Luis Gomez-Raya

Swine leukocyte antigen (SLA) diversity in Sinclair and Hanford swine.

The swine leukocyte antigen (SLA) haplotype B is associated with increased penetrance of the tumor traits in Sinclair swine cutaneous melanoma (SSCM). We established a series of SinclairxHanford swine crosses to facilitate genetic mapping of the tumor-associated loci. In this study, the SLA diversity in the founding animals was characterized for effective selection of maximum tumor penetrance in the pedigrees. Using the sequence-based typing (SBT) method we identified a total of 29 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing six class I and five class II haplotypes. We subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the crossbred progeny. In a total of 469 animals we identified three crossovers within the class I region and three between the class I and class II regions, which corresponded to recombination frequencies of 0.39% and 0.56%, respectively. We also confirmed the presence of two expressed SLA-1 loci in three of the class I haplotypes and were able to determine the relative chromosomal arrangement of the duplicated loci in two haplotypes. This study furthers our understanding of the allelic architecture and polymorphism of the SLA system and will facilitate the mapping of loci associated with the expression of SSCM.

Genotype by environment interaction and breeding for robustness in livestock

The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond.

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine

This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between -0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (+/-0.03) and 0.25 (+/-0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (+/-0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).

Acclimation in Simulated Lake Water Increases Survival of Lahontan Cutthroat Trout Challenged with Saline, Alkaline Water from Walker Lake, Nevada

Abstract We investigated the effect of acclimation and condition factor (K) on short-term survival of subyearling Lahontan cutthroat trout Oncorhynchus clarkii henshawi reared at Lahontan National Fish Hatchery, Gardnerville, Nevada, and challenged for 1 week with saline, alkaline water from Walker Lake, Nevada. The effect of acclimation and lake-water challenge on plasma osmolality was also investigated. Fish were acclimated for 0, 8, or 17 d in simulated lake water with gradual and simultaneous increases in total dissolved solids and pH. Mean (±SE) survival rates (proportion) during three replicate, weeklong challenges in Walker Lake water for the 0-, 8-, and 17-d acclimation groups were 0.153 ± 0.0409, 0.236 ± 0.0371, and 0.487 ± 0.1040, respectively. During all three challenge replicates, fish acclimated for 17 d experienced a lower hazard of death than unacclimated fish; fish in the 0- and 8-d acclimation groups survived at similar rates. Higher K-values were associated with a lower hazard of death d...

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 (SD 0.00) and 0.19 (SD 0.03) for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by: a) estimation of the recombination fraction and LD in consecutive SNPs using family information, b) linkage analyses between fragments, c) phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual (sire level). SNPs for which the sire and calf were heterozygotes became informative (over 90%) after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes (with at least 20 SNP) in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.

Acclimation Improves Short-Term Survival of Hatchery Lahontan Cutthroat Trout in Water From Saline, Alkaline Walker Lake, Nevada

We investigated the effectiveness of two acclimation protocols for 8-month-old Lahontan cutthroat trout Oncorhynchus clarkii henshawi, reared at Lahontan National Fish Hatchery in terms of survival during a week-long challenge in water from saline, alkaline Walker Lake, Nevada. Fish were acclimated for 0 (control), 3, and 8 d by increasing the ratio of lake water to hatchery water. For the 3-d acclimation treatment, 50% of the tank water was replaced with lake water each day. For the 8-d treatment, 33% of the water was replaced with lake water on the first through fourth day of acclimation. Survival during acclimation (i.e., prior to the challenge) was lowest for fish acclimated 3 d. Median survival time during the lake water challenge was 8 h for unacclimated fish, and 8 and 12 h for fish surviving the 3- and 8-d acclimation treatments, respectively. No fish survived the entire week-long challenge. Compared with no acclimation, 3- and 8-d acclimation decreased the hazard of mortality during the challenge. Increased fork length also reduced the hazard of death. Our results indicate acceptable survival rates cannot be achieved for subyearling, hatchery-reared Lahontan cutthroat trout stocked in Walker Lake without acclimation or with the acclimation methods employed in this study. Our results indicate that the acclimation method might be improved by the use of longer fish, longer acclimation, and better control of water temperature, ammonia concentration, and alkalinity.

Estimation of Recombination Rate and Maternal Linkage Disequilibrium in Half-Sibs

A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been proposed for estimating these parameters in half-sibs without phasing the progeny. It, however, overlooks the fact that the underlying likelihood function may have two maxima. The magnitudes of the maxima depend on the maternal allele frequencies at the investigated marker pair. Which maximum the algorithm converges to depends on the chosen start values. We present a stepwise procedure in which the relationship between the two modes is exploited. The expectation maximization algorithm for the parameter estimation is applied twice using different start values, followed by a decision process to assess the most likely estimate. This approach was validated using simulated genotypes of half-sibs. It was also applied to a dairy cattle dataset consisting of multiple half-sib families and 39,780 marker genotypes, leading to estimates for 12,759,713 intrachromosomal marker pairs. Furthermore, the proper order of markers was verified by studying the mean of estimated recombination rates in a window adjacent to the investigated locus as well as in a window at its most distant chromosome end. Putatively misplaced markers or marker clusters were detected by comparing the results with the revised bovine genome assembly UMD 3.1.1. In total, 40 markers were identified as candidates of misplacement. This outcome may help improving the physical order of markers which is also required for refining the bovine genetic map.

Observations Concerning Reproductive Temperature Requirements of Captive Lahontan Cutthroat Trout

Abstract The effects of holding temperature during late oocyte development and spawning on the timing of ovulation, fecundity, and egg survival in female Lahontan cutthroat trout Oncorhynchus clarkii henshawi in three postovulatory regimes were investigated. The timing of ovulation was similar for females held at 7.2°C and 12.4°C from 2.5 to 6.0 months before the time of ovulation until spawning. Mean fecundity was higher for females held at 7.2°C. Mean egg eye-up, hatch, and swim-up rates were also higher for females held at 7.2°C. Eggs collected 1, 4, and 7 d postovulation exhibited similar survival rates within females regardless of holding temperature.