Janet Fulton - Profile on Academia.edu (original) (raw)

Papers by Janet Fulton

Introduction 2 Specific advantages of genomics for selection of egg production traits 3 Genomic s... more Introduction 2 Specific advantages of genomics for selection of egg production traits 3 Genomic selection versus phenotypic selection 4 Factors impacting genomic selection 5 Analysis methods for genomic selection 6 Conclusion 7 Future trends 8 Where to look for further information 9 References

Poultry Science, Nov 1, 2001

Alloantisera directed against chicken class I MHC (BFIV) antigens were produced by using transfec... more Alloantisera directed against chicken class I MHC (BFIV) antigens were produced by using transfected cell lines expressing cloned BFIV sequences. The cloned BFIV sequences were from haplotypes *12, *13, and *21. Two laboratory-derived class I mutant sequences (BFIV13m126 and BFIV21m78) were developed to analyze cross-reactive epitopes and to induce specific alloantisera. Antisera were tested in hemagglutination and flow cytometry assays. The antisera produced were highly specific and had minimal cross-reactivity. The antisera induced by the BFIV21m78 mutant confirmed the significance of amino acids 78 and 81 in cross-reactivity

Marek's Disease (MD) has a significant impact on both the global poultry economy and animal welfa... more Marek's Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F 6 population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here, we mapped MD QTLRs on GGZ in the previously utilized F 6 population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by individuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of p-values and Linkage Disequilibrium (LD) pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the non-significant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD.

Research Square (Research Square), Jul 5, 2023

Dramatic improvements in measuring genetic variation across agriculturally relevant populations (... more Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in the area of genome to phenome (G2P) research is the focus of this paper. Previously (Tuggle et al. 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with US federal government agencies, including USDA, expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome-to-phenome (AG2P) work and envision the future of the AG2P field. To tackle some of these big challenges, we designed this workshop to include diverse voices with the intention of hearing the different

Achieving sustainable production of eggs Volume 1, 2017

Multiple tools for the molecular analysis of variation at both the DNA and protein level have rec... more Multiple tools for the molecular analysis of variation at both the DNA and protein level have recently been developed. These molecular tools that include low cost sequencing, simultaneous genotyping of large numbers of single nucleotide polymorphisms chips, real-time polymerase chain reaction (PCR) and RNAseq (for gene expression) are enabling scientists to better understand the fundamental bases of egg-quality traits in poultry. Genomic selection methods have been developed to improve egg quality and have been implemented by major poultry breeding companies. This chapter looks at ways to improve external egg quality and internal egg quality utilizing these molecular tools. The Animal Genome Quantitative Trait Loci (QTL) database currently includes 4676 chicken QTLs curated from 224 publications for 316 different chicken traits (www.animalgenome.org). Targeted genomic analysis of specific genes allows in-depth study of genes involved in the determination of egg quality. Further insi...

Poultry Science, 2021

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Poultry Science, 2020

The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which... more The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which contains numerous immune response genes, and is known to influence disease susceptibility and resistance in chickens. Variability of MHC-B haplotypes in various well-known and commercially utilized breeds has previously been identified. This study aims to understand MHC-B diversity in the Silkie breed using a high-density SNP panel that encompasses the chicken MHC-B region. DNA was obtained from 74 females and 27 males from a commercial Silkie breeder colony that is maintained through minimal genetic selection practices. A previously described panel of 90 SNPs, all located within the MHC-B region, was used to evaluate MHC-B variability in the commercial Silkie breeder colony. MHC-B haplotypes identified from the individual SNP information in the Silkie colony were compared to published haplotypes from the same region. Of the 27 haplotypes identified in the Silkie population, 8 have been previously described. Nineteen haplotypes are unique to the Silkie population and include one novel recombinant and 2 additional possible novel recombinants. Six haplotypes were found at a frequency greater than 5% of the population, of which 4 are novel. Finally, Hardy Weinberg Equilibrium (HWE) was calculated for the observed haplotypes, which were found to be in HWE. This study shows considerable MHC-B diversity in the Silkie breed and adds further information on variability of the MHC-B region in the chicken.

Poultry Science, 2019

The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chrom... more The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chromosome 16. The chicken MHC-B is known to be highly associated with resistance to numerous diseases caused by viruses, bacteria, and parasitic pathogens. Since the level of resistance varies with MHC-B haplotypes, identification and classification of different haplotypes within lines is important for sustaining lines. The “Campero-INTA” chicken breed is a meat-type free-range poultry breed that was developed specifically for small producers in Argentina. Campero-INTA was started by selection in populations produced by crosses between a variety of established lines. MHC-B variation was examined in 65 samples obtained in 2002 using the VNTR marker LEI0258, a marker for MHC-B region. These samples plus and an additional 55 samples from 2018 were examined for variation using the MHC-B specific SNP panel that encompasses ∼230,000 bp of the MHC-B region. Eleven MHC-B SNP haplotypes with 6 LEI025...

Frontiers in Genetics, 2019

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute f... more In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The

Genetics Selection Evolution, 2018

Background: Copy number variations (CNV) are an important source of genetic variation that has ga... more Background: Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis for 18,719 individuals from four pure lines and one commercial cross of layer chickens. Samples were genotyped on four single nucleotide polymorphism (SNP) genotyping platforms, i.e. the Illumina 42K, Affymetrix 600K, and two different customized Affymetrix 50K chips. CNV recovered from the Affymetrix chips were identified by using the Axiom ® CNV Summary Tools and PennCNV software and those from the Illumina chip were identified by using the cnvPartition in the Genome Studio software. The mean number of CNV per individual varied from 0.50 to 4.87 according to line or cross and size of the SNP genotyping set. The length of the detected CNV across all datasets ranged from 1.2 kb to 3.2 Mb. The number of duplications exceeded the number of deletions for most lines. Between the lines, there were considerable differences in the number of detected CNV and their distribution. Most of the detected CNV had a low frequency, but 19 CNV were identified with a frequency higher than 5% in birds that were genotyped on the 600K panel, with the most common CNV being detected in 734 birds from three lines. Commonly used SNP genotyping platforms can be used to detect segregating CNV in chicken layer lines. The sample sizes for this study enabled a detailed characterization of the CNV landscape within commercially relevant lines. The size of the SNP panel used affected detection efficiency, with more CNV detected per individual on the higher density 600K panel. In spite of the high level of inter-individual diversity and a large number of CNV observed within individuals, we were able to detect 19 frequent CNV, of which, 57.9% overlapped with annotated genes and 89% overlapped with known quantitative trait loci.

BMC Genomics, Jul 31, 2015

Poultry Science, Jun 1, 2019

Improving the Outcome of a Marek's Disease Challenge in Multiple Lines of Egg Type Chickens

Avian Diseases, Jun 1, 2013

A challenge test following inoculation with a standard amount of a vv+ strain of the Marek&am... more A challenge test following inoculation with a standard amount of a vv+ strain of the Marek's disease (MD) virus in multiple lines and multiple generations of egg type chicken and the corresponding phenotypic trend are described. This program significantly reduced mortality of progeny from selected sires for three to 11 generations in eight of the nine elite lines studied herein. In brown egg lines, a retrospective analysis of DNA indicated an association between the blood type B (major histocompatibility complex) of the sire and the MD mortality in the challenge of its progeny. As a result of the multigeneration stock amplification and crossbreeding processes used in the commercial breeding industry, improvement in survival after challenge at the elite level will translate to improved welfare for millions of birds at the commercial production level.

Accuracy of genomic prediction was compared in two layer lines using medium density SNP chip and ... more Accuracy of genomic prediction was compared in two layer lines using medium density SNP chip and lowpass sequencing. Three thousand individuals representing two lines were sequenced for the project. Thirtyfour genomic regions were identified as genome-wide significant across 11 egg quality traits and their genotypes were added to the chip. Multi-trait single-step animal model was used for genomic prediction. A slight increase in accuracy for some of the traits was obtained by adding the significant SNPs to those present on the chip. Fitting all sequence SNPs had no advantage for predictive ability over chip despite explaining 15% more of phenotypic variance in the Genome Wide Association Study. Further optimization of the utilization of sequence data and cost reduction are required to make low-pass sequence competitive to medium density SNP chips for genomic prediction.

Poultry Science, 2019

High environmental temperature is a serious stress affecting economic and biological efficiency o... more High environmental temperature is a serious stress affecting economic and biological efficiency of poultry production in tropical and subtropical countries that is expected to become more prominent with global climate change. Iowa experienced 3 acute heat waves of 11, 3, and 4 d of heat index above 38°C in the summer of 2012, which led to production losses and increased bird mortality. For the current study, the proportion of daughters that died from heat stress during this period was calculated for 118 sire families of an elite White Leghorn layer line. The number of daughters per sire ranged from 25 to 111 and averaged 68. Average mortality due to heat stress was 8.2%, ranging from 0 to 24.6%. All sires were genotyped using a 600 K Affymetrix chip. After stringent quality filtering (clustering quality, parentage, missing genotypes, MAF) 113,344 SNPs were retained for the analysis. Method BayesB with π equal to 0.999, for the number of markers fitted not to exceed the number of observations, was applied. Markers explained 8% of the phenotypic variance. One 1-Mb window on chromosome 5 explained 1.2% of genetic variance. When the number of daughters was fitted as a weight in the analysis, the proportion of variance explained by markers dropped to 1%, but 9 1-Mb windows explained more than 1% of genetic variance on chromosomes 1, 3, 5 (the same top window as in the unweighted analysis), 9, 17, and 18. Although the support of the genomic regions associated with heat stress resistance identified in this study was not very strong, they overlapped with previously reported quantitative trait loci regions for immune response and physiological traits in chickens and contained genes that have been associated with response to heat stress in other studies. Further research is needed to validate the results.

Acta Agriculturae Scandinavica Section A-animal Science, Feb 21, 2020

The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins t... more The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins to almost 1,000 years ago. Today, remnant populations of phenotypically distinct lineages are maintained by a network of volunteer hobbyists in Finland, managed by Natural Resources Institute Finland (Luke). Guided by a prior Major Histocompatibility Complex B-locus haplotype study, we sought now to characterize genetically Finnish Landrace chickens using denser genomic sampling. A new panel of 101 selectively neutral SNP sites was used to interrogate genetic variation in 192 individuals sampled from 13 putatively distinctive population units. Individuals partitioned into K = 11 genetic clusters characterized by high levels of genetic diversity, strong patterns of genetic structure and low levels of inbreeding. Evidence of an undocumented genetic lineage was also discovered. Facilitated by an inexpensive SNP assay, this study shows that the genetic integrity of the Finnish Landrace persists and represents a rich resource of natural (adaptive) genomic variation.

Defective feathers in Japanese quail

Journal of Heredity, May 1, 1983

Page 1. The Journal of Heredity 74:184-188. 1983. Defective feathers in Japanese quail A two-locu... more Page 1. The Journal of Heredity 74:184-188. 1983. Defective feathers in Japanese quail A two-locus model for a new trait ABSTRACT: A new feather-structure mutation In Japanese quail {Cotumlx coturnlx Japonl-ca) is characterized ...

Journal of Virology, Oct 1, 1995

The interaction between the major histocompatibility complex (MHC) and cytotoxic T lymphocytes (C... more The interaction between the major histocompatibility complex (MHC) and cytotoxic T lymphocytes (CTLs) is an important component of the host's resistance to viral infections and tumor formation. In this study, an avian leukosis virus (ALV) vector system, RCASBP, expressing MHC chicken class I (B-F) cDNA was used to develop target cells expressing the chicken class I glycoproteins complexed with ALV antigens on the cell surface. Peripheral blood from chickens inoculated with ALV was shown to contain antigen-specific, MHCrestricted, CD8 ؉ effector CTLs, using a 51 Cr release assay utilizing the RCASBP B-F target cells. The stimulated effector cells were also predominantly ␣␤ T-cell receptor-positive (TCR2) T cells. The CTL response varied between two haplotypes of chickens which differed in their response to Rous sarcoma virus (RSV)induced tumors. Chickens with the B 21 haplotype which regress RSV-induced tumors showed maximal cytolytic activity, while chickens with the B 13 haplotype which do not regress RSV-induced tumors had minimal to no cytolytic activity. In addition to assessing the CTL response to ALV, the creation of MHC-specific immortal target cell lines will be extremely useful in evaluating CTL responses to other viral disease in chickens.

Genome wide association analysis of cuticle deposition in laying hens

Poultry Science

Introduction 2 Specific advantages of genomics for selection of egg production traits 3 Genomic s... more Introduction 2 Specific advantages of genomics for selection of egg production traits 3 Genomic selection versus phenotypic selection 4 Factors impacting genomic selection 5 Analysis methods for genomic selection 6 Conclusion 7 Future trends 8 Where to look for further information 9 References

Poultry Science, Nov 1, 2001

Alloantisera directed against chicken class I MHC (BFIV) antigens were produced by using transfec... more Alloantisera directed against chicken class I MHC (BFIV) antigens were produced by using transfected cell lines expressing cloned BFIV sequences. The cloned BFIV sequences were from haplotypes *12, *13, and *21. Two laboratory-derived class I mutant sequences (BFIV13m126 and BFIV21m78) were developed to analyze cross-reactive epitopes and to induce specific alloantisera. Antisera were tested in hemagglutination and flow cytometry assays. The antisera produced were highly specific and had minimal cross-reactivity. The antisera induced by the BFIV21m78 mutant confirmed the significance of amino acids 78 and 81 in cross-reactivity

Marek's Disease (MD) has a significant impact on both the global poultry economy and animal welfa... more Marek's Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F 6 population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here, we mapped MD QTLRs on GGZ in the previously utilized F 6 population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by individuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of p-values and Linkage Disequilibrium (LD) pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the non-significant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD.

Research Square (Research Square), Jul 5, 2023

Dramatic improvements in measuring genetic variation across agriculturally relevant populations (... more Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in the area of genome to phenome (G2P) research is the focus of this paper. Previously (Tuggle et al. 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with US federal government agencies, including USDA, expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome-to-phenome (AG2P) work and envision the future of the AG2P field. To tackle some of these big challenges, we designed this workshop to include diverse voices with the intention of hearing the different

Achieving sustainable production of eggs Volume 1, 2017

Multiple tools for the molecular analysis of variation at both the DNA and protein level have rec... more Multiple tools for the molecular analysis of variation at both the DNA and protein level have recently been developed. These molecular tools that include low cost sequencing, simultaneous genotyping of large numbers of single nucleotide polymorphisms chips, real-time polymerase chain reaction (PCR) and RNAseq (for gene expression) are enabling scientists to better understand the fundamental bases of egg-quality traits in poultry. Genomic selection methods have been developed to improve egg quality and have been implemented by major poultry breeding companies. This chapter looks at ways to improve external egg quality and internal egg quality utilizing these molecular tools. The Animal Genome Quantitative Trait Loci (QTL) database currently includes 4676 chicken QTLs curated from 224 publications for 316 different chicken traits (www.animalgenome.org). Targeted genomic analysis of specific genes allows in-depth study of genes involved in the determination of egg quality. Further insi...

Poultry Science, 2021

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Poultry Science, 2020

The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which... more The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which contains numerous immune response genes, and is known to influence disease susceptibility and resistance in chickens. Variability of MHC-B haplotypes in various well-known and commercially utilized breeds has previously been identified. This study aims to understand MHC-B diversity in the Silkie breed using a high-density SNP panel that encompasses the chicken MHC-B region. DNA was obtained from 74 females and 27 males from a commercial Silkie breeder colony that is maintained through minimal genetic selection practices. A previously described panel of 90 SNPs, all located within the MHC-B region, was used to evaluate MHC-B variability in the commercial Silkie breeder colony. MHC-B haplotypes identified from the individual SNP information in the Silkie colony were compared to published haplotypes from the same region. Of the 27 haplotypes identified in the Silkie population, 8 have been previously described. Nineteen haplotypes are unique to the Silkie population and include one novel recombinant and 2 additional possible novel recombinants. Six haplotypes were found at a frequency greater than 5% of the population, of which 4 are novel. Finally, Hardy Weinberg Equilibrium (HWE) was calculated for the observed haplotypes, which were found to be in HWE. This study shows considerable MHC-B diversity in the Silkie breed and adds further information on variability of the MHC-B region in the chicken.

Poultry Science, 2019

The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chrom... more The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chromosome 16. The chicken MHC-B is known to be highly associated with resistance to numerous diseases caused by viruses, bacteria, and parasitic pathogens. Since the level of resistance varies with MHC-B haplotypes, identification and classification of different haplotypes within lines is important for sustaining lines. The “Campero-INTA” chicken breed is a meat-type free-range poultry breed that was developed specifically for small producers in Argentina. Campero-INTA was started by selection in populations produced by crosses between a variety of established lines. MHC-B variation was examined in 65 samples obtained in 2002 using the VNTR marker LEI0258, a marker for MHC-B region. These samples plus and an additional 55 samples from 2018 were examined for variation using the MHC-B specific SNP panel that encompasses ∼230,000 bp of the MHC-B region. Eleven MHC-B SNP haplotypes with 6 LEI025...

Frontiers in Genetics, 2019

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute f... more In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The

Genetics Selection Evolution, 2018

Background: Copy number variations (CNV) are an important source of genetic variation that has ga... more Background: Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis for 18,719 individuals from four pure lines and one commercial cross of layer chickens. Samples were genotyped on four single nucleotide polymorphism (SNP) genotyping platforms, i.e. the Illumina 42K, Affymetrix 600K, and two different customized Affymetrix 50K chips. CNV recovered from the Affymetrix chips were identified by using the Axiom ® CNV Summary Tools and PennCNV software and those from the Illumina chip were identified by using the cnvPartition in the Genome Studio software. The mean number of CNV per individual varied from 0.50 to 4.87 according to line or cross and size of the SNP genotyping set. The length of the detected CNV across all datasets ranged from 1.2 kb to 3.2 Mb. The number of duplications exceeded the number of deletions for most lines. Between the lines, there were considerable differences in the number of detected CNV and their distribution. Most of the detected CNV had a low frequency, but 19 CNV were identified with a frequency higher than 5% in birds that were genotyped on the 600K panel, with the most common CNV being detected in 734 birds from three lines. Commonly used SNP genotyping platforms can be used to detect segregating CNV in chicken layer lines. The sample sizes for this study enabled a detailed characterization of the CNV landscape within commercially relevant lines. The size of the SNP panel used affected detection efficiency, with more CNV detected per individual on the higher density 600K panel. In spite of the high level of inter-individual diversity and a large number of CNV observed within individuals, we were able to detect 19 frequent CNV, of which, 57.9% overlapped with annotated genes and 89% overlapped with known quantitative trait loci.

BMC Genomics, Jul 31, 2015

Poultry Science, Jun 1, 2019

Improving the Outcome of a Marek's Disease Challenge in Multiple Lines of Egg Type Chickens

Avian Diseases, Jun 1, 2013

A challenge test following inoculation with a standard amount of a vv+ strain of the Marek&am... more A challenge test following inoculation with a standard amount of a vv+ strain of the Marek's disease (MD) virus in multiple lines and multiple generations of egg type chicken and the corresponding phenotypic trend are described. This program significantly reduced mortality of progeny from selected sires for three to 11 generations in eight of the nine elite lines studied herein. In brown egg lines, a retrospective analysis of DNA indicated an association between the blood type B (major histocompatibility complex) of the sire and the MD mortality in the challenge of its progeny. As a result of the multigeneration stock amplification and crossbreeding processes used in the commercial breeding industry, improvement in survival after challenge at the elite level will translate to improved welfare for millions of birds at the commercial production level.

Accuracy of genomic prediction was compared in two layer lines using medium density SNP chip and ... more Accuracy of genomic prediction was compared in two layer lines using medium density SNP chip and lowpass sequencing. Three thousand individuals representing two lines were sequenced for the project. Thirtyfour genomic regions were identified as genome-wide significant across 11 egg quality traits and their genotypes were added to the chip. Multi-trait single-step animal model was used for genomic prediction. A slight increase in accuracy for some of the traits was obtained by adding the significant SNPs to those present on the chip. Fitting all sequence SNPs had no advantage for predictive ability over chip despite explaining 15% more of phenotypic variance in the Genome Wide Association Study. Further optimization of the utilization of sequence data and cost reduction are required to make low-pass sequence competitive to medium density SNP chips for genomic prediction.

Poultry Science, 2019

High environmental temperature is a serious stress affecting economic and biological efficiency o... more High environmental temperature is a serious stress affecting economic and biological efficiency of poultry production in tropical and subtropical countries that is expected to become more prominent with global climate change. Iowa experienced 3 acute heat waves of 11, 3, and 4 d of heat index above 38°C in the summer of 2012, which led to production losses and increased bird mortality. For the current study, the proportion of daughters that died from heat stress during this period was calculated for 118 sire families of an elite White Leghorn layer line. The number of daughters per sire ranged from 25 to 111 and averaged 68. Average mortality due to heat stress was 8.2%, ranging from 0 to 24.6%. All sires were genotyped using a 600 K Affymetrix chip. After stringent quality filtering (clustering quality, parentage, missing genotypes, MAF) 113,344 SNPs were retained for the analysis. Method BayesB with π equal to 0.999, for the number of markers fitted not to exceed the number of observations, was applied. Markers explained 8% of the phenotypic variance. One 1-Mb window on chromosome 5 explained 1.2% of genetic variance. When the number of daughters was fitted as a weight in the analysis, the proportion of variance explained by markers dropped to 1%, but 9 1-Mb windows explained more than 1% of genetic variance on chromosomes 1, 3, 5 (the same top window as in the unweighted analysis), 9, 17, and 18. Although the support of the genomic regions associated with heat stress resistance identified in this study was not very strong, they overlapped with previously reported quantitative trait loci regions for immune response and physiological traits in chickens and contained genes that have been associated with response to heat stress in other studies. Further research is needed to validate the results.

Acta Agriculturae Scandinavica Section A-animal Science, Feb 21, 2020

The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins t... more The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins to almost 1,000 years ago. Today, remnant populations of phenotypically distinct lineages are maintained by a network of volunteer hobbyists in Finland, managed by Natural Resources Institute Finland (Luke). Guided by a prior Major Histocompatibility Complex B-locus haplotype study, we sought now to characterize genetically Finnish Landrace chickens using denser genomic sampling. A new panel of 101 selectively neutral SNP sites was used to interrogate genetic variation in 192 individuals sampled from 13 putatively distinctive population units. Individuals partitioned into K = 11 genetic clusters characterized by high levels of genetic diversity, strong patterns of genetic structure and low levels of inbreeding. Evidence of an undocumented genetic lineage was also discovered. Facilitated by an inexpensive SNP assay, this study shows that the genetic integrity of the Finnish Landrace persists and represents a rich resource of natural (adaptive) genomic variation.

Defective feathers in Japanese quail

Journal of Heredity, May 1, 1983

Page 1. The Journal of Heredity 74:184-188. 1983. Defective feathers in Japanese quail A two-locu... more Page 1. The Journal of Heredity 74:184-188. 1983. Defective feathers in Japanese quail A two-locus model for a new trait ABSTRACT: A new feather-structure mutation In Japanese quail {Cotumlx coturnlx Japonl-ca) is characterized ...

Journal of Virology, Oct 1, 1995

The interaction between the major histocompatibility complex (MHC) and cytotoxic T lymphocytes (C... more The interaction between the major histocompatibility complex (MHC) and cytotoxic T lymphocytes (CTLs) is an important component of the host's resistance to viral infections and tumor formation. In this study, an avian leukosis virus (ALV) vector system, RCASBP, expressing MHC chicken class I (B-F) cDNA was used to develop target cells expressing the chicken class I glycoproteins complexed with ALV antigens on the cell surface. Peripheral blood from chickens inoculated with ALV was shown to contain antigen-specific, MHCrestricted, CD8 ؉ effector CTLs, using a 51 Cr release assay utilizing the RCASBP B-F target cells. The stimulated effector cells were also predominantly ␣␤ T-cell receptor-positive (TCR2) T cells. The CTL response varied between two haplotypes of chickens which differed in their response to Rous sarcoma virus (RSV)induced tumors. Chickens with the B 21 haplotype which regress RSV-induced tumors showed maximal cytolytic activity, while chickens with the B 13 haplotype which do not regress RSV-induced tumors had minimal to no cytolytic activity. In addition to assessing the CTL response to ALV, the creation of MHC-specific immortal target cell lines will be extremely useful in evaluating CTL responses to other viral disease in chickens.

Genome wide association analysis of cuticle deposition in laying hens

Poultry Science