Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

Abstract

BackgroundThe aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED).ResultsThe average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands.ConclusionsLow FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.

Genome‐wide scan for runs of homozygosity in the composite Montana Tropical® beef cattle

“…The most extreme animal exhibited an ROH genome coverage encompassing 786.84 Mb of the total autosomal genome extension (UMD3.1) covered by markers (31.47% of the cattle genome). Similar results were described in several cattle breeds, whose findings reported a coverage varying from 25% to 29.20% of the cattle genome (Marras et al, 2015;Mastrangelo et al, 2016;Peripolli, Metzger, et al, 2018;Purfield et al, 2012;Szmatoła et al, 2016).…”

“…Additionally, by not allowing any heterozygous call within an ROH, long ROH might not have been overestimated. In fact, these results contradict those reported in the cattle (Ferenčaković et al, ; Ferenčaković, Hamzić, et al, ; Marras et al, ; Peripolli, Metzger, et al, ; Peripolli, Stafuzza, et al, ; Szmatoła et al, ; Zhang, Calus, et al, ), sheep (Purfield, McParland, Wall, & Berry, ), and pigs (Saura et al, ), in which the total length of ROH was composed mostly of high number of shorter ROH. It is noteworthy to highlight that the inconsistency amongst the criteria for defining ROH make the comparison of ROH studies not straightforward.…”

“…The number of ROH per chromosome was greater for BTA5 (532 segments) and the greater fraction of chromosome covered with ROH was found on BTA25 (16.91% of chromosomal length within an ROH; Figure ). Our previous studies in indicine cattle (Peripolli, Metzger, et al, ; Peripolli, Stafuzza, et al, ) also have described the greatest number of ROH on BTA5, whereas others have found on BTA1 (Gurgul et al, ; Mastrangelo et al, ; Purfield et al, ).…”

Detection of runs of homozygosity in conserved and commercial pig breeds in Poland

“…These loci are called “ROH hotspots” and are likely created as a result of the presence of alleles which have undergone selection and are close to fixation (Bosse et al., 2012; Pemberton et al., 2012; Quilez et al., 2011; Ramey et al., 2013; Zhang et al., 2015). In this sense, analysis of ROH hotspots may reveal the locations of variants that are under selection and reveal the genetic background of traits selected in the different populations (Bosse et al., 2012; Peripolli et al., 2017, 2018; Quilez et al., 2011; Ramey et al., 2013; Smith & Haigh, 1974).…”

Genomic Tools for Effective Conservation of Livestock Breed Diversity

“…The simultaneous analyses on LD to estimate past and present Ne, and ROH, provided valuable insights to settle future management strategies in Iberian Peninsula pig breeds. Further studies developed in cattle, goats and sheep allowed the detection of selection signatures based on common shared runs of homozygosity (ROH islands) [69,[71][72][73]. As selection is distinguished by local reductions in haplotype diversity, depending on the distribution of ROH patterns across the genome, results allow the identification of genomic regions that have been subjected to either recent and/or ancient selective pressure events [74,75].…”