) white nails, ocular ratio, and back length (Wilks’ lambda values of 0.191, 0.357, and 0.429, respectively) to have the highest discriminant power in female morphological characterization. For males, ocular ratio and black/corneous and white beak colors (Wilks’ lambda values of 0.180, 0.210, and 0.349, respectively) displayed the greatest discriminant potential. The first two functions explained around 90% intergroup variability. A stepwise discriminant canonical analysis (DCA) was used to determine genotype clustering patterns. Interbreed and varieties proximity was evaluated through Mahalanobis distances. Despite the adaptability capacity to alternative production systems ascribed to both avian breeds, Sureña and Utrerana morphologically differ. Breed dimorphism may evidence differential adaptability mechanisms linked to their aptitude (dual purpose/egg production). The present tool may serve as a model for the first stages of breed protection to be applicable in other endangered avian breeds worldwide.

SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.

Genotypic and Dietary Effects on Egg Quality of Local Chicken Breeds and Their Crosses Fed with Faba Beans

The quality of chicken eggs is an important criterion for food safety and the consumers' choice at the point of sale. Several studies have shown that egg quality can be influenced by the chickens' genotype and by the composition of the diet. The present study aimed to evaluate the effect of faba beans as a substitute for soybeans in the diet of chickens originating from traditional low-performance breeds in comparison with high-performing laying type hens and their crosses on egg quality parameters. Chickens of six different genotypes were fed either with a feed mix containing 20% faba beans with high or low vicin contents or, as a control, a feed mix containing soybeans. The genotypes studied were the local breeds Vorwerkhuhn and Bresse Gauloise, as well as commercial White Rock parent hens and their crosses. Yolk weight, Haugh units, yolk and shell color, the frequency of blood and meat spots and the composition of the eggs were significantly influenced by the genotype. The feeding of faba beans had an effect on yolk and shell color, Haugh units and shell portion, while there was no significant influence on the frequency of blood and meat spots.

Selection Response Due to Different Combination of Antagonistic Milk, Beef, and Morphological Traits in the Alpine Grey Cattle Breed

Selection in local dual-purpose breeds requires great carefulness because of the need to preserve peculiar traits and also guarantee the positive genetic progress for milk and beef production to maintain economic competitiveness. A specific breeding plan accounting for milk, beef, and functional traits is required by breeders of the Alpine Grey cattle (AG), a local dual-purpose breed of the Italian Alps. Hereditability and genetic correlations among all traits have been analyzed for this purpose. After that, different selection indexes were proposed to identify the most suitable for this breed. Firstly, a genetic parameters analysis was carried out with different datasets. The milk dataset contained 406,918 test day records of milk, protein, and fat yields and somatic cells (expressed as SCS). The beef dataset included performance test data conducted on 749 young bulls. Average daily gain, in vivo estimated carcass yields, and carcass conformation (SEUROP) were the phenotypes obtained from the performance tests. The morphological dataset included 21 linear type evaluations of 11,320 first party cows. Linear type traits were aggregated through factor analysis and three factors were retained, while head typicality (HT) and rear muscularity (RM) were analyzed as single traits. Heritability estimates (h2) for milk traits ranged from 0.125 to 0.219. Analysis of beef traits showed h2 greater than milk traits, ranging from 0.282 to 0.501. Type traits showed a medium value of h2 ranging from 0.238 to 0.374. Regarding genetic correlation, SCS and milk traits were strongly positively correlated. Milk traits had a negative genetic correlation with the factor accounting for udder conformations (-0.40) and with all performance test traits and RM. These latter traits showed also a negative genetic correlation with udder volume (-0.28). The HT and the factor accounting for rear legs traits were not correlated with milk traits, but negatively correlated with beef traits (-0.32 with RM). We argue that the consequence of these results is that the use of the current selection index, which is mainly focused on milk attitude, will lead to a deterioration of all other traits. In this study, we propose more appropriate selection indexes that account for genetic relationships among traits, including functional traits.

Payments for Conservation of Animal Genetic Resources in Agriculture: One Size Fits All?

Simple Summary

Maintaining minimum population sizes for local livestock breeds is a key goal in the conservation of animal genetic resources. As markets and livestock production systems have tended to favour a narrow base of high-output improved breeds, countries have had to use financial and other incentives to motivate breeders to keep local breeds. This paper explores the potential for more cost-effective alternatives to the most commonly used financial incentive, a fixed payment per animal or livestock unit. We compare the current fixed payment incentives for local breeds under the Slovenian Rural Development Programmme with those instead determined through a competitive tender approach. A stated preference survey was realised to determine the conditions under which breeders would be willing to participate in such an incentive system based on differentiated payments. Willingness to accept (WTA) payment for conservation was found to differ significantly from actual payment levels, being lower for the local sheep and goat breeds, and higher for the local pig breed. This suggests that implementation of differentiated payments would be more cost-effective; particularly when accompanied by measures to streamline administrative requirements, improve access to breeding stock and target support for local breed market valorisation (e.g., promotion of value chains based on designated quality schemes).

Abstract

Local livestock breeds in Slovenia have been eligible for financial incentives in the form of a fixed payment per livestock unit (LU) since 2002. The scheme has however not been successful in reversing the erosion of animal genetic resources (AnGR). This paper investigates an alternative, whereby incentive payments would better reflect breeders’ actual opportunity costs. The paper contributes to the limited existing body of knowledge related to the use of tender mechanisms in the design of the payments for agrobiodiversity conservation schemes (PACS), particularly for AnGR. Empirical findings draw on the results of a stated preference survey involving 301 farmers in Slovenia, engaging, or being potentially able to engage, in the rearing of local pig, sheep and goat breeds. Interval and logistic regression model results suggest that willingness to accept (WTA) conservation support significantly differs from actual payment levels. The estimated WTA was found to be 27% lower for the local sheep and goat breeds and 5% higher for the local pig breed, suggesting that differentiated incentive payments would provide a more cost-effective alternative. Additional analysis of breeders’ preferences and motives for engaging in local livestock breed production further informs understanding regarding AnGR conservation policy and the importance of accompanying actions to reverse negative population trends. These include reducing administrative barriers and enhancing the market valorisation of local breeds.

Welfare-Related Behaviors in Chickens: Characterization of Fear and Exploration in Local and Commercial Chicken Strains

Fear and exploration are crucial traits determining how animals behave in novel situations, and thus, they influence animal welfare. The aim of this study was the characterization of these behavioral traits among different strains to identify interesting alternatives for future poultry production. Whereas the Novel Object Test (NOT) focuses on fear and exploration of novel objects, the Avoidance Distance Test (ADT) addresses this in the context of humans. Here, a commercial hybrid line, a dual-purpose hybrid and a local adapted strain were tested. For the differences between strains and development of fear, Lohmann Brown (n = 714), Lohmann Dual (n = 844) and Rhinelander (n = 458) were observed weekly until maturity. Results show that fear and exploration towards unknown objects and humans are breed-specific (all p < 0.01). Additionally, development of fear in NOT and ADT differed between all three strains (both p < 0.01). The expressions of fear of humans or objects should be regarded as characteristics adapted for different husbandry systems and breeding goals, e.g., high exploratory behavior in aviary or high avoidance of predators in free-ranging husbandry or at least a balanced ratio between fear and exploration. Characterization of behavioral traits among different strains, understanding diversity and integrating these behaviors into future breeding and husbandry systems might reflect the need to preserve local strains and the potential to improve animal welfare.

Genetic basis of thermotolerance in 2 local dairy sheep populations in the Iberian Peninsula

Sheep milk production in the Northern Mediterranean countries heavily relies on local breeds subject to selection schemes to improve milk production. Climate change may shift the range of thermal loads on the animals and challenge their adaptation to the new thermal gradient. The objective of this study was to characterize the genetic component of thermal tolerance of 2 local breeds from the Iberian Peninsula, Latxa and Manchega, belonging to different genetic types that have evolved under different climatic environments (Oceanic for Latxa and Continentalized Mediterranean for Manchega). A total of 79,243 and 2,388,853 test day monthly records of milk, fat and protein yields from 12,882 and 277,904 ewes of Latxa and Manchega breeds, respectively, along a 12-yr period, were matched with the value of the average temperature-humidity index (THI) on the day of milk recording of the closest weather station to the flocks. These data were used to fit individual reaction norms (Legendre polynomials) describing changes in yields along the THI gradient. Genetic values for thermal tolerance were obtained from the slopes of those reaction norms under cold or heat stress and variances and covariances between yield and thermal tolerance were derived from the (co)variance matrices of the polynomial random regression coefficients. Results showed differing patterns in the 2 breeds. The Latxa breed showed clearer signs of genotype by environment interaction than did Manchega. Estimated correlations between yields under extremes of cold and heat were always above 0.8 for Manchega and around 0.4 for Latxa for all traits. Estimates of correlations between comfort and thermal stress were again over 0.8 for Manchega and lower for the higher (hot end) values (down to 0.6) than for the lower (cold end) values (down to 0.84) of the THI gradient for Latxa, indicating greater thermal stress expected from high than from low temperatures in this breed. Substantial variability in thermal tolerance under the more extreme THI values was found in both breeds. Estimated genetic correlations between yield and thermal tolerance were close to 0 and 0.2 for Latxa and Manchega in the cold and down to -0.6 and -0.3 in the heat end, although small variation was observed for fat in Latxa. Estimated realized trends from the average estimated breeding value, by year of birth, showed a positive response for yields in both breeds [around 0.1 standard deviation (SD) unit], but a detrimental correlation for thermal tolerance (down to -0.03 SD units for heat tolerance in Latxa). These results can be used to design optimal selection strategies for sustainable improvement of productivity under a rising-temperature scenario associated with climate change.

Evaluation of Greek Cattle Carcass Characteristics (Carcass Weight and Age of Slaughter) Based on SEUROP Classification System

In Greece, all cattle carcasses produced from a variety of breed types are classified according to the SEUROP system. The objective of this study was to evaluate Greek carcass characteristics such as carcass weight and age of slaughter based on SEUROP classification system (muscle conformation and fat deposit classes) and to describe the effect of main factors such as breed, gender, year of slaughter, farm's geographical region and month of slaughter on these carcass parameters. It is the first study that evaluates local breeds, revealing the wide diversity of the Greek cattle breeding conditions. The analyzed records consisted of 323,046 carcasses from 2011 to 2017. All the examined factors significantly affected the mean carcass weight (298.9 ± 0.2 kg) and the mean slaughter age (559.1 ± 0.3 days). Carcasses from beef meat breeds had on average higher mean carcass weight while the local breeds had lower. The mean slaughter age and carcass weight were higher in winter than in summer. The local and the dairy breeds were classified in similar muscle conformation classes. Finally, Greek cattle carcasses from almost all regions were satisfactory for their quality carcass traits with good muscle conformation (R, O and U class) and low-fat deposit (class 1 to 3).

Resequencing and signatures of selection scan in two Siberian native sheep breeds point to candidate genetic variants for adaptation and economically important traits

Russian sheep breeds represent an important economic asset by providing meat and wool, whilst being adapted to extreme climates. By resequencing two Russian breeds from Siberia: Tuva (n = 20) and Baikal (n = 20); and comparing them with a European (UK) sheep outgroup (n = 14), 41 million variants were called, and signatures of selection were identified. High-frequency missense mutations on top of selection peaks were found in genes related to immunity (LOC101109746) in the Baikal breed and wool traits (IDUA), cell differentiation (GLIS1) and fat deposition (AADACL3) in the Tuva breed. In addition, genes found under selection owing to haplotype frequency changes were related to wool traits (DSC2), parasite resistance (CLCA1), insulin receptor pathway (SOCS6) and DNA repair (DDB2) in the Baikal breed, and vision (GPR179) in the Tuva breed. Our results present candidate genes and SNPs for future selection programmes, which are necessary to maintain and increase socioeconomic gain from Siberian breeds.

Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability

Simple Summary

Russia has diverse specifically selected and multipurpose goat resources. However, the origin of the local goats is still enigmatic. In this study, we sequenced and analyzed mitochondrial DNA (mtDNA) fragments of seven Russian local goat populations to provide the first insight into their maternal lineage.

Abstract

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.

Egg Production and Bone Stability of Local Chicken Breeds and Their Crosses Fed with Faba Beans

Poultry production is raising concerns within the public regarding the practice of culling day-old chicks and the importation of soy from overseas for feedstuff. Therefore, an alternative approach to poultry production was tested. In two consecutive experiments, two traditional chicken breeds, Vorwerkhuhn and Bresse Gauloise, and White Rock as a commercial layer genotype as well as crossbreds thereof were fed diets containing either 20% vicin-rich or vicin-poor faba beans, though addressing both subjects of debate. Hen performance traits and bone stability were recorded. All parameters were considerably influenced by the genotype with White Rock showing the significantly highest (p < 0.05) laying performance (99.4% peak production) and mean egg weights (56.6 g) of the purebreds, but the lowest bone breaking strength (tibiotarsus 197.2 N, humerus 230.2 N). Regarding crossbreds, the Bresse Gauloise × White Rock cross performed best (peak production 98.1%, mean egg weight 58.0 g). However, only limited dietary effects were found as only the feeding of 20% vicin-rich faba beans led to a significant reduction of egg weights of at most 1.1 g (p < 0.05) and to a significant reduction of the shell stability in the crossbred genotypes. In terms of dual-purpose usage, crossing of Bresse Gauloise with White Rock seems to be the most promising variant studied here.

Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed-The Ramo Grande Cattle from the Azores

Simple Summary

Inbreeding control is a key concern in managing local endangered breeds, which often have developed unique adaptation features. Ramo Grande is a local cattle breed raised in the Azores archipelago under very harsh conditions, with a census of about 1300 cows dispersed by various islands. This fragmentation is a challenge when the goal is to keep inbreeding under control. Currently, panels of genetic markers are available which enable the assessment of inbreeding and the occurrence of previous bottlenecks in a population. These panels also allow the identification of genes associated with specific production traits, if reliable phenotypic information is available. We used a panel of genetic markers and estimated that the degree of inbreeding was approaching a level of concern, while some exotic gene inflow may have occurred in the past. We were able to identify genetic markers significantly associated with longevity, which reflects the ability of these cattle to remain productive under severe environmental conditions. Genetic markers were also identified as significantly associated with age at first calving and calf growth rate. The results indicate that genomic information can be used to control inbreeding and to implement genomic selection in Ramo Grande cattle to enhance adaptation and production traits.

Abstract

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds

The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r²) across autosomes. Moreover, r² values were used to calculate historical and contemporary effective population size (N_e) in each breed. Average r² was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11-0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in N_e across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation.

Growth Performance Analysis of Two Italian Slow-Growing Chicken Breeds: Bianca di Saluzzo and Bionda Piemontese

Simple Summary

Bianca di Saluzzo and Bionda Piemontese are two Italian slow-growing chicken breeds of the Piemonte region (Northwest Italy) and are reared mainly for meat. They conserve adaptation to free ranging low input rearing systems and are promising for antibiotic-free farming. We aimed to analyze their growth using a mathematical model and to obtain some advice for improving performance. Polymorphism of the PAX7 gene was also studied to increase conservation value. The results confirmed that these breeds are late-maturing. Whereas selection would increase inbreeding, a mating scheme to bring inbreeding under control could be the most proper way to increase growth rate and reach commercial maturity earlier.

Abstract

Bianca di Saluzzo (BS) and Bionda Piemontese (BP) are two Italian chicken breeds, mainly reared for meat production, primarily in antibiotic-free farming. However, technical information on their growth pattern is still missing. At hatching, 150 unsexed chicks of each breed were weighed, labeled, and reared in indoor pens up to 8 w of age. At 8 w of age, the chicks were separated by sex and randomly transferred to growing pens with access to an external paddock (15 birds/pen; 4 pens/sex for each breed). The body weight (BW) was recorded biweekly for each bird, from hatching to 32 w of age. In order to identify an improvement strategy, the objectives of our study were to analyze the growth pattern of these birds using the Gompertz mathematical model and compare results with other chicken breeds. Polymorphism of the PAX7 gene was also analyzed to test its association with growth traits. Both BS and BP are close to unselected native breeds and, among the Italian local poultry, they are confirmed to be slow-growing birds with an intermediate size between heavy and light chicken breeds. Regarding the PAX7 gene, two alleles were found, F and G, and showed an association with the actual BW in the BP females from 14 w of age onwards. The G allele always exhibited a more favorable effect than the F allele. In small size poultry population, a delicate balance between preservation of biodiversity and performance improvement should be considered. Consequently, the most proper way could be an approach based on a mating scheme to keep inbreeding under control, increase growth rate, and improve commercial maturity.

Growth Performance of Local Chicken Breeds, a High-Performance Genotype and Their Crosses Fed with Regional Faba Beans to Replace Soy

Simple Summary

The culling of day-old male chicks and the ecological impact of high soy imports from overseas as animal feed are intensively discussed by the Western European agricultural sector and society. One possible approach to mitigate these problems could be the use of dual-purpose chickens for meat and egg production in combination with a predominant use of regionally grown protein plants. In the present study the suitability of six different chicken genotypes for fattening was evaluated while feeding them two different faba bean varieties. No adverse effects of the faba bean feeding on the performance and the health of the birds could be detected.

Abstract

The faba bean (Vicia faba L.) is a native protein crop and considered a promising alternative to soybeans. Due to its anti-nutritive substances such as vicin and convicin (VC) its use in animal nutrition has been restricted. In the present study, two consecutive experiments were conducted to analyse the effects of feeding 20% faba beans, which differ in their VC content on fattening performance and slaughter traits of different chicken genotypes. In a first trial, purebred male chickens of the local breeds Bresse Gauloise and Vorwerkhuhn as well as of a high-performance White Rock line were tested. In a second trial, crossbreds of them were evaluated: Vorwerkhuhn × Bresse Gauloise, Vorwerkhuhn × White Rock, Bresse Gauloise × White Rock. Daily weight gain and feed intake were recorded until slaughter at approximately 2100 g. At slaughter the final live weight, carcass yield and the weights of the valuable parts (breasts and legs) were measured. For the genotypes studied, no adverse or undesirable effects of both VC−rich and VC−poor faba beans in the feedstuff were detected regarding body weight development, carcass quality, and fattening parameters. Furthermore, there was no indication that the birds’ health was impaired.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (F_ROH>4Mb = 0.400 and F_ROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (F_ROH>4Mb = 0.098 and F_ROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.

Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review

Modern pig breeds, which have been genetically improved to achieve fast growth and a lean meat deposition, differ from local pig breeds with respect to fat deposition, fat specific metabolic characteristics and various other properties. The present review aimed to elucidate the mechanisms underlying the differences between fatty local and modern lean pig breeds in adipose tissue deposition and lipid metabolism, taking into consideration morphological, cellular, biochemical, transcriptomic and proteomic perspectives. Compared to modern breeds, local pig breeds accumulate larger amounts of fat, which generally contains more monounsaturated and saturated fatty acids; they exhibit a higher adipocyte size and higher activity of lipogenic enzymes. Studies using transcriptomic and proteomic approaches highlighted several processes like immune response, fatty-acid turn-over, oxidoreductase activity, mitochondrial function, etc. which differ between local and modern pig breeds.

Community-based sheep breeding programs generated substantial genetic gains and socioeconomic benefits

Community-based breeding programs (CBBPs) for small ruminants have been suggested as alternatives to centralised, government-controlled breeding schemes which have been implemented in many developing countries. An innovative methodological framework on how to design, implement and sustain CBBPs was tested in three sites in Ethiopia: Bonga, Horro and Menz. In these CBBPs, the main selection trait identified through participatory approaches was 6-month weight in all three sites. In Horro and Bonga, where resources such as feed and water permitted larger litter sizes, twinning rate was included. Ten-year (2009 to 2018) performance data from the breeding programs were analysed using Average Information Restricted Maximum Likelihood method (AI-REML). Additionally, the socioeconomic impact of CBBPs was assessed. Results indicated that 6-month weight increased over the years in all breeds. In Bonga, the average increase was 0.21 ± 0.018 kg/year, followed by 0.18 ± 0.007 and 0.11 ± 0.003 kg/year in Horro and Menz, respectively. This was quite substantial in an on-farm situation. The birth weight of lambs did not improve over the years in Bonga and Horro sheep but significant increases occurred in Menz. Considering that there was no direct selection on birth weight in the community flock, the increased weights observed in Menz could be due to correlated responses, but this was not the case in Bonga and Horro. The genetic trend for prolificacy over the years in both Bonga and Horro flocks was positive and significant (P < 0.01). This increase in litter size, combined with the increased 6-month body weight, increased income by 20% and farm-level meat consumption from slaughter of one sheep per year to three. The results show that CBBPs are technically feasible, result in measurable genetic gains in performance traits and impact the livelihoods of farmers.

Detailed macro- and micromineral profile of milk: Effects of herd productivity, parity, and stage of lactation of cows of 6 dairy and dual-purpose breeds

The aim of this study was to quantify the major sources of variation in the levels of 15 minerals in individual milk samples collected from cows raised in multibreed dairy herds. The herds (n = 27) were classified into 2 categories, according to milk productivity. Milk productivity was based on the net energy of lactating cows' average daily milk yield. Milk samples were collected from 240 cows of 6 different breeds: 3 specialized dairy (Holstein-Friesian, Brown Swiss, and Jersey) and 3 dual-purpose (Simmental, Rendena, and Alpine Grey). The samples were analyzed for macro-elements (Na, Mg, P, S, K, and Ca), essential micro-elements (Mn, Fe, Cu, Zn, and Se), and environmental micro-elements (B, Si, Sr, and Sn), using inductively coupled plasma-optical emission spectrometry. Data were analyzed using a linear mixed model that included fixed effects of days in milk (DIM), parity, breed, and herd productivity, and a random effect of herd-date within productivity level. Results showed that the effect of herd-date varied across minerals. It was especially large for environmental minerals (ranging from 47 to 91% of total variance) and ranged from 11 to 61% for macrominerals and essential microminerals. Milk samples collected from farms with a high level of herd productivity had a richer mineral profile than samples from low-productivity herds. Parity only influenced macrominerals, with the exception of S and Ca, while DIM influenced almost all minerals, with a few exceptions among the environmental elements. Differences in mineral profile were small between specialized and dual-purpose breeds, but they were large within the group of the specialized cows. These breed differences were reduced after adjusting for milk quality and yield, particularly in the case of milk Mg, S, Ca, Mn, and Zn levels. Milk samples from the Jersey and Brown Swiss cows had higher mineral levels (Sn excluded) than milk from the Holstein-Friesian cows; the other breeds of Alpine origin produced milk of intermediate quality. Our findings suggest that breed has a stronger effect on macrominerals and some of the essential microminerals than herd productivity, parity, and DIM. The modification of the mineral profile in milk seems possible for many minerals, but it likely depends on genetics (e.g., breed, selection) and on environmental and management factors in variable proportions according to the mineral considered.

Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between F_PED and F_ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F_ROH estimates from medium-density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep, the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion, we identified differences in the genetic make-up of Swiss sheep breeds, and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.

Modelling Nutritional Requirements of Growing Pigs from Local Breeds Using InraPorc

Models such as InraPorc enable the growth of pigs to be simulated and their nutrient requirements to be determined. However, so far, these models have not been applied to local breeds. We used InraPorc to determine the nutrient requirements of growing pigs from local breeds (H2020 European Union project TREASURE). Data on feed composition, allowance and intake, and body weight (BW) were obtained from literature reports or experiments conducted within the project. Data were used in InraPorc to calibrate 16 growth and intake profiles from nine breeds (Alentejana, Basque, Bísara, Apulo Calabrese, Cinta Senese, Iberian, Krškopolje pig, Mangalitsa, and Moravka), with one to three profiles per breed depending on the experimental conditions or data source. On the 40-100 kg BW range, mean protein deposition (PDm) was low for all breeds (below 116 g/d vs. over 130 g/d in conventional breeds). The age of pigs at 40 kg BW (110 to 206 days) denoted different types of feeding management in addition to genetic differences. The PDm and the lysine requirements were the highest in breeds with the highest average daily gain. In all breeds, a small proportion of total body energy retention was dedicated to protein, with the greatest proportion of energy retention in the form of lipids. Despite some methodological limitations, this study provides initial insights into the nutrient requirements of some local breeds.

Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap

Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.

Assessing patterns of genetic admixture between sheep breeds: Case study in Algeria

In developing countries, cross-breeding between local breeds and indigene or exotic breeds represents one of the main threats to the livestock diversity, leading to genetic dilution and loss of unique allelic combination underlying essential local adaptive traits. In this study, two Algerian sheep breeds, known to be highly admixed, were considered as a case study, to demonstrate how combination of different methodologies coupled with the use of specific softwares can be efficient to assess the spatial structuration of a hybrid zone, even in a case of extreme admixture. A fine sampling covering distribution areas of both breeds was implemented in order to study the admixture area and adjacent zones from a phenotypic (i.e., 19 quantitative traits were considered) and a genetic point of view (i.e., 21 microsatellites markers were used). Both approaches gave concordant patterns, highlighting areas with sheep most differentiated (or less admixed) for each breed. In detail, the region of Biskra appeared as the most preserved for the Ouled-Djellal breed and the northwest of Laghouat was identified as the most preserved area for the Rembi breed. The approach proposed in the study offers a low-cost solution to identify the most representative flocks of a breed, allowing the implementation of efficient conservation plans.

On the origins and genetic diversity of South American chickens: one step closer

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.