Selection signatures scan in water buffaloes

• Published in: CES medicina veterinaria y zootecnia Vol. 11; no. 3; p. 188
• Main Authors: Vieira do Nascimento, André, Herrera Rios, Ana Cristina, Francisco Cardoso, Diercles, de Abreu Santos, Daniel Jordan, Ferreira de Camargo, Gregório Miguel, Fernandes de Andrade, Willian Bruno, Becker Scalez, Daiane Cristina, Hurtado- Lugo, Naudin Alejandro, Muñoz Berrocal, Milthon, Tonhati, Humberto
• Format: Journal Article
• Language: Spanish
• Published: Universidad del CES 01.09.2016
• Subjects: Animal genetics; Dairy products industry; DNA; Genes; Genomes; Genomics; Milk; Milk production; Phenotypes; Public relations executives; Quantitative genetics; Skin; Water
• ISSN: 1900-9607; 1900-9607

In contrast to demographic factors, the positive selection influences only genomic regions related to selected phenotypes, leaving special patterns of DNA called selection signatures. The statistics "Runs of Homozygosity (ROH) enable the identification of parts of genome presenting reduced local diversity due selection. The current study aimed to detect selection signatures in the water buffaloes genome, by scanning ROH hotspots. A sample of 352 Murrah buffaloes, explored to milk production in Brazil, were genotyped with Axiom[R] Buffalo Genotyping Array (Affymetrix). This array is based coordinates of cattle genome reference (UMD3.1), however, our group previously perform a LD based alignment to predict buffalo genome position to each marker, enabling this first selection signature scan in this specie. A total of 55,560 autosomal markers with predicted position to buffalo genome and presenting call-rate>0.95 were used to the ROH scan, with the PLINK v.1.7 software. The uninterrupted sequences with more than 30 homozygous SNPs were assumed ROHs. Then, a local autozygozity coefficient was estimated to each marker, as the proportion of individuals presenting a ROH enclosing the marker, being values higher than 0.3 assumed selection signals. Gene and QTL within selection signatures were retrieved from Ensembl e CattleQTL databases, based on bovine homologue regions. Four genomic regions were ROH hotspots, located at BBU3 (60094330-65022593), BBU4 (43407621-44282612), BBU5 (57022610-60442072) e BBU16 (4616653250868968). Based on bovine information, there were 202 annotated genes e 631 known QTL over these selection signatures. The ILK gene that has a central role in hair follicle development and skin thickness, is a notable gene in this list, specially, because buffaloes are markedly represented by animals of low hair density and thick skin. In addition, this first study of selection signatures in buffaloes underscore the utility of this practice to evidence signals of past selection and genetics regions underlying important traits.