Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Abstract

Summary ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed‐specific ROH islands was obtained via over‐representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo‐Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

“…The distribution of runs among different length classes (Table 1) confirms the predominance of short segments (<4 Mb) already observed in sheep (Dzomba et al., 2021; He et al., 2020; Purfield et al., 2017; Signer‐Hasler et al., 2019), as well as in other livestock species (Macciotta et al., 2021; Marras et al., 2015; Schiavo et al., 2021). Short ROHs are considered as evidence of ancient inbreeding.…”

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

“…F ROH>10 made a major contribution to F ROH of the two Duroc lines, revealing the recent reduction in genetic diversity and increase in homozygosity in two Duroc lines. Due to the differences in computational methods and parameters, tested populations, sample sizes, and SNP arrays, the Duroc populations in this study displayed different ROH numbers and lengths compared with previous studies of ROH in Duroc pigs ( 10 , 28 – 30 ). Two Duroc populations had low degrees of F HOM , likely due to the two Duroc populations raised in the same company (Wen's Foodstuff Group Co., Ltd.), which had the better inbreeding control and breeding programs.…”

“…For instance, Schiavo et al ( 10 ) used the 60 K single-nucleotide polymorphism (SNP) data of 573 Italian Duroc pigs to reveal the distribution of ROH and F ROH . They also used the 80 K SNP data of 48 Italian Duroc pigs to detect an ROH island including genes that have been shown to affect body size ( 28 ). Grossi et al ( 29 ) evaluated the F ROH using the 60 K SNP data of 1,066 Canadian Duroc pigs.…”

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

“…Genomic inbreeding level was estimated with several methods that used genotyping information. The ROH were computed with PLINK 1.9 according to previous works (Ferenčaković et al, 2013a,b;Marras et al, 2015;Lashmar et al, 2018;Schiavo et al, 2021a) and using the following parameters: (1) the minimum number of consecutive homozygous SNP was 15; (2) the minimum region length to define a ROH was 1 Mb, which excluded short ROH due to high linkage disequilibrium; (3) a maximum of 2 heterozygous SNP was allowed; (4) the minimum allowed density of SNP in a genome window was one SNP in 100 kb; (5) the maximum allowed distance between consecutive SNP was 1 Mb. Five classes of ROH were defined depending on the ROH length, according to Kirin et al (2010): 1 to 2 Mb, 2 to 4 Mb, 4 to 8 Mb, 8 to 16 Mb, >16 Mb.…”

“…For example, the average length of all ROH of an individual and the genome coverage of ROH are indicators of the occurrence of inbreeding events and whether these events were recent (in case of long ROH) or remote (short ROH), because many recombination events can disrupt the recent long ROH inherited from common ancestors (Ceballos et al, 2018). The accumulation of ROH in some genome regions, indicated as ROH island or ROH hotspots, can be due to natural or artificial directional selection at certain loci, which reduce genetic variability at these regions, leaving signatures of selections particularly useful for the identification of variants affecting economically relevant and breed-specific traits (Mastrangelo et al, 2016;Bertolini et al, 2018;Schiavo et al, 2020aSchiavo et al, , 2021a.…”