Associations between microsatellite markers and traits related to performance, carcass and organs in chickens

Associations between four microsatellite markers on chromosome 11 and five on chromosome 13 with performance, carcass and organs traits were investigated in chickens using a least-squares approach applied to single-marker analysis. Three hundred and twenty seven F 2 chickens from the EMBRAPA broiler×layer experimental population were evaluated for 16 traits: five related to performance, five to carcass and five to organs, plus the hematocrit. Two significance thresholds were considered: p<0.05 and p<0.0056; the last value resulted from the application of a multiple tests analyses correction. On chromosome 11, six associations (p<0.05) between the genotypes of two markers with four growth related and one carcass trait were found. On chromosome 13, six associations (p<0.05) between marker genotypes and three performance traits, eight associations (p<0.05) between marker genotypes and two carcass traits and eight associations (p<0.05) between marker genotypes and four organs traits were detected. These associations were indications of the presence of quantitative trait loci on these chromosomes, especially on chromosome 13. In this chromosome, the strongest evidence was for body weight at 41 days of age and percentage of carcass because the p-values exceeded the multiple test threshold (p<0.0056), but also for breast percentage and heart weight due to the large number of markers (four) on chromosome 13 associated with each one of these traits. These associations should be further investigated by interval mapping analyses to find QTL positions and to allow the estimation of their effects. © Asian Network for Scientific Information, 2009.

Genetic correlations between mature cow weight and productive and reproductive traits in Nellore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens

In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellulardifferentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P < 0.05), and SNP g.651G>A in FGFBP2 was associated with thawing loss and meat redness content (P < 0.05). Four haplotypes were constructed based on 2 SNPs and were associated with breast weight, thawing loss, and meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits. © FUNPEC-RP.

Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens

Two functional and positional candidate genes were selected in a region of chicken chromosome 1 (GGA1), based on their biological roles, and also where several quantitative trait loci (QTL) have been mapped and associated with performance, fatness and carcass traits in chickens. The insulin-like growth factor 1 (IGF1) gene has been associated with several physiological functions related to growth. The lysine (K)-specific demethylase 5A (KDM5A) gene participates in the epigenetic regulation of genes involved with the cell cycle. Our objective was to find associations of selected single-nucleotide polymorphisms (SNPs) in these genes with performance, fatness and carcass traits in 165 F2 chickens from a resource population. In the IGF1 gene, 17 SNPs were detected, and in the KDM5A gene, nine SNPs were detected. IGF1 SNP c. 47673G > A was associated with body weight and haematocrit percentage, and also with feed intake and percentages of abdominal fat and gizzard genotype × sex interactions. KDM5A SNP c. 34208C > T genotype × sex interaction affected body weight, feed intake, percentages of abdominal fat (p = 0. 0001), carcass, gizzard and haematocrit. A strong association of the diplotype × sex interaction (p < 0. 0001) with abdominal fat was observed, and also associations with body weight, feed intake, percentages of carcass, drums and thighs, gizzard and haematocrit. Our findings suggest that the KDM5A gene might play an important role in the abdominal fat deposition in chickens. The IGF1 and KDM5A genes are strong candidates to explain the QTL mapped in this region of GGA1. © 2012 Institute of Plant Genetics, Polish Academy of Sciences, Poznan.

Genetic Parameters for Growth Traits of Mediterranean Buffaloes from Brazil, Estimated By Bayesian Inference

Quantitative analysis of growth genetic parameters is not available for many breeds of buffaloes making selection and breeding decisions an empirical process that lacks robustness. The objective of this study was to estimate heritability for birth weight (BW), weight at 205 days (W205) and 365 days (W365) of age using Bayesian inference. The Brazilian Program for Genetic Improvement of Buffaloes provided the data. For the traits BW, W205 and W365 of Brazilian Mediterranean buffaloes 5169, 3792 and 3883 observations have been employed for the analysis, respectively. In order to obtain the estimates of variance, univariate analyses were conducted using the Gibbs sampler included in the MTGSAM software. The model for BW, W205 and W365 included additive direct and maternal genetic random effects, random maternal permanent environmental effect and contemporary group that was treated as a fixed effect. The convergence diagnosis was performed employing Geweke, a method that uses an algorithm from the Bayesian Output Analysis package that was implemented using R software environment. The average values for weight traits were 37.6 +/- 4.7 kg for BW, 192.7 +/- 40.3 kg for W205 and 298.6 +/- 67.4 kg for W365. The heritability posterior distributions for direct and maternal effects were symmetric and close to those expected in a normal distribution. Direct heritability estimates obtained using the modes were 0.30 (BW), 0.52 (W205) and 0.54 (W365). The maternal heritability coefficient estimates were 0.31, 0.19 and 0.21 for BW, W205 and W365, respectively. Our data suggests that all growth traits and mainly W205 and W365, have clear potential for yield improvement through direct genetic selection.

A Genome-Wide Association Study for Morphometric Traits in Quarter Horse

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of IGF1, GH, and PIT1 markers on the genetic parameters of growth and reproduction traits in Canchim cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

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.

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.

QUANTITATIVE TRAIT LOCI FOR AGRONOMIC AND END-USE QUALITY PERFORMANCE AND THE EFFECT OF SOILBORNE WHEAT MOSAIC VIRUS IN A HARD WINTER WHEAT POPULATION IN NEBRASKA

To better understand agronomic and end-use quality in wheat (Triticum aestivum L.) we developed a population containing 154 F6:8 recombinant inbred lines (RILs) from the cross TAM107-R7/Arlin. The parental lines and RILs were phenotyped at six environments in Nebraska and differed for resistance to Wheat soilborne mosaic virus (WSBMV), morphological, agronomic, and end-use quality traits. Additionally, a 2300 cM genome-wide linkage map was created for quantitative trait loci (QTL) analysis. Based on our results across multiple environments, the best RILs could be used for cultivar improvement. The population and marker data are publicly available for interested researchers for future research. The population was used to determine the effect of WSBMV on agronomic and end-use quality and for the mapping of a resistance locus. Results from two infected environments showed that all but two agronomic traits were significantly affected by the disease. Specifically, the disease reduced grain yield by 30% of susceptible RILs and they flowered 5 d later and were 11 cm shorter. End-use quality traits were not negatively affected but flour protein content was increased in susceptible RILs. The resistance locus SbmTmr1 mapped to 27.1 cM near marker wPt-5870 on chromosome 5DL using ELISA data. Finally, we investigated how WSBMV affected QTL detection in the population. QTLs were mapped at two WSBMV infected environments, four uninfected environments, and in the resistant and susceptible RIL subpopulations in the infected environments. Fifty-two significant (LOD≥3) QTLs were mapped in RILs at uninfected environments. Many of the QTLs were pleiotropic or closely linked at 6 chromosomal regions. Forty-seven QTLs were mapped in RILs at WSBMV infected environments. Comparisons between uninfected and infected environments identified 20 common QTLs and 21 environmentally specific QTLs. Finally, 24 QTLs were determined to be affected by WSBMV by comparing the subpopulations in QTL analyses within the same environment. The comparisons were statistically validated using marker by disease interactions. These results showed that QTLs can be affected by WSBMV and careful interpretation of QTL results is needed where biotic stresses are present. Finally, beneficial QTLs not affected by WSBMV or the environment are candidates for marker-assisted selection.

Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus)

Abstract Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

Gene expression and phenotypic traits of Aggregatibacter actinomycetemcomitans in response to environmental changes

Background and Objective: Periodontopathogens experience several challenges in the oral cavity that may influence their transcription profile and resulting phenotype. This study evaluated the effect of environmental changes on phenotype and gene expression in a serotype b Aggregatibacter actinomycetemcomitans isolate. Material and Methods: Cultures in early exponential phase and at the start of stationary growth phase in microaerophilic and anaerobic atmospheres were evaluated. Cell hydrophobic properties were measured by adherence to n-hexadecane; in addition, adhesion to, and the ability to invade, KB cells was evaluated. Relative transcription of 12 virulence-associated genes was determined by real-time reverse transcritption quantitative PCR. Results: The culture conditions tested in this study were found to influence the phenotypic and genotypic traits of A. actinomycetemcomitans. Cells cultured in microaerophilic conditions were the most hydrophobic, reached the highest adhesion efficiency and showed up-regulation of omp100 (which encodes an adhesion) and pga (related to polysaccharide synthesis). Cells grown anaerobically were more invasive to epithelial cells and showed up-regulation of genes involved in host-cell invasion or apoptosis induction (such as apaH, omp29, cagE and cdtB) and in adhesion to extracellular matrix protein (emaA). Conclusion: Environmental conditions of different oral habitats may influence the expression of factors involved in the binding of A. actinomycetemcomitans to host tissues and the damage resulting thereby, and thus should be considered in in-vitro studies assessing its pathogenic potential.

A candidate gene approach to identify DNA markers associated with meat quality and production traits: investigation of several cathepsin genes in Italian heavy pigs.

The cathepsin enzymes represent an important family of lysosomal proteinases with a broad spectrum of functions in many, if not in all, tissues and cell types. In addition to their primary role during the normal protein turnover, they possess highly specific proteolytic activities, including antigen processing in the immune response and a direct role in the development of obesity and tumours. In pigs, the involvement of cathepsin enzymes in proteolytic processes have important effects during the conversion of muscle to meat, due to their influence on meat texture and sensory characteristics, mainly in seasoned products. Their contribution is fundamental in flavour development of dry-curing hams. However, several authors have demonstrated that high cathepsin activity, in particular of cathepsin B, is correlated to defects of these products, such as an excessive meat softness together with abnormal free tyrosine content, astringent or metallic aftertastes and formation of a white film on the cut surface. Thus, investigation of their genetic variability could be useful to identify DNA markers associated with these dry cured hams parameters, but also with meat quality, production and carcass traits in Italian heavy pigs. Unfortunately, no association has been found between cathepsin markers and meat quality traits so far, in particular with cathepsin B activity, suggesting that other genes, besides these, affect meat quality parameters. Nevertheless, significant associations were observed with several carcass and production traits in pigs. A recent study has demonstrated that different single nucleotide polymorphisms (SNPs) localized in cathepsin D (CTSD), F (CTSF), H and Z genes were highly associated with growth, fat deposition and production traits in an Italian Large White pig population. The aim of this thesis was to confirm some of these results in other pig populations and identify new cathepsin markers in order to evaluate their effects on cathepsin activity and other production traits. Furthermore, starting from the data obtained in previous studies on CTSD gene, we also analyzed the known polymorphism located in the insulin-like growth factor 2 gene (IGF2 intron3-g.3072G>A). This marker is considered the causative mutation for the quantitative trait loci (QTL) affecting muscle mass and fat deposition in pigs. Since IGF2 maps very close to CTSD on porcine chromosome (SSC) 2, we wanted to clarify if the effects of the CTSD marker were due to linkage disequilibrium with the IGF2 intron3-g.3072G>A mutation or not. In the first chapter, we reported the results from these two SSC2 gene markers. First of all, we evaluated the effects of the IGF2 intron3-g.3072G>A polymorphism in the Italian Large White breed, for which no previous studies have analysed this marker. Highly significant associations were identified with all estimated breeding values for production and carcass traits (P<0.00001), while no effects were observed for meat quality traits. Instead, the IGF2 intron3-g.3072G>A mutation did not show any associations with the analyzed traits in the Italian Duroc pigs, probably due to the low level of variability at this polymorphic site for this breed. In the same Duroc pig population, significant associations were obtained for the CTSD marker for all production and carcass traits (P < 0.001), after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A polymorphism were also confirmed in a group of Italian Large White pigs homozygous for the IGF2 intron3-g.3072G allele G (IGF2 intron3-g.3072GG) and by haplotype analysis between the markers of the two considered genes. Taken together, all these data indicated that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition in pigs. In the second chapter, we reported the analysis of two new SNPs identified in cathepsin L (CTSL) and cathepsin S (CTSS) genes and the association results with meat quality parameters (including cathepsin B activity) and several production traits in an Italian Large White pig population. Allele frequencies of these two markers were evaluated in 7 different pig breeds. Furthermore, we mapped using a radiation hybrid panel the CTSS gene on SSC4. Association studies with several production traits, carried out in 268 Italian Large White pigs, indicated positive effects of the CTSL polymorphism on average daily gain, weight of lean cuts and backfat thickness (P<0.05). The results for these latter traits were also confirmed using a selective genotype approach in other Italian Large White pigs (P<0.01). In the 268 pig group, the CTSS polymorphism was associated with feed:gain ratio and average daily gain (P<0.05). Instead, no association was observed between the analysed markers and meat quality parameters. Finally, we wanted to verify if the positive results obtained for the cathepsin L and S markers and for other previous identified SNPs (cathepsin F, cathepsin Z and their inhibitor cystatin B) were confirmed in the Italian Duroc pig breed (third chapter). We analysed them in two groups of Duroc pigs: the first group was made of 218 performance-tested pigs not selected by any phenotypic criteria, the second group was made of 100 Italian Duroc pigs extreme and divergent for visible intermuscular fat trait. In the first group, the CTSL polymorphism was associated with weight of lean cuts (P<0.05), while suggestive associations were obtained for average daily gain and backfat thickness (P<0.10). Allele frequencies of the CTSL gene marker also differed positively among the visible intermuscular extreme tails. Instead, no positive effects were observed for the other DNA markers on the analysed traits. In conclusion, in agreement with the present data and for the biological role of these enzymes, the porcine CTSD and CTSL markers: a) may have a direct effect in the biological mechanisms involved in determining fat and lean meat content in pigs, or b) these markers could be very close to the putative functional mutation(s) present in other genes. These findings have important practical applications, in particular the CTSD and CTSL mutations could be applied in a marker assisted selection (MAS) both in the Italian Large White and Italian Duroc breeds. Marker assisted selection could also increase in efficiency by adding information from the cathepsin S genotype, but only in the Italian Large White breed.

A multiparental cross population for mapping QTL for relevant agronomic traits in durum wheat (Triticum durum Desf.)

Multiparental cross designs for mapping quantitative trait loci (QTL) in crops are efficient alternatives to conventional biparental experimental populations because they exploit a broader genetic basis and higher mapping resolution. We describe the development and deployment of a multiparental recombinant inbred line (RIL) population in durum wheat (Triticum durum Desf.) obtained by crossing four elite cultivars characterized by different traits of agronomic value. A linkage map spanning 2,663 cM and including 7,594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs with a wheat-dedicated 90k SNP chip. A cluster file was developed for correct allele calling in the framework of the tetraploid durum wheat genome. Based on phenotypic data collected over four field experiments, a multi-trait quantitative trait loci (QTL) analysis was carried out for 18 traits of agronomic relevance (including yield, yield-components, morpho-physiological and seed quality traits). Across environments, a total of 63 QTL were identified and characterized in terms of the four founder haplotypes. We mapped two QTL for grain yield across environments and 23 QTL for grain yield components. A novel major QTL for number of grain per spikelet/ear was mapped on chr 2A and shown to control up to 39% of phenotypic variance in this cross. Functionally different QTL alleles, in terms of direction and size of genetic effect, were distributed among the four parents. Based on the occurrence of QTL-clusters, we characterized the breeding values (in terms of effects on yield) of most of QTL for heading and maturity as well as yield component and quality QTL. This multiparental RIL population provides the wheat community with a highly informative QTL mapping resource enabling the dissection of the genetic architecture of multiple agronomic relevant traits in durum wheat.

Sequential Quantitative Trait Locus Mapping in Experimental Crosses

The etiology of complex diseases is heterogeneous. The presence of risk alleles in one or more genetic loci affects the function of a variety of intermediate biological pathways, resulting in the overt expression of disease. Hence, there is an increasing focus on identifying the genetic basis of disease by sytematically studying phenotypic traits pertaining to the underlying biological functions. In this paper we focus on identifying genetic loci linked to quantitative phenotypic traits in experimental crosses. Such genetic mapping methods often use a one stage design by genotyping all the markers of interest on the available subjects. A genome scan based on single locus or multi-locus models is used to identify the putative loci. Since the number of quantitative trait loci (QTLs) is very likely to be small relative to the number of markers genotyped, a one-stage selective genotyping approach is commonly used to reduce the genotyping burden, whereby markers are genotyped solely on individuals with extreme trait values. This approach is powerful in the presence of a single quantitative trait locus (QTL) but may result in substantial loss of information in the presence of multiple QTLs. Here we investigate the efficiency of sequential two stage designs to identify QTLs in experimental populations. Our investigations for backcross and F2 crosses suggest that genotyping all the markers on 60% of the subjects in Stage 1 and genotyping the chromosomes significant at 20% level using additional subjects in Stage 2 and testing using all the subjects provides an efficient approach to identify the QTLs and utilizes only 70% of the genotyping burden relative to a one stage design, regardless of the heritability and genotyping density. Complex traits are a consequence of multiple QTLs conferring main effects as well as epistatic interactions. We propose a two-stage analytic approach where a single-locus genome scan is conducted in Stage 1 to identify promising chromosomes, and interactions are examined using the loci on these chromosomes in Stage 2. We examine settings under which the two-stage analytic approach provides sufficient power to detect the putative QTLs.