Whole-genome sequencing of alpaca revealed variants in KIT gene potentially associated with the white coat phenotype

The association between variants on TYRP1, TYRP2, MC1R, KITLG, KIT, ASIP and MITF genes and fleece color has been described for alpaca and llama (Zhu et al., 2019; Feeley et al., 2016; Chandramohan et al., 2015; Anello et al., 2022; Pallotti et al., 2020; Shah et al., 2023; Jones et al., 2019; Tan et al., 2022). In this regard, variants on KIT were associated to white and blue-eyed white phenotype in alpaca (Jones et al., 2019; Tan et al., 2022) due to its important role in melanogenesis (Roskoski, 2005). Moreover, previous segregation analysis suggested that the inheritance of white color in alpaca was due to a single gene which is completely dominant over black and brown pigmentation (Valbonesi et al., 2011). In the present study, the segregation of KITLG, KIT and MITF genes was analyzed to find variants associated to white coat phenotype in alpaca. Six Peruvian alpacas belonging to two test-cross families were tested: white huacaya male × pigmented suri female and white suri male x pigmented huacaya female which gave birth to one white suri and one pigmented huacaya, respectively (Table 1). The animals were raised at the experimental station of the INIA (the Peruvian National Institute for Agronomic Innovation) located in Quimsachata, Peru. Sampling of the animals and genomics analysis were performed as reported in Pallotti et al. (2023). Briefly, genomic DNA extracted from skin biopsies underwent whole-genome sequencing on Illumina NovaSeq 6000 System, with a 150x2 bp mode, and an average sequencing depth of 25X. After quality control and alignment to VicPac3 reference genome, the variants were called using the standard joint-call GATK pipeline. All the variants were annotated using SNPeff and filtered according to the segregation of the white coat phenotype. No segregating variants for white coat color were identified in KITLG and MITF. On the contrary, two different KIT variants segregated in white animals (Table 1): two white alpacas, belonging to family 1, were heterozygous (G/A) for the c.35G>A (p.Arg12His) variant, while one white alpaca, belonging to family 2, was heterozygotes (G/C) for c.982G>C (p.Val328Leu) variant. Conversely, all the pigmented animals showed a homozygous G/G genotype. The protein functional domains predicted using InterProScan (Quevillon et al., 2005) suggested that the two mutations were in the N-terminal region of the signal peptide and in the extracellular region which are essential for the binding of the appropriate ligand and consequent activation of KIT (Roskoski, 2005). In addition, such results may suggest a dominant inheritance for alpaca white color as proposed by previous segregation studies (Valbonesi et al., 2011). Although these results must be validated on larger sample, our findings refine the current understanding of the association between gene variants and white color in alpaca and suggest new potential KIT variants as a starting point for further studies on the genetics of white color in alpaca

Estimates of non-genetic effects for measures of hunting performance in short-haired and rough-haired Italian hound

The aim of this work was to estimate the effects of eight non-genetic factors (sex, type of coat, pigmentation, type of the trial, the number of the judges in the jury, the location where the competition took place, the subjectivity of the judge and the breeders) on the assessment of seven hunting traits (morphology, the breed style, search, approach, find, pursuit and voice) for the short-haired and rough-haired Italian Hound. The data consisted of 3172 field trial records between the years 2016 and 2017. The Mann–Whitney test and Kruskal–Wallis test showed that each factor was statistically significant for some traits: the sex of the dogs was statistically significant only for the evaluation of the morphology the type of coat for breed style, search, approach, find and voice; the pigmentation for all traits excluding approach; the number of judges for morphology, approach and find; the type of trial for all traits excluding voice. Spearman's ρ (rho) correlation showed that high phenotypic correlations were between morphology, breed style and search. These traits showed low to moderate correlations with the other traits except breed style and search vs. pursuit. Furthermore, principal component analysis for the factor judge, location and breeders showed that among the seven traits assessed during the trials, the morphology and the breed style had the highest loading on the final score. Our results suggest that the effect of all the non-genetic factors analysed must be taken into account by the judges during the evaluation of the dogs.Highlights We evaluated the effects of eight non-genetic factors on the assessment of seven hunting traits for the Italian Hound. All the non-genetic factors had influence on some of the hunting traits considered. Principal component analysis showed that the highest loading for morphology and breed style are on location, judge and breeder. High phenotypic correlations were between morphology, breed style, search and pursuit

solar thermal based orc power plant for micro cogeneration performance analysis and control strategy

Abstract The paper deals with the performance assessment of a small scale cogeneration system for building applications, featuring an Organic Rankine Cycle-based plant bottoming a solar collector array for combined heat and electricity generation. A sliding vanes rotary expander and a water cooled condenser are employed in the recovery section. A comprehensive MATLAB® model accounts for the dynamic of each component, as both a stand-alone device and a plant-integrated unit: a parametric study is presented and an off-design analysis is performed to properly assess the performances of both the heat exchanger and the expander. Heat availability to the ORC heat exchanger is evaluated, based on solar availability, thermal losses in the pipes and plant requirements, in terms of operating temperature and pressures, having the collection area, the mass flowrate for the fluid in the solar collector branch and the fluid type in the recovery section as main variables. Due to the need for DHW production, a storage unit for hot water is present, upstream the recovery branch: dependently on the ability the fluid at the collector outlet has to meet the ORC requirements for proper operation (about 110°C), the ORC evaporator is fed and the recovery section enabled. Both continuous and unsteady operation underwent an in-depth analysis, as well as the benefits associated with different discharge times for the storage unit: dependently on whether the electrical output or the thermal one need to be maximized, a different control logic for the whole system comes out (e.g. either a flash or a progressive tank discharge). The virtual platform allowed the setting-up of a pilot plant, for direct performance assessment and model validation

Genome-wide scan for runs of homozygosity in South American Camelids

Background: Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results: A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions: The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies

Meat and carcass quality from peruvian llama (Lama glama) and alpaca (Lama pacos)

An experiment based on 20 llama males and 40 alpaca males reared in Peru has been carried out with the aim to evaluate the live growth performances, carcass quality, the nutritional characteristics of meat from animals slaughtered at 25 months of age, and to determine the physical and chemical parameters of meat obtained from these animals. The live body weights registered during the 25 months of the experiment were significantly lower in alpaca compared with llama. In llama carcasses were significantly higher both warm and cold carcass weight (P<0.001) but dressing percentage was higher in alpacas (P<0.01). The glycolityc fine-course was very similar both in llama and in alpaca muscle Longissimus Thoracis et Lumborum. Chemical composition of muscle Longissimus Thoracis et Lumborum taken from llama and alpaca carcasses was significantly different (P<0.01) in ash content; cholesterol content was significantly higher (P<0.001) in llama meat compared with alpaca

Global second-order estimates in anisotropic elliptic problems

We deal with boundary value problems for second-order nonlinear elliptic equations in divergence form, which emerge as Euler-Lagrange equations of integral functionals of the Calculus of Variations built upon possibly anisotropic norms of the gradient of trial functions. Integrands with non polynomial growth are included in our discussion. The $W^{1,2}$-regularity of the stress-field associated with solutions, namely the nonlinear expression of the gradient subject to the divergence operator, is established under the weakest possible assumption that the datum on the right-hand side of the equation is a merely $L^2$-function. Global regularity estimates are offered in domains enjoying minimal assumptions on the boundary. They depend on the weak curvatures of the boundary via either their degree of integrability or an isocapacitary inequality. By contrast, none of these assumptions is needed in the case of convex domains. An explicit estimate for the constants appearing in the relevant estimates is exhibited in terms of the Lipschitz characteristic of the domains, when their boundary is endowed with H\"older continuous curvatures

inheritance of suri and huacaya type of fleece in alpaca

The inheritance of the two types of fleece, Suri and Huacaya, observed in Alpaca (Lama pacos L.) is still not clearly defined. The objective of this work is to investigate the patter of inheritance of these two phenotypes, throughout 588 Suri x Suri and 2126 Huacaya x Huacaya offspring. The single gene and the three two-phenotype epistatic models were tested in the 19 Suri x Suri segregating families. The single dominant gene hypothesis best fitted our segregation data and could be, therefore, accepted (GT=20.276, P=0.378). The gene frequency of the recessive Huacaya allele was 0.295, being the frequency of the dominant Suri allele 0.705. The frequency of heterozygotes, estimated in the whole population and among dominant individuals, was 0.416 and 0.455, respectively, with a "carrier" Suri to Huacaya ratio of 4.780. In three Huacaya families, 3 Suri were born, as a result of a new dominant mutation on some germinal lines of Huacaya animals. The direct mutation rate can be estimated at 0.0014