Inbreeding, effective population size, and coancestry in the Latxa dairy sheep breed

摘要

Traditionally, breeding programs have estimated andmanaged inbreeding based on pedigree information. Theavailability of genomic marker panels has made possiblenew alternatives to achieve more precise estimates, forexample in case of missing pedigree. The objective ofthe present study was to assess and compare, differentestimation methods (pedigree-based methodologies,single SNP-based approach (homozygosity) and runsof homozygosity-based method) to analyze the evolutionof genetic diversity measured as inbreeding or ascoancestry of 3 selected populations of Latxa dairysheep (Latxa Cara Rubia and Latxa Cara Negra fromEuskadi and Navarre). Genomic data came from 972artificial insemination rams genotyped with the IlluminaOvineSNP50 BeadChip (Illumina Inc., San Diego,CA) whose genealogy consisted of 4,484 animals. Inbreedingestimates based on molecular data were moresimilar between them than compared with those basedon pedigree information. However, the SNP-based approachestimations of effective population size differedmore, reflecting the sensitivity of effective populationsize to small changes in the evolution of inbreeding.The 2 Latxa Cara Negra populations showed increasesof inbreeding rates with time and effective populationsizes between 64 and 103 animals, depending on breedand methodology used. The Latxa Cara Rubia populationdid not show an increase in inbreeding rate, mainlydue to semen importation from the related Frenchpopulation of Manech Tête Rousse. The effective sizeestimates based on coancestry increase show a highervariability and they are more sensitive to the source ofinformation and the data structure considered. Realizedeffective population size based on individual increase ininbreeding were in agreement with the previous estimates.Coancestry evolution analysis based on DNAinformation showed an increase on coancestry duringthe last 10 yr in all breeds, as a consequence of theselection process. Moreover, the increase on coancestrybetween Latxa Cara Rubia and Manech Tête Roussewas more noticeable between than within each of thosebreeds.