Ye Shaopan, Chen Zi-Tao, Zheng Rongrong, Diao Shuqi, Teng Jinyan, Yuan Xiaolong, Zhang Hao, Chen Zanmou, Zhang Xiquan, Li Jiaqi, Zhang Zhe
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Front Genet. 2020 Apr 3;11:243. doi: 10.3389/fgene.2020.00243. eCollection 2020.
Poultry feed constitutes the largest cost in poultry production, estimated to be up to 70% of the total cost. Moreover, there is pressure on the poultry industry to increase production to meet the protein demand of humans and simultaneously reduce emissions to protect the environment. Therefore, improving feed efficiency plays an important role to improve profits and the environmental footprint in broiler production. In this study, using imputed whole-genome sequencing data, genome-wide association analysis (GWAS) was performed to identify single-nucleotide polymorphisms (SNPs) and genes associated with residual feed intake (RFI) and its component traits. Furthermore, a transcriptomic analysis between the high-RFI and the low-RFI groups was performed to validate the candidate genes from GWAS. The results showed that the heritability estimates of average daily gain (ADG), average daily feed intake (ADFI), and RFI were 0.29 (0.004), 0.37 (0.005), and 0.38 (0.004), respectively. Using imputed sequence-based GWAS, we identified seven significant SNPs and five candidate genes [MTSS I-BAR domain containing 1, folliculin, COP9 signalosome subunit 3, 5',3'-nucleotidase (mitochondrial), and gametocyte-specific factor 1] associated with RFI, 20 significant SNPs and one candidate gene (inositol polyphosphate multikinase) associated with ADG, and one significant SNP and one candidate gene (coatomer protein complex subunit alpha) associated with ADFI. After performing a transcriptomic analysis between the high-RFI and the low-RFI groups, both 38 up-regulated and 26 down-regulated genes were identified in the high-RFI group. Furthermore, integrating regional conditional GWAS and transcriptome analysis, ras-related dexamethasone induced 1 was the only overlapped gene associated with RFI, which also suggested that the region (GGA14: 4767015-4882318) is a new quantitative trait locus associated with RFI. In conclusion, using imputed sequence-based GWAS is an efficient method to identify significant SNPs and candidate genes in chicken. Our results provide valuable insights into the genetic mechanisms of RFI and its component traits, which would further improve the genetic gain of feed efficiency rapidly and cost-effectively in the context of marker-assisted breeding selection.
家禽饲料成本占家禽生产总成本的比例最大，估计高达总成本的70%。此外，家禽行业面临着增加产量以满足人类蛋白质需求并同时减少排放以保护环境的压力。因此，提高饲料效率对于提高肉鸡生产的利润和环境足迹起着重要作用。在本研究中，利用推算的全基因组测序数据，进行了全基因组关联分析（GWAS），以鉴定与剩余采食量（RFI）及其组成性状相关的单核苷酸多态性（SNP）和基因。此外，对高RFI组和低RFI组进行了转录组分析，以验证来自GWAS的候选基因。结果表明，平均日增重（ADG）、平均日采食量（ADFI）和RFI的遗传力估计值分别为0.29（0.004）、0.37（0.005）和0.38（0.004）。利用基于推算序列的GWAS，我们鉴定出7个与RFI相关的显著SNP和5个候选基因[含MTSS I-BAR结构域1、卵泡抑素、COP9信号体亚基3、5',3'-核苷酸酶（线粒体）和配子细胞特异性因子1]，20个与ADG相关的显著SNP和1个候选基因（肌醇多磷酸多激酶），以及1个与ADFI相关的显著SNP和1个候选基因（衣被蛋白复合体亚基α）。在高RFI组和低RFI组之间进行转录组分析后，在高RFI组中鉴定出38个上调基因和26个下调基因。此外，整合区域条件GWAS和转录组分析，ras相关地塞米松诱导蛋白1是与RFI相关的唯一重叠基因，这也表明该区域（GGA14:4767015-4882318）是一个与RFI相关的新数量性状位点。总之，利用基于推算序列的GWAS是鉴定鸡中显著SNP和候选基因的有效方法。我们的结果为RFI及其组成性状的遗传机制提供了有价值的见解，这将在标记辅助育种选择的背景下快速且经济高效地进一步提高饲料效率的遗传进展。
