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BMC genomics
Nov 11, 2020;21 (1): 783.

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 Vanvanhossou, Carsten Scheper, Luc Hippolyte Dossa, Tong Yin, Kerstin Brügemann, Sven König
Author Information
  1. Sèyi Fridaïus Ulrich Vanvanhossou: Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
  2. Carsten Scheper: Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
  3. Luc Hippolyte Dossa: School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin.
  4. Tong Yin: Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
  5. Kerstin Brügemann: Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
  6. Sven König: Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany. sven.koenig@agrar.uni-giessen.de.
PMID: 33176675 DOI: 10.1186/s12864-020-07170-0

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 genome-wide 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, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).
CONCLUSIONS: Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Keywords

Endangered cattle breeds Functional annotations Morphometric traits Multi-breed GWAS Potential candidate genes SNP-based genetic parameters

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MeSH Term

Animals
Cattle
Genome
Genome-Wide Association Study
Genomics
Phenotype
Polymorphism, Single Nucleotide
Journal Article

Word Cloud

Created with Highcharts 10.0.0traitsgenesbreeds0cattlebodygeneticGWASassociatedconformationcarcasscandidateadaptiveincludingindigenousheightSNPMulti-breedmorphometricfunctionallocidetectedpotentialfeaturesgrowthBeninbreedcharacterizationsmorphologicalmeasurementsHGHWlengthfourgenomicgenome-wideSNP-basedrangedHW-BLHAW-SHdifferentlocatedsizeannotationsimmuneresponsefeedefficiencyBACKGROUND:SpecificdiseaseresistanceabilitiesharshenvironmentsattributedendangeredduecrossbreedingfarlacksystematictraitrecordingbasisstructuredbreedingprogramdesignsaimingconservationBridginggapphenotypingconsideredwithersHAWsacrumSHheartgirthhipwidthBLearEL449LaguneSombaBorgouPabliorderutilizerecenttoolsevaluationsphenotypesnovelmergedhigh-densitymarkerdataparameterestimationsassociationstudiessixcarriedContinuativelyaimedinferringregionspotentiallyRESULTS:heritabilityestimates46 ± 01474 ± 013Phenotypiccorrelations25 ± 00589 ± 00114 ± 01085 ± 002respectivelyThree25chromosome-widesignificantpositionedchromosomesclosechromosomaldistance±25 kb15withinPIK3R6PIK3R1showeddirectassociationsinferredVEPH1CNTNAP5GYPCweightfatdepositionAccordingstressPTAFRPBRM1ADAMTS12MEGF11SLC16A4CCDC117CONCLUSIONS:Accuratecontributedlargeheritabilitiesevensmallmixed-breedsampleidentifiedindicatorsreflectevolutionarydevelopmentadaptabilitymulti-breedBenineserevealsEndangeredFunctionalMorphometricPotentialparameters

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