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Scaning of Selection Signatures in Dairy Buffalo (Bubalus bubalis)

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André Vieira do Nascimento
Total Authors: 1
Document type: Doctoral Thesis
Press: Jaboticabal. 2020-09-16.
Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
Defense date:
Advisor: Humberto Tonhati; Diercles Francisco Cardoso

The aim of the present work was to improve the map of Axiom Buffalo Genotyping array with determining the positions of ~10 thousand SNPs and to predict the genomic location of QTL (Quantitative Trait Loci) cattle in the buffalo genome using local alignment. In addition to identifying signature of selection in a Murrah breed herd, looking for genes and QTL related to racial and productive aspects of the specie. A population of 865 animals genotyped with the Axiom Buffalo Genotyping (ABG) panel was used. All probe sequences (123,040) have been realigned with buffalo genome (UOA_WB_1) using BLAST, however the sequences of bovine QTL were aligned with the buffalo genome using the Burrows-Wheeler Aligner. The quality control of the genotypes was carried out with the removal of duplicate non-autosomal markers, with call rateSNP and call rateSample less than 0.95 and 0.90 respectively. For the detection of signature of selection by ROH (Runs of homozygosity), the following parameters were used: genomic region with homozygous length greater than 1Mb; minimum of 30 SNP in homozygosis; at least 1 SNP per 100 kb; maximum interval between two SNPs up to 500 kb; and no more than 1 heterozygous locus per segment. Integrated Haplotype Score (iHS) analysis was performed with the SELSCAN software. The averages of |iHS| were estimated in 500 kb windows, with 250 kb of overlap allowed. Where selection signatures were the windows with mean values of |iHS| greater than 2.36 (top 0.1%). The inbreeding of coefficients were calculated from the genomic relationship matrix (FGRM), pedigree (FPED) and ROH (FROH). The number of SNP mapped increased from 106,778 in ABG map to 116,708 in our map. We identified signatures of selection using the new map and the ABG map. There was an intensification of peaks of autozygosity and the appearance of new ones in the BBU5 and BBU11 when we used all the markers on the new map were. After alignment and quality control, 63,995 cattle QTL were successfully mapped to the buffalo genome. Thus, the new SNP map can improve the results of genomic analyzes, by increasing 9,930 SNPs and reducing the average marker spacing by ~ 2kb. Due to the homology between cattle and buffaloes, the coordinates of the QTL presented in this work can be considered potential buffalo QTLs, leading to the presentation of the first buffalo QTL database. Of the total animals, 350 had ROHs greater than 10 Mb and average length per animal of 4.28 ± 1.85 Mb. Inbreeding estimates of the pedigree had a low correlation with genomic estimates. The estimates of FGRM were higher compared to FPED and FROH. Analysis of selection signatures based on ROH highlighted regions on autosomal chromosomes 1, 2, 3, 5, 16 and 18, while iHS identified regions located on chromosomes 1, 6, 7, 9, 14 and 23. The regions of both analyzes were in overlap with genes and QTL previously related to traits of milk production, reproduction, morphology and immune response. Inbreeding levels in this population are still low, but must be managed to avoid future losses due to inbreeding depression. (AU)

FAPESP's process: 17/10542-6 - Scaning of selection signatures in dairy buffalo (Bubalus bubalis)
Grantee:André Vieira do Nascimento
Support Opportunities: Scholarships in Brazil - Doctorate