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Open Access
A Bayesian analysis of the effect of selection for growth rate on growth curves in rabbits
(BioMed Central, 2003) Blasco, Agustín; Piles, Miriam; Varona Aguado, Luís
Gompertz growth curves were tted to the data of 137 rabbits from control (C) and selected (S) lines. The animals came from a synthetic rabbit line selected for an increased growth rate. The embryos from generations 3 and 4 were frozen and thawed to be contemporary of rabbits born in generation 10. Group C was the offspring of generations 3 and 4, and group S was the contemporary offspring of generation 10. The animals were weighed individually twice a week during the rst four weeks of life, and once a week thereafter, until 20 weeks of age. Subsequently, the males were weighed weekly until 40 weeks of age. The random samples of the posterior distributions of the growth curve parameters were drawn by using Markov Chain Monte Carlo (MCMC) methods. As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve. Adult body weight, estimated as a parameter of the Gompertz curve, was 7% higher in the selected line. The other parameters of the Gompertz curve were scarcely affected by selection. When selected and control growth curves are represented in a metabolic scale, all differences disappear.
Open Access
A bivalent dendrimeric peptide bearing a T-cell epitope from foot-and-mouth disease virus protein 3A improves humoral response against classical swine fever virus
(Elsevier, 2017) Bohórquez, José Alejandro; Defaus, Sira; Muñoz González, Sara; Perez-Simó, Marta; Rosell, Rosa; Fraile Sauce, Lorenzo José; Sobrino, Francisco; Andreu, David; Ganges, Llilianne
Three dendrimeric peptides were synthesized in order to evaluate their immunogenicity and their potential protection against classical swine fever virus (CSFV) in domestic pigs. Construct 1, an optimized version of a previously used dendrimer, had four copies of a B-cell epitope derived from CSFV E2 glycoprotein connected to an also CSFV-derived T-cell epitope through maleimide instead of thioether linkages. Construct 2 was similarly built but included only two copies of the B-cell epitope, and in also bivalent construct 3 the CSFV T-cell epitope was replaced by a previously described one from the 3A protein of foot-and-mouth disease virus (FMDV). Animals were inoculated twice with a 21-day interval and challenged 15days after the second immunization. Clinical signs were recorded daily and ELISA tests were performed to detect antibodies against specific peptide and E2. The neutralising antibody response was assessed 13days after challenge. Despite the change to maleimide connectivity, only partial protection against CSFV was again observed. The best clinical protection was observed in group 3. Animals inoculated with constructs 2 and 3 showed higher anti-peptide humoral response, suggesting that two copies of the B-cell epitope are sufficient or even better than four copies for swine immune recognition. In addition, for construct 3 higher neutralizing antibody titres against CSFV were detected. Our results support the immunogenicity of the CSFV B-cell epitope and the cooperative role of the FMDV 3A T-cell epitope in inducing a neutralising response against CSFV in domestic pigs. This is also the first time that the FMDV T-cell epitope shows effectivity in improving swine immune response against a different virus. Our findings highlight the relevance of dendrimeric peptides as a powerful tool for epitope characterization and antiviral strategies development.
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A classification of feline skulls by means of geometric morphometric techniques
(World Science and Research Publishing, 2014-10-25) Parés Casanova, Pere-Miquel; De la Cruz Bueno, Sara
Geometric morphometrics is a powerful tool for the study of morphological variation that possesses numerous advantages over more traditional approaches based on linear measurements. Here, the skull morphologies of 42 adult museum specimens of different species belonging to the family Felidae were analysed in order to assess the reliability of classifying two specimens labelled as Panthera sp. Using this technique. According to the results obtained, these specimens can be assigned to Panthera pardus. This is not just a contribution to the traceability of these museum pieces, but primarily an exemplification of the validity of geometric morphometric methods for classifying biological specimens.
Open Access
A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction
(Public Library of Science, 2018) Royo Sánchez-Palencia, José Luis; Valls Marsal, Joan; Acemel, Rafael D.; Gómez-Marin, Carlos; Pascual Pons, Mariona; Lupiañez, Arantxa; Gomez-Skarmeta, Jose Luis; Fibla Palazón, Joan
Previous reports have proposed that personality may have played a role on human Out-Of- Africa migration, pinpointing some genetic variants that were positively selected in the migrating populations. In this work, we discuss the role of a common copy-number variant within the SIRPB1 gene, recently associated with impulsive behavior, in the human Out-Of-Africa migration. With the analysis of the variant distribution across forty-two different populations, we found that the SIRPB1 haplotype containing duplicated allele significantly correlated with human migratory distance, being one of the few examples of positively selected loci found across the human world colonization. Circular Chromosome Conformation Capture (4C-seq) experiments from the SIRPB1 promoter revealed important 3D modifications in the locus depending on the presence or absence of the duplication variant. In addition, a 3' enhancer showed neural activity in transgenic models, suggesting that the presence of the CNV may compromise the expression of SIRPB1 in the central nervous system, paving the way to construct a molecular explanation of the SIRPB1 variants role in human migration.
Open Access
A comparison of processed sorghum grain using different digestion techniques
(Taylor & Francis, 2016) González García, Ulises Alejandro; Corona, Luis; Castrejon Pineda, Francisco; Balcells Terés, Joaquim; Castelan Ortega, Octavio; González Ronquillo, Manuel
This study compares in situ, in vitro (DaisyII and gas production) and in vivo techniques to estimate the degradation of dry matter (DM), organic matter (OM), and N of sorghum grain. We used whole dried sorghum (WDS), dry cracked sorghum (DCS), the reconstituted whole sorghum silage (WSS) and reconstituted cracked sorghum silage (CSS). The residues obtained from the ruminal digestion in vitro (DaisyII) and in situ were analysed for their intestinal digestion (pepsin–pancreatin). OM was similar (981.32 ± 0.52) in all treatments, WSS showed the highest (P < .001) crude protein (CP) concentration compared with the other treatments, whereas CSS showed the highest amount of starch (P < .001) compared to other treatments. The apparent degraded substrate (ADS) was higher (P < .038) for whole sorghums, rumen degradable protein (RDP) was higher for WDS and WSS (P = .003), while protein digestible in the intestine (PDI) was higher for sorghums silage (P < .001) compared with dry sorghums. ADS was higher (P < .022) using the in sacco technique compared with the other methods, while for the RDP and PDI methods in sacco and in vitro (Daisy) showed the better degradation compared with in vivo. The reconstituted ensiling sorghum grains had a favourable response in the availability of nutrients, compared with dried sorghums.
Open Access
A comparison of traditional and geometric morphometric techniques for the study of basicranial morphology in horses: a case study of the Araucanian horse from Colombia
(MDPI, 2020-01-10) Parés Casanova, Pere-Miquel; Salamanca-Carreño, Arcesio; Crosby-Granados, René; Bentez-Molano, Jannet
Skull size and shape have been widely used to study domestic animal populations and breeds. Although several techniques have been proposed to quantify cranial form, few attempts have been made to compare the results obtained by di erent techniques. While linear morphometrics has traditionally been used in breed characterization, recent advances in geometric morphometrics have created new techniques for specifically quantifying shape and size. The objective of this study was to compare two morphometric methods for their ability to describe external morphology. For this purpose, 20 skull specimens of adult male Araucanian horses were examined. Two age categories were established (the 'mature group',M3 not fully erupted to moderately worn, n = 7; and the 'senile group', M3 totally erupted and highly worn, n = 13). Both methods showed that there were statistical di erences between generations, but discrimination rates were di erent between methods with the geometric morphometric analysis obtaining a rate of 97.5%. Although linear morphometrics was found to be compatible with geometric morphometrics, the latter was better able to discriminate the two groups and it also provides more information on shape.
Open Access
A computational model approach to assess the effect of climate change on the growth and development of tadpoles
(Elsevier, 2021) Colomer, M. Àngels (Maria Àngels); Margalida, Antoni; Sanuy, Isabel; Llorente, Gustavo A.; Sanuy i Castells, Delfí; Pujol-Buixó, Eudal
All of the environmental conditions in nature act on an organism simultaneously. However, in experimental studies of the factors influencing metamorphosis, each factor needs to be examined individually in order to disentangle its specific effects. However, it is challenging to then build properly integrated models which include data on all of the different factors evaluated in different experiments. This study set out to develop a predictive model which could synthesize the results of several experiments on survival, development and growth of Natterjack toad (Epidalea calamita) tadpole guilds. The proposed Population Dynamic P System (PDP) model enables estimates of growth and development during the larval phase, under different environmental conditions, weather conditions, predator density, and pond characteristics and management. The architecture of the model allows the inclusion of an indefinite number of parameters and interactions, with all inputs interacting in parallel, and enables solutions to complex modeling approaches. Using the model with a range of field data, we found that the importance of predation pressure on Natterjack toad tadpole guilds exceeds the potential effects of variations in temperature and precipitation. The impact of introduced invasive predators therefore arguably poses the greatest threat to this species. This type of model holds promise as a reliable management and conservation tool for this and other species, especially where interactions between environmental factors make the impacts of individual factors difficult to predict.
Open Access
A cow-calf farming system fully adapted to elevation and harsh conditions in Andorra (Europe)
(MDPI, 2021) Armengol Gelonch, Ramon; Bassols, Marta; Fraile Sauce, Lorenzo José
The use of natural resources is an important topic to optimize the efficiency of cattle production. The purpose of this work is to describe the project of the Bruna d'Andorra; a local cow breed under an extensive cow-calf system in Andorra (Europe), as an example of local farming and marketing of its meat products in an area with adverse environmental conditions. This breed is located in Andorra, a microstate that consists predominantly of rugged mountains and harsh weather conditions. The cow-calf Bruna d'Andorra extensive system is thoroughly described and productive and reproductive performance, compiled over 21 years (2000-2020), has been analyzed by years with the Chi-square test or ANOVA to compare proportions or means, respectively, and regression analysis was used to decipher evolution across years. The results show a population with a census large and stable enough to avoid inbreeding. Moreover, a sustained improvement of the productive performance and maternal fitness has been observed along the studied period for Bruna d'Andorra. The work concludes that local breeds can achieve sustainable animal production, especially when farmers, public administration and commercial circuits in the area agree to cooperate on such projects. The study also concludes that the Bruna d'Andorra cow breed can still improve in meat and reproductive performance.
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A cryopreservation procedure for the rumen protozoon Entodinium caudatum: estimation of its viability by fluorescence microscopy
(Blackwell Science, 2004) de la Fuente Oliver, Gabriel; Cebrián, J. A.; Fondevila, Manuel
Aims: To study the viability of a culture of the rumen protozoon Entodinium caudatum after a cryopreservation procedure by a fluorescence microscopy staining method. Methods and Results: Fluorescence method is based on the different colour of cells depending on their membrane integrity. When the temperature effect was studied either by fluorescence or motility, the techniques were correlated (r = 0·727) and their slopes and intercepts were not different (P > 0·05). However, motility showed a higher variation coefficient (0·40 vs 0·12). There were no differences between cooling rates at cryopreservation (1 and 4°C min−1) at 38, 15 or 5°C, nor after thawing. Conclusions: Fluorescence staining is more accurate than motility for assessing protozoal viability. Viability after thawing was 0·50, and the number of viable cells per 250 μl straw was 320 and 420 for 1 and 4°C min−1. Significance and Impact of the Study: This cryopreservation procedure seems to ensure culture recovery for E. caudatum.
Open Access
A dilated pore of winer in a young Iberian Lynx (Lynx pardinus)
(Sciendo, 2023-06) Pérez, Estela; Lima-Barbero, José Francisco; Pinczowski, Pedro; Serra, Rodrigo; Asín, Javier; Molín, Jéssica; Luján, Lluís; Pérez, Marta
A 1.5-year-old male Iberian lynx born in captivity presented with a 2.2 cm exophytic nodular alopecic mass at the left tarsus medial aspect, before being released into the wild. The lesion had keratinised material protruding through a 1.2 cm pore, forming a cutaneous horn. Histopathology revealed a cystic dermo-epidermal lesion lined by psoriasiform hyperplasia of the epithelium, thicker at the base of the cyst, together with abrupt to progressive keratinization and keratin pearls. The central cystic cavity was filled with fibrillary keratin and ghost cells. Immunohistochemistry for pan-cytokeratin showed strong positive immunolabeling in the hyperplastic epithelium and a weaker immunolabeling at the content of the cyst. A final diagnosis of a Dilated Pore of Winer was made. This paper is the first reported case of a DPW in a lynx and a wild felid.
Open Access
A functional variant in the Stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork
(Public Library of Science (PLoS), 2014) Estany Illa, Joan; Ros Freixedes, Roger; Tor i Naudí, Marc; Pena i Subirà, Ramona Natacha
There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.
Open Access
A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants
(BioMed Central, 2014-09-10) Manunza, Arianna; Casellas, Joaquim; Quintanilla Aguado, Raquel; González-Prendes, Rayner; Pena i Subirà, Ramona Natacha; Tibau, Joan; Mercadé Carceller, Anna; Castelló, Anna; Aznarez, Nitdia; Hernández-Sánchez, Jules; Amills i Eras, Marcel
Background: The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even in model organisms, little is known about how the genetic determinants of lipid traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) for cholesterol (CHOL), triglyceride (TRIG) and low (LDL) and high (HDL) density lipoprotein concentrations measured in Duroc pigs at two time points (45 and 190 days). Results: Analysis of data with mixed-model methods (EMMAX, GEMMA, GenABEL) and PLINK showed a low positional concordance between trait-associated regions (TARs) for serum lipids at 45 and 190 days. Besides, the proportion of phenotypic variance explained by SNPs at these two time points was also substantially different. The four analyses consistently detected two regions on SSC3 (124 Mb, CHOL and LDL at 190 days) and SSC6 (135 Mb, CHOL and TRIG at 190 days) with highly significant effects on the porcine blood lipid profile. Moreover, we have found that SNP variation within SSC3, SSC6, SSC10, SSC13 and SSC16 TARs is associated with the expression of several genes mapping to other chromosomes and related to lipid metabolism. Conclusions: Our data demonstrate that the effects of genomic determinants influencing lipid concentrations in pigs, as well as the amount of phenotypic variance they explain, are influenced by age-related factors.
Open Access
A genome-wide screen for resilient responses in growing pigs
(BMC, 2022-07-04) Laghouaouta, Houda; Fraile Sauce, Lorenzo José; Suárez-Mesa, Rafael; Ros Freixedes, Roger; Estany Illa, Joan; Pena i Subirà, Ramona Natacha
Background There is a growing interest to decipher the genetic background of resilience and its possible improvement through selective breeding. The objective of the present study was to provide new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. Commercial Duroc pigs were challenged with an attenuated Aujeszky vaccine at 12 weeks of age. Two resilience indicators were used: deviation from the expected body weight at 16 weeks of age given the growth curve of non-vaccinated pigs (∆BW) and the increase in acute-phase protein haptoglobin at four days post-vaccination (∆HP). Genome-wide association analyses were carried out on 445 pigs, using genotypes at 41,165 single nucleotide polymorphisms (SNPs) and single-marker and Bayesian multiple-marker regression approaches. Results Genomic regions on pig chromosomes 2, 8, 9, 11 (∆BW) and 8, 9, 13 (∆HP) were found to be associated with the resilience indicators and explained high proportions of their genetic variance. The genomic regions that were associated explained 27 and 5% of the genetic variance of ∆BW and ∆HP, respectively. These genomic regions harbour promising candidate genes that are involved in pathways related to immune response, response to stress, or signal transduction ( CD6 , PTGDR2 , IKZF1 , RNASEL and MYD88 ), and growth ( GRB10 and LCORL ). Conclusions Our study identified novel genomic regions that are associated with two resilience indicators (∆BW and ∆HP) in pigs. These associated genomic regions harbour potential candidate genes involved in immune response and growth pathways, which emphasise the strong relationship between resilience and immune response.
Open Access
A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits
(Blackwell Verlag GmbH, 2019) Sosa‐Madrid, Bolívar Samuel; Santacreu, María Antonia; Blasco, Agustín; Fontanesi, Luca; Pena i Subirà, Ramona Natacha; Ibáñez-Escriche, N.
Uterine capacity (UC), defined as the total number of kits from unilaterally ovariectomized does at birth, has a high genetic correlation with litter size. The aim of our research was to identify genomic regions associated with litter size traits through a genomewide association study using rabbits from a divergent selection experiment for UC. A high‐density SNP array (200K) was used to genotype 181 does from a control population, high and low UC lines. Traits included total number born (TNB), number born alive (NBA), number born dead, ovulation rate (OR), implanted embryos (IE) and embryo, foetal and prenatal survivals at second parity. We implemented the Bayes B method and the associations were tested by Bayes factors and the percentage of genomic variance (GV) explained by windows. Different genomic regions associated with TNB, NBA, IE and OR were found. These regions explained 7.36%, 1.27%, 15.87% and 3.95% of GV, respectively. Two consecutive windows on chromosome 17 were associated with TNB, NBA and IE. This genomic region accounted for 6.32% of GV of TNB. In this region, we found the BMP4, PTDGR, PTGER2, STYX and CDKN3 candidate genes which presented functional annotations linked to some reproductive processes. Our findings suggest that a genomic region on chromosome 17 has an important effect on litter size traits. However, further analyses are needed to validate this region in other maternal rabbit lines.
Open Access
A genome‑wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines
(BMC, 2023-06-15) Desire, Suzanne; Johnsson, Martin; Ros Freixedes, Roger; Chen, Ching-Yi; Holl, Justin; Herring, William O.; Gorjanc, Gregor; Mellanby, Richard J.; Hickey, John M.; Jungnickel, Melissa K.
Background Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong (≥ 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. Results Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. Conclusions For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.
Open Access
A horizon scan exercise for aquatic invasive alien species in Iberian inland waters
(Elsevier, 2023) Oficialdegui, Francisco J.; Zamora-Marín, José M.; Guareschi, Simone; Anastácio, Pedro M.; García-Murillo, Pablo; Ribeiro, Filipe; Miranda, Rafael; Cobo, Fernando; Gallardo, Belinda; García-Berthou, Emili; Boix, Dani; Arias, Andrés; Cuesta, Jose A.; Medina, Leopoldo; Almeida, David; Banha, Filipe; Barca, Sandra; Biurrun, Idoia; Cabezas, M. Pilar; Calero, Sara; Sánchez-González, Jorge Rubén
As the number of introduced species keeps increasing unabatedly, identifying and prioritising current and potential Invasive Alien Species (IAS) has become essential to manage them. Horizon Scanning (HS), defined as an exploration of potential threats, is considered a fundamental component of IAS management. By combining scientific knowledge on taxa with expert opinion, we identified the most relevant aquatic IAS in the Iberian Peninsula, i.e., those with the greatest geographic extent (or probability of introduction), severe ecological, economic and human health impacts, greatest difficulty and acceptability of management. We highlighted the 126 most relevant IAS already present in Iberian inland waters (i.e., Concern list) and 89 with a high probability of being introduced in the near future (i.e., Alert list), of which 24 and 10 IAS, respectively, were considered as a management priority after receiving the highest scores in the expert assessment (i.e., top-ranked IAS). In both lists, aquatic IAS belonging to the four thematic groups (plants, freshwater invertebrates, estuarine invertebrates, and vertebrates) were identified as having been introduced through various pathways from different regions of the world and classified according to their main functional feeding groups. Also, the latest update of the list of IAS of Union concern pursuant to Regulation (EU) No 1143/2014 includes only 12 top-ranked IAS identified for the Iberian Peninsula, while the national lists incorporate the vast majority of them. This fact underlines the great importance of taxa prioritisation exercises at biogeographical scales as a step prior to risk analyses and their inclusion in national lists. This HS provides a robust assessment and a cost-effective strategy for decision-makers and stakeholders to prioritise the use of limited resources for IAS prevention and management. Although applied at a transnational level in a European biodiversity hotspot, this approach is designed for potential application at any geographical or administrative scale, including the continental one.
Open Access
A limit for antler length in captive Marals
(Sociedad Chilena de Anatomía, 2014) Korzhikenova, N.; Sambetbaev, A.; Iglikov, O.; Parés Casanova, Pere-Miquel
The main aim of this study was to estimate phenotypic correlations among live weight, withers height, rump height, chest depth, chest width, thoracic girth, body length, hip widths (between iliac tuberosities and between ischial tuberosities) and forelimb cannon perimeter with antler length measured during the growth of marals on a Kazakh farm. The data comprised 18 animals studied during their growth (at 18 months and at 24 months). In maral, the first period of antler productivity takes place at the age of 24 months. This fact should be taken into account in order to select the best animals for antler production, which is the main purpose for farming this species.
Open Access
A limit for horn length in White of Rasquera Goat
(Labome, 2014) Parés Casanova, Pere-Miquel
Well-preserved adult skulls (twenty-two male and 27 female) from White of Rasquera Goat breed were studied. The greatest length of the skull has been used to estimate head size. Horn length was measured with a tape along the whole length of the right sheath. The equations obtained were [log y = 3.231
1.417 log x] and [log y = 3.248
1.538 log x] for males and females respectively. It is possible that, although horn traits can be important for this breed, which is mainly naturally selected, other important traits must exist when choosing a mate.
Open Access
A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals
(BMC (part of Springer Nature), 2017-10-25) Ros Freixedes, Roger; Gonen, Serap; Gorjanc, Gregor; Hickey, John M.
Background: This paper describes a heuristic method for allocating low-coverage sequencing resources by target- ing haplotypes rather than individuals. Low-coverage sequencing assembles high-coverage sequence information for every individual by accumulating data from the genome segments that they share with many other individuals into consensus haplotypes. Deriving the consensus haplotypes accurately is critical for achieving a high phasing and imputation accuracy. In order to enable accurate phasing and imputation of sequence information for the whole population, we allocate the available sequencing resources among individuals with existing phased genomic data by targeting the sequencing coverage of their haplotypes. Results: Our method, called AlphaSeqOpt, prioritizes haplotypes using a score function that is based on the fre- quency of the haplotypes in the sequencing set relative to the target coverage. AlphaSeqOpt has two steps: (1) selec- tion of an initial set of individuals by iteratively choosing the individuals that have the maximum score conditional on the current set, and (2) refinement of the set through several rounds of exchanges of individuals. AlphaSeqOpt is very effective for distributing a fixed amount of sequencing resources evenly across haplotypes, which results in a reduction of the proportion of haplotypes that are sequenced below the target coverage. AlphaSeqOpt can provide a greater proportion of haplotypes sequenced at the target coverage by sequencing less individuals, as compared with other methods that use a score function based on haplotype frequencies in the population. A refinement of the initially selected set can provide a larger more diverse set with more unique individuals, which is beneficial in the context of low-coverage sequencing. We extend the method with an approach for filtering rare haplotypes based on their flanking haplotypes, so that only those that are likely to derive from a recombination event are targeted. Conclusions: We present a method for allocating sequencing resources so that a greater proportion of haplotypes are sequenced at a coverage that is sufficiently high for population-based imputation with low-coverage sequencing. The haplotype score function, the refinement step, and the new approach for filtering rare haplotypes make AlphaSe- qOpt more effective for that purpose than previously reported methods for reducing sequencing redundancy.
Open Access
A method for the allocation of sequencing resources in genotyped livestock populations
(BMC (part of Springer Nature), 2017-05-18) Gonen, Serap; Ros Freixedes, Roger; Battagin, Mara; Gorjanc, Gregor; Hickey, John M.
Background: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. Methods: We present two algorithms. The rst selects focal individuals that collectively represent the maximum pos‐ sible portion of the haplotype diversity in the population. The second allocates a xed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level. We tested the performance of the two algorithms in simulated pedigrees. For each pedigree, we evaluated the proportion of population haplo‐ types that are carried by the focal individuals and compared our results to a variant of the widely‐used key ancestors approach and to two haplotype‐based approaches. We calculated the expected phasing accuracy of the haplotypes of a focal individual at the sequence level given the proportion of the xed sequencing budget allocated to its family. Results: AlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, it selects focal individuals that collectively represent a larger portion of the population haplotype diversity than existing methods. Second, it selects focal individuals from across the pedigree whose haplotypes can be easily phased using family‐based phasing and imputation algorithms, thus maximises the ability to impute sequence into the rest of the population. Third, it allocates more of the xed sequencing budget to focal individuals whose haplotypes are more frequent in the population than to focal individuals whose haplotypes are less frequent. Unlike existing methods, we additionally present an algorithm to allocate part of the sequencing budget to the families (i.e. immediate ancestors) of focal individuals to ensure that their haplotypes can be phased at the sequence level, which is essential for enabling and maximising subsequent sequence imputation. Conclusions: We present a new method for the allocation of a xed sequencing budget to focal individuals and their families such that the nal sequenced haplotypes, when phased at the sequence level, represent the maximum pos‐ sible portion of the haplotype diversity in the population that can be sequenced and phased at that budget.