Jesus Arango - Academia.edu (original) (raw)

Papers by Jesus Arango

Research paper thumbnail of Genetic parameters of egg defects and egg quality in layer chickens

Research paper thumbnail of Identifying the genetic basis for resistance to avian influenza in commercial egg layer chickens

Research paper thumbnail of Genome wide association analysis of cuticle deposition in laying hens

Research paper thumbnail of Repeatability vs. multiple-trait models to evaluate shell dynamic stiffness for layer chickens

Journal of Animal Science, 2017

Shell quality is one of the most important traits for improvement in layer chickens. Proper consi... more Shell quality is one of the most important traits for improvement in layer chickens. Proper consideration of repeated records can increase the accuracy of estimated breeding values and thus genetic improvement of shell quality. The objective of this study was to compare different models for genetic evaluation of the collected data. For this study, 81,646 dynamic stiffness records on 21,321 brown egg layers and 93,748 records on 24,678 white egg layers from 4 generations were analyzed. Across generations, data were collected at 2 to 4 ages (at approximately 26, 42, 65, and 86 wk), with repeated records at each age. Seven models were compared, including 5 repeatability models with increasing complexity, a random regression model, and a multitrait model. The models were compared using Akaike Information Criteria with significance testing of nested models with a Log Likelihood Ratio test. Estimates of heritability were 0.31–0.36 for the brown line and 0.23–0.26 for the white line, but r...

Research paper thumbnail of Breed Comparisons of Weight, Weight Adjusted for Condition Score, Height, and Condition Score of Beef Cows1

The Professional Animal Scientist, Feb 1, 2004

Research paper thumbnail of Genome‐wide association studies for egg quality traits in White Leghorn layers using low‐pass sequencing and SNP chip data

Journal of Animal Breeding and Genetics

Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (... more Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.

Research paper thumbnail of MOESM2 of Effects of number of training generations on genomic prediction for various traits in a layer chicken population

Additional file 2: Figure S1. Scatter plot of accuracies of genomic predictions across different ... more Additional file 2: Figure S1. Scatter plot of accuracies of genomic predictions across different validation sets over training generations for each trait. The blue line is the regression of the accuracy on the number of training generations. The red line indicates the optimal number of training generations. The R-squared of regression line is presented as r2.

Research paper thumbnail of Producción porcina a campo: un modelo alternativo y sostenible (experiencias europeas e hispanoamericanas)

Research paper thumbnail of Detection of CNVs in layer chickens using 42K, 50K and 600K SNP chips

The development of SNP chips has enabled rapid genotyping of hundreds of thousands of loci at a r... more The development of SNP chips has enabled rapid genotyping of hundreds of thousands of loci at a relatively low cost. In addition to providing SNP genotype information, copy number variation (CNV) can also be inferred from intensity data generated by the same chips. The aim of this study was to detect and describe CNVs in five lines of layer chickens using different SNP chips. A total of 18,719 individuals from four pure lines and one commercial cross were genotyped using four different SNP chips (Illumina 42K, Affymetrix 600K, and two customized Affymetrix 50K chips). Analysis software Axiom® CNV Summary Tools and PennCNV were used to identify CNVs from Affymetrix chips and cnvPartition in Genome Studio was used to identify CNV’s from the Illumina chip. The CNV regions (CNVR) within lines were defined using the BedTools software, through merging CNVs overlapping by at least 1 bp. CNVRs identified across all panels were selected with BedTools intersect to choose regions with highest ...

Research paper thumbnail of See Profile

Variation in the ovocalyxin-32 gene in commercial egg-laying chickens and its relationship with e... more Variation in the ovocalyxin-32 gene in commercial egg-laying chickens and its relationship with egg production and egg quality traits

Research paper thumbnail of Additional file 7: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S7. Proportion of genetic variance explained by 1-Mb regions across the genome for GRN in ... more Figure S7. Proportion of genetic variance explained by 1-Mb regions across the genome for GRN in BL. (PDF 10 kb)

Research paper thumbnail of Additional file 4: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S4. Variation in recombination rate in males (red solid line) and females (blue dashed lin... more Figure S4. Variation in recombination rate in males (red solid line) and females (blue dashed line) within 0.5-Mb windows across the 28 autosomes in BL (except GGA16). (PPTX 164 kb)

Research paper thumbnail of Additional file 3: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S3. Variation in recombination rate in males (red solid line) and females (blue dashed lin... more Figure S3. Variation in recombination rate in males (red solid line) and females (blue dashed line) within 0.5-Mb windows across the 28 autosomes in WL (except GGA16). (PPTX 152 kb)

Research paper thumbnail of Investigating the genetic determination of clutch traits in laying hens

Research paper thumbnail of Genetics and genomics of egg production traits in poultry species

Advances in poultry genetics and genomics, 2020

Research paper thumbnail of Model comparison to evaluate a shell quality bio-complex in layer hens

Research paper thumbnail of Additional file 1: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S1. Variation in recombination rate within 0.5-Mb windows across the 28 autosomes (except ... more Figure S1. Variation in recombination rate within 0.5-Mb windows across the 28 autosomes (except GGA6). The black line corresponds to recombination rates estimated from segregating 173K SNPs in WL. The grey line corresponds to recombination rate estimated from segregating 23K SNPs in BL. (PPTX 127 kb)

Research paper thumbnail of Can Lighting Programs be Manipulated in the Growing Phase to Improve the Skeletal Integrity of Commercial Egg Layers Patricia

Osteoporosis, a progressive decrease in the amount of mineralized structural bone, leads to skele... more Osteoporosis, a progressive decrease in the amount of mineralized structural bone, leads to skeletal fragility and susceptibility to bone fracture in egg laying strains of chickens. Approximately 5% of birds grown in conventional cages were shown to have old breaks and 29% of all hens have one or more broken bones during time spent in cages, depopulation, and transport for processing (Gregory and Wilkins, 1989). In addition to the bone breakage of live birds, economic losses arise due to high fracture incidences during carcass processing. Because of bone splinters in the meat of spent hens, the egg industry has lost the majority of its market to companies manufacturing chicken based soup products. Most soup companies now use broiler meat in place of spent hen meat.

Research paper thumbnail of Breeder management and its relation to commercial chick quality and layer performance

The objective of a livestock breeding company is to maximize genetic progress in elite pedigreed ... more The objective of a livestock breeding company is to maximize genetic progress in elite pedigreed populations (pure lines) and to find the right combination of these pure lines to produce the final commercial product (Figure 1). Several biological processes are involved in the design and implementation of a breeding program. The most important one is selection at the pure line level. Once the best individuals are chosen to reproduce the elite populations, a robust multiplication process needs to be in place to ensure that: (a) the best combination of lines is used to produce commercials, and (b) new combinations of lines are tested in a continual basis to search for final product improvement or to develop new products. To maximize the results of crossbreeding (a and b) other biological processes Breeder management and its relation to commercial chick quality and layer performance

Research paper thumbnail of Heritability of perching behavior and its genetic relationship with incidence of floor eggs in Rhode Island Red chickens

Background As cage-free production systems become increasingly popular, behavioral traits such as... more Background As cage-free production systems become increasingly popular, behavioral traits such as nesting behavior and temperament have become more important. The objective of this study was to estimate heritabilities for frequency of perching and proportion of floor eggs and their genetic correlation in two Rhode Island Red lines. Results The percent of hens observed perching tended to increase and the proportion of eggs laid on the floor tended to decrease as the test progressed. This suggests the ability of hens to learn to use nests and perches. Under the bivariate repeatability model, estimates of heritability in the two lines were 0.22 ± 0.04 and 0.07 ± 0.05 for the percent of hens perching, and 0.52 ± 0.05 and 0.45 ± 0.05 for the percent of floor eggs. Estimates of the genetic correlation between perching and floor eggs were − 0.26 ± 0.14 and − 0.19 ± 0.27 for the two lines, suggesting that, genetically, there was some tendency for hens that better use perches to also use nes...

Research paper thumbnail of Genetic parameters of egg defects and egg quality in layer chickens

Research paper thumbnail of Identifying the genetic basis for resistance to avian influenza in commercial egg layer chickens

Research paper thumbnail of Genome wide association analysis of cuticle deposition in laying hens

Research paper thumbnail of Repeatability vs. multiple-trait models to evaluate shell dynamic stiffness for layer chickens

Journal of Animal Science, 2017

Shell quality is one of the most important traits for improvement in layer chickens. Proper consi... more Shell quality is one of the most important traits for improvement in layer chickens. Proper consideration of repeated records can increase the accuracy of estimated breeding values and thus genetic improvement of shell quality. The objective of this study was to compare different models for genetic evaluation of the collected data. For this study, 81,646 dynamic stiffness records on 21,321 brown egg layers and 93,748 records on 24,678 white egg layers from 4 generations were analyzed. Across generations, data were collected at 2 to 4 ages (at approximately 26, 42, 65, and 86 wk), with repeated records at each age. Seven models were compared, including 5 repeatability models with increasing complexity, a random regression model, and a multitrait model. The models were compared using Akaike Information Criteria with significance testing of nested models with a Log Likelihood Ratio test. Estimates of heritability were 0.31–0.36 for the brown line and 0.23–0.26 for the white line, but r...

Research paper thumbnail of Breed Comparisons of Weight, Weight Adjusted for Condition Score, Height, and Condition Score of Beef Cows1

The Professional Animal Scientist, Feb 1, 2004

Research paper thumbnail of Genome‐wide association studies for egg quality traits in White Leghorn layers using low‐pass sequencing and SNP chip data

Journal of Animal Breeding and Genetics

Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (... more Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.

Research paper thumbnail of MOESM2 of Effects of number of training generations on genomic prediction for various traits in a layer chicken population

Additional file 2: Figure S1. Scatter plot of accuracies of genomic predictions across different ... more Additional file 2: Figure S1. Scatter plot of accuracies of genomic predictions across different validation sets over training generations for each trait. The blue line is the regression of the accuracy on the number of training generations. The red line indicates the optimal number of training generations. The R-squared of regression line is presented as r2.

Research paper thumbnail of Producción porcina a campo: un modelo alternativo y sostenible (experiencias europeas e hispanoamericanas)

Research paper thumbnail of Detection of CNVs in layer chickens using 42K, 50K and 600K SNP chips

The development of SNP chips has enabled rapid genotyping of hundreds of thousands of loci at a r... more The development of SNP chips has enabled rapid genotyping of hundreds of thousands of loci at a relatively low cost. In addition to providing SNP genotype information, copy number variation (CNV) can also be inferred from intensity data generated by the same chips. The aim of this study was to detect and describe CNVs in five lines of layer chickens using different SNP chips. A total of 18,719 individuals from four pure lines and one commercial cross were genotyped using four different SNP chips (Illumina 42K, Affymetrix 600K, and two customized Affymetrix 50K chips). Analysis software Axiom® CNV Summary Tools and PennCNV were used to identify CNVs from Affymetrix chips and cnvPartition in Genome Studio was used to identify CNV’s from the Illumina chip. The CNV regions (CNVR) within lines were defined using the BedTools software, through merging CNVs overlapping by at least 1 bp. CNVRs identified across all panels were selected with BedTools intersect to choose regions with highest ...

Research paper thumbnail of See Profile

Variation in the ovocalyxin-32 gene in commercial egg-laying chickens and its relationship with e... more Variation in the ovocalyxin-32 gene in commercial egg-laying chickens and its relationship with egg production and egg quality traits

Research paper thumbnail of Additional file 7: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S7. Proportion of genetic variance explained by 1-Mb regions across the genome for GRN in ... more Figure S7. Proportion of genetic variance explained by 1-Mb regions across the genome for GRN in BL. (PDF 10 kb)

Research paper thumbnail of Additional file 4: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S4. Variation in recombination rate in males (red solid line) and females (blue dashed lin... more Figure S4. Variation in recombination rate in males (red solid line) and females (blue dashed line) within 0.5-Mb windows across the 28 autosomes in BL (except GGA16). (PPTX 164 kb)

Research paper thumbnail of Additional file 3: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S3. Variation in recombination rate in males (red solid line) and females (blue dashed lin... more Figure S3. Variation in recombination rate in males (red solid line) and females (blue dashed line) within 0.5-Mb windows across the 28 autosomes in WL (except GGA16). (PPTX 152 kb)

Research paper thumbnail of Investigating the genetic determination of clutch traits in laying hens

Research paper thumbnail of Genetics and genomics of egg production traits in poultry species

Advances in poultry genetics and genomics, 2020

Research paper thumbnail of Model comparison to evaluate a shell quality bio-complex in layer hens

Research paper thumbnail of Additional file 1: of Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

Figure S1. Variation in recombination rate within 0.5-Mb windows across the 28 autosomes (except ... more Figure S1. Variation in recombination rate within 0.5-Mb windows across the 28 autosomes (except GGA6). The black line corresponds to recombination rates estimated from segregating 173K SNPs in WL. The grey line corresponds to recombination rate estimated from segregating 23K SNPs in BL. (PPTX 127 kb)

Research paper thumbnail of Can Lighting Programs be Manipulated in the Growing Phase to Improve the Skeletal Integrity of Commercial Egg Layers Patricia

Osteoporosis, a progressive decrease in the amount of mineralized structural bone, leads to skele... more Osteoporosis, a progressive decrease in the amount of mineralized structural bone, leads to skeletal fragility and susceptibility to bone fracture in egg laying strains of chickens. Approximately 5% of birds grown in conventional cages were shown to have old breaks and 29% of all hens have one or more broken bones during time spent in cages, depopulation, and transport for processing (Gregory and Wilkins, 1989). In addition to the bone breakage of live birds, economic losses arise due to high fracture incidences during carcass processing. Because of bone splinters in the meat of spent hens, the egg industry has lost the majority of its market to companies manufacturing chicken based soup products. Most soup companies now use broiler meat in place of spent hen meat.

Research paper thumbnail of Breeder management and its relation to commercial chick quality and layer performance

The objective of a livestock breeding company is to maximize genetic progress in elite pedigreed ... more The objective of a livestock breeding company is to maximize genetic progress in elite pedigreed populations (pure lines) and to find the right combination of these pure lines to produce the final commercial product (Figure 1). Several biological processes are involved in the design and implementation of a breeding program. The most important one is selection at the pure line level. Once the best individuals are chosen to reproduce the elite populations, a robust multiplication process needs to be in place to ensure that: (a) the best combination of lines is used to produce commercials, and (b) new combinations of lines are tested in a continual basis to search for final product improvement or to develop new products. To maximize the results of crossbreeding (a and b) other biological processes Breeder management and its relation to commercial chick quality and layer performance

Research paper thumbnail of Heritability of perching behavior and its genetic relationship with incidence of floor eggs in Rhode Island Red chickens

Background As cage-free production systems become increasingly popular, behavioral traits such as... more Background As cage-free production systems become increasingly popular, behavioral traits such as nesting behavior and temperament have become more important. The objective of this study was to estimate heritabilities for frequency of perching and proportion of floor eggs and their genetic correlation in two Rhode Island Red lines. Results The percent of hens observed perching tended to increase and the proportion of eggs laid on the floor tended to decrease as the test progressed. This suggests the ability of hens to learn to use nests and perches. Under the bivariate repeatability model, estimates of heritability in the two lines were 0.22 ± 0.04 and 0.07 ± 0.05 for the percent of hens perching, and 0.52 ± 0.05 and 0.45 ± 0.05 for the percent of floor eggs. Estimates of the genetic correlation between perching and floor eggs were − 0.26 ± 0.14 and − 0.19 ± 0.27 for the two lines, suggesting that, genetically, there was some tendency for hens that better use perches to also use nes...