Source: UNIVERSITY OF DELAWARE submitted to
TARGETING GENOMIC REGIONS IDENTIFIED THROUGH GENOME-WIDE ASSOCIATION STUDY OF WOODEN BREAST
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1026102
Grant No.
2021-67015-34543
Project No.
DEL00815
Proposal No.
2020-02675
Multistate No.
(N/A)
Program Code
A1231
Project Start Date
Jul 1, 2021
Project End Date
Jun 30, 2024
Grant Year
2021
Project Director
Abasht, B.
Recipient Organization
UNIVERSITY OF DELAWARE
(N/A)
NEWARK,DE 19717
Performing Department
Animal & Food Science
Non Technical Summary
Wooden Breast myopathy (WB) has emerged as a global threat to broiler production due to severe deterioration of meat quality in affected muscles. Despite its prevalence and the fact that broiler producers and primary breeding companies have expressed immense interest in a timely and economic solution, there is currently no approach available to effectively prevent this disease. Through association analyses, we have recently identified genomic regions associated with WB. The purpose of our project is to conduct an in-depth analysis of these genomic regions to identify and characterize candidate mutations that cause WB. We aim to (i) validate while at the same time increase mapping precision of these regions, (ii) identify candidate mutations that cause WB in each target region and determine their roles in metabolic dysregulation andcellular dysfunction. A new sequencing approach will be used to sequence target genomic regions in 800 broiler chickens.The application of this new technology is revolutionary in that it will enable detecting all types of changes in DNA among individuals [single nucleotide ("1-letter" changes), insertion/deletion (< 50-letter changes) and structural (>= 50-letter changes)], allowing identification of top significant changes (mutations) causing WB.Additionally, association analysis using these mutations in each target region and molecular phenotypes (gene expression and metabolites) will allow studying the cause of WB.
Animal Health Component
0%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
30832201080100%
Goals / Objectives
As a part of a grant funded by the USDA-NIFA, we have conducted a genome-wide association study (GWAS) and identified genomic regions significantly associatedwith Wooden Breast disease in broiler chickens.The overall objectiveof this project is to identify and characterize candidate causal variants intarget genomic regions,so that long-term solutions for reducing incidence of WB can be achieved.
Project Methods
Methods that will be used include targeted sequencing, variant-trait association analysis using a mixed-model, histopathologic analysis of breast muscle samples, allele-specific expression analysis, functional annotation of variants in target regions, gene expression analysis using 3'UTR sequencing, metabolomics analysis and manipulation of gene expression.

Progress 07/01/21 to 06/30/22

Outputs
Target Audience:Scientific community, poultry breeders, students Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunities were provided for 8 undergrad and 2 grad students. Student participated in a wide range of activities, including but not restricted to feeding breeders (hens and roosters), collecting eggs, setting eggs in an incubator, candling eggs to identify viable embryos, hatching eggs, raising chicks, tagging chicks (wing-band), recording live weight, routine checking on live chickens, postmortem tissue sample and data collection, tissue sample processing (homogenization) and RNA isolation from tissue samples. RNA quality and quantity checks, blood sample collection and separating plasma from blood cells. 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? Histopathologic Analysis of 567 p. major muscle samples harvested at necropsy Spatial transcriptomic analysis using Visium Spatial Transcriptomic method RNA and DNA isolation from blood and tissue samples RNAi assays for candidate genes to knock-down gene expression in satellite cells in co-PI's lab

Impacts
What was accomplished under these goals? Live animal experiment: A new experiment was conducted using commercial broiler chickensat the University of Delaware. Cobb Breeders including 30 hens (Cobb500) and 6 roosters (Cobb Vantage)were obtained from abreeders farm in New Holland, PA.Breeders were randomly placed in 2 breeder houses, 15 hens and 3 roosters per house. Egg were collected twice daily and stored in a cold room until incubation.Eggs from one week of egg collection were incubated in an egg incubator at 100 °F, 70% humidity, and checked by candling at embryonic day 11;non-viableeggs were disposed properly.Upon hatching,chickenswere placed in chicken houses at the University of Delawareand raised in accordance with the Animal Care and Use Handbook 2019 of the UD College of Agriculture and Natural Resources. Chicks had free access to feed and water throughout the experiment.Tissue samples were harvested post-euthanasia at day 14 15, 16, 17 post-hatch immediately frozen in liquid nitrogen, and stored in a −80 °C freezer until subsequent analysis.Sex was determined post-euthanasia during necropsy by visual inspection of gonads and will subsequently be confirmed by PCR-based sexing, as we described before (Zhuo et al., 2017). During necropsy, the entire p. major muscle was removed, weighed, and samples from the p. major muscle were taken from the cranial aspect (which is typically the fastest growing part of the muscle) of the left p. major muscle. Two sets of samples, one for histopathologic analysis and another for gene expression analysis were collected from the same sampling location.While this project is focused on the p. major muscle, two important metabolic tissues (liver and adipose) were also collected forpotentialfuture studies.Body weight were recorded and cardiac blood samples were collectedpost-euthanasia. In total, tissue and blood samples were collected from 534 chicks over 5 hatches. Histopathologic Analysis: One set of p. majorsamples harvested at necropsy were placed in 10% neutral buffered formalin for histologic analysis. Tissues were trimmed, embedded transversely and longitudinally in paraffin, sectioned to 4 μm thickness, and autostained with Hematoxylin and Eosin. Slides will be analyzed microscopically in a blinded manner by students trained by the project collaborator Dr. Brannick-board certified veterinary anatomic pathologist screening for lesions of vasculitis/phlebitis, abnormal lipid deposition, and WB (myofiber damage, myositis, regeneration, fibrosis, edema, etc.).

Publications