Biobanking animal genetic resources: critical infrastructure and growth opportunities

National animal gene banks have acquired substantial quantities of germplasm that protect and preserve a wide range of livestock breeds. New challenges and growth opportunities are emerging. A key challenge will be increased gene bank use, but this requires increased characterization of phenotypes and genotypes for populations and collections.

Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study

Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbreeding is implemented when leveraging autochthonous and cosmopolitan breeds to obtain most of the hybrid vigor.

Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity

In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.

Analysis of milk leukocyte differential measures for use in management practices for decreased mastitis incidence

The aim of this study was to assess the usefulness of measures derived from milk leukocyte differential (MLD) in practices that improve fresh cow mastitis monitoring and decrease mastitis incidence. Quarter milk samples were collected from Holstein and Jersey cows on d 4 and 11 postcalving. Samples were analyzed using MLD, whereby cell counts and quarter infection diagnosis were obtained. Measures derived from MLD included cell scores (total leukocyte, neutrophil, macrophage, and lymphocyte scores), cell proportions (neutrophil, macrophage, and lymphocyte percentages), cell thresholds (total leukocyte, neutrophil, macrophage, and lymphocyte thresholds), and MLD diagnosis at different threshold settings (A, B, and C). Microbiological culturing of milk samples was used to determine infection status to compare the MLD diagnosis and serve as an indicator of infection. Measures derived from the microbiological analysis included occurrence of major pathogens, minor pathogens, and infection. Data analysis was based on a linear mixed model, which was used on all measures for the estimation of the fixed effects of breed, lactation number, day of sample collection, time of sampling, and quarter location, and the random effects of animal and week of sampling. All the fixed effects studied were significant for one or more of the analyzed measures. The results of this study showed that MLD-derived measures justify further study on their use for management practices for mastitis screening and prevention in early lactation.