Quantitative trait loci for morphometric and mineral composition traits of the tibia bone in a broiler × layer cross.

Many economic losses occur in the poultry industry due to leg fragility. Knowing the genomic regions that influence traits associated with the growth and composition of the leg's bone can help to improve the selection process leading to increased leg resistance to fracture. The present study aimed to map quantitative trait loci (QTL) for mineral composition and morphometric traits of the tibia in 478 animals from an F2 broiler × layer cross. The measurement of weight, length and width of Tibia was carried out at 42 days of age. Ash, dry matter, levels of calcium (Ca), phosphorus (P), magnesium (Mg), Zinc (Zn) and Calcium:Phosphorus (Ca:P) ratio were also recorded. The population was genotyped for 128 microsatellite markers and one single nucleotide polymorphism, covering 2630 cM of the chicken genome. A likelihood ratio test was performed to find QTLs. Additive and dominance effects of the QTLs were included in the model. In the chromosomes 2 (GGA2), 6 (GGA6), 8 (GGA8), 24 (GGA24) and 26 (GGA26) some suggestive QTLs (P<0.00276) were mapped for tibia weight (GGA2 and GGA26), ash percentage (GGA2 and GGA6), dry matter percentage (GGA2), Ca (GGA8 and GGA24) and Ca:P ratio (GGA8), many of which are close to genes already identified as good candidates for those traits. The suggestive QTL on GGA2 has a pleiotropic effect on ash percentage, dry matter and bone weight, whereas in the GGA8 there seems to be two QTLs, one for Ca and another for Ca:P ratio. Thus, this study identified at least five genomic regions, in different chromosomes, that can be targeted for further research to identify potential mutations influencing the development and composition of leg bones in Gallus gallus.

Whole transcriptome analysis of the pectoralis major muscle reveals molecular mechanisms involved with white striping in broiler chickens.

White striping (WS) is one of the most common myopathies identified in broiler chickens leading to substantial production losses, where the incidence reaches 12% in commercial chickens. It occurs primarily in heavier chickens being a modification of the breast muscle characterized by the presence of pale parallel streaks in the same orientation of the muscle fibers. Since the WS etiology remains unclear, we aimed to identify the biological and genetic mechanisms involved in its occurrence through the whole transcriptome analysis of WS in affected and unaffected chicken breast muscles. A total of 11,177 genes were expressed in the pectoralis major muscle. Out of those, 1,441 genes were differentially expressed (FDR ≤ 0.01) between the two analyzed groups, being, respectively, 772 genes upregulated and 669 downregulated in the WS affected group. A total of 36 significantly overrepresented GO terms related to WS myopathy were enriched, and the most relevant biological processes were activation of immune system, angiogenesis, hypoxia, cell death, and striated muscle contraction. The unbalance of those biological processes may trigger the occurrence of the WS phenotype in broilers. The possible lack of capillary blood supply homogeneously in the muscle triggers the hypoxia, following the activation of glycolysis, calcium signaling and apoptosis related genes facilitating the tissue damage and WS incidence.

Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

Association of RUNX2 and TNFSF11 genes with production traits in a paternal broiler line.

Intense selection for production traits has improved the genetic gain of important economic traits. However, selection for performance and carcass traits has led to the onset of locomotors problems and decreasing bone strength in broilers. Thus, genes associated with bone integrity traits have become candidates for genetic studies in order to reduce the impact of bone disorders in broilers. This study investigated the association of the RUNX2 and TNFSF11 genes with 79 traits related to performance, carcass composition, organs, and bone integrity in a paternal broiler line. Analyses of genetic association between single-nucleotide polymorphisms (SNPs) and traits were carried out using the maximum likelihood procedures for mixed models. Genetic associations (P < 0.05) were found between SNP g.124,883A>G in the RUNX2 gene and chilled femur weight (additive plus dominance deviation effects within sex) and with performance traits (additive within sex and additive effects). The SNP g.14,862T>C in the TNFSF11 gene presented genetic associations (P < 0.05) with additive plus dominance deviation effects within sex for performance traits. Suggestive genetic associations (P < 0.10) were found with abdominal fat and its yield. Selection based on SNPs g.14,862T>C in TNFSF11 and g.124,883A>G in RUNX2 could be used to improve performance and carcass quality traits in the population studied, although SNP g.14,862T>C was not in Hardy-Weinberg equilibrium because it was not undergoing a selection process. Furthermore, it is important to validate these markers in an unrelated population for use in the selection process.

The involvement of RUNX2 and SPARC genes in the bacterial chondronecrosis with osteomyelitis in broilers.

Economic losses due to an increase of leg disorders in broilers have become a major concern of the poultry industry. Despite the efforts to reduce skeletal abnormalities in chickens, insufficient progress has been made. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main disorders that affect bone integrity in broilers. However, the genetic pathways and genes involved in most bone problems, including BCO, remains unclear. In this study, femoral samples from male broilers with 45 days of age affected or not with BCO were used to compare the relative expression with a reverse transcription real time PCR approach of 13 candidate genes: SPP1 (osteopontin), TNFRSF11B (osteoprotegerin), SPARC (osteonectin), CALB1 (calbidin 1), CALM (Calmodulin 2), IBSP (sialoprotein), COL1A2 (collagen, type I, α 2), BMP2 (bone morphogenetic protein 2), BMP3 (bone morphogenetic protein 3), RANKL (κ-B nuclear factor ligand), SMAD1 (SMAD family member 1), LEPR (leptin receptor) and RUNX2 (related transcription factor Runt 2). Differential expression test between affected and non-affected groups was performed using the REST software. The RUNX2 and SPARC genes were downregulated (P<0.05) in the affected group, with reduced expression of fourfold when compared with the non-affected group. This result indicates that the downregulation of RUNX2 and SPARC can contribute to an increased incidence of BCO in broilers.

Parâmetros genéticos e efeitos de sexo e cruzamento recíproco sobre características de interesse econômico em aves F2 / Genetic parameters and effects of sex and reciprocal cross on economic traits in F2 broilers

Este estudo teve por objetivo estimar os parâmetros genéticos de características de interesse econômico, mensuradas em populações F2 desenvolvidas pela Embrapa Suínos e Aves utilizando cruzamento recíproco entre linhagens de corte e de postura. Ainda, foram avaliados os efeitos de sexo e de cruzamento recíproco sobre as características em estudo. Os pesos com um, 35 e 42 dias de idade; ganho de peso; consumo de ração e conversão alimentar entre 35 e 41 dias de idade; pesos dos pulmões, fígado, coração, moela, peito, pernas, carcaça, dorso, asas, cabeça, pés e gordura abdominal, além do comprimento do intestino, foram os fenótipos estudados. Foram estimados os componentes de variâncias genética aditiva e residual, além dos coeficientes de herdabilidade e das correlações genética e fenotípica. Os machos apresentaram maior peso para todas as características estudadas, nos dois cruzamentos recíprocos, exceto para gordura abdominal na população oriunda do cruzamento de machos de postura com fêmeas de corte. Os animais oriundos do cruzamento de machos de postura com fêmeas de corte foram mais pesados que os recíprocos, para todas as idades, além de apresentarem maior comprimento de intestino e maiores pesos de moela, carcaça, dorso, peito e cabeça. Os coeficientes de herdabilidade foram altos para consumo de ração e para os pesos ao nascimento, da moela e da gordura abdominal. As correlações fenotípicas estimadas foram, em sua maioria, baixas ou moderadas, contudo muitas correlações genéticas altas foram observadas. Ressalta-se que houve expressiva diferença nos coeficientes de herdabilidade de algumas características em função do cruzamento recíproco estudado, o que pode ser devido a efeitos materno, citoplasmático, ligados ao sexo ou imprinting.(AU)

This study aimed to estimate genetic parameters for several economic traits in F2 populations developed by Embrapa Swine and Poultry National Research Center, through reciprocal crosses of broilers and layer lines. Furthermore, sex and reciprocal cross effects were evaluated. Weights at 1, 35 and 42 days of age; weight gain, feed intake and feed conversion between 35 and 41 days of age; weights of the lungs, heart, liver, gizzard, breast, thighs, carcass, back, wings, head, legs and abdominal fat; and intestine length were studied. Residual and genetic additive variance components, heritability coefficients, and genetic and phenotypic correlations were estimated. Males were heavier than females for all studied traits in both reciprocal crosses, except for abdominal fat weight in chickens from the male layer x female broiler cross. Chickens from male layer x female broiler cross were heavier than those from its reciprocal cross, also having larger intestine length and gizzard, carcass, back, breast and head weights. The heritability coefficients were high for feed intake and body weight at birth, gizzard, and abdominal fat. The estimated phenotypic correlations were mostly lower or moderate, however, most high genetic correlations were observed. We found significant differences in heritability coefficients for some traits due to the reciprocal cross, which may be due maternal, cytoplasmic, sex-linked or imprinting effects.(AU)

Genome-wide association study of periweaning failure-to-thrive syndrome (PFTS) in pigs.

Porcine periweaning-failure-to-thrive syndrome (PFTS) is a condition that affects newly weaned piglets. It is characterised by a progressive debilitation leading to death, in the absence of infectious, nutritional, management or environmental factors. In this study, we present the first report of PFTS in South America and the results of a genome-wide association study to identify the genetic markers associated with the appearance of this condition in a crossbred swine population. Four chromosomal regions were associated with PFTS predisposition, one located on SSCX, one on SSC8, and the two other regions on SSC14. Regions on SSC8 and SSC14 harbour important functional candidate genes involved in human depression and might have an important role in PFTS. Our findings contribute to the increasing knowledge about this syndrome, which has been investigated since 2007, and to the identification of the aetiology of this disease.

Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross.

Rapid growth in broilers is associated with susceptibility to metabolic disorders such as pulmonary hypertension syndrome (ascites) and sudden death. This study describes a genome search for QTL associated with relative weight of cardio respiratory and metabolically important organs (heart, lungs, liver and gizzard), and hematocrit value in a Brazilian broiler-layer cross. QTL with similar or different effects across sexes were investigated. At 42 days of age after fasted for 6 h, the F2 chickens were weighed and slaughtered. Weights and percentages of the weight relative to BW42 of gizzard, heart, lungs, liver and hematocrit were used in the QTL search. Parental, F1 and F2 individuals were genotyped with 128 genetic markers (127 microsatellites and 1 SNP) covering 22 linkage groups. QTL mapping analyses were carried out using mixed models. A total of 11 genome-wide significant QTL and five suggestive linkages were mapped. Thus, genome-wide significant QTL with similar effects across sexes were mapped to GGA2, 4 and 14 for heart weight, and to GGA2, 8 and 12 for gizzard %. Additionally, five genome-wide significant QTL with different effects across sexes were mapped to GGA 8, 19 and 26 for heart weight; GGA26 for heart % and GGA3 for hematocrit value. Five QTL were detected in chromosomal regions where QTL for similar traits were previously mapped in other F2 chicken populations. Seven novel genome-wide significant QTL are reported here, and 21 positional candidate genes in QTL regions were identified.

Comparison of iterated single-step and Bayesian regressions on genomic evaluations for age at 100 kg in swine.

The effects of modified single-step genomic best linear unbiased prediction (ssGBLUP) iterations on GEBV and SNP were investigated using 85,388 age at 100 kg phenotypes from the BRF SA breeding program Landrace pure line animals, off-tested between 2002 and 2013. Pedigree data comprised animals born between 1999 and 2013. A total of 1,068 animals were assigned to the training population, in which all of them had genotypes, original and corrected age at 100 kg phenotypes, and weighted deregressed proof records. A total of 100 genotyped animals, with high accuracy age at 100 kg estimated breeding values, were assigned to the validation population. After applying the quality control workflow, a set of 41,042 SNP was used for the analysis. Standard and modified ssGBLUP, BayesCπ, and Bayesian Lasso were compared, and their predictive abilities were accessed by approximate true and GEBV correlations. Modified ssGBLUP iteration effects on SNP estimates and GEBV were relevant, in which assigned differential weights and shrinkage caused important losses on ssGBLUP predictive ability for age at 100 kg GEBV. Even though ssGBLUP accuracy can be equal or better than the compared Bayesian methods, additional gains can be obtained by correctly identifying the number of iterations required for best ssGBLUP performance.

Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers.

This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P<0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24±0.06 to 0.45±0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02±0.18 for LIVY and BMY to 0.97±0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.

Phenotypic, genetic and environmental parameters for traits related to femur bone integrity and body weight at 42 days of age in a broiler population.

Intense selection among broilers, especially for performance and carcass traits, currently favors locomotion problems and bone resistance. Conducting studies relating to development and growth of bone tissue in broilers is necessary to minimize losses. Thus, genetic parameters were estimated for a broiler population's phenotypic traits such as BW at 42 d of age (BW42), chilled femur weight (CFW) and its yield (CFY), and femur measurements: calcium, DM, magnesium, phosphorus, and zinc content; breaking strength; rigidity; length; and thickness. Variance components were estimated through multitrait analyses using the restricted maximum likelihood method. The model included a fixed group effect (sex and hatch) and additive and residual genetic random effects. The heritability estimates we obtained ranged from 0.10 ± 0.05 to 0.50 ± 0.08 for chilled femur yield and BW42, respectively, and indicated that the traits can respond to the selection process, except for CFY, which presented low-magnitude heritability coefficients. Genetic correlation estimates between breaking strength, rigidity, and traits related to mineral content indicated that selection that aims to improve the breaking strength resistance of the femur is highly correlated with mineral content. Given the genetic correlation estimates between BW42 and minerals, it is suggested that in this population, selection for BW42 can be performed with greater intensity without affecting femoral integrity.

Identification of polymorphisms associated with production traits on chicken (Gallus gallus) chromosome 4.

Genetic selection for production traits has resulted in a rapid improvement in animal performance and development. Previous studies have mapped quantitative trait loci for body weight at 35 and 41 days, and drum and thigh yield, onto chicken chromosome 4. We investigated this region for single nucleotide polymorphisms and their associations with important economic traits. Three positional candidate genes were studied: KLF3 (Krüeppel-like factor 3), SLIT2 (Slit homolog 2), and PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha). Fragment sequencing of these genes was conducted in 11 F1 animals, and one polymorphism in each gene was selected and genotyped in an F2 population (N = 276) and a paternal broiler line TT (N = 840). Associations were identified with growth, carcass, and fat traits in the F2 and the paternal line (P < 0.05). Using single markers in both the F2 and the TT line, KLF3 was associated with weight gain (P < 0.05), PPPARGC1A was associated with liver and wing-parts weights and yields (P < 0.05), and SLIT2 was associated with back yield (P < 0.05) and fat traits (P < 0.05). Using multiple markers, KLF3 lost its significance in both populations, and SLIT2 was associated with feed conversion only in the TT population (P < 0.05). The QTLs mapped in the F2 population could be partly explained by PPARGC1A and SLIT2, which were associated with body weight at 35 and 41 days, respectively, and with drum and thigh yield in the same population. The results of this study indicate the importance of these genes for production traits.

SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition.

Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105,849-112,649 kb). Initially, 94,674 unique SNPs and 10,448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85,765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non-synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non-frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non-tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss-of-function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects.

Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens.

Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci (QTL) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next-generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). A total of 136,054 unique SNPs and 15,496 unique INDELs were detected in this region, and after quality filtering, 123,985 SNPs and 11,298 INDELs were retained. Of these variants, 386 SNPs and 15 INDELs were located in coding regions of genes related to important metabolic pathways. Loss-of-function variants were identified in several genes, and six of those, namely LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1, were related to fat deposition. Therefore, these loss-of-function variants are candidate mutations for conducting further studies on this important trait in chickens.

Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers.

Selection among broilers for performance traits is resulting in locomotion problems and bone disorders, once skeletal structure is not strong enough to support body weight in broilers with high growth rates. In this study, genetic parameters were estimated for body weight at 42 days of age (BW42), and tibia traits (length, width, and weight) in a population of broiler chickens. Quantitative trait loci (QTL) were identified for tibia traits to expand our knowledge of the genetic architecture of the broiler population. Genetic correlations ranged from 0.56 ± 0.18 (between tibia length and BW42) to 0.89 ± 0.06 (between tibia width and weight), suggesting that these traits are either controlled by pleiotropic genes or by genes that are in linkage disequilibrium. For QTL mapping, the genome was scanned with 127 microsatellites, representing a coverage of 2630 cM. Eight QTL were mapped on Gallus gallus chromosomes (GGA): GGA1, GGA4, GGA6, GGA13, and GGA24. The QTL regions for tibia length and weight were mapped on GGA1, between LEI0079 and MCW145 markers. The gene DACH1 is located in this region; this gene acts to form the apical ectodermal ridge, responsible for limb development. Body weight at 42 days of age was included in the model as a covariate for selection effect of bone traits. Two QTL were found for tibia weight on GGA2 and GGA4, and one for tibia width on GGA3. Information originating from these QTL will assist in the search for candidate genes for these bone traits in future studies.

Genetic and phenotypic parameters of carcass and organ traits of broiler chickens.

The objective of this study was to estimate the genetic and environmental parameters for carcass, carcass part, and organ weights in a paternal strain of broiler chickens that was selected mainly for body weight at 42 days of age (BW42) to provide support for poultry genetic improvement programs. A total of 1448 chickens were used that resulted from the expansion of a pure paternal strain named TT, which was developed by Embrapa Suínos e Aves. The following weights were evaluated: BW42, chilled carcass, wing, drumstick meat, thigh meat, breast meat, breast fillet, back, liver, heart (HRT), and gizzard (GIZ). The variance component was estimated by the restricted maximum likelihood method using a multi-trait animal model. The general model included the additive genetic and residual random effects and the fixed effect of the sex-hatch group (10 levels). The heritability estimates ranged from 0.27 ± 0.06 for HRT to 0.44 ± 0.08 for GIZ. These results indicated that all the traits have enough additive genetic variability to respond to selection. The genetic correlation estimates between BW42 and the carcass and carcass part weights were high and positive. However, the genetic correlation estimates between BW42 and organ weights were low. In this population, the carcass traits might respond indirectly to selection applied to BW42. It can be concluded that selection to increase BW42 is not effective in improving broiler organ weight. Therefore, to obtain suitable genetic improvement for these traits, the selection indexes for broilers should include organ weight-based criteria.

Identification and characterization of microRNAs expressed in chicken skeletal muscle.

MicroRNAs (miRNAs, miRs) encompass a class of small non-coding RNAs that often negatively regulate gene expression. miRNAs play an essential role in skeletal muscle, determining the proper development and maintenance of this tissue. In comparison to other organs and tissues, the full set of muscle miRNAs and its expression patterns are still poorly understood. In this report, a chicken skeletal muscle miRNA library was constructed, and the expression of selected miRNAs was further characterized during muscle development in chicken lines with distinct muscling phenotypes. Clone library sequence analysis revealed 40 small RNAs with similarities to previously described chicken miRNAs, seven miRNAs that were never identified before in chicken, and some sequence clusters representing other possible novel miRNAs. Temporal expression profiles of three miRNAs associated with cell proliferation and differentiation (miR-125b, miR-221, and miR-206) in two chicken lines (broiler and layer) revealed the differential steady-state levels of these miRs during skeletal muscle growth and suggests that miR-206 is involved in the muscling phenotype that is observed in growth-selected chicken lines.

Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4.

Interval mapping (IM) implemented in QTL Express or GridQTL is widely used, but presents some limitations, such as restriction to a fixed model, risk of mapping two QTL when there may be only one and no discrimination of two or more QTL using both cofactors located on the same and other chromosomes. These limitations were overcome with composite interval mapping (CIM). We reported QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4 through implementation of CIM and analysis of phenotypic data using mixed models. Thirty-four microsatellite markers were used to genotype 360 F2 chickens from crosses between males from a layer line and females from a broiler line. Sixteen QTL were mapped using CIM and 14 QTL with IM. Furthermore, of those 30 QTL, six were mapped only when CIM was used: for body weight at 35 days (first and third peaks on GGA4), body weight at 41 days (GGA1B and second peak on GGA4), and weights of back and legs (both on GGA4). Three new regions had evidence for QTL presence: one on GGA1B associated with feed intake 35-41 d at 404 cM (LEI0107-ADL0183) and two on GGA4 associated with weight of back at 163 cM (LEI0076-MCW0240) and weight gain 35-41 d, feed efficiency 35-41 d and weight of legs at 241 cM (LEI0085-MCW0174). We dissected one more linked QTL on GGA4, where three QTL for BW35 and two QTL for BW41 were mapped. Therefore, these new regions mapped here need further investigations using high-density SNP to confirm these QTL and identify candidate genes associated with those traits.

Genetic parameters and principal component analysis for egg production from White Leghorn hens.

The objectives of this study were to estimate genetic parameters for accumulated egg production over 3-wk periods and for total egg production over 54 wk of egg-laying, and using principal component analysis (PCA), to explore the relationships among the breeding values of these traits to identify the possible genetic relationships present among them and hence to observe which of them could be used as selection criteria for improving egg production. Egg production was measured among 1,512 females of a line of White Leghorn laying hens. The traits analyzed were the number of eggs produced over partial periods of 3 wk, thus totaling 18 partial periods (P1 to P18), and the total number of eggs produced over the period between the 17 and 70 wk of age (PTOT), thus totaling 54 wk of egg production. Estimates of genetic parameters were obtained by means of the restricted maximum likelihood method, using 2-trait animal models. The PCA was done using the breeding values of partial and total egg production. The heritability estimates ranged from 0.05 ± 0.03 (P1 and P8) to 0.27 ± 0.06 (P4) in the 2-trait analysis. The genetic correlations between PTOT and partial periods ranged from 0.19 ± 0.31 (P1) to 1.00 ± 0.05 (P10, P11, and P12). Despite the high genetic correlation, selection of birds based on P10, P11, and P12 did not result in an increase in PTOT because of the low heritability estimates for these periods (0.06 ± 0.03, 0.12 ± 0.04, and 0.10 ± 0.04, respectively). The PCA showed that egg production can be divided genetically into 4 periods, and that P1 and P2 are independent and have little genetic association with the other periods.