# Whole-Genome Resequencing Reveals Population Structure and Loci Associated with Growth and Meat-Quality Traits in Meigu Yanying Chickens

## TL;DR

This study uses whole-genome sequencing to identify genetic factors linked to growth and meat quality in a local Chinese chicken breed.

## Contribution

The study provides the first genome-wide insights into the genetic basis of growth and meat traits in Meigu Yanying chickens.

## Key findings

- The breed shows high genetic diversity and low inbreeding, which is beneficial for conservation and breeding.
- Several genetic regions were linked to muscle and liver weight, protein, and cholesterol levels in meat.
- Candidate genes were identified for traits related to growth and meat quality, offering targets for breeding programs.

## Abstract

The Meigu Yanying chicken is an important local meat breed from the mountains of southwest China, but little is known about the genes that make it strong, productive and good to eat. In this study, we combined detailed body and meat measurements with modern genetic sequencing in 211 birds to explore how differences in their genetic code relate to growth and meat quality. We focused on leg muscle weight, liver weight, protein content in leg meat and cholesterol content in leg meat, which are all closely linked to both farmer profit and consumer health. Our analyses showed that this breed still has rich genetic diversity and only low levels of inbreeding, which is positive for long-term conservation and breeding. We also found several regions in the genetic code that were strongly associated with heavier muscles and livers, higher protein and differences in cholesterol level. These results provide a scientific basis to protect this local breed and to design breeding programs that produce chickens with better growth, tastier meat and potentially healthier nutritional profiles for consumers.

Liangshan Meigu Yanying chicken is an indigenous high-altitude breed in Sichuan, China, but its population genetic structure and the genetic basis of key growth and meat-quality traits remain unclear. In this study, 211 Meigu Yanying chickens were whole-genome resequenced, and leg muscle weight, liver weight, leg muscle total protein content and leg muscle total cholesterol content were recorded at slaughter. After quality control, high-confidence single-nucleotide polymorphisms were used to analyze linkage disequilibrium, population structure and genome-wide associations. Linkage disequilibrium decayed rapidly with distance, and multivariate analyses indicated an overall homogeneous genetic background with only mild substructure and few closely related individuals. Genome-wide association studies for the four traits detected several significant or suggestive regions harboring biologically plausible candidate genes, including CPNE4, PLXNB2, SMAP1, SDHAF4, FAM135A, LCP1, MAPK15 and SCRIB. Gene Ontology enrichment showed that candidate genes for leg muscle weight and liver weight were mainly involved in cellular processes and tissue development, whereas those for leg muscle total cholesterol content were enriched in phosphorus metabolism and phosphate-containing compound metabolism. These results provide a genome-wide resource for Meigu Yanying chickens and lay a basis for conservation and genomic breeding aimed at improved growth performance, meat quality and nutritional value.