Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds

Abstract

The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation.

Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds

“…It is known that in local breeds, the imputation accuracies might be overestimated mostly due to either highly structured and related population (Bolormaa et al., 2015) or due to a low effective population size (Druet et al., 2014). Although all tested breeds were limited in size, there are recent evidence that their inbreeding level is modest since all breeds except Sarda showed average inbreeding between 1% and 6% based on Runs of Homozygosity estimate ($$$ {F}_{\mathrm{ROH}}\Big) $$$ (Cortellari et al., 2022). The Sarda breed showed an average $$$ {F}_{\mathrm{ROH}} $$$ of 13.5%, which might partially explain, together with the highest number of animals considered in the study, why the highest concordance rate was found in this breed.…”

Demography and Genealogical Analysis of Massese Sheep, a Native Breed of Tuscany

“…Genomic data aid in studying inbreeding depression without the need for extensive parentage analysis over multiple generations [55][56][57], as these two inbreeding coefficients are related [42]. While studies demonstrate a slight correlation between genomic and pedigree-based inbreeding values in Massese sheep, other breeds with more complete pedigrees show a stronger correlation between these values [58]. Genealogical data represent the primary information source for assessing genetic variability in livestock populations [59].…”

Estimation of the Central Rhodope Sheep pedigree quality in 2005-2023

“…С преустройството на селското стопанство в България, започва и реорганизация на селекционния процес, като за повишаване ефективността на селекционната дейност в животновъдството се създават неправителствени организацииразвъдни асоциации, към които се прехвърля тази дейност. Създадени са две организации, осъществяващи развъдна дейност със Среднородопската овца, Сдружение организация за развъждане на цигайски, романовски и местни породи овце в Република България (ОРЦМПО -Троян) и Асоциация за развъждане на Среднородопска, Каракачанска и Родопски цигай овце (АРСРККРЦО -Смолян За изследване на популационната структура и генетично разнообразие при дребните преживни животни все още масово се използва родословната информацията (Cortellari et al, 2022). В това отношение, пълнотата и качеството на педигрето са критични, тъй като грешките в педигрето могат да доведат до вземането на неправилни решения при съхранението на породите (Oliehoek & Bijma, 2009).…”