Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.

BACKGROUND: Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated. RESULTS: Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. CONCLUSIONS: The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.

Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle.

BACKGROUND: The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (R H,B ) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. RESULTS: Mean LD estimates, measured using the squared correlation of alleles at two loci (r (2)), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r(2) was > 0.2 and 0.3, respectively, for 34 and 25% of adjacent markers in Herefords, and 26 and 17% in Brafords. Estimated N e for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (R H,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (R H,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r(2) > 0.2) was found spanning to ~50 Kb. CONCLUSIONS: Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.

Comparison of three larval bioassays to evaluate susceptibility of Rhipicephalus (Boophilus) microplus to amitraz / Comparação de três bioensaios larvais para avaliar a suscetibilidade de Rhipicephalus (Boophilus) microplus ao amitraz

Field samples of Rhipicephalus (Boophilus) microplus from the state of Rio Grande do Sul, Brazil, were assessed using the following methods: larval packet test (LPT), larval immersion test (LIT) and syringe immersion test (SIT). The following parameters were determined for each population and for the Mozo susceptible reference strain: lethal concentration for 50% (LC50) with its 95% confidence interval (95% CI), regression line slope and resistance ratio (RR). Using the LPT, only one population was susceptible to amitraz, presenting a RR of 1.9. Using the same technique, the other populations presented RRs of between 92.9 and 3445.8 and were considered resistant. The LC50 of the Mozo strain calculated using the LPT, LIT and SIT was 2.9, 27.3, and 52.7 µg/mL, respectively. In general, a good fit to the probit statistical model was only achieved using the LPT. The results obtained in this study impair recommendations for using the LIT and SIT to diagnose amitraz resistance in R. (B.) microplus populations. Additional studies are required to improve the sensitivity of these tests in relation to the LPT.

Amostras de Rhipicephalus (Boophilus) microplus coletadas à campo no Rio Grande do Sul, Brasil, foram analisadas pelos seguintes métodos: teste do pacote de larvas (TPL), teste de imersão de larvas (TIL) e teste de imersão em seringas (TIS). Os seguintes parâmetros foram determinados para cada população e para a amostra referência suscetível Mozo: concentração letal para 50% (CL50) e seu intervalo de confiança de 95% (IC95%), inclinação da reta de regressão e os fatores de resistência (FR). Pelo TPL, apenas uma população foi sensível ao amitraz, com FR de 1,9. Utilizando a mesma técnica, as outras amostras apresentaram FR entre 92,9 e 3445,8 sendo consideradas resistentes. As CL50 da cepa Mozo calculadas por meio do TPL, TIL e TIS foram 2,9, 27,3 e 52,7 µg/mL, respectivamente. De forma geral, a adequação ao modelo estatístico de probitos só foi alcançada com o uso do TPL. Os resultados obtidos no presente estudo limitam a recomendação de uso do TIL e TIS para diagnóstico de resistência ao amitraz em populações de R. (B.) microplus. Estudos adicionais são necessários para aprimorar a sensibilidade destes testes em relação ao LPT.

Comparison of three larval bioassays to evaluate susceptibility of Rhipicephalus (Boophilus) microplus to amitraz.

Field samples of Rhipicephalus (Boophilus) microplus from the state of Rio Grande do Sul, Brazil, were assessed using the following methods: larval packet test (LPT), larval immersion test (LIT) and syringe immersion test (SIT). The following parameters were determined for each population and for the Mozo susceptible reference strain: lethal concentration for 50% (LC50) with its 95% confidence interval (95% CI), regression line slope and resistance ratio (RR). Using the LPT, only one population was susceptible to amitraz, presenting a RR of 1.9. Using the same technique, the other populations presented RRs of between 92.9 and 3445.8 and were considered resistant. The LC50 of the Mozo strain calculated using the LPT, LIT and SIT was 2.9, 27.3, and 52.7 µg/mL, respectively. In general, a good fit to the probit statistical model was only achieved using the LPT. The results obtained in this study impair recommendations for using the LIT and SIT to diagnose amitraz resistance in R. (B.) microplus populations. Additional studies are required to improve the sensitivity of these tests in relation to the LPT.