Abstract
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 interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.
Highlights
Livestock contributes 40% of the worldwide estimation of agricultural yield [1]
The results indicated that responses to hypoxia, development of new blood vessels and their dilatation in stress conditions are the important factors that allow highland Pakistani-indicine cattle to cope with the oxygen depletion at higher altitudes (Please see S1 File for all identified genes enriching KEGG pathways in Pakistani indicine breeds)
This study presented extensive genome analysis of eleven indigenous Pakistani cattle breeds following whole-genome resequencing using BGISEQ-500 sequencing platform
Summary
Livestock contributes 40% of the worldwide estimation of agricultural yield [1]. It provides employment to nearly 1.3 billion people worldwide and directly helps the livings of 0.6 billion farmers in the developing countries [2]. Domestic cattle plays important role in agricultural economy of developing countries, its contribution goes beyond the direct production of milk and meat to skins, fiber, fertilizer and fuel production [3, 4]. Significantly less susceptibility to ticks, low maintenance cost and resistance to gastrointestinal parasites are the key physiological strengths of indicine over taurine [7]. These physiological advantages enable indicine to grow in tropical and subtropical regions, such as Africa, South-east Asia, Brazil, northern Australia, southern China, and parts of the United States. Population studies using genomic SNP data showed at least three major geographical divisions of cattle; European, Indian, and African cattle [9, 10]
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