A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with confor
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RESEARCH ARTICLE
Open Access
A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits Sèyi Fridaïus Ulrich Vanvanhossou1, Carsten Scheper1, Luc Hippolyte Dossa2, Tong Yin1, Kerstin Brügemann1 and Sven König1*
Abstract Background: Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genomewide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results: SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAM TS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). (Continued on next page)
* Correspondence: [email protected] 1 Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in t
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