High-Density Genomic Characterization of Native Croatian Sheep Breeds

Abstract

A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (FROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.

An empirical test of the estimation of historical effective population size using Drosophila melanogaster

“…Even so, this artefact may have occurred in some of the estimations made so far, for example, in two or three Croatian sheep breeds analysed by Drzaic et al (2022) or one of the horse breeds analysed by Criscione et al (2022). Note, however, that it is possible that a great decline in size can be expected to occur in the last few generations, for example, when a selection program has started within that period (Saura et al, 2021).…”

“…The method of Santiago et al (2020) has now been applied to different species, particularly in the last year, including insects, such as honeybees (Sang et al, 2022); birds, such as Black Robin (von Seth et al, 2022); fishes, such as turbot, seabream and seabass (Saura et al, 2021), Baltic herring (Atmore et al, 2022), pikeperch (De Los Ríos-Pérez et al, 2022, coho salmon (Martinez et al, 2022), catfish (Coimbra et al, 2023) and sailfish (Ferrette et al, 2023); wild mammals, such as grey wolf (Pacheco et al, 2022), killer whales (Kardos et al, 2023), sika deer (Iijima et al, 2023), scimitar-horned oryx (Humble et al, 2023) and gorilla (Alvarez-Estape et al, 2023); humans (Bird et al, 2023); domestic species, such as pigs (Krupa et al, 2022), cattle (Jin et al, 2022;Magnier et al, 2022), sheep (Djokic et al, 2023;Drzaic et al, 2022), horse (Criscione et al, 2022) and chicken (Gao et al, 2023;Liu et al, 2023); plants, such as walnut (Ding et al, 2022); crustaceans, such as Daphnia (Wersebe & Weider, 2023) and fungi (Singh et al, 2021). As suggested by Santiago et al (2020), the method is generally reliable for about 200 generations in the past, although…”

Impact of population structure in the estimation of recent historical effective population size by the software GONE

“…This can make it difficult to distinguish whether there has been a real sharp decline in N e in the most recent generations in a closed population or whether it is an artefact caused by population admixture. This type of result can be seen in some recent analyses such as those in two or three Croatian sheep breeds analysed by Drzaic et al [ 23 ] and one of the horse breeds analysed by Criscione et al [ 25 ]. In addition, a similar result has been found in experimental populations of Drosophila melanogaster maintained in bottles with 50% mixture between them every generation [ 19 ].…”

“…The possibility of estimating changes in population size in the recent past is particularly useful in livestock species, for which the start of breeding programs may imply substantial changes in N e . To date, this software has been applied to various breeds of pigs [ 20 ], cattle [ 21 , 22 ], sheep [ 23 , 24 ], horses [ 25 ] and chickens [ 26 , 27 ], and fish species such as turbot, seabream and seabass [ 16 ], Baltic herring [ 28 ], pikeperch [ 29 ], coho salmon [ 30 ], catfish [ 31 ] and sailfish [ 32 ].…”

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

“…Sheep production is deeply rooted in the eastern Adriatic and was introduced during the Neolithic migrations [ 4 – 6 ] so all populations have the same non-native origin. Croatian production primarily includes traditional systems without specialized breeding for carcass or milk yield [ 7 ] making local breeds such as Istrian sheep, Cres Island sheep, Pag Island sheep, Krk Island sheep, Rab Island sheep, Lika Pramenka sheep, Dalmatian Pramenka sheep, and Dubrovnik Ruda sheep valuable genetic resources. These breeds are bred for milk, meat and to a limited extent wool, but are hardy and resilient in harsh environments.…”