Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan

• Published in: PloS one 2019-04, Vol.14 (4), p.e0215065
• Main Authors: Iqbal, Naveed, Liu, Xin, Yang, Ting, Huang, Ziheng, Hanif, Quratulain, Asif, Muhammad, Khan, Qaiser Mahmood, Mansoor, Shahid
• Format: Article
• Language: English
• Subjects: Adaptation; Animal genetic engineering; Animal genetics; Animals; Annotations; Artificial chromosomes; Beef; Beef cattle; Bias; Biology; Biology and Life Sciences; Biotechnology; Bos taurus; Bovidae; Breeding; Breeding - methods; Cattle; Cattle - classification; Cattle - genetics; Chromosomes; Climate; Comparative analysis; Consortia; DNA sequencing; Drought; Economic analysis; Endothelial growth factors; Endothelium; Enrichment; Extracellular matrix; Extreme values; Gene expression; Gene mapping; Gene sequencing; Genes; Genetic engineering; Genetic polymorphisms; Genome; Genomes; Genomics; Genomics - methods; Genotype; Growth factors; High altitude; High-altitude environments; Hot climates; Hypoxia; Hypoxia-inducible factor 1; Hypoxia-inducible factors; INDEL Mutation; Kinases; Life sciences; Livestock breeding; Mapping; Metabolism; Milking; Molecular modelling; Molecular Sequence Annotation; Multiprocessing; Muscle contraction; Muscles; Muscular function; Next-generation sequencing; Novels; Pakistan; People and Places; Phenotype; Phenotypes; Physiology; Polymorphism; Polymorphism, Single Nucleotide; Research and Analysis Methods; Selection, Genetic; Signal transduction; Signaling; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Smooth muscle; Technology; Toll-like receptors; Vascular endothelial growth factor; Whole Genome Sequencing - veterinary; Wnt protein
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0215065

The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor int