Genome‐wide survey on three local horse populations with a focus on runs of homozygosity pattern

Abstract

Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the Arab as well as between Sanfratellano, Siciliano and Maremmano. The highest expected heterozygosity (H e ) and contemporary effective population size (cNe) were reported in Siciliano (H e = 0.323, cNe = 397), and the lowest were reported in Purosangue Orientale Siciliano (H e = 0.277, cNe = 10). The analysis of the runs of homozygosity and the relative derived inbreeding revealed high internal homogeneity in Purosangue Orientale Siciliano and Arab horses, intermediate values in Maremmano and Sanfratellano and high heterogeneity in the Siciliano population. The genome-wide SNP analysis showed the selective pressure on Purosangue Orientale Siciliano towards traits related to endurance performance.Our results underline the importance of planning adequate conservation and exploitation programmes to reduce the level of inbreeding and, therefore, the loss of genetic diversity.

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

“…Previous studies have followed this recommendation and some of them assumed an even lower threshold ( c < 0.01; Ding et al, 2022; Alvarez‐Estape et al, 2023; or c < .02, Kardos et al, 2023). 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…”

Unlocking Horse Y Chromosome Diversity

“…Recently, many studies have been focused on the loss of biodiversity [ 23 , 24 , 25 ] or the increase in deleterious genotypes [ 26 ] caused by such inbreeding (as reviewed in [ 7 ]). In the last 200 years, the inbreeding practice led to the phenotypical expression at homozygous sites of deleterious variants [ 27 ], as highlighted when the coefficients are calculated in order to evaluate the genetic diversity among different horse breeds [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ,…”

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

“…HRR islands per breed were identified comparing the results of SW and CR methods of detection. Based on the standard normal z-score, obtained from all the SNPs-within-HRR incidence per breed and method, p -values were calculated and the top 0.1% of SNPs were selected to constitute an island 14 , 76 , 77 . Only those markers identified simultaneously with both methods were considered.…”