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We proposed a genome association study for pig growth curves based on Bayesian hierarchical framework considering different sets of SNP markers and pedigree. Additionally, we aimed also to identify possible chromosome regions affecting the growth curve parameters using empirical weight-age data from an outbred F2 (Brazilian Piau vs commercial) pig population. Under the proposed hierarchical approach, individual growth trajectories were modeled by the nonlinear Gompertz function, so that the parameter estimates were considered to be affected by additive polygenic, systematic and SNP markers effects. The model assuming jointly pedigree and SNP markers presented the best fit based on Deviance Information Criterion. Heritability estimates ranged from 0.53 to 0.56 and from 0.55 to 0.57, respectively for the parameters mature weight (a) and maturing rate (k). Additionally, we found high and positive genetic correlation (0.78) between “a” and “k”. The percentages of the genetic variances explained by each SNP allowed identifying the most relevant chromosome regions for each phenotype (growth curve parameters). The majority of these regions were closed to QTL regions previously reported for growth traits. However, we identified three relevant SNPs (55840514 bp at SSC17, 55814469 at SSC17 and 76475804 at SSC X) affecting “a” and “k” simultaneously, and three SNPs affecting only “a” (292758 bp at SSC1, 67319 bp at SSC8 and 50290193 bp at SSC17), that are located in regions not previously described as QTL for growth traits in pigs.

A major objective of pork producers is to reduce production cost. Feeding may account for over 75% of pork production costs. Thus, selecting pigs for feed efficiency (FE) traits is a priority in pig breeding programs. While in the Americas, pigs are typically fed high-input diets, based on corn and soybean meal (CS); in Western Europe, pigs are commonly fed diets based on wheat and barley with high amounts of added protein-rich coproducts (WB), e.g., from milling and seed-oil industries. These two feeding scenarios provided a realistic setting for investigating a specific type of genotype by environment interaction; thus, we investigated the genotype by feed interaction (GxF). In the presence of a GxF, different feed compositions should be considered when selecting for FE. This study aimed to 1) verify the presence of a GxF for FE and growth performance traits in different growth phases (starter, grower, and finisher) of 3-way crossbred growing-finishing pigs fed either a CS (547 boars and 558 gilts) or WB (567 boars and 558 gilts) diet; and 2) to assess and compare the expected responses to direct selection under the 2 diets and the expected correlated responses for one diet to indirect selection under the other diet. We found that GxF did not interfere in the ranking of genotypes under both diets for growth, protein deposition, feed intake, energy intake, or feed conversion rate. Therefore, for these traits, we recommend changing the diet of growing-finishing pigs from high-input feed (i.e., CS) to feed with less valuable ingredients, as WB, to reduce production costs and the environmental impact, regardless of which diet is used in selection. We found that GxF interfered in the ranking of genotypes and caused heterogeneity of genetic variance under both diets for lipid deposition (LD), residual energy intake (REI), and residual feed intake (RFI). Thus, selecting pigs under a diet different from the diet used for growing-finishing performance could compromise the LD in all growth phases, compromise the REI and RFI during the starter phase, and severely compromise the REI during the grower phase. In particular, when pigs are required to consume a WB diet for growing-finishing performance, pigs should be selected for FE under the same diet. Breeding pigs for FE under lower-input diets should be considered, because FE traits will become more important and lower-input diets will become more widespread in the near future.

The LocalPork project aims to improve the efficiency of pork production in Brazil. Pigs in Brazil are usually fed a diet based on corn and soybean. Growing these pigs on a diet that includes local alternative ingredients raises a number of questions related to breeding for such an environment. First, what is the economic and environmental impact of alternative local diets. Second, what are the purebred-crossbred genetic correlations and the extent of genotype by environment interaction. Third, how to accurately predict breeding values based on crossbred performance. Performance of pigs in Brazil that are fed a reference or alternative diets was predicted and alternative diets that include Macaúba or other co-products were found to improve the economic and environmental performance of pork production. Genotype by feed interaction was investigated in crossbred pigs that were fed either a corn and soybean based diet or a diet based on wheat, barley and co-products. Genetic correlations between the diets for growth and residual feed intake were found to be high. The genetic correlation between purebreds and crossbreds for residual feed intake was however found to be only moderate, 0.62. Taking into account the breed origin of haplotypes in crossbreds when predicting breeding values did not substantially increase their accuracies. We speculate that the moderate value of the purebred-crossbred genetic correlation is mainly due to GxE caused by differences in environmental factors, other than diet.

We aimed to estimate genetic parameters for semen quality and quantity traits as well as for within-boar variation of these traits to evaluate their inclusion in breeding goals. Genetic parameters were estimated within line using a multiple-trait (4 × 4) repeatability animal model fitted for 5 pig lines, considering 4 semen traits: sperm motility (MOT), sperm progressive motility (PROMOT), log-transformed number of sperm cells per ejaculate (lnNcells), and total morphological abnormalities (ABN). The within-boar variation of these traits was analyzed based on a multiple-trait (2 × 2) approach for SD and average (AVG) and a single-trait analysis for CV. The average heritabilities across the 5 lines estimated by multiple-trait analysis were 0.18 ± 0.07 (MOT), 0.22 ± 0.08 (PROMOT), 0.16 ± 0.04 (lnNcells), and 0.20 ± 0.04 (ABN). The average genetic correlations were favorable between MOT and PROMOT (0.86 ± 0.10), between MOT and ABN (−0.66 ± 0.25), and between PROMOT and ABN (−0.65 ± 0.25). As determined by within-boar variation analysis, AVG exhibited the greatest heritabilities followed by SD and CV, respectively, for the traits MOT and ABN. For PROMOT, average SD heritability was lower than CV heritability, whereas for lnNcells, they were the same. The average genetic correlations between AVG and SD were favorable for MOT (−0.60 ± 0.13), PROMOT (−0.79 ± 0.14), and ABN (0.78 ± 0.17). The moderate heritabilities indicate the possibility of effective selection of boars based on semen traits. Average and SD are proposed as appropriate traits for selection regarding uniformity.

Genome association analyses have been successful in identifying quantitative trait loci (QTLs) for pig body weights measured at a single age. However, when considering the whole weight trajectories over time in the context of genome association analyses, it is important to look at the markers that affect growth curve parameters. The easiest way to consider them is via the two-step method, in which the growth curve parameters and marker effects are estimated separately, thereby resulting in a reduction of the statistical power and the precision of estimates. One efficient solution is to adopt nonlinear mixed models (NMM), which enables a joint modeling of the individual growth curves and marker effects. Our aim was to propose a genome association analysis for growth curves in pigs based on NMM as well as to compare it with the traditional two-step method. In addition, we also aimed to identify the nearest candidate genes related to significant SNP (single nucleotide polymorphism) markers. The NMM presented a higher number of significant SNPs for adult weight (A) and maturity rate (K), and provided a direct way to test SNP significance simultaneously for both the A and K parameters. Furthermore, all significant SNPs from the two-step method were also reported in the NMM analysis. The ontology of the three candidate genes (SH3BGRL2, MAPK14, and MYL9) derived from significant SNPs (simultaneously affecting A and K) allows us to make inferences with regards to their contribution to the pig growth process in the population studied.

Number of teats (NT) is an important trait affecting both piglet’s welfare and the production level of pig farms. Biologically, embryonic mammary gland development requires the coordination of many signaling pathways necessary for the proper development of teats. Several QTL for NT have been identified; however, further analysis is still lacking. Therefore, gene networks derived from genomewide association study (GWAS) results can be used to examine shared pathways and functions of putative candidate genes. Besides, such analyses may also be helpful to understand the genetic diversity between populations for the same trait or traits. In this study, we identified significant SNP for Landrace-based (line C) and Large White–based (line D) dam lines. Besides, gene– transcription factor (TF) networks were constructed aiming to obtain the most likely candidate genes for NT in each line followed by a comparative analysis between both lines to access similarities or dissimilarities at the marker and gene level. We identified 24 and 19 significant SNP (Bayes factor ≥ 100) for lines C and D, respectively. Only 1 significant SNP overlapped both lines. Network analysis illustrated gene interactions consistent with known mammal’s breast biology and captured known TF. We observed different sets of putative candidate genes for NT in each line evaluated that may have common effects on the phenotype. Based on these results, we demonstrated the importance of post-GWAS analyses increasing the biological understanding of relevant genes for a complex trait. Moreover, we believe that this genomic diversity across lines should be taken into account, considering breed-specific reference populations for genomic selection.

The local Brazilian pig breed Piau is a lard-type pig that has undergone a breeding and selection process devised by the veterinarian Antonio Teixeira Vianna in 1939. The objective of the program was to develop a dual purpose animal, that is an animal suitable for the production of both fat and meat. The main characteristics of the Piau breed are rusticity, adaptability and high disease resistance. The conservation status of the breed is threatened, and in 1998, the Pig Breeding Farm at Universidade Federal de Viçosa (UFV, Viçosa, MG, Brazil) started a Piau herd for the purposes of conservation and use in genetic studies. The objectives of the present study were to describe the Piau genetic conservation program of the Universidade Federal de Viçosa (UFV) and to evaluate a range of population parameters to generate information for monitoring and improving the program. Population genetic structure analysis was performed using a pedigree file of 1349 animals and ENDOG v 4.8 software. The Piau conservation program has data and a collection of pedigree registers going back to the introduction of the first animals to the Pig Breeding Farm. The program used mating control, which is based on the mating of animals with the lowest pedigree-based relationships and on the maintenance of all the population's founding families. The effective numbers of founders and ancestors in the studied Piau population are 9 and 8 animals, respectively. The average inbreeding coefficient (F), the average relatedness coefficient (AR) and the effective population size are 6.55 %, 19.74 % and 18.59, respectively. The findings support an increase in the effective population size of this population through the introduction of animals from other populations, as the small number of founders makes inbreeding control difficult. A raça local brasileira Piau é um suíno tipo banha a qual passou por um processo de seleção realizado pelo médico veterinário Antonio Teixeira Vianna em 1939, com o intuito de desenvolver um animal de dupla aptidão, em outras palavras que fosse adequado para a produção de carne e gordura. As principais características da raça são rusticidade, adaptabilidade e resistência a doenças. O status de conservação da raça é ameaçado e em 1998 a Granja de Melhoramento de Suínos da Universidade Federal de Viçosa (UFV, Viçosa, MG, Brazil) iniciou uma criação de suínos da raça Piau com o objetivo de conservála e utilizá-la em estudos genéticos. O objetivo do presente estudo é descrever o programa de conservação da raça Piau da UFV e avaliar uma série de parâmetros populacionais, a fim de gerar informações que possibilitem o monitoramento e a melhoria do programa. Para a análise da estrutura populacional foi utilizado arquivo de pedigree com 1349 indivíduos por meio do software ENDOG v. 4.8. O programa de conservação da raça possui boa estrutura com registro de dados zootécnicos e pedigree desde a introdução dos primeiros animais na granja de melhoramento de suínos, juntamente com o controle de acasalamentos, o qual é baseado no acasalamento de animais com menor coancestralidade e na manutenção das famílias fundadoras. A população de Piau avaliada possui número efetivo de fundadores e ancestrais iguais a 9 e 8, respectivamente. O coeficiente de endogamia médio, coeficiente de relação médio e tamanho efetivo da população são 6,55 %, 19,74 % e 18,59, respectivamente. De acordo com os parâmetros avaliados é recomendado aumentar o tamanho efetivo da população, por meio da introdução de animais de outra população, uma vez que o pequeno número de fundadores torna difícil o controle da endogamia.

Mapeou-se quantitative trait loci (QTL) associados a características de desempenho nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos pertencentes a uma população F2, formada a partir do cruzamento entre dois machos da raça naturalizada brasileira Piau e 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa genético de ligação da população foi construído após a genotipagem dos animais para 35 marcadores microssatélites. As estimativas do conteúdo de informação polimórfica indicaram que os marcadores microssatélites foram adequados para as análises de QTL. Os dados foram analisados pelo mapeamento por intervalo usando-se o programa GridQTL. Encontraram-se seis QTL, sendo que o QTL genômico para idade ao abate atingiu a significância de 5% de probabilidade. As informações dos QTL detectados neste estudo são úteis para identificar genes que podem ser usados em conjunto com os métodos convencionais de seleção, aumentar a acurácia deles e prover uma compreensão dos fenótipos produtivos de suínos. The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this population was constructed after genotyping the animals for 35 microsatellite markers. Estimates of polymorphic information content indicated that the microsatellite markers were appropriate for QTL analyses. The genotypes were analyzed by interval mapping using the GridQTL program. A total of six QTL were found, of which the QTL for slaughter age (days) was significant at the 5% genome-wise level. The information of the significant QTL detected in this study is useful for future fine-mapping studies for the identification of genes. Such information can be used together with traditional methods in breeding programs or even for a better understanding of the phenotypes of swine production.

The components of the insulin-like growth factor (IGF) system appear to be involved in regulation of ovarian follicular growth and atresia in the pig. We investigated the expression pattern of mRNAs for IGF1 (IGF1), its binding proteins (IGFBP1, IGFBP2, IGFBP3, and IGFBP5), and epidermal growth factor in swine follicle cells and ovarian tissue throughout the estrous cycle using the real-time quantitative PCR technique. The results of gene expression were analyzed using linear regression with gene expression as a dependent variable and days of estrous cycle as an independent variable. Additionally, an analysis was made of the correlation of expression levels with plasma concentration of follicle-stimulating hormone, luteinizing hormone, estradiol-17β, progesterone, and prolactin. Expression of mRNA of all of these genes was detected in granulosa cells and ovarian tissue. IGFBP3 mRNA showed a quadratic expression pattern (P ≤ 0.001) and was significantly and positively correlated with progesterone (r = 0.81; P ≤ 0.01) but negatively correlated with prolactin (r = -0.596; P ≤ 0.05). Expression of the other genes was unaffected by the stage of the estrous cycle. Realtime quantitative PCR effectively detected all transcripts, including the very low levels of IGFBP1 transcripts, and could be used for studies of follicle dynamics.

The bovine tick Rhipicephalus (Boophilus) microplus causes major losses in cattle production systems in tropical regions. Bos indicus breeds are more resistant to ticks than B. taurus breeds. Resistance genes could be an alternative to control this parasite. We examined the pattern of gene expression of three calcium-binding-protein genes: translationally controlled tumor protein 1 (TPT1), allergen Bos d3 (S100A7), calcium channel protein transient receptor potential vanilloid 6 (TRPV6), and the cysteine proteinase inhibitor gene (CST6). These genes were selected from cDNA libraries prepared from skin biopsies taken from resistant and susceptible Gyr x Holstein F₂ animals. These biopsies were also used to study the expression level of these genes through real-time PCR analysis. The relative expression levels of the S100A7, TPT1, TRPV6, and CST6 genes were 2.01 ± 0.6, 1.32 ± 0.9, 1.53 ± 1.2, and 2.03 ± 0.7 times higher in the susceptible group, respectively. Skin lesion tissue from the susceptible animals showed significantly more mRNA transcripts of these genes in comparison with the resistant animals (P = 0.001). However, this hypersensitivity does not seem to protect the susceptible animals against tick infestation.

Seventy-two pigs of three genetic groups (Brazilian indigenous breed Piau, Commercial line and Crossbred) of both sexes were slaughtered at four live weights (30, 60, 90 and 120 kg). Intramuscular fat (IMF) content in Longissimus dorsi muscle of each animal was extracted and correlated with candidate gene mRNA expression (ATN1, EEF1A2, FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1). Within slaughter weight of 120 kg, Piau and Crossbred pigs showed higher IMF content (p < 0.05) than commercial animals, with 2.48, 2.08 and 1.00% respectively. Barrows presented higher values of IMF (p < 0.05) than gilts (1.54 and 1.30% respectively). Gene expression of EEF1A2, FABP3, LDLR, OBSCN, PDHB, TRDN and RYR1 were correlated with IMF (p < 0.05) using the whole dataset. For Piau data only, expression of FABP3, LDLR, MGP, OBSCN, PDHB, TRDN and RYR1 showed correlation with IMF (p < 0.05). Genes that have important roles in lipid transportation inside the cell (FABP3) and tissues (LDLR) showed correlation with IMF of, respectively, 0.68 and 0.63 using the whole data set, and 0.90 and 0.91 using data from Piau animals. The highly positive correlation of the LDLR and FAPB3 expression with IMF content may confirm that these genes are important for fat deposition in the porcine L. dorsi muscle.

Using principal component analysis, records of 435 animals from an F2 swine population were used to identity independent and informative variables of economically important performance. The following performance traits were recorded: litter size at birth (BL), litter size at weaning (WL), teat number (TN), birth weight (BW), weight at 21 (W21), 42 (W42), 63 (W63) and 77 (W77) days of age, average daily gain (ADG), feed intake (FI) and feed:gain ratio (FGR) from 77 to 105 days of age. Six principal components expressed variation lower than 0.7 (eigen values lower than 0.7) suggesting that six variables could be discarded with little information loss. The discarded variables present significant simple linear correlation with the retained variables. Retaining variables BL, TN, W77, FI and FGR and eliminating all the rest would retain most of the relevant information in the original data set. Dados de 435 animais de uma população F2 de suínos foram utilizados para avaliar a possibilidade de redução da dimensão do espaço multivariado, por meio da técnica de componentes principais. Foram avaliadas as seguintes características de desempenho: tamanho da leitegada ao nascer (TLN), tamanho da leitegada à desmama (TLD), número de tetos (NT), pesos ao nascer (PN), aos 21 (P21), aos 42 (P42), aos 63 (P63) e aos 77 (P77) dias de idade e ganho médio de peso diário (GPD), consumo de ração (CR) e conversão alimentar (CA) dos 77 aos 105 dias de idade. Seis componentes principais, obtidos a partir da matriz de correlação, apresentaram variância inferior a 0,7 (autovalores inferiores a 0,7), o que sugere seis variáveis para descarte, por apresentarem maiores coeficientes, em valor absoluto, a partir do último componente principal. As variáveis descartadas apresentaram correlação linear simples significativa com as demais. Em razão do grande número de variáveis redundantes, 54,5% delas podem ser eliminadas, sendo recomendada a avaliação de apenas TLN, NT, P77, CR e CA, sem que haja perda considerável da informação.