Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing

R-Q Zhang; F-N Lai; J-J Wang; H-L Zhai; Y. Zhao; Y-J Sun; L-J Min; W. Shen

doi:10.1016/j.gene.2017.12.002

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Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing

Journal article

Peer reviewed

Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing

R-Q Zhang, F-N Lai, J-J Wang, H-L Zhai, Y. Zhao, Y-J Sun, L-J Min and W. Shen

Gene, Vol.643, pp.1-6

2018

DOI: https://doi.org/10.1016/j.gene.2017.12.002

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Abstract

Genome flanking regions surrounding transcription start sites (TSSs) are critical for the regulation of gene expression, containing many translational regulatory elements. To investigate whether critical single nucleotide polymorphisms (SNPs) exist around TSSs in the dairy goat genome, we performed high throughput DNA sequencing to compare two dairy goat groups with discrepant litter sizes. After genome mapping, SNP calling, and annotation, we screened the SNPs within 2 kb scales surrounding annotated TSSs in high fecundity (HF) and low fecundity (LF) groups, respectively. We attempted to identify distinct SNPs and motifs near the TSSs in both groups. The SNPs near the TSSs most were consistent; 318 new SNPs were uncovered in the HF group, of which 305 were heterozygote SNPs, 13 were homozygote SNPs, and majority of which were distributed on chromosome 2 and 29. After validation by Sanger sequencing we found that a SNP in CHI16: 27612330 C > A in the PSEN2

Details

Title: Analysis of the SNP loci around transcription start sites related to goat fecundity trait base on whole genome resequencing
Authors/Creators: R-Q Zhang (Author/Creator) - Qingdao Agricultural University
F-N Lai (Author/Creator) - Qingdao Agricultural University
J-J Wang (Author/Creator) - Qingdao Agricultural University
H-L Zhai (Author/Creator) - Shandong International Biotechnology Park, Yantai 264670, China
Y. Zhao (Author/Creator) - Qingdao Agricultural University
Y-J Sun (Author/Creator) - Qingdao Agricultural University
L-J Min (Author/Creator) - Qingdao Agricultural University
W. Shen (Author/Creator) - Qingdao Agricultural University
Publication Details: Gene, Vol.643, pp.1-6
Publisher: Elsevier BV
Identifiers: 991005540533107891
Copyright: © 2017 Elsevier B.V.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Citation topics: 1 Clinical & Life Sciences; 1.81 Reproductive Biology; 1.81.1408 Fertility Preservation
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics