臺灣商用紅羽土雞不同族群遺傳結構之研析

Abstract

家雞（Gallus gallus domesticus）是全球分布最廣泛的經濟動物，其所生產的雞肉與雞蛋在世界各地都是非常重要的食物來源。經濟動物性狀會受到多種因子影響，包含環境因素與遺傳背景因素，而品種/系內性狀表型的不一致與不整齊是很重要的議題。2022年臺灣家禽總產值初次超越臺灣畜牧總產值五成，可見家禽產業在臺灣畜牧界的重要性，雞為家禽產業中最重要的物種，可區分為肉用與蛋用兩大類別，肉用雞種可分為白肉雞與有色肉雞，而有色肉雞產業可再細分為商用紅羽土雞、商用黑羽土雞、烏骨雞、鬥雞、文昌雞及閹雞等多樣品種。在商業生產上，以商用紅羽土雞與黑羽土雞為大宗，佔整體土雞總產量85%，可知商用紅羽土雞與商用黑羽土雞在臺灣家禽產業的重要性。 隨著分子技術的進步，次世代定序（Next-generation sequencing；NGS）當中的全基因組定序（Whole genome sequencing；WGS）是能夠針對物種的基因組全長進行完整的測序技術，因此能夠完整瞭解物種的基因組，在育種選拔和疾病的篩選有非常大的貢獻，且有助於進行物種的保種及瞭解演化過程。在雞隻方面第一個進行全基因組定序的品種為紅色叢林雞（Red Junglefowl），而目前在國外已有許多以全基因組重定序（Whole genome re-sequencing）的研究應用在動物族群遺傳結構分析及尋找品種/系的特異性基因。但目前臺灣尚未針對紅羽土雞進行過遺傳結構的解析，因此本研究與國內四場紅羽土雞種雞場合作，其所飼養的紅羽土雞種母雞佔全國紅羽土雞種母雞總量35.3%，並收集種母雞的血液及屠體性狀資料作為紅羽土雞遺傳結構的解析。 本研究針對臺灣商用紅羽土雞種母雞進行MC1R毛色基因序列定序與基因型鑑定，並應用全基因組重定序技術進行全基因組序列定序，以研究其族群遺傳結構，並搭配收集的屠體性狀數據，包含屠體重、屠宰率與各部位肉重，並應用全基因組關聯性分析（Genome-wide association study；GWAS），以探討屠體重、屠宰率與各部位肉重之特定位點與相鄰基因，並依照候選位點繪製層次聚類（Hierarchical clustering）分析圖，瞭解候選位點在樣本之間的基因型分布情況，再利用基因功能分類分析候選基因，包含：GO分析（Gene Ontology）與KEGG分析（Kyoto Encyclopedia of Genes and Genomes；KEGG），以尋找可能影響屠體表型性狀的候選基因。 研究結果顯示，從屠體性狀資料分析發現，四場商用紅羽土雞品系內屠體重性狀及腿肉重的標準差較大，表示品系內表型性狀並不整齊。在族群遺傳結構分析中，不論是主成分分析圖（Principal component analysis；PCA）、親緣關係樹（Phylogenetic tree）及層次聚類分析熱圖（Heat map）皆顯示臺灣商用紅羽土雞不同品系之間的基因組有所差異。 本研究初次揭示臺灣商用紅羽土雞的族群遺傳結構，對於商用紅羽土雞的基因組有初步的瞭解，篩選出與屠體重、屠宰率與各部位肉重的相關位點及基因，並開發鑑別不同紅羽土雞族群品系之分子標記之檢測平台，未來可提供臺灣商用紅羽土雞之育種及建立新品系的參考。

The domestic chicken (Gallus gallus domesticus) is the most widely distributed economic animal globally, with its meat and eggs being crucial food sources worldwide. Economic traits in animals are influenced by various factors, including environmental and genetic background. The inconsistency and irregularity of phenotypic traits within breeds/lines being significant issues. In 2022, the poultry production value exceeded half of total livestock production value in Taiwan, indicating the importance of the poultry industry in the livestock sector. Poultry is categorized into meat chickens and egg-laying chickens, with meat chickens further classified into broiler and colored-feathered chickens. The colored-feathered chicken industry includes various breeds such as commercial red-feathered country chickens, commercial black-feathered country chickens, Silkies, fighting cocks, Wen-Chang chickens, and capons, among which commercial red-feathered and black-feathered country chickens constitute the majority, accounting for 85% of the total chicken production in Taiwan, highlighting their significance in the country's poultry industry. With the advancement of molecular techniques, whole-genome sequencing (WGS) within next-generation sequencing (NGS) has emerged as a comprehensive sequencing technique capable of sequencing the entire genome of a species, facilitating a thorough understanding of the species genome. This technology has made significant contributions to breeding selection, disease screening, species conservation, and understanding evolutionary processes. The red junglefowl was the first chicken breed subjected to whole-genome sequencing. Many studies abroad have utilized whole-genome re-sequencing to understand the population genetic structure and specific genes of local chickens, yet Taiwan has not conducted genetic structural analysis of commercial red-feathered country chickens. This study collected blood and carcass samples from commercial red-feathered country chicken breeding hens in four Taiwanese farms. Initial data surveys revealed that the four collaborating farms accounted for 35.3% of the total number of breeding hens nationwide, representing a significant portion of the genetic information of Taiwan's commercial red-feathered country chickens. This research involved sequencing and genotyping the MC1R feather color gene in commercial red-feathered Taiwan country chicken breeding hens. Additionally, whole-genome resequencing was employed to sequence their entire genome to study their population genetic structure. Combining collected carcass trait data, including carcass weight, dressing percentage, and meat weights of various parts, with genome-wide association analysis (GWAS), the study aimed to explore specific SNPs and adjacent genes. Hierarchical clustering analysis was conducted to understand the genotype distribution of candidate SNPs among samples, followed by gene functional classification analysis, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to identify candidate genes potentially affecting carcass phenotype traits. The results revealed significant variability in carcass weight and thighs weight among the four commercial red-feathered country chicken lines, indicating inconsistency in phenotypic traits within these lines. Population genetic structure analysis, including principal component analysis (PCA), phylogenetic tree, and hierarchical clustering analysis heatmap, showed genetic differences among different of Taiwan's commercial red-feathered country chickens. This study provides initial insights into the population genetic structure of Taiwan's commercial red-feathered country chickens, offering preliminary understanding of their genomic characteristics. It identified relevant SNPs and genes associated with carcass weight, dressing percentage, and various meat weights, and developed molecular markers to differentiate between different population lines, providing a reference for breeding and establishing new lines of Taiwan's commercial red-feathered country chickens in the future.