Short communication: Imputing genotypes using PedImpute fast algorithm combining pedigree and population information

Routine genomic evaluations frequently include a preliminary imputation step, requiring high accuracy and reduced computing time. A new algorithm, PedImpute (http://dekoppel.eu/pedimpute/), was developed and compared with findhap (http://aipl.arsusda.gov/software/findhap/) and BEAGLE (http://faculty.washington.edu/browning/beagle/beagle.html), using 19,904 Holstein genotypes from a 4-country international collaboration (United States, Canada, UK, and Italy). Different scenarios were evaluated on a sample subset that included only single nucleotide polymorphism from the Bovine low-density (LD) Illumina BeadChip (Illumina Inc., San Diego, CA). Comparative criteria were computing time, percentage of missing alleles, percentage of wrongly imputed alleles, and the allelic squared correlation. Imputation accuracy on ungenotyped animals was also analyzed. The algorithm PedImpute was slightly more accurate and faster than findhap and BEAGLE when sire, dam, and maternal grandsire were genotyped at high density. On the other hand, BEAGLE performed better than both PedImpute and findhap for animals with at least one close relative not genotyped or genotyped at low density. However, computing time and resources using BEAGLE were incompatible with routine genomic evaluations in Italy. Error rate and allelic squared correlation attained by PedImpute ranged from 0.2 to 1.1% and from 96.6 to 99.3%, respectively. When complete genomic information on sire, dam, and maternal grandsire are available, as expected to be the case in the close future in (at least) dairy cattle, and considering accuracies obtained and computation time required, PedImpute represents a valuable choice in routine evaluations among the algorithms tested

Procjena genetskih parametara za osobine plodnosti talijanskog Holstein-frizijskog goveda

Data from insemination and calving events of Italian Holstein cows and heifers collected from January 1996 until December 2002 were used to estimate phenotypic and genetic parameter for some fertility traits. A validation procedure of the data based on gestation length and information on service sire was used. According to these procedure, in Italy 75.9 % of the calvings are associated to service or inseminations events. Days to first service (DTPS), calving interval (CI), number of service per conception (NSC) and non return rate at 90 days (NRR90) were the main traits analysed. The effect of month and year of calving (or insemination), of sampling bull code, of age of cow and of herd-year-season of calving were included in the model and were significant for all the traits analysed. A decreasing efficiency in cow fertility was observed over the last 5 years, with a longer days to first service interval and a higher proportion of cows being re-bred after 90 days. Different data sets were successively defined according to the parities in order to validate the hypothesis that different parities have to be considered as different traits. Heritabilities for the five fertility traits were low ranging from 0,014 for NRR90 to 0,065 for CI. Estimates of c2 for score traits (NSC, NRR56 and NRR90) ranged from 0,010 to 0,025 and were lower than those for CI and DTPS. Genetic correlation were high between traits related to time period but were moderate between those traits and score traits. Heritabilities of interval traits (CI, DTPS) vary over parities, with some indication that higher parities show higher estimates. Results in terms of genetic correlations confirmed the high relationships with interval traits between parities.Podaci o teljenju i osjemenjivanju talijanskih Holstein krava i junica, sakupljeni od siječnja 1996. do prosinca 2002., korišteni su za procjenu fenotipskog i genetskog parametra nekih osobina plodnosti. Primijenjen je postupak neospornosti podataka na temelju dužine gestacije i informacije o servisnom biku. Prema tom postupku u Italiji 75,9% teljenja povezano je sa servisom ili osjemenjivanjem. Glavne analizirane osobine bile su dani do prvog servisa (DTFS), interval teljenja (CI), broj servisa po koncepciji (NSC) i stopa bez rezultata u 90 dana (NRR90). Djelovanje mjeseca i godine teljenja (ili inseminacije), uzimanje šifre bika, dobi krave i stado-godina-sezona teljenja bili su značajni za sve analizirane osobine. Smanjenje djelotvornosti u plodnosti krava zapaženo je u zadnjih 5 godina, s više dana do prvog intervala servisa i veći omjer ponovo pripuštenih krava nakon 90 dana. Postepeno su određene skupine različitih podataka prema analogiji radi vrednovanja hipoteze da razne paritete treba smatrati kao različite osobine. Nasljednosti za pet osobina plodnosti bile su male u rasponu od 0.014 za NRR90 do 0.065 za CI. Procjena c2 za osobine skora (NSC, NRR56 i NRR90) kretale su se od 0.010 do 0.025 i bile su niže od onih za CI i DTFS. Genetske korelacije bile su visoke između osobina u vezi s vremenskim razdobljem ali su bile umjerene između tih osobina i osobina skora. Nasljednosti osobina intervala (CI, DTFS) variraju nad paritetom s nekim naznakama da viši pariteti pokazuju više procjene. Rezultati u smislu genetskih korelacija potvrdili su visoku povezanost s osobinama intervala među paritetima

Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers

The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasing on pedigrees. Despite several algorithmic advances and refinements that led to some efficient algorithms, its applicability to real datasets has been limited by the absence of some important characteristics of these data in its formulation, such as mutations, genotyping errors, and missing data. In this work, we propose the Haplotype Configuration with Recombinations and Errors problem (HCRE), which generalizes the original MRHC formulation by incorporating the two most common characteristics of real data: errors and missing genotypes (including untyped individuals). Although HCRE is computationally hard, we propose an exact algorithm for the problem based on a reduction to the well-known Satisfiability problem. Our reduction exploits recent progresses in the constraint programming literature and, combined with the use of state-of-the-art SAT solvers, provides a practical solution for the HCRE problem. Biological soundness of the phasing model and effectiveness (on both accuracy and performance) of the algorithm are experimentally demonstrated under several simulated scenarios and on a real dairy cattle population.Comment: 14 pages, 1 figure, 4 tables, the associated software reHCstar is available at http://www.algolab.eu/reHCsta

Body measurements from selective hunting: biometric features of red deer (Cervus elaphus) from Northern Apennine, Italy

Morphometric studies on European red deer (Cervus elaphus L.) living in sub-Mediterranean areas are rare. In this paper, we provide the first morphometric description of red deer from Apennine living in Prato Province, as well as a description of its skeletal growth pattern. We analysed 18 body, cranial and antler measurements from 905 deer carcasses, collected during 12 hunting seasons (2000–2012). The body size of red deer from Prato appeared comparable to that of other populations from Northern Apennine and Central Alps. A significant variation in weight during the hunting season was detected only in adult stags: they were estimated to lose 23% of their eviscerated body weight from the beginning of the rutting season until the end of winter. The relationship between eviscerated body weight (EW) and whole body weight (WW) was highly significant in both sexes within every age class (R2 always higher than 0.75), thus linear regressions were assessed in order to estimate EW from WW, allowing to complete datasets when such information is missing. Growth equations were utilised to describe the development of a subset of skeletal measures (height at shoulder, hind foot length, mandible length, head–trunk length) commonly collected on hunted cervids. Hind foot length was the measure which first ceased to grow and with the highest growth constant; although the relationship between cohort hind foot length and environmental, climatic and demographic variables has to be tested for red deer from Apennine, these bones appeared a suitable biological indicator for long-term monitoring of the species