Progress 10/01/19 to 09/30/20
Outputs
Target Audience:Animal and poultry breeders and geneticists, veterinarians, researchers and students in animal health and in poultry breeding and genetics, commercial breeders of poultry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate students, post-doctoral fellows, and visiting international scholars were mentored and trained in conducting research in this project. Faculty, graduate students and staff of the project participated in relevant regional, national and international scientific conferences. How have the results been disseminated to communities of interest?The results have been disseminated by publication of peer-reviewed journal papers, presentation of research at conferences and in seminars at other universities, web-hosted industry reports, and direct communications with poultry genetics companies. What do you plan to do during the next reporting period to accomplish the goals?Publish peer-reviewed journal papers on the completed studies. Continue research progress on the study of genetics and genomics of response to Newcastle disease virus in African ecotypes of chickens. Complete analysis of effects of heat-stress on the meta-transcriptome of mature layer chickens. Maintain the ISU genetic lines of chickens.
Impacts
What was accomplished under these goals?
Overall impact statement: Poultry eggs and meat provide a major source of nutrient-dense animal protein for human consumption. To enhance production efficiency, improve product quality and safety, meet consumer preferences, and to maintain US competitiveness in a global market, new information and technologies must be developed to enable continued genetic improvements in poultry. The aim of this research project was to identify genes, genomic regions and heritable biomarkers associated with important economic traits in chickens using unique genetic populations, and to develop and test new methods for optimally integrating molecular data into programs for poultry genetic improvement.Candidate genes, regions and markers form the basis for hypothesis-testing through additional studies to determine the feasibility of future use in commercial breeding programs. Studies on both long-term and micro-evolution in chickens helps to define the genetic architecture of the species, relationships among populations, and genomic elements that may be associated with geography, environment or genetic selection. Objective 1. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene editing. Iowa State University maintained and reproduced eight unique chicken research lines that served as resources for identifying genes, quantitative trait loci, and genetic pathways associated with traits of economic importance. These lines included highly inbred lines (the oldest was established in 1925), MHC-congenic pairs of lines, a closed broiler population, and advanced intercross lines (now at the F31 generation) formed from crossing a broiler (meat-type) sire with Fayoumi (village-type chicken originating in Egypt) inbred hens. Because of defined and distinct responses among these lines, the ISU genetic lines served as a discovery platform for genetics and genomics research in several studies supported by grants from the USDA, USAID and other sources. In the past year, transcriptomic analyses of tissues from birds challenged with several different types of pathogens, and on in vitro characteristics of cells from these lines, was conducted. In two major collaborative projects, we explored the origin, domestication and the long-term and microevolution of the chicken species. The geographic and temporal origins of the domestication of chickens are controversial. We participated in a major global consortium of researchers that analyzed 863 genomes from a global sampling of domestic chickens and of all four species of wild jungle fowl and the five subspecies of red jungle fowl. Our study provides novel insights into the evolutionary history of domestic chickens and provides a foundation for future genetic and functional studies. Stringent artificial selection is typically applied to improve productivity and efficiency of poultry production systems. Little is known, however, about the microevolution of genomes due to intensive breeding. We determined the dynamic changes of chicken genomes under divergent selection for fat content (adiposity) over 19 generations, using whole-genome sequencing. Our study provides insights into the microevolutionary dynamics of chicken genomes under human-directed selection. Additionally, understanding genetic predisposition to obesity may contribute to understanding the condition in other species including humans. Objective 2. Elucidate genetic mechanisms that underlie economically important traits, including genetic variants and functional regulatory elements within the genomes of poultry species, and develop new methods to apply that knowledge to poultry breeding practices. Newcastle Disease (ND) is a global threat to domestic poultry, especially in the developing countries, where entire small holder flocks are often lost to the disease. Local chicken ecotypes are important to rural family households through provision of high-quality protein in the form of eggs and meat and serve as a source of income. Collaborative studies were conducted in two countries, Ghana and Tanzania. In each country, three popular chicken ecotypes were naturally infected with a velogenic NDV strain by exposure to seeder birds that had been naturally infected with a velogenic strain of NDV. Various traits including natural antibodies, pre-exposure growth, and other host response traits, including viral load at 2, 4 and 6 days post exposure (dpe), viral shedding at 2, 4, and 6dpe, anti-NDV antibody levels at 7 dpe, viral lesion score in the trachea, proventriculus, intestine, and caecal tonsil, survival time and growth up to 3 weeks post-exposure, were recorded or measured. All birds were genotyped on a low density 5000K panel using genotyping by sequencing and imputed to a 600K SNP high-density panel for downstream analyses. We estimated genetic parameters and performed genome-wide association study (GWAS) analyses, using data on about 1300 and 1500 birds for Ghana and Tanzania, respectively. Data analyses indicated that various traits, including pre-exposure growth rate, natural antibody levels, proventriculus lesions, and survival time were heritable for both Ghana and Tanzania with heritabilities ranging between 0.12-0.37. Moderate heritabilities (0.10 - 0.44) were noted for average lesions, intestinal lesions, tear viral load at 6 dpe, and swabs viral load at 4 and 6 dpe for either Tanzania or Ghana. Preliminary analyses revealed high genetic correlation between survival time and swabs viral load at 4 and 6 dpe. Twelve and six genomic regions explaining >1% of the genetic variance were identified by the Bayes B GWAS analysis method for Tanzania and Ghana, respectively. Genomic prediction for survival time using BayesB and BayesCo indicated an accuracy of 0.42. The moderate estimates of heritability and identified QTL suggest that host response to NDV can be improved through selective breeding of African local chicken ecotypes to enhance increased NDV resilience and vaccine efficacy.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Mushi, J.R., Chiwanga, G.H., Amuzu-Aweh, E.N., Walugembe, M., Max, R.A., Lamont, S.J., Kelly, T.R., Mollel, E.L., Msoffe, P.L., Dekkers, J., Gallardo, R., Zhou, H., and Muhairwa, A.P. 2020. Phenotypic variability and population structure analysis of Tanzanian free-range local chickens. BMC Vet. Res. 16, 360 doi.org/10.1186/s12917-020-02541-x
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wang, Y., Saelao, P., Kern, C., Jin, S., Gallardo, R.A., Kelly, T., Dekkers, J.M., Lamont, S.J., Zhou, H. 2020. Liver transcriptome responses to heat stress and Newcastle Disease virus infection in genetically distinct chicken inbred lines. GENES 11, 1067; doi:10.3390/genes11091067
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Chanthavixay, G., Kern, C., Wang, Y., Saelao, P., Lamont, S.J., Gallardo, R.A., Rincon, G., Zhou, H. 2020. Integrated transcriptome and histone modification analysis reveals NDV infection under heat stress affects bursa development and proliferation in susceptible chicken line. Front. Genet. 11:567812. doi: 10.3389/fgene.2020.567812
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Zhang, J., Kaiser, M.G., Gallardo, R.A., Kelly, T. R., Dekkers, J.C.M., Zhou, H., Lamont, S.J. 2020. Transcriptome analysis reveals inhibitory effects of lentogenic Newcastle disease virus on cell survival and immune function in spleen of commercial layer chicks. Genes 11:1003; doi:10.3390/genes11091003
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Walugembe, M., Amuzu-Aweh, E.N., Botchway, P.K., Naazie, A., Aning, G., Wang, Y., Saelao, P., Kelly, T., Gallardo, R.A., Zhou, H., Lamont, S.J., Kayang, B., Dekkers, J. 2020. Genetic basis of response of Ghanaian local chickens to infection with a lentogenic Newcastle disease virus. Frontiers Genetics doi: 10.3389/fgene.2020.00739
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Zhang, H., Liang, Q., Wang, N., Wang, Q., Leng, L., Mao, J., Wang, Y., Wang, S., Zhang, J., Liang, H., Zhou, X., Li, Y., Cao, Z., Luan, P., Wang, Z., Yuan, H., Wang, Z., Zhou, X., Lamont, S.J., Da, Y., Li, R., Tian, S., Du, Z., and Li, H. Microevolutionary dynamics of chicken genomes under divergent selection for adiposity. 2020. iScience. 23:101193. doi: 10.1016/j.isci.2020.101193.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wang, M.-S., Thakur, M., Peng, M.-S., Jiang, Y., Frantz, L.A.F., Li, M., Zhang, J.-J., Wang, S., Peters, J., Otecko, N.O., Suwannapoom, C., Guo, X., Zheng, Z.-Q., Esmailizadeh, A., Yasoda, N., Hirimuthugoda, Ashari, H., Suladari, S., Zein, M.S.A., Kusza, S., Sohrabi, S., Kharrati-Koopaee, H., Shen, Q.-K., Zeng, L., Yang, M.-M., Wu, Y.-J., Yang, X.-Y., Xue-Mei Lu, X.-M., Jia, X.-Z., Nie, Q.-H., Lamont, S.J., Lasagna, E., Ceccobelli, S., Gunwardana, H.G.T.N., Senasige, T.M., Feng, S.-H., Si, J.-F., Zhang, H., Jin, J.-Q., Li, M.-L., Liu, Y.-H., Chen, H.-M., Ma, C., Dai, S.-S., Bhuiyan, A.K.F.H., Khan, M.S., Silva, G. L. L. P., Le, T.-T., Mwai, O.A., Nawaz, M., Ibrahim, M., Supple, M., Shapiro, B., Hanotte, O., Zhang, G., Larson, G., Han, J.-L., Wu, D.-D. and Zhang, Y.-P. 2020. 863 genomes reveal the origin and domestication of chicken. Cell Research 30, 693701. https://doi.org/10.1038/s41422-020-0349-y
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Deist, M.S., Gallardo, R.A., Dekkers, J.C.M., Zhou, H. Lamont, S.J. 2020. Novel combined tissue transcriptome analysis after lentogenic Newcastle disease virus challenge in inbred chicken lines of differential resistance. Frontiers Genet. 11:11. doi: 10.3389/fgene.2020.00011
- Type:
Book Chapters
Status:
Published
Year Published:
2020
Citation:
Cheng, H.H. and Lamont, S.J. 2020. Genetics of disease resistance. Pp. 90-108. In: Diseases of Poultry. 14th ed. D.E. Swayne, M. Boulianne, C.M. Logue, L.R. McDougald, V. Nair, and D.L. Suarez, Eds. Wiley-Blackwell, Hoboken
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wolc, A., Drobik-Czwarno, W., Jankowski, T., Arango, J., Settar, P., Fulton, J.E., Fernando, R.L., Garrick, D.J. and Dekkers, J.C.M. 2020. Accuracy of genomic prediction of shell quality in a White Leghorn line. Poultry Science. 99: 2833-2840
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wolc, A., Arango, J., Rubinoff, I. and Dekkers, J.C. 2020. A biphasic curve for modeling, classifying, and predicting egg production in single cycle and molted flocks. Poultry Science. doi.org/10.1016/j.psj.2019.11.037
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Animal and poultry breeders and geneticists, veterinarians, researchers and students in animal health and in poultry breeding and genetics, commercial breeders of poultry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate students, post-doctoral fellows, and visiting international scholars were mentored and trained in conducting research in this project. Courses in animal breeding and genetics were taught to graduate students. Faculty, graduate students and staff of the project participated in relevant regional, national and international scientific conferences. How have the results been disseminated to communities of interest?The results have been disseminated by publication of peer-reviewed journal papers, presentation of research at conferences and in seminars at other universities, web-hosted industry reports, and direct communications with poultry genetics companies. Special efforts were made to have project trainees attend conferences and present their research. What do you plan to do during the next reporting period to accomplish the goals?Publish peer-reviewed journal papers on the completed studies. Maintain the ISU genetic lines of chickens. Continue research progress on the study of genetics and genomics of response to Newcastle disease virus. Complete analysis of effects of heat-stress on microbiome of layer chickens.
Impacts
What was accomplished under these goals?
Overall impact statement: Poultry eggs and meat provide a major source of nutrient-dense animal protein for human consumption. To enhance production efficiency, improve product quality and safety, meet consumer preferences, and to maintain US competitiveness in a global market, new information and technologies must be developed to enable continued genetic improvements in poultry. The aim of this research project was to identify genes and genomic regions associated with important economic traits in chickens using unique genetic populations, and to develop and test new methods for optimally integrating molecular data into programs for poultry genetic improvement. Objective 1. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene editing. Iowa State University maintained and reproduced eight unique chicken research lines that served as resources for identifying genes, quantitative trait loci, and genetic pathways associated with traits of economic importance. These lines included highly inbred lines (the oldest was established in 1925), MHC-congenic pairs, a closed broiler population, and advanced intercross lines formed from crossing a broiler (meat-type) sire with Fayoumi (village-type chicken originating in Egypt) inbred hens. Because of defined and distinct responses among these lines, the ISU genetic lines served as a discovery platform for genetics and genomics research in several studies supported by grants from the USDA, USAID and other sources. Phenotypes were collected on live birds challenged with several different types of pathogens, and on in vitro characteristics of cells from these lines. Objective 2. Elucidate genetic mechanisms that underlie economically important traits, including genetic variants and functional regulatory elements within the genomes of poultry species, and develop new methods to apply that knowledge to poultry breeding practices. Broiler production has improved greatly over the past several decades, but excessive abdominal fat deposition remains a problem. Fat deposition is a result of excess energy intake, in which the intestine plays a role by digesting feed and absorbing nutrients. The association of the intestine with broiler abdominal fat deposition has not been investigated at the transcriptome level. Therefore, to explore intestinal gene expression associated with broiler lines selected for abdominal fat deposition, we collected the duodenum, jejunum, ileum, and cecum of 10 high- and 10 low-abdominal fat line (HL and LL) male broilers from Generation 21 of the Northeast Agricultural University High- and Low-Fat (NEAUHLF) broiler lines that had been divergently selected for abdominal fat. We identified differentially expressed genes (DEGs) in the four intestine tissues in comparisons of the HL vs LL, and in comparisons across tissues within the HL and LL using RNA-seq. Ingenuity Pathway Analysis (IPA) predicted that duodenal cell turnover functions would be inhibited of the HL vs LL. IPA predicted that ileal transport of lipids would be inhibited in the HL vs LL. Catabolism of lipids and transport of lipids were significantly predicted to be inhibited in ileum vs duodenum and ileum vs jejunum within the HL, but no differences were predicted within the LL. Our data suggest that more lipids might be absorbed in the duodenum and jejunum within the HL. The current study's results provide a foundation for understanding of transcriptional regulation of broiler abdominal fat deposition and intestinal lipid digestion and absorption. Newcastle Disease (ND) is a global threat to domestic poultry, especially in the developing countries, where entire small holder flocks are often lost to the disease. Local chicken ecotypes are important to rural family households through provision of high-quality protein in the form of eggs and meat and serve as a source of income. Studies were conducted in two countries, Ghana and Tanzania. In each country, three popular chicken ecotypes were challenged with a lentogenic (vaccine) strain of NDV. Various host response phenotypes, including viral load at 2 and 6 dpi, anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and growth to 38 days of age, were measured. All birds were genotyped using a 600K Single Nucleotide Polymorphism (SNP) panel. We estimated genetic parameters and performed genome-wide association study (GWAS) analyses, using data on about 1400 birds per country. Heritability estimates for the various traits ranged from moderate to high (0.18 - 0.55). Six and twelve quantitative trait loci (QTL) were identified by single-SNP analyses for growth and/or response to NDV for Tanzania and Ghana, respectively. Several locations of these QTL corresponded in location with genomic regions explaining >1% of the genetic variance identified by the Bayes B GWAS analysis method. Immune related genes were located in the QTL regions for some response traits. Significant SNPs from GWAS and other important SNPs from separate studies, along with SNPs spread across the genome were used in the development of a 5K SNP panel for use in imputation. The moderate estimates of heritability and identified QTL suggest that host response to NDV can be improved through selective breeding of Africa local chicken ecotypes to enhance increased NDV resilience and vaccine efficacy.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Adentunji, M., Lamont, S.J., Abasht, B.A., and Schmidt, C. J. 2019. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLOS ONE 14(9): e0216838.doi.org/10.1371/journal.pone.0216838
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Monson, M.S., Van Goor, A.G., Persia, M.E., Rothschild, M. F., Schmidt, C.J., Lamont, S.J. 2019. Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide. Scientific Reports 9:13649 doi.org/10.1038/s41598-019-50051-0
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Barrett, N.W., Schmidt, C.J., Lamont, S.J., Ashwell, C.M., Persia, M.E. 2019. Effects of acute and chronic heat stress on the performance, egg quality, body temperature and blood gas parameters of laying hens. Poultry Science. http://dx.doi.org/10.3382/ps/pez541
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Walugembe, M. Mushi, J., Amuzu-Aweh, E., Chiwanga, G., Msoffe, P., Wang, Y., Saelao, P., Kelly, T., Gallardo, R., Zhou, H., Lamont, S., Muhairwa, A., Dekkers. J. 2019. Genetic analyses of Tanzania local chicken ecotypes challenged with Newcastle disease virus. Genes 10, 546; doi:10.3390/genes10070546
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Rowland, K., Ashwell, C.M. Persia, M.P., Rothschild, M.F., Schmidt, C., Lamont, S.J. 2019. Genetic analysis of production, physiologic, and egg quality traits in heat-challenged commercial white egg-laying hens using 600k SNP array data. Genetics Selection Evolution 51:31 doi.org/10.1186/s12711-019-0474-6
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Elbeltagy, A.R., Bertolini, F., Fleming, D.S., Van Goor, A., Ashwell, C.M., Schmidt, C.J., Kugonza, D., Lamont, S.J., Rothschild, M.F. 2019. Natural selection footprints among African chicken breeds and village ecotypes. Front. Genet. 10:376. doi: 10.3389/fgene.2019.00376
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Rowland, K., Persia, M., Rothschild, M., Schmidt, C., Lamont, S. 2019. Blood gas and chemistry components are moderately heritable in commercial white egg-laying hens under acute or chronic heat exposure. Poultry Science 0:15 http://dx.doi.org/10.3382/ps/pez204
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Saelao, P., Wang, Y., Chanthavixay, G., Gallardo, R.A., Wolc, A., Dekkers, J.C.M., Lamont, S.J., and Zhou, H. 2019. Genetics and genomic regions affecting response to Newcastle disease virus infection under heat stress in layer chickens. Genes 10(1), 61; https://doi.org/10.3390/genes10010061
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Walugembe, M., Bertolini, F., Dematawewa, C.M.B., Reis, M.P., Elbeltagy, A.R., Schmidt, C.J., Lamont, S.J., and Rothschild, M.F. 2019. Detection of selection signatures among Brazilian, Sri Lankan, and Egyptian chicken populations under different environmental conditions. Front. Genet. doi: 10.3389/fgene.2018.00737
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Zhuo, Z., Lamont, S., Abasht, B. 2019. RNA-Seq analyses identify additivity as the predominant gene expression pattern in F1 chicken embryonic brain and liver. Genes 10, 27; doi:10.3390/genes10010027
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
A.1. Drobik-Czwarno, W., Wolc, A., Kucharska, K., Martyniuk. E., Genetic basis of resistance to highly pathogenic avian influenza in chicken. Review article in Polish. Scientific Annals of Polish Society of Animal Production.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
A.2. Wolc, A., Arango, J., Settar, P., Fulton, J.E., OSullivan, N.P. and Dekkers, J.C., 2019. Genetics of male reproductive performance in White Leghorns. Poultry science, 98(7), pp.2729-2733.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
A.3. Weng, Z., Wolc, A., Su, H., Fernando, R.L., Dekkers, J.C., Arango, J., Settar, P., Fulton, J.E., OSullivan, N.P. and Garrick, D.J., 2019. Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens. Journal of animal science and biotechnology, 10(1), p.20.
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