Table1_Differential gene expression and identification of growth-related genes in the pituitary gland of South African goats.DOCX

Growth and carcass quality are economically important traits in goat production. This study investigated differentially expressed genes from the caprine pituitary gland transcriptome of South African indigenous goat breeds of varying growth performances and carcass quality parameters. Tissues were harvested from the pituitary gland of three South African Boer goats and three village ecotype goats all raised under similar conditions simulating intensive commercial production systems. Three additional tissues were harvested from village ecotype goats that were raised extensively on village farms. Between breed differences were investigated by comparing differential gene expression among three South African Boer and three village goats that were both raised under intensive commercial production system at a research farm. Within-breed differences were investigated by comparing differential gene expression among three village goats raised under extensive conditions (on-farm in Pella, S.A. village farming community) and three village goats raised under intensive commercial production system (at ARC research farm in Pretoria, South Africa. Total RNA was isolated from the pituitary gland of 36-week-old animals (n = 9) and sequenced individually in triplicates. An average of 28,298,512 trimmed, and quality-controlled reads/animal were mapped to the goat genome (Capra_hircus.ARS1.94) using HiSat2 software. Transcript assembly and quantification yielded 104 differentially expressed genes for village goats raised under extensive system and 62 for village goats raised under the intensive production system at the false discovery rate (FRD) of ≤0.05 and a fold change of ≥2. Growth-related genes such as POU3F4 and TSHZ1 were highly expressed within breeds raised under both production systems. Conversely, growth-related genes such as FGFR2 and SMPX genes were highly expressed between breeds raised under similar production systems. Ballgown analysis revealed a high expression of GH1 and IGF1 in the intensively raised compared to extensively raised goats. Both genes were also highly expressed in the village goats when compared to the Boer. The differential gene expression data provided insights into genes and molecular mechanisms associated with growth and growth development in goats.

生长性能与胴体品质是山羊养殖中具有重要经济价值的性状。本研究针对生长性能与胴体品质参数存在差异的南非本土山羊品种的垂体转录组，开展差异表达基因（differentially expressed genes）的分析。

研究样本采集自以下群体：3只南非波尔山羊（South African Boer goats）与3只乡村生态型山羊，所有受试个体均在模拟集约化商品养殖模式的相同条件下饲养；另从乡村放牧农场散养的乡村生态型山羊中采集3份垂体组织样本。

为分析品种间的基因表达差异，本研究对比了均在研究农场集约化商品养殖模式下饲养的3只波尔山羊与3只乡村生态型山羊的基因表达情况；为分析品种内的基因表达差异，则对比了3只散养（位于南非佩拉乡村农场养殖社区）与3只集约化商品养殖（位于南非比勒陀利亚ARC研究农场）的乡村生态型山羊的基因表达差异。

本研究共纳入9只36周龄受试山羊，从其垂体中提取总RNA，对每份样本单独开展3次重复测序。利用HiSat2软件，将平均每条受试个体的28,298,512条经修剪与质量控制的测序读段比对至山羊基因组（Capra_hircus.ARS1.94）。经转录组组装与定量分析，在错误发现率（false discovery rate，原文此处误写为FRD）≤0.05且折叠变化（fold change）≥2的筛选标准下，散养乡村生态型山羊共获得104个差异表达基因，集约化养殖的乡村生态型山羊则获得62个差异表达基因。

在两种养殖模式下饲养的山羊品种内，POU3F4与TSHZ1等生长相关基因均呈现高表达；反之，在相同养殖模式下饲养的山羊品种间，FGFR2与SMPX等生长相关基因呈现高表达。Ballgown分析显示，相较于散养山羊，集约化养殖山羊的GH1与IGF1基因表达量更高；相较于波尔山羊，乡村生态型山羊的这两个基因同样呈现高表达。本研究获得的差异表达基因数据，为解析山羊生长与发育相关的基因及分子机制提供了新的研究视角。