ADVANCED TECHNOLOGIES FOR THE GENETIC IMPROVEMENT OF POULTRY (WAS NC-168)

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1011590
• Multistate No.: NC-_old1170
• Project Start Date: Oct 1, 2015
• Project End Date: Sep 30, 2018
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIVERSITY OF GEORGIA
200 D.W. BROOKS DR
ATHENS,GA 30602-5016

Performing Department
Poultry Science

Non Technical Summary
1. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expressions by targeting the mRNAs especially in the 3'UTR regions. The identification of miRNAs has been done by biological experiment, however, computation methods could be developed for rapid identification prior to biological confirmation. We developed the program mir-Explore which relies on within miRNA class alignment to predict mirRNA precursors. Compared with global alignment, grouping miRNA by classes yields a better sensitivity with very high specificity for pre-miRNA prediction even when a simple positional based secondary and primary structure alignment are used.2. Selection for residual feed intake will lead to reduced feed intake and no changes in weight gain. High feed efficiency birds are characterized by rapid conversion of carbohydrates to ATP, high fat oxidation, increased in de novo amino acid synthesis, cell division and proliferation, and efficient nitrogen recycling. Low feed efficiency birds are characterized by low ATP production, increased apoptosis, increased lipogenesis and increased ammonium production and excretion.

Animal Health Component

10%

Research Effort Categories

Basic

60%

Applied

10%

Developmental

30%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3220	1080	50%
302	3220	1010	50%

Knowledge Area
303 - Genetic Improvement of Animals; 302 - Nutrient Utilization in Animals;

Subject Of Investigation
3220 - Meat-type chicken, live animal;

Field Of Science
1010 - Nutrition and metabolism; 1080 - Genetics;

Keywords

feed efficiency

nutrigenomics

genome breeding values

methionine

Goals / Objectives
Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices.

Project Methods
Use nutrigenomic approaches to decipher traits of economic importance. Elucidate the molecular dynamics of sulfur amino acids and feed conversion ratio. We have genotype our control population for several single nucleotide polymorphisms. We are testing the conventional statistical approaches, e.g. multiple regression analysis for association of SNPs to traits of economic importance. We are also using a machine learning approach to analyze association of SNP to traits of economic importance. The ant colony optimization algorithm (ACA) coupled with logistic regression on haplotypes will be adapted for association studies involving large numbers of SNP markers. The ACA uses artificial ants that communicate through a probability density function (PDF) that is updated at each iteration with weights, which are analogous to the chemical pheromones used by real ants. In the case of SNP association studies, the weights can be ascertained by the strength of the association between selected haplotypes and the traits of interest. The SNPs selected by ACA could be a combination of both additive and interactive effects of SNPs. The ACA will remove redundant SNPs. The candidate SNPs will be further tested via regular multiple regression analysis.

Progress 10/01/15 to 09/30/18

Outputs
Target Audience:Quantitative Geneticists Poultry Breeders Poultry Producers NutriGenomicist Functional Genomicist Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has trained Dr. Walid Habashy, Mr. Bryan Ortega, Mr. James Foutz, Dr. Sajjad Toghiani and currently training, James Foutz, Gustavo Ortega, Jennifer Richter and Marie Milfort How have the results been disseminated to communities of interest?Results have been presented in several meetings and published in appropriate scientific journals What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. Multi-generational imputation of SNP markers genotypes and accuracy of genomic selection (a) Imputed genotypes provide a viable alternative, even after several generations, as long as teh reference and training populations are appropriately updated to reflect the genetic changes in the population 2. Genomic differentiation as a tool for SNP prioritization for genome wide association of phenotype prediction Using different empirical cut off values for FST, most QTLs were correctly detected using as few as 2.5% of SNP markers in the panels. Genomic similarity, calculated based on the selected SNPs, was very high (>0.80) for individuals with similar genetic and phenotypic values despite having limited to no pedigree relationship Filtering SNPs using FST could be beneficial for use in GWAS by focusing on genome regions under selection pressure. d. High functional genomic similarity based on selected markers indicates similarity in SNP signatures, regardless of relatedness, and translates into high phenotypic correlation that could be used in decision making. 3. Amino acid, protein utilization and nutrient transport under heat stress Heat stress affect growth possible via changes in nutrient and amino acid transporters Broiler chickens maintain the same level of amino acid digestibility under heat stress Heat stressed birds incorporate more amino acids into growth than birds raised in a thermos-neutral environment Cysteine is the amino acid incorporated most under heat stress.

Publications

• Type: Book Chapters Status: Published Year Published: 2017 Citation: Aggrey, S. E, F. Gonz�lez-Cer�n and R. Rekaya, 2017. Gene associated with functional traits in poultry: implications for sustainable genetic improvement. In: Achieving sustainable production of poultry meat, Volume 2. Breeding and Nutrition, Editor: Todd Applegate, Burleigh Dodd Science Publishing Ltd, Cambridge, UK Pg 3-24. DOI: 10.19103/AS.2016.0011.02
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Habashy, W. S., M. C. Milfort, K. Adomako, Y. A. Attia, R. Rekaya and S. E. Aggrey, 2017. Effect of Heat Stress on Amino Acid Digestibility and Transporters in meat-type Chickens. Poultry Science. 96: 2312-2319.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: 101. Toghiani, S., L.-Y. Chang, A. Ling, S. E. Aggrey, and R. Rekaya, Genomic differentiation o fa tool for single nucleotide polymorphism prioritization for genome wide association and phenotypic predication in livestock. Livestock Science 205:25-30.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Habashy, W., M. C. Milfort, A. L. Fuller, Y. A. Attia, R. Rekaya and S. E. Aggrey, 2017. Effect of heat stress on protein utilization and nutrient transporters in meat-type chickens. International Journal of Biometerology 61: 2111-2118
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Resnyk, C. W., W. Carr�; X. Wang, T. E. Porter, J. Simon, E. Le Bihan- Duval, M. J. Duclos, S. E. Aggrey and L. A. Cogburn, 2017. Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: Validating visceral adipose tissue as a dynamic endocrine and metabolic organ, BMC Genomics 18(1)626 doi: 10.1186/s12864-017-4035-5.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Yuan, J., E. Du, D. Yin, J. Gao, S. E. Aggrey and Y. Guo, 2017. Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces the effect of necrotic enteritis caused by Clostridium perfringes in broiler chickens. Scientific Reports 17(1) 7734. DOI: 10.1038/s41598-017-07420-4
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Chang, L.-Y., S. Toghiani, A. Ling, E. H. Hay, S. E. Aggrey and R. Rekaya, 2017. Analysis of multiple binary responses using a threshold model. J. Agric. Biol. And Environ. Stat. 22: 640-651
• Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Milfort M., J. Foutz, C. Dunkley, A. Davis, R. Rekaya and S. Aggrey, 2017. Amino acid composition and digestibility of organic feed ingredients. Poultry Science 95 (E-Suppl. 1): 156.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Poultry Breeders Poultry Producers Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has trained Mr. Walid S. Habashy and currently training James Foutz, Bryan Aguanta, Eduardo Ortega and Gustavo Scheiders How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?1. Molecular mechanisms of sulfur amino acids 2. Sulfur amino acids and immunity 3. Molecular and cellular bases of heat tolerance

Impacts
What was accomplished under these goals? 1. Multi-generational imputation of SNP marker genotypes and accuracy of genomic selection Imputed genotypes provide a viable alternative, even after several generations, as long the reference and training populations are appropriately updated to reflect the genetic change in the population. Dietary methionine deficiency seems to be associated with: Muscular inflammation Compromised immunity Inflammation in the digestive system Molecular basis of heat stress Initial molecular response under heat stress is to reduce both protein synthesis and degradation. When heat stress persists, protein breakdown is elevated.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Toghiani, S, S.E. Aggrey and R. Rekaya, 2016. Multi-generational imputation of SNP marker genotypes and accuracy of genomic selection. ANIMAL 10: 1077-1085.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Fulton, J. A. Lund, A. McCarron, K. Pinegar, D. Korver, H. Classen, S. Aggrey, C. Utterback, N. Anthony and M. Berres, 2016. MHC variability in heritage chicken breeds. Poultry Science 95:393-399.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Collins KE, HL Marks, S. E. Aggrey, M. P. Lacy and J. L., 2016. History of the Athens Canadian Random Bred control populations. Poultry Science 95: 997-1004.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Lee, J. A. and S. E. Aggrey, 2016. Transcriptomic differences in the avian mechanistic target of rapamycin (avTOR) pathway in a divergent line selected for feed efficiency in meat type chicken. Genetics and Molecular Research 15 (2): doi: 10.4238/gmr.15027120.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Rekaya, R., S. Smith, E. H. Hay, N. Farhart and S. E. Aggrey, 2016. Analysis of binary responses with outcomes specific misclassification probability in genome-wide association studies. The Application of Clinical Genetics: 9 169-177.