BUZANKAS, M. E.

CANTAO, M. E.

JOAQUIM, L. B.

LEDUR, M. C.

MARCHESI, J. P.

MUNARI, D. P.

PEIXOTO, J. de O.

SBARDELLA, A. P.

English

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Linkage disequilibrium and effective population size in a paternal broiler line. Jorge A. P. Marchesi*1,3, Ana P. Sbardella1,3, Letícia B. Joaquim1,4, Mauricio E. Cantão2, Jane O. Peixoto2,Marcos E. Buzanskas1,5, Mônica C. Ledur2 and Danísio P. Munari1,6. 1UNESP – Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, SP,Brazil,  2Embrapa Swine and Poultry,  Concórdia,  SC,  Brazil.3CAPES/EMBRAPA,  4CAPES,  5FAPESP(2013/19335-2), 6CNPq.The patterns of linkage disequilibrium (LD) in the genome of livestock play a major role in genome-wide association studies (GWAS) and genomic selection.  For quantitative trait  loci (QTL) mapping,strong LD between markers and QTL are needed. By definition, LD is the non-random relationship ofalleles  between two loci  within  a  population.  The LD information  can  be  used  to  infer  populationdemography based on the changes in the historical effective population size (Ne), which is a measure ofgenetic variability and genetic contribution of ancestors. This study aimed to characterize the LD anddetermined Ne of a paternal broiler line (called TT) developed by Embrapa Swine and Poultry. A total of1,430 chickens (652 males and 778 females) were genotyped with the 600K Affymetrix® Axiom® HDpanel. For genotype quality control, SNPs with call rate <98%, MAF <0.03 and that deviated from HWE(p <10-6) were removed, remaining 353,589 SNPs for LD analyses using Plink v.1.9 software. The LDwas calculated by the correlation between two consecutive SNPs (r²) considering different distancesaccording  to  the  autosomal  chromosomes:  macrochromosomes  (GGA1  to  GGA5),  intermediatechromosomes (GGA 6 to GGA10) and microchromosomes (GGA11 to GGA28). The Ne was calculatedfrom the LD data for up to 200 generations ago using SNP1101 v.1.0 software. The LD decreased as thephysical distance between the markers in all classes of chromosomes increased. The average r² whichwas equal to or higher than 0.30 extended for up to 500-550 Kb in macro, 350-400 Kb in intermediate,and 150-200 Kb in microchromosomes. The average LD between adjacent SNPs in all autosomes was0.37 and ranged from 0.38 to 0.43, 0.36 to 0.40, and 0.29 to 0.41 in macrochromosomes, intermediatechromosomes, and microchromosomes, respectively. The  Ne from LD data showed that the ancestralpopulation of 200 generations ago was much higher (548 animals) than the recent population of 5 pastgenerations (157 animals). The LD generally decayed rapidly while the distance increased; however,there were differences in the persistence and extent of LD in different classes of chromosomes. The LDinformation  is  an  important  measure  to  characterize  the  broiler  population  and  essential  for  othergenomic analyses. Key Words: animal breeding, genetic markers, genomics, poultryInternational Meeting of Advances in Animal ScienceISSN: 2448-4385Vol. 1 - 2016Galoá {Este trabalho foi publicado utilizando o Galoá Proceedings

Linkage disequilibrium and effective population size in a paternal broiler line.

http://www.alice.cnptia.embrapa.br/bitstream/doc/1053164/1/final8167.pdf

Linkage disequilibrium and effective population size in a paternal broiler line.

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