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Rapid Communications

Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

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References

  • Silpa MV, Naicy T, Aravindakshan TV, Radhika G, Boswell A, Mini M. Sirtuin3 (SIRT3) gene molecular characterization and SNP detection in prolific and low prolific goat breeds. Theriogenology. 2018;122:47–52.
  • Henkel J, Saif R, Jagannathan V, et al. Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes. PLoS Genet. 2019;15(12):e1008536.
  • Das A, Shaha M, Gupta MD, Dutta A, Miazi OF. Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat. Trop Anim Health Prod. 2021;53(2):230.
  • Gootwine E. Invited review: Opportunities for genetic improvement toward higher prolificacy in sheep. Small Ruminant Res. 2020;186:106090.
  • Abdolahi S, Shokrollahi B, Saadati N, Morammazi S. No polymorphism of melatonin receptor 1A (MTNR1A) gene was found in Markhoz goat. Vet Med Sci. 2019;5(2):157–161.
  • Kang Z, Bai Y, Lan X, Zhao H. Goat AKAP12: Indel mutation detection, association analysis with litter size and alternative splicing variant expression. Front Genet. 2021;12:648256.
  • Wang J-J, Zhang T, Chen Q-M, et al. Genomic signatures of selection associated with litter size trait in Jining Gray Goat. Front Genet. 2020;11:286.
  • Guan D, Luo N, Tan X, et al. Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus). Sci Rep. 2016;6(1):36372.
  • Liu Z, Ji Z, Wang G, Chao T, Hou L, Wang J. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics. 2016;17(1):863.
  • Siddiki AZ, Miah G, Islam MS, et al. Goat genomic resources: The search for genes associated with its economic traits. Int J Genomics. 2020;2020:5940205.
  • Babraham Bioinformatics – FastQC. A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed June 12, 2018.
  • Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079.
  • DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491–498.
  • Danecek P, Auton A, Abecasis G, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–2158.
  • Rubin CJ, Zody MC, Eriksson J, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464(7288):587–591.
  • Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009;4(3):363–371.
  • Islam R, Li Y, Liu X, et al. Genome-wide runs of homozygosity, effective population size, and detection of positive selection signatures in six Chinese goat breeds. Genes (Basel). 2019;10(11):938.
  • Sabeti PC, Schaffner SF, Fry B, et al. Positive natural selection in the human lineage. Science. 2006;312(5780):1614–1620.
  • Buffalo V, Coop G. Estimating the genome-wide contribution of selection to temporal allele frequency change. Proc Natl Acad Sci USA. 2020;117(34):20672–20680.
  • Wang K, Liu X, Qi T, et al. Whole-genome sequencing to identify candidate genes for litter size and to uncover the variant function in goats (Capra hircus). Genomics. 2021;113(1):142–150.
  • Yao Y, Pan Z, Di R Liu Q, et al. Whole genome sequencing reveals the effects of recent artificial selection on litter size of Bamei mutton sheep. Animals (Basel). 2021;11(1):157.
  • Yao Z, Zhang S, Wang X, et al. Genetic diversity and signatures of selection in BoHuai goat revealed by whole-genome sequencing. BMC Genomics. 2023;24(1):116.
  • Chong Y, Jiang X, Liu G. An ancient positively selected BMPRIB missense variant increases litter size of Mongolian sheep populations following latitudinal gradient. Mol Genet Genomics. 2022;297(1):155–167.
  • Tao L, He XY, Jiang YT, et al. Combined approaches to reveal genes associated with litter size in Yunshang black goats. Anim Genet. 2020;51(6):924–934.
  • Guo J, Tao H, Li P, et al. Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds. Sci Rep. 2018;8(1):10405.
  • Saif R, Henkel J, Mahmood T, Ejaz A, Ahmad F, Zia S. Detection of whole genome selection signatures of Pakistani Teddy goat. Mol Biol Rep. 2021;48(11):7273–7280.
  • Yang BG, Yuan Y, Zhou DK, et al. Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development. Anim Genet. 2021;52(4):550–555.
  • Goymer P. Synonymous mutations break their silence. Nat Rev Genet. 2007;8(2):92–92.
  • Minde DP, Anvarian Z, Rüdiger SG, Maurice MM. Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer? Mol Cancer. 2011;10(1):101.
  • Chen Y, Lu H, Zhang N, Zhu Z, Wang S, Li M. PremPS: Predicting the impact of missense mutations on protein stability. PLoS Comput Biol. 2020;16(12):e1008543.
  • Sallam AM. A missense mutation in the coding region of the toll-like receptor 4 gene affects milk traits in Barki sheep. Anim Biosci. 2021;34(4):489–498.
  • An XP, Hou JX, Zhao HB, et al. Polymorphism identification in goat GNRH1 and GDF9 genes and their association analysis with litter size. Anim Genet. 2013;44(2):234–238.
  • Hou JX, An XP, Han P, Peng JY, Cao BY. Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size. Anim Genet. 2015;46(1):87–90.
  • Peaston AE, Evsikov AV, Graber JH, et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell. 2004;7(4):597–606.
  • Stenhouse C, Hogg CO, Ashworth CJ. Association of foetal size and sex with porcine foeto-maternal interface integrin expression. Reproduction. 2019;157(4):317–328.
  • Claycombe-Larson KJ, Bundy AN, Kuntz T, et al. Effect of a maternal high-fat diet with vegetable substitution on fetal brain transcriptome. J Nutr Biochem. 2022;108:109088.
  • Sims MA, Field SD, Barnes MR, et al. Cloning and characterisation of ITGAV, the genomic sequence for human cell adhesion protein (vitronectin) receptor alpha subunit, CD51. Cytogenet Cell Genet. 2000;89(3-4):268–271.
  • Lin H, Wang H, Wang Y, Liu C, Wang C, Guo J. Transcriptomic Analysis of the Porcine Endometrium during Embryo Implantation. Genes (Basel). 2015;6(4):1330–1346.
  • Pierzchała M, Pierzchała D, Ogłuszka M, et al. Identification of differentially expressed gene transcripts in porcine endometrium during early stages of pregnancy. Life (Basel). 2020;10(5):68.
  • Frank JW, Seo H, Burghardt RC, Bayless KJ, Johnson GA. ITGAV (alpha v integrins) bind SPP1 (osteopontin) to support trophoblast cell adhesion. Reproduction. 2017;153(5):695–706.
  • Massuto DA, Kneese EC, Johnson GA, et al. Transforming growth factor beta (TGFB) signaling is activated during porcine implantation: proposed role for latency-associated peptide interactions with integrins at the conceptus-maternal interface. Reproduction. 2010;139(2):465–478.
  • Astrof NS, Salas A, Shimaoka M, JianFeng Chen J, Springer TM. Importance of force linkage in mechanochemistry of adhesion receptors. Biochemistry. 2006;45(50):15020–15028.
  • Burghardt RC, Burghardt JR, Taylor JD, et al. Enhanced focal adhesion assembly reflects increased mechanosensation and mechanotransduction at maternal-conceptus interface and uterine wall during ovine pregnancy. Reproduction. 2009;137(3):567–582.
  • Beyeler J, Katsaros C, Chiquet M. Impaired contracture of 3D collagen constructs by fibronectin-deficient murine fibroblasts. Front Physiol. 2019;10:166.
  • Li Y, Pohl E, Boulouiz R, et al. Mutations in TPRN cause a progressive form of autosomal-recessive nonsyndromic hearing loss. Am J Hum Genet. 2010;86(3):479–484.
  • Wang CCN, Li CY, Cai J-H, et al. Identification of prognostic candidate genes in breast cancer by integrated bioinformatic analysis. J Clin Med. 2019;8(8):1160.
  • Wang R, Wang G. Protein modification and autophagy activation. Adv Exp Med Biol. 2019;1206:237–259.
  • Cusack MP, Thibert B, Bredesen DE, del Rio G. Efficient identification of critical residues based only on protein structure by network analysis. PLoS One. 2007;2(5):e421.
  • Yan W, Zhou J, Sun M, Chen J, Hu G, Shen B. The construction of an amino acid network for understanding protein structure and function. Amino Acids. 2014;46(6):1419–1439.
  • Hino T, Yanagimachi R. Active peristaltic movements and fluid production of the mouse oviduct: their roles in fluid and sperm transport and fertilization†. Biol Reprod. 2019;101(1):40–49.
  • Boutin C, Labedan P, Dimidschstein J, et al. A dual role for planar cell polarity genes in ciliated cells. Proc Natl Acad Sci USA. 2014;111(30):E3129–3138.
  • Gross N, Taylor T, Crenshaw T, Khatib H. The intergenerational impacts of paternal diet on DNA methylation and offspring phenotypes in sheep. Front Genet. 2020;11:597943.
  • Usami FM, Arata M, Shi D, et al. Intercellular and intracellular cilia orientation is coordinated by CELSR1 and CAMSAP3 in oviduct multi-ciliated cells. J Cell Sci. 2021;134(4): jcs257006.
  • Shi D, Komatsu K, Hirao M, et al. Celsr1 is required for the generation of polarity at multiple levels of the mouse oviduct. Development. 2014;141(23):4558–4568.
  • Goffinet AM, Tissir F. Seven pass cadherins CELSR1-3. Semin Cell Dev Biol. 2017;69:102–110.
  • Prömel S, Langenhan T, Araç D. Matching structure with function: the GAIN domain of adhesion-GPCR and PKD1-like proteins. Trends Pharmacol Sci. 2013;34(8):470–478.
  • Shashidhar S, Lorente G, Nagavarapu U, et al. GPR56 is a GPCR that is overexpressed in gliomas and functions in tumor cell adhesion. Oncogene. 2005;24(10):1673–1682.