Abstract
BackgroundIn the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip.ResultDe-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent.ConclusionThe key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
Highlights
Sahiwal is a well-known breed belonging to the humped zebu cattle group (Bos indicus), having its origin in the northwestern region of the Indian subcontinent (Muhuyi et al, 1999)
Selection signatures in Sahiwal were identified by the De-correlated composite of multiple selection signals (DCMS) method, which combined the p-values from five different statistics into a new statistic, in contrast to the studies that considered the overlap in the genomic regions among the different methods
The methodology of DCMS was used in the computation of p-values from different univariate statistics into a composite signal, and the most significant regions were mapped onto BTA 6, 20, and 23
Summary
Sahiwal is a well-known breed belonging to the humped zebu cattle group (Bos indicus), having its origin in the northwestern region of the Indian subcontinent (Muhuyi et al, 1999) Apart from their high milk-producing ability, these cattle breed possesses unique adaptability to hot and humid climate prevailing in their native tract and their known resistance to tropical disease, ticks, and parasites (Singh et al, 2005). Sahiwal cattle are utilized in crossbreeding programs around the world because of their higher milk production qualities and endurance to harsh environments (Maule, 1990) Such crossbreeding work has affected the numbers and distribution of indigenous purebred cattle to some extent in recent years (DAHDF, 2018/2019). The present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip
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