台灣主要種豬族群候選基因分析與表型關聯性研究

Abstract

台灣養豬業一直是畜牧業裡最重要的產業之一，本試驗旨在解析臺灣主要種豬族群之候選基因多型性分布與其經濟性狀間之關聯性，並建立豬隻基因型資料庫，以評估不同基因型對生長、繁殖與屠體性狀之遺傳效應，期為未來精準育種與基因體選拔（genomic selection, GS）提供基礎依據。試驗材料取自財團法人中央畜產會種豬性能檢定站（Central Breeding Swine Performance Testing Station, CBSPTS），整體分析資料涵蓋自第200005期至第202505期共23,647頭豬隻之歷史檢定紀錄，包含杜洛克（Duroc, D）、藍瑞斯（Landrace, L）及約克夏（Yorkshire, Y）三主要純種族群。自第202309期至第202505期另實際採集樣本1,633頭，進行基因型分析。所有個體均依中央檢定標準化作業程序進行飼養、測定及資料登錄。 本試驗分為兩部分。實驗一針對七個候選基因（PSS、ESR、H-FABP、IGF2-In3、IGF2-In7、PRLR與MSTN）共十一個單核苷酸多型性（single nucleotide polymorphism, SNP）位點進行分型，採用MassArray平台進行單鹼基延伸（SBE）質譜分型。所得基因型資料結合中央畜產會自202309期至202505期之生長與繁殖性狀資料，包含平均日增重（average daily gain, ADG）、飼料換肉率（feed conversion ratio, FCR）、修正背脂厚度（adjusted backfat thickness, adjBF）及育種選拔指數（selection index, SI）等性狀，利用SAS進行一般線性模式（GLM）與Tukey多重比較分析。實驗二則依據生長指數極端分群之樣本進行全基因組定序（whole-genome sequencing, WGS），藉由全基因組關聯分析（genome-wide association study, GWAS）比對高、低選拔指數組間之基因變異，篩選潛在影響生長性狀之新候選基因。 分析結果顯示，PSS基因在三品系間已趨於固定（AA型>98%）；ESR基因於三品系間呈高度分化（p<0.05），約克夏族群保留最高的基因多樣性，其MM型與窩仔數顯著相關（p<0.05）。H-FABP基因三個限制酶切位點（HinfI、MspI、HaeIII）組成之基因指數在不同族群間呈顯著差異，公約克夏族群中，其指數值與ADG、FCR及選拔指數具有顯著影響（p<0.05）。增長基因（IGF2-In3 gene）自202309期後在三品種豬種間均為QQ型，在公藍瑞斯族群中，增肌基因（IGF2-In7 gene）與窩仔數及飼料換肉率有顯著影響（p<0.05）。PRLR基因在三品系中顯示不同的分布型態，其中杜洛克以LP型為主（約50%），藍瑞斯以LL型為主（約63%），在藍瑞斯族群中，PRLR基因與ADG有顯著影響（p<0.05）。本研究特別關注之MSTN基因，於三個位點（435、447與879）均呈現顯著多型性，並可形成多種haplotype組合。MSTN之A/KS與A/SS型在藍瑞斯與約克夏族群中與窩仔數及生長性狀顯著相關（p<0.05）。實驗二透過 WGS 分析，本研究進一步觀察到杜洛克、藍瑞斯與約克夏族群間具有明顯的基因組分化，主成分分析（PCA）結果亦證實三品種形成獨立聚群。WGS 差異分析顯示，生長與適應性相關的基因多分布於非編碼調控區域，突顯調控變異於複雜性狀中的重要性。整體而言，候選基因方法可針對特定位點提供生物意義，而 WGS 則能補足其限制，揭示更完整的基因組變異與多基因調控架構。整體而言，本研究結果顯示，不同候選基因於三品系間皆具有顯著的基因結構分化，且部分位點與主要經濟性狀呈現顯著關聯，反映臺灣種豬族群在長期育種選拔下的遺傳變化趨勢。 綜合而言，本研究成功整合中央畜產會近二十五年間之性能資料與分子分型結果，建立完整的候選基因與表型關聯分析架構。所得結果不僅可作為臺灣種豬族群分子育種與選拔的參考基礎，亦有助於未來建立基因體選拔模型與精準育種策略，推動臺灣種豬產業發展。

The swine industry has long been one of the most important sectors of animal husbandry in Taiwan. This study aimed to investigate the distribution of the candidate gene polymorphisms in Taiwan’s main breeding pig populations and analyze their associations with key economic traits. A comprehensive genotypic database was established to evaluate genetic effects on growth, reproduction, and carcass characteristics, providing a foundation for precision breeding and Marker-Assisted Selection (MAS). Experimental materials and data were collected from the Central Breeding Swine Performance Testing Station, including 23,647 performance records from period 200005 to 202505 and 1,633 DNA samples (including 909 Duroc, 460 Landrace, and 264 Yorkshire pigs) collected from period 202309 to period 202505. This study consisted of two parts. In Experiment 1, eleven single nucleotide polymorphisms (SNPs) from seven candidate genes (PSS, ESR, H-FABP, IGF2-In3, IGF2-In7, PRLR, and MSTN) were genotyped using the MassArray platform based on the single base extension (SBE) mass spectrometry method. The resulting genotypes were integrated with performance data from Periods 202309 to 202505, including average daily gain (ADG), feed conversion ratio (FCR), adjusted backfat thickness (adjBF), and the selection index (SI). Statistical analyses were conducted using SAS with the general linear model (GLM) and Tukey’s multiple comparison test. In Experiment 2, whole-genome sequencing (WGS) was performed on pigs representing extreme ends of the growth index, and genome-wide association study (GWAS) analyses were used to identify genomic variants differentiating high- and low-index groups, with the goal of discovering novel candidate genes associated with growth traits. Results showed that the PSS gene was nearly fixed across all three breeds (AA > 98%). The ESR gene exhibited significant genetic differentiation among breeds (p < 0.05), with Yorkshire maintaining the highest genetic diversity, and the MM genotype showing a significant association with litter size (p < 0.05). For the H-FABP gene, genotype indices derived from three restriction enzyme sites (HinfI, MspI, HaeIII) differed significantly among breeds; in male Yorkshire pigs, this index was significantly associated with ADG, FCR, and SI (p < 0.05). The IGF2-In3 gene was fixed as the QQ genotype in all breeds after Period 202309. In male Landrace pigs, the IGF2-In7 gene showed significant associations with litter size and feed conversion ratio (p < 0.05). The PRLR gene displayed distinct distribution patterns among breeds, with LP predominating in Duroc (50%), and LL predominating in Landrace (63%). In Landrace, PRLR genotypes were significantly associated with ADG (p < 0.05). The MSTN gene exhibited marked polymorphism at all three loci (435, 447, 879), forming multiple haplotype combinations. Among these, A/KS and A/SS haplotypes were significantly associated with litter size and growth traits in both Landrace and Yorkshire (p < 0.05). In Experiment 2, WGS analysis revealed clear genomic differentiation among the three breeds, and principal component analysis (PCA) confirmed distinct clustering patterns. Differential genomic analysis further indicated that many growth- and adaptation-related variants were located in non-coding regulatory regions, highlighting the crucial role of regulatory variation in complex traits. Overall, candidate gene analysis provides biologically meaningful insights at specific loci, whereas WGS compensates for its limitations by revealing more comprehensive genomic variation and polygenic regulatory architecture. The combined results demonstrate significant genetic differentiation among breeds and identify multiple loci associated with key economic traits, reflecting the long-term genetic impacts of selective breeding in Taiwan’s commercial pig populations. In conclusion, this study integrates nearly 25 years of performance data with molecular genotyping to establish a comprehensive framework for analyzing candidate genes and their phenotypic associations. The findings not only provide a scientific basis for molecular breeding and selection in Taiwanese pig populations but also support future development of genomic selection models and precision breeding strategies, contributing to the advancement and sustainability of Taiwan’s swine industry.