title: Transcriptomic analysis provides insight into high-altitude acclimation in domestic goats.
abstract: Domestic goats are distributed in a wide range of habitats and have acclimated to their local environmental conditions. To investigate the gene expression changes of goats that are induced by high altitude stress, we performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung, and skeletal muscle) in three indigenous populations from distinct altitudes (600 m, 2000 m, and 3000 m). We generated 129Gb of high-quality sequencing data (~4Gb per sample) and catalogued the expression profiles of 12,421 annotated hircine genes in each sample. The analysis showed global similarities and differences of high-altitude transcriptomes among populations and tissues as well as revealed that the heart underwent the most high-altitude induced expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and nonsynonymous single nucleotide variant-containing genes that were highly differentiated between the high- and low-altitude populations. These genes have known or potential roles in hypoxia response and were enriched in functional gene categories potentially responsible for high-altitude stress. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to high-altitude acclimation.
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Qianzi
authors.initials: Q
authors.lastname: Tang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Wenyao
authors.initials: W
authors.lastname: Huang
authors.affiliation: Sichuan Academy of Grassland Science, Chengdu 611731, China.
authors.forename: Jiuqiang
authors.initials: J
authors.lastname: Guan
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Long
authors.initials: L
authors.lastname: Jin
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Tiandong
authors.initials: T
authors.lastname: Che
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Yaodong
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100083, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100083, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100083, China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Xuewei
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China. Electronic address: mingzhou.li@163.com.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
mesh_terms: D000064:Acclimatization; D000531:Altitude; D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D006041:Goats / Q000502:physiology*; D018482:Muscle, Skeletal / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D054875:Ubiquitination
keywords: Differential expression; Hypoxia response; RNA-seq; Single nucleotide variant