Genomic adaptation of Mediterranean and Alpine local cattle breeds to the climate variables

Abstract. – Adaptive ability of livestock to climate variations is a factor of first importance in the context of global climate change. Domestic species such as cattle represent attractive biological models to characterize the genetic basis of short domestication history. Local cattle breeds are valuable genetic resources to decipher the molecular mechanisms of cattle adaptation to their specific environments. Using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 Mediterranean and 24 Alpine cattle breeds and performed genome‐wide association analyses with covariables discriminating the different Mediterranean and Alpine climate subtypes. This provided insights into both the demographic and adaptive histories. A detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean and Alpine climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified. Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean and Alpine area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens. Taken together, our results highlight the genetic uniqueness of local Mediterranean and Alpine cattle breeds and strongly support conservation of these populations

Evaluation of the trend of the inbreeding from 1970 to 2011 in the Bracco Italiano dog breed

The Bracco Italiano is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time. In this study we analysed the pedigree information to evaluate the trend of the inbreeding of the breed in the course of time since 1970 to 2011. Pedigree records of 24,613 animals were considered. 16,832 dogs were inbreds. The average inbreeding coefficient in the reference population (23,997 animals) resulted 4.1%, while the average inbreeding of the inbreds was 6%. The inbreeding coefficient was <0.05 in 9849 dogs (58.51%) whereas it was >0.20 in 623 dogs (2.53%). The percentage of inbreds per year increased from 2.44% in 1976-1980 to 100% in 2003. 16 traced generations were highlighted. The evolution of inbreeding indicates a steady increase over time, from a mean value of 0.5% for dogs born in 1979, to an average value of 7.6% in dogs born in 2011. Nevertheless a regular monitoring of genetic variability of the population is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variation

Genetic variability in Bracco Italiano dog breed assessed by pedigree data

The Bracco Italiano is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time. The complete electronic record of the breed was downloaded from the ENCI database [whole population (WP) = 24,613 animals registered since 1970 to 2011] with the aim to estimate genetic variability in Bracco Italiano dog breed using pedigree records. Up to 97% of the individuals had registered parents and 86% registered grand-fathers. Average generation interval was 4.68±0.545 for stallions and 4.08±0.321 year for dams. Reference population (RP) was defined as the population of interest that include living reproductive animals approaching the last three generations and include 9006 dogs of which 34% were inbreds. The number of ancestors was 564 in WP and 188 in RP, while the effective number of ancestors was 46 and 34 respectively. To explain 50% of the genetic variability, a total of 18 and 9 ancestors enough, respectively in the WP and RP. The average inbreeding coefficient in the RP resulted 6.7% while the average increase in inbreeding was estimated to be 1.29% (Ne=38.86). Nevertheless a regular monitoring of genetic variability of the population is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variatio

Genetic variability of the Braque Français Type Pyrénées dog breed assessed by pedigree data

The Braques français are hunting dogs, from a very old type of gun dog used for pointing the location of game birds for a hunter. There are two breeds of Braque français, both from the South of France, the Braque français type Gascogne (larger size) and the Braque français type Pyrénées (smaller size). The original Braque français type of pointing dog has existed since the fifteenth century. The first breed club was formed in 1850, and the standards for both breeds were written in 1880. Both types belong to group 7 of ENCI classification. The complete electronic record of the Braque français type Pyrénées was downloaded from the ENCI database with the aim to estimate the genetic variability of the breed. In Italy 921 puppies (479 males and 442 females) were registered from 2003 to 2014 (average value: 76.6±40.24 dogs per year). Pedigree records of all registered animals (Reference Population=RP) were considered. The whole population (WP =RP and its genealogy) included 1,250 dogs (826 males and 622 females). 783 dogs were inbred. Up to 89% of the individuals had registered parents and 83% registered grand-parents. To explain 50% of the genetic variability, a total of 9 and 7 ancestors were enough, respectively in the WP and RP. The average inbreeding coefficient in the RP resulted 4.3%, while the average inbreeding of the inbred was 5.19%. The inbreeding coefficient was 0.20 in only 13 dogs (1.66% of inbred). Inbreeding coefficient per year ranged from 0.98% for dogs born in 2003 (27 dogs) to 7.05% in 204 dogs born in 2009. Puppies born in 2014 had an average inbreeding coefficient of 1.78%. Ten traced generations were highlighted; the maximum average inbreeding value (6.62%) was observed in the dogs with 10 traced generations (inbred: 93.15% with an inbreeding average value of 7.11%) while Ne for RP computed via individual increase in inbreeding was 42.42. A regular monitoring of genetic variability of the breed is important and must be adopted, in order to avoid the danger of an excessive increase of inbreeding in the future, which would result in significant inbreeding depression and in significant loss of genetic variation

Leccese sheep breed from Apulia: evidence of genetic substructuring from STR loci

Leccese is an originally triple-purpose sheep breed from Southern Italy. Due to major changes in rural society and livestock production, the breed has experienced in the last decades a drastic population size reduction. Nowadays roughly one thousand animals are reared in about ten farms located in Apulia. In order to evaluate the genetic variability within the Leccese breed, a total of 97 animals, sampled from five different farms in the provinces of Bari, Taranto, Brindisi, and Lecce were genotyped at 19 microsatellite loci belonging to the ISAG-FAO panel for Domestic Animal Diversity. Samples were chosen according to genealogical records in order to minimize relatedness among animals. Although being a local bottlenecked breed, the Leccese sample displayed a valuable number of alleles (187 over 19 loci, with a minimum of 4 in BM1824 and OarFCB193 and a maximum of 16 in MAF70 and MCM140). A high proportion of private alleles was observed for each farm (7.7 alleles on average). In addition, a high level of linkage disequilibrium was observed in the total sample, also among non syntenic locus pairs, suggesting the presence of population sub-structuring. To test the hypothesis of a genetic partitioning at the farm hierarchical level we first calculated the pair-wise FST between the different farms, which highlighted significant (P<0.001) though moderate values (0.055 to 0.065). Then, we performed both a likelihood-based and a Bayesian population assignment test, respectively implemented in the Arlequin and Structure software packages, in order to verify the degree of differentiation between the five farms. A correct allocation was obtained for 96.9% of animals by using the Arlequin software and 92.8% when using Structure, thus highlighting a clear genetic differentiation at the farm level, counterbalanced by a marked within-herd genetic similarity. These results suggest that reproductive isolation and/or different selection strategies across farms contributed to the observed pattern of genetic sub-structuring; this should be seriously taken into consideration, due to the critical implications for the breed conservation

Demographic approach on the study of genetic parameters in the dog Braque Français type Pyrénées Italian population

The complete electronic record of the Braque Franc¸ais type Pyrénées reared in Italy was downloaded from the ENCI database in order to estimate the genetic variability of the breed. Pedigree records of all active registered animals (reference population¼RP) were considered. The whole population (WP¼RP and its genealogy) included 1250 dogs (628 males and 622 females). Seven hundred eighty-three dogs were inbred. To explain 50% of the genetic variability, a total of seven ancestors were sufficient in the RP. The average inbreeding coefficient (F) in the RP was 4.3%, while the average inbreeding of the inbred was 5.19%. F was&lt;0.05 in 511 dogs (65.3% of inbred), whereas it was&gt;0.20 in only 13 dogs (1.66% of inbred). F per year ranged from 0.98% for dogs born in 2003 (27 dogs) to 7.05% in 204 dogs born in 2009. Ten traced generations were highlighted. A maximum average inbreeding value (6.62%) was observed in the dogs with 10 traced generations. This research highlighted the good genetic variability of the breed obtained through the efficient management by the Italian Club of Braque Franc¸ais Type Pyrenees (CIBF), in collaboration with the member breeders and the active cooperation of the French Club. The CIBF has made arrangements with our genetic centre to constantly monitor the genetic variability of the breed in order to prevent excessive increases in inbreeding in the future. © 2016 The Author(s)

Morphological characteristics of “Bracco Italiano” dog

The Italian Bracco is one of the oldest pointing dog breed, used for hunting ever since the Renaissance time; paintings of the 14th century show hunting sceneries with dogs similar to the present day Bracco. The breed has been officially registered by ENCI (the Italian cynological club) in 1949, when the definitive standard was established. In this work, we report the first results of a study aimed at measuring morphological traits in this breed, as a part of a more comprehensive study whose objective is to identify the characters that have the potential of being genetically improved. Body measures were taken from 121 adult (mean age 4.09±2.64 years) Bracco Italiano dogs (65 males and 56 females). For each animal the following biometrical measurements were considered: withers height, chest height, length of the rump (RL), iliac width of rump, chest and cannon circumference. The ratio chest/cannon circumference was calculated, as index of body compactness. The proportion rump length-withers height (RLWH) was also calculated. ANOVA was used to test the differences between males and females for morphological measurements (sex as fixed factor and age at measurement as covariate). Data were analysed by JMP software version 5.0 of SAS Inst. Significant differences were observed between the means of females and males for withers height (59.0±2.95 cm in females and 62.1±2.73 cm in males; P<0.01), chest circumference (71.3±5.46 cm and 73.9±3.97 cm, in females and males respectively; P<0.01) and cannon circumference (12.6±0.98 cm and 13.6±0.90 cm in females and males respectively; P<0.05). The other measurements were not different between sexes. Sexual dimorphism was evident and generally the measures coincided with what reported in the standard, except for the length of the rump, which was around ¼ of the withers height instead of the value of 1/3 required in the standard

Genome-wide homozygosity in Maremmana Cattle

The current availability of large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of patterns of genetic diversity and of genome-wide homozygosity in animal populations. The aim of this work was to estimate genetic diversity and homozygosity in the Maremmana cattle breed. We used a sample of 149 animals (males and females) genotyped with the BovineSNP50 v2 (54K) Illumina BeadChip. After editing for call-rate >0.9 and removing SNP unassigned or on the sex chromosomes, 128 animals and 50,814 SNPs were left. We estimated the following genetic parameters: observed and expected heterozygosity (Ho and He), minor allele frequency (MAF), and the FIS statistic. We also scanned the genome for runs of homozygosity (ROH). In the present study, ROH were detected based on 20-SNP-long sliding-windows, and allowing for a maximum of 1 missing and 1 heterozygote genotype, and a maximum gap between consecutive SNP of 105 bp. ROH contained minimum 10 SNPs, and had a minimum length of 1 Mb and a minimum density of 1 SNP every 50 kbps. The average Ho and He were 0.374 ± 0.132 and 0.365 ± 0.120, respectively, and the average MAF was 0.274 ± 0.130. These values are consistent with the range observed in other cattle breeds. We obtained some negative values for FIS (-0.162 to 0.180) which corresponded to animals with lower than average homozygosity. In total, 10,465 ROH were detected (81.75 per animal), with an average length of 2.69 Mb. Most ROH (74%) had length 2 Mb. ROH are contiguous lengths of homozygous genomic segments where the two inherited haplotypes are identical. ROH indicate genomic regions where a reduction in heterozygosity occurred, and offer new opportunities to estimate inbreeding (F). The inbreeding coefficient based on ROH (FROH) was estimated by the ratio between the total ROH length and the size of the genome in each animal. Average FROH was 0.0869 ± 0.032. Unlike inbreeding estimated based on Ho, FROH is not influenced by allele frequencies (sampling) and can distinguish recent from ancient inbreeding. However, FROH requires SNP positions to be known (unlike Ho). Two genomic regions with ROH in over 60% of the animals were found: one on BTA6 (38.6-39.7 Mbps), one on BTA13 (54.3-54.8 Mbps). These may highlight regions where selective pressures have shaped the genome of the Maremmana breed

Carcass traits and meat quality of two different rabbit genotypes

To evaluate the effect of genotype on carcass traits and meat quality, thirty-two rabbits for two genotypes (local population – LP; commercial hybrids – HY) were used. Rabbits were weaned at 35 days old and slaughtered at 103 days of age for LP and 87 days of age for HY. Comparing the slaughtering traits of two genotypes, LP provided higher dressing out (59.4% vs 56.2%, P<0.01) and skin percentage (16.0% vs 14.2%, P<0.05), lower incidence of full gastrointestinal tract (18.5% vs 22.3, P<0.01) and higher incidence of head (9.5% vs 8,9%, P<0.05) and kidneys (0.99 vs 0.86%, P<0.05) than HY. Reference carcasses from LP had greater incidence of perirenal fat (2.04% vs 1.12%; P<0.01), loin (21.5% vs 19.2%; P<0.01) and hind leg (34.4% vs 31.6%; P<0.01) than HY. Hind leg meat-to-bone ratio was significantly higher in HY than LP (4.7% vs 3.8%; P<0.01). The comparison between the variances of slaughter weight, chilled carcass weight, kidneys percentage, reference carcass weight, perirenal fat and hind leg percentage showed the great variability in the local population. Meat derived from LP showed lower lightness (L*), higher redness (a*), yellowness (b*) and C* value than HY (P<0.01). In conclusion, LP showed good slaughter traits and favourable meat quality and the great variability observed in the local population could allow to improve the productive performances without loss the rusticity and the capacity to fit to different local environmental conditions

Genetic variability of the Bracco Italiano dog breed based on microsatellite polimorphism

The Bracco Italiano is one of the oldest breeds of Italian pointing dogs, used for hunting ever since Renaissance times. After the Second World War it was included among the breeds officially recorded by the ENCI (the Italian Cynological Club), and since 1970 more than 23,000 animals have been registered; there are currently approximately 750 births per year. In this paper, we present the breed characterization of the population at the molecular level using 21 STR markers from the panels recommended for the 2006, 2008 and 2010 ISAG canine comparison test. Number of alleles, allele frequencies, deviations from Hardy-Weinberg proportions, linkage disequilibrium among loci, genetic similarity, genetic distances and molecular co-ancestry-based parameters were calculated. The number of alleles ranged from 3 to 9 (mean 6.43) whereas the expected heterozygosity ranged from 0.44 to 0.81 (mean 0.64). There was a high genetic similarity within the whole population (0.455) showing the great homogeneity of the sampled animals, as confirmed also by the small kinship distance (0.336), by the high values of the self molecular coancestry (0.703) and of the inbreeding coefficient (0.406). These results suggest the need for a careful genetic management of the population in order to avoid the risk of an excessive increase in the inbreeding level which would result in significant inbreeding depression and in significant loss of genetic variation