In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBV) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits, such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential for choosing the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season, HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree ( A: ) and genomic ( G: ) relationship matrices were considered. The genetic parameters (variance components, h(2) and genetic correlations) were very similar when estimated using the A: and G: relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G: matrix analysis, SNP by environment interactions were observed. For some SNP, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBV for "juvenile" boars varying from 0.14 to 0.44 across different HYS levels, while the accuracy of the standard genomic prediction model, without reaction norms, varied from 0.09 to 0.28. These results show that it is important and feasible to consider G×E interactions in evaluations of sires using genomic prediction models and that genomic information can increase the accuracy of selection across environments.
BackgroundIn recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines.ResultsWe identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway.ConclusionsWe identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0412-z) contains supplementary material, which is available to authorized users.
Linkage disequilibrium (LD) across the genome is critical information for association studies and genomic selection because it determines the number of SNP that should be used for a successful association analysis and genomic selection. Linkage disequilibrium also influences the accuracy of genomic breeding values. Some studies have demonstrated that SNP in strong LD are organized into discrete blocks of haplotypes, which are separated by possibly hot spots of recombination. To reduce the number of markers needed to be genotyped for association mapping, a set of SNP can be selected that labels all haplotype blocks. We estimated the LD, calculated the average haplotype block size for 6 pig lines, and compared the block size between lines. Six commercial pig lines were genotyped using the Illumina PorcineSNP60 (number of markers M = 62,163) Genotyping BeadChip (Illumina Inc.); on average, a panel of 37,623 SNP with an average minor allelic frequency (MAF) of 0.283 was included in the analysis. The LD declined as a function of distance. All pig lines had an average r(2) above 0.3 for markers 100 to 150 apart. The estimated average block size was 394.885 kb, and blocks between 100 and 400 kb were most prominent (49.96%) in all lines. These results showed that the extent of LD in pigs is much larger than in the cattle population, in accordance with the genetic map length of pigs, which is much shorter than cattle. The evaluated lines have 2,640 to 3,037 blocks, covering 45% of the pig genome, on average. Differences in haplotype block size between lines were observed for some chromosomes (i.e., SSC 3, 5, 7, 13, 14, and 18), which provide a direction for future studies of haplotype block conservation or divergence across lines.
BackgroundReproductive traits such as number of stillborn piglets (SB) and number of teats (NT) have been evaluated in many genome-wide association studies (GWAS). Most of these GWAS were performed under the assumption that these traits were normally distributed. However, both SB and NT are discrete (e.g. count) variables. Therefore, it is necessary to test for better fit of other appropriate statistical models based on discrete distributions. In addition, although many GWAS have been performed, the biological meaning of the identified candidate genes, as well as their functional relationships still need to be better understood. Here, we performed and tested a Bayesian treatment of a GWAS model assuming a Poisson distribution for SB and NT in a commercial pig line. To explore the biological role of the genes that underlie SB and NT and identify the most likely candidate genes, we used the most significant single nucleotide polymorphisms (SNPs), to collect related genes and generated gene-transcription factor (TF) networks.ResultsComparisons of the Poisson and Gaussian distributions showed that the Poisson model was appropriate for SB, while the Gaussian was appropriate for NT. The fitted GWAS models indicated 18 and 65 significant SNPs with one and nine quantitative trait locus (QTL) regions within which 18 and 57 related genes were identified for SB and NT, respectively. Based on the related TF, we selected the most representative TF for each trait and constructed a gene-TF network of gene-gene interactions and identified new candidate genes.ConclusionsOur comparative analyses showed that the Poisson model presented the best fit for SB. Thus, to increase the accuracy of GWAS, counting models should be considered for this kind of trait. We identified multiple candidate genes (e.g. PTP4A2, NPHP1, and CYP24A1 for SB and YLPM1, SYNDIG1L, TGFB3, and VRTN for NT) and TF (e.g. NF-κB and KLF4 for SB and SOX9 and ELF5 for NT), which were consistent with known newborn survival traits (e.g. congenital heart disease in fetuses and kidney diseases and diabetes in the mother) and mammary gland biology (e.g. mammary gland development and body length).Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0189-x) contains supplementary material, which is available to authorized users.
BackgroundGenomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses.ResultsAlmost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb.ConclusionsThis study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0126-3) contains supplementary material, which is available to authorized users.
RESUMO -Foram utilizados 960 pintos, metade machos e metade fêmeas, no período de 1 a 21 dias idade, com peso inicial médio de 42,5 e 42,1g, respectivamente. O delineamento experimental utilizado foi em blocos casualizados, com seis tratamentos, dois sexos, quatro repetições por sexo e vinte aves por unidade experimental. Os tratamentos consistiram de uma dieta basal deficiente em fósforo (0,150%), suplementada com fósforo disponível, provenientes do fosfato bicálcico (0,0; 0,10; 0,20; 0,30; 0,40; e 0,50%). As variáveis avaliadas foram ganho de peso (GP), consumo de ração (CR), conversão alimentar (CA), resistência dos ossos à quebra (ROQ), cinzas (CO) e fósforo no osso (PO). As exigências em fósforo disponível foram estimadas por intermédio dos modelos de regressão polinomial e LRP. As suplementações com fósforo disponível influenciaram o GP, CR, CA, ROQ, CO e PO, tanto para os machos como para as fêmeas. As estimativas de exigências de P-disp variaram de 0,259 (0,085%/Mcal de EM) a 0,559% (0,184%/Mcal de EM), para os machos, e de 0,307% (0,092%/Mcal de EM) a 0,575% (0,190%/Mcal de EM) para as fêmeas. Entretanto, considerando as respostas biológicas, para as variáveis de desempenho e características ósseas, pode-se sugerir que a exigência de fósforo disponível, para frangos de corte machos e fêmeas, de 1 a 21 dias de idade, é de 0,45 ou 0,148% de Pdisp/Mcal de EM. Palavras-chave: exigência de fósforo disponível, frangos, fase inicial Available Phosphorus Requirement of Male and Female Broilers from 1 to 21 Days of AgeABSTRACT -Ninety and sixty Hubbard one-day-old broilers chicks, half male and half female, were used at the initial phase, from 1 to 21 days of age, with initial weight of 42.5 and 42.1g, respectively. The chicks were allotted to a randomized block design, with six treatments, two sexes, four replicates per sex and twenty animals per experimental unity. The treatments consisted on deficient basal diet in available phosphorus (.15%), supplemented with available phosphorus from dicalcium phosphate (0, 0.10, 0.20, 0.30, 0.40, and 0.50%). The weight gain (GP), feed intake (CR), feed: gain (CA), bone fracture resistance (BFR), ashes (AO) and phosphorus in the bone (PO) were the evaluated variables. The available phosphorus requirements were estimated by means of the regression polynomial and linear response plateau models. The supplemented levels of available phosphorus affected the GP, CR, CA, BFR, AO and PO, for males and females. The requirement estimates of available phosphorus ranged from 0,259 (.089%/Mcal ME) to .559%
RESUMO -Utilizaram-se 153.963 controles mensais de produção de leite e 13.273 primeiras lactações de vacas da raça Holandesa, com partos entre 1989 a 1998, com o objetivo de estimar parâmetros genéticos, fenotípicos e de meio ambiente para produção de leite no dia do controle (PLDC) e produção até 305 dias de lactação (P305), bem como verificar a conveniência de se utilizar a PLDC em avaliações genéticas, em substituição à P305. Foram utilizados quatro modelos (modelo animal). Em dois, modelos 1 e 2, consideraramse os controles mensais de produção, coletados ao longo da lactação, como medidas repetidas de um animal, diferenciados segundo o critério de formação de grupos de animais contemporâneos. No modelo 1 (PLDCM01), as produções dos animais foram agrupadas segundo o rebanho-ano-estação de controle de produção, enquanto, no modelo 2 (PLDCM02), o agrupamento considerou o rebanho-ano-estação de parto. No modelo 3, analisaram-se os controles mensais de produção, como características individuais (C01 até C10); e no modelo 4, analisou-se a tradicional P305. As análises foram realizadas utilizando-se o método da Máxima Verossimilhança Restrita, por meio do sistema MTDFREML. As estimativas de herdabilidade para PLDC, com o uso do modelo 1, modelo 2 e para P305, foram de 0,27, 0,15 e 0,25, respectivamente. As herdabilidades para os controles mensais variaram de 0,11±0,02 (C01) a 0,21±0,03 (C08), e os maiores valores ocorreram a partir do quarto mês. A correlação de ordem entre os valores genéticos obtidos, para P305 e para PLDC (modelo 1), foi de 0,62, para touros, e de 0,78, para vacas. Concluiu-se que é viável a utilização da PLDC em estudos envolvendo a produção de leite e que os controles do meio da lactação, se usados para seleção, podem apresentar vantagens em relação à P305.Palavras-chave: controle mensal, método REML, modelo animal, produção de leite, raça Holandesa Genetic Evaluation of Holstein Cattle Using Test Day Milk YieldABSTRACT -153,963 test day milk yield records and 13,273 first lactations of Holstein cows calving between 1989 and 1998, were used with the objective of estimating genetic, phenotypic and environmental parameters for test day milk yield (PLDC) and 305 day milk yield (P305) and to study the convenience of using test day yields in genetic evaluations to replace P305. Four models were used. Models 1 and 2 differed according contemporary grouping and monthly milk records were considered as repeated measures. In model 1 (PLDCM01) records were grouped by herd-year-season of test day yield and in model 2 (PLDCM02) by herd-year-season of calving. In a third (model 3), monthly yield records were analyzed as individual traits (C01 to C10); and the fourth (model 4) was the traditional 305-day model. Restricted Maximum Likelihood methodology was used with the MTDFREML system. The estimates of heritability for PLDC, using model 1, model 2 and for P305 were 0.27, 0.15 and 0.25, respectively. Heritabilities for monthly milk records ranged from 0.11+0.02 (C01) to 0.21+0.03 (C08), with the largest valu...
The objective of this work was to evaluate the efficiency of the supervised independent component regression (SICR) method for the estimation of genomic values and the SNP marker effects for boar taint and carcass traits in pigs. The methods were evaluated via the agreement between the predicted genetic values and the corrected phenotypes observed by cross-validation. These values were also compared with other methods generally used for the same purposes, such as RR-BLUP, SPCR, SPLS, ICR, PCR and PLS. The SICR method was found to have the most accurate prediction values.
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