Traits Of Economic Interest Research Articles

Genetic variability in ultrasound records of breast muscle in a broiler breeding program

Breast weight is one of the most economically important traits in the poultry industry, but direct selection for weight is expensive. The use of ultrasonography enables in vivo measurements of the broiler’s breast muscle size, which may be much more feasible for broiler selection. Previous studies of broilers concluded that ultrasound of the breast muscle is feasible and favorable for meat production. According to previously obtained genetic parameters, breast weight could be efficiently improved by ultrasound of the breast muscle. The use of ultrasonography for the indirect selection of breast weight does not affect the body composition or meat quality of broilers, despite the meat’s paleness and shear force; therefore, the use of ultrasound as a selection criterion might be a useful monitoring tool. Studies on the utilization of ultrasound in broiler breeding programs allow a better understanding of the relationship between traits of economic interest and the establishment of the selection schemes.

Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens

Meat quality is an important feature for the poultry industry and is associated with consumer satisfaction. The calpain 1 (CAPN1) gene is related to the tenderness process of meat post- mortem, and the calpain 3 (CAPN3) gene plays an important role in myofibrillar organization and growth. The objective of the present study was to identify polymorphisms in these genes and to determine the association between these polymorphisms and traits of economic interest in poultry. Eleven animals (F₁) from an experimental poultry population at Embrapa Swine and Poultry were used to identify the polymorphisms. Four single nucleotide polymorphisms (SNPs) were found in the CAPN1 gene, and one SNP was found in the CAPN3 gene. A polymorphism from each gene was selected for genotyping in 152 chickens from the Embrapa F₂ experimental population and 311 chickens from a commercial population. Polymorphism g.2554T>C (CAPN1) was associated with body weight at 35 to 42 days, thigh weight, breast weight, carcass weight, and meat lightness content. SNP g.15486C>T (CAPN3) was associated with thigh yield, thawing-cooking loss, and shear force. Results suggest the possibility of using molecular markers in CAPN1 and CAPN3 genes as a tool for performance and meat quality traits in poultry breeding programs.

Genetic variability in ultrasound records of breast muscle in a broiler breeding program

Breast weight is one of the most economically important traits in the poultry industry, but direct selection for weight is expensive. The use of ultrasonography enables in vivo measurements of the broiler’s breast muscle size, which may be much more feasible for broiler selection. Previous studies of broilers concluded that ultrasound of the breast muscle is feasible and favorable for meat production. According to previously obtained genetic parameters, breast weight could be efficiently improved by ultrasound of the breast muscle. The use of ultrasonography for the indirect selection of breast weight does not affect the body composition or meat quality of broilers, despite the meat’s paleness and shear force; therefore, the use of ultrasound as a selection criterion might be a useful monitoring tool. Studies on the utilization of ultrasound in broiler breeding programs allow a better understanding of the relationship between traits of economic interest and the establishment of the selection schemes.

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds1

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.

Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins

Genome-enabled prediction of breeding values using high-density panels (HDP) can be highly accurate, even for young sires. However, the cost of the assay may limit its use to elite animals only. Low-density panels (LDP) containing a subset of single nucleotide polymorphisms (SNP) may give reasonably accurate predictions and could be used cost-effectively with young males and females. This study evaluates strategies for selecting subsets of SNP for several traits, compares predictive ability of LDP with that of HDP, and assesses the benefits of including parent average (PA) as a predictor in models using LDP. Data consisting of progeny-test predicted transmitting ability (PTA) for net merit and 6 other traits of economic interest from 4,783 Holstein sires were evaluated using testing and training sets with regressions on their high-density genotypes and parent averages for net merit index. Additionally, SNP subsets of different sizes were selected using different strategies, including the “best” SNP based on the absolute values of their estimated effects from HDP models for either the trait itself or lifetime net merit, and evenly spaced (ES) SNP across the genome. Overall, HDP models had the best predictive ability, setting an upper bound for the predictive ability of LDP sets. Low-density panels targeting the SNP with strongest effects (for either a single trait or lifetime net merit) provided reasonably accurate predictions and generally outperformed predictions based on evenly spaced SNP. For example, evenly spaced sets would require at least 5,000 to 7,500 SNP to reach 95% of the predictive ability provided by HDP. On the other hand, this level of predictive ability can be achieved with sets of 2,000 SNP when SNP are selected based on magnitude of estimated effects for the trait. Accuracy of predictions based on LDP can be improved markedly by including parent average as a fixed effect in the model; for example, a set with the 1,000 best SNP using the parent average achieved the 95% of the accuracy of a HDP model.

Strategies for Map-Based Cloning in Apple

The apple, Malus × domestica Borkh, is one of the most important temperate fruit crops grown around the world. Although the apple is a diploid (2n = 34), it originated as an allopolyploid and has a relatively small genome size of 750 Mb/haploid. The apple is self-incompatible, highly heterozygous, and displays a juvenile period of 6 to 10 years or more. These characteristics contribute to long-term and difficult efforts to breed new cultivars of apple. However in the past 15 years, significant advances have been made to develop molecular markers linked to traits of economic interest for apple. In turn, these molecular markers have been used to map, clone, and isolate genes. Efforts to pursue map-based cloning in apple have been quite successful in identifying and characterizing target genes, particularly those controlling disease and pest resistance. Strategies of chromosome walking and chromosome landing have provided viable approaches to locate, isolate, and clone some of these genes. In this review, we provide detailed information for these strategies and their use to clone some of these target genes controlling qualitative traits.

SHORT COMMUNICATION: MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits

SummaryThe Mx1 gene in mice is induced by type I interferons and is the major determinant of resistance to influenza virus and related orthomyxoviruses. It has been previously shown that a SNP in exon 13 of the chicken MX1 gene determines differential antiviral activity of the protein. We evaluated this SNP and two additional SNPs in elite broiler lines by PCR amplification and sequence analysis. Associations between MX1 exon 13 SNPs and several traits of economic interest were evaluated. Significant associations were found between the SNP determining antiviral activity and mortality in one line and leg defects in another line.

QTL analysis of production traits on SSC3 in a Large White×Meishan pig resource family

In order to locate the genetic regions that are responsible for economically important traits, a resource population was established by crossing Large White boars and Meishan sows. Phenotypic data of a total of 287 F2 offspring were collected from 1998 to 2000 and QTL analysis conducted using nine microsatellites on Sus scrofa chromosome 3 (SSC3). Least square regression interval mapping revealed two significant QTL effects on dressing percentage and moisture in m. longissimus dorsi, respectively. They were located at 136 cM and 22 cM in the genetic linkage map, near the marker Sw349 and Swr1637, respectively. QTL for dressing percentage had an additive effect of -1.035 ± 0.296% and a dominance effect of 1.056 ± 0.481%, and the explained phenotypic variance was 15.9%. The additive and dominance effects of QTL for moisture in m. longissimus dorsi were -0.025 ± 0.076% and 0.365 ± 0.101%, respectively, indicating that this QTL seemed to be significantly dominant in action. The present study confirms previously identified QTL and provides an important step in the search for the actual major genes involved in the traits of economic interest. South African Journal of Animal Science Vol. 36(2) 2006: 122-125

Identification of a single nucleotide polymorphism at intron 16 of the caprine Acyl-Coenzyme A: diacylglycerol acyltransferase 1 (DGAT1) gene

The DGAT1 gene encodes a microsomal enzyme that catalyses the only committed step in triacylglycerol synthesis by joining diacylglycerol and fatty acyl coenzyme A. In cattle, a K232A substitution in the DGAT1 molecule has a significant effect on enzyme activity and milk fat content. The prominent role of this gene in lipid metabolism led us to undertake the structural characterization of DGAT1 in goats. In this way, we have sequenced a 1552 bp fragment of the goat DGAT1 cDNA, which encompasses most of the coding sequence (from exon 1 to 17), and a genomic fragment covering exons 12 to 17. Multiple alignment of the goat DGAT1 sequences revealed the existence of a single nucleotide polymorphism (SNP) involving a T to C substitution at intron 16. We optimized a primer extension based genotyping method that allowed us to determine that the C variant is a minority allele with frequencies ranging from 0.062 (Murciano-Granadina) to 0.109 (Malagueña). This SNP, although not expected to have any functional effect, might be useful as a genetic marker in association studies to detect additional DGAT1 polymorphisms which might influence fat milk content and other traits of economic interest.

Mapping of Quantitative Trait Loci on Porcine Chromosome 7 Using Combined Data Analysis

To further investigate the regions on porcine chromosome 7 that are responsible for economically important traits, phenotypic data from a total of 287 F2 individuals were collected and analyzed from 1998 to 2000. All animals were genotyped for eight microsatellite loci spanning the length of chromosome 7. QTL analysis was performed using interval mapping under the line-cross model. A permutation test was used to establish significance levels associated with QTL effects. Observed QTL effects were (chromosomewide significance, position of maximum significance in centimorgans): Birth weight (<0.01, 3); Carcass length (<0.05, 80); Longissimus muscle area (<0.01, 69); Skin percentage (<0.01, 69); Bone percentage (<0.01, 74); Fat depths at shoulder (<0.05, 54); Mean fat depth (<0.05, 81); Moisture in m. Longissimus Dorsi (<0.05, 88). Additional evidence was also found which suggested QTL for dressing percentage and fat depths at buttock. This study offers confirmation of several QTL affecting growth and carcass traits on SSC7 and provides an important step in the search for the actual major genes involved in the traits of economic interest. (Asian-Aust. J. Anim. Sci. 2004. Vol 17, No. 10 : 1350-1354)

Advances in pig genomics and functional gene discovery

Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health.

Genetic changes in layer breeding: Historical trends and future prospects

SummaryIn commercial egg type chicken breeding three and four way crosses are used to produce commercial layers. The primary breeders are using closed nucleus breeding programmes, with birds kept under maximum biosecurity. All grand parents and parents are produced from a closed nucleus for the world wide demand of commercial layers. The breeding goals have been focused for several decades on increasing number of eggs per hen housed. Additional traits have become more important during the last decade, i.e. feed efficiency, internal and external egg quality and general adaptability. Prior to each selection, weights for individual traits within the selection index are adjusted to meet market demands. Breeding stock and commercial layers have to be bred to perform adequately in a variety of systems ranging from large intensive cage units to free range management under different environmental conditions world-wide.Despite intensive selection for egg production the decrease in genetic variation observed in closed commercial lines is not yet critical. Peak production is approaching the biological limit of one egg a day. During this period genetic and phenotypic variation have been significantly reduced. But for early production (sexual maturity) and late production (persistency) genetic variation is still high. In a mating scheme avoiding full and half sib matings no serious inbreeding depression is observed. To achieve continued future genetic progress, selection pressure will shift to other traits like internal and external egg quality and perhaps behaviour traits which still respond to selection.Primary breeders are responding to this challenge by testing pedigreed cross-line hens in a wide range of environments and housing systems while the pure-line elite stock is kept under conditions of maximum biosecurity. Marker assisted selection is already part of commercial breeding programmes. In the past, blood typing has been used to improve Marek's resistance, whereas today anonymous microsatellites which are linked to traits of economic interest are used for selection. In particular, selection between full sib males can give a major improvement.The whole industry is getting more specialised. While the genetic potential of the birds is improved management and nutrition have also to be adapted to changing demands. The general goal for the future is to breed chickens with the ability to function well within a wider range of production conditions and do not respond to the slightest stress.

Isolation of genomic DNA from milk samples by using Chelex resin.

A rapid procedure for isolating genomic DNA from milk samples has been devised, based on the use of Chelex resin. By using this protocol, genomic DNA was extracted from milk samples from 15 cows and 15 goats. The suitability of these DNA preparations as a template for performing the polymerase chain reaction (PCR) was tested by amplifying three different loci of the bovine genome: exon 4 of the kappa-casein gene and the INRA5 and INRA23 microsatellites, together with two others: exon 19 of the alpha s1-casein gene and exon 2 and part of intron 2 of the DRB gene of the caprine genome. No amplification products could be obtained from any sampless at 30 cycles. In contrast, at 45 cycles the number of amplified samples ranged from 86 to 100% and at 65 cycles all the DNA targets were amplified, indicating that the number of cycles was a critical factor to be optimized for obtaining the desired PCR target. These results suggest that this method may be a useful tool for analysing genetic polymorphism at the DNA level by PCR and relating it to milk composition and other traits of economic interest.