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

Abstract

The aim of this study was to assess the distribution of runs of homozygosity (ROH) and autozygosity islands in the composite Montana Tropical® beef cattle to explore hotspot regions which could better characterize the different biological types within the composite breed. Montana animals (n = 1,436) were genotyped with the GGP‐LD BeadChip (~30,000 markers). ROH was identified in every individual using the plink v1.90 software. Medium and long ROH prevailed in the genome, which accounted for approximately 74% of all ROH detected. On an average, 2.0% of the genome was within ROH, agreeing with the pedigree‐based inbreeding coefficient. The Montana cattle with a higher proportion of productive breed types showed the highest number of autozygosity islands (n = 17), followed by those with a higher proportion of breeds adapted to tropical environments (n = 15). Enriched terms (p < .05) associated with the immune and inflammatory response, homeostasis, reproduction, mineral absorption, and lipid metabolism were described within the autozygosity islands. In this regard, over‐represented GO terms and KEGG pathways described in this population may play a key role in providing information to explore the genetic and biological mechanisms together with the genomic regions underlying each biological type that favoured their optimal performance ability in tropical and subtropical regions.

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

“…Nevertheless, we did not find any signs that our results are distinct from previous findings and could be biased in comparison with other results obtained with medium‐density arrays. However, it should be noted that arrays with low or medium marker density are overestimating the number of short ROH (length approximately 1 Mb) (Peripolli et al, 2019; Purfield et al., 2012). The breed‐specific differences observed in this study in both the number and length of ROH were also described in other studies and resulted from breed characteristics and their breeding or demographic histories (Druml et al., 2017; Grilz‐Seger et al., 2018).…”

Ancient Homozygosity Segments in West African Djallonké Sheep Inform on the Genomic Impact of Livestock Adaptation to the Environment

“…ROH segments have been shown to be informative in population genetics to estimate inbreeding or effective size [13,14] and to assess inbreeding depression [15]. However, the use of ROH as markers for the identification of genomic areas potentially subjected to non-recent evolutionary selective events is not straightforward.…”

Efeitos da endogamia sobre a uniformidade de progênie de touros Nelore

“…• 15 (FERENČAKOVIĆ et al 2011 ;GURGUL et al, 2016) • 30 (KARIMI, 2013;MESZAROS et al, 2015;ZAVAREZ et al, 2015;SUMREDDEE et al, 2018) • 40 (MASTRANGELO et al, 2016;PERIPOLLI et al, 2019) • 58 (PURFIELD et al, 2012) Número de dados perdidos dentro de um ROH: SCRAGGS et al, 2014) • 2 (PURFIELD et al, 2012;WILLIAMS et al, 2015;MASTRANGELO et al, 2016;PERIPOLLI et al, 2019) • 4 (KARIMI, 2013), 5 (FERENČAKOVIĆ et al, 2013) Número de heterozigotos permitidos em um ROH: 2013a;BJELLAND et al, 2013 ;GURGUL et al, 2016;PERIPOLLI et al, 2019) • 1 (PURFIELD et al, 2012;KARIMI, 2013;SCRAGGS et al, 2014) • 2 (SUMREDDEE et al, 2018) Distância entre SNPs, dentro de ROH, consecutivos:…”

“…• 1000 (PURFIELD et al, 2012;MARRAS et al, 2014 ;MASTRANGELO et al, 2016;GURGUL et al, 2016 ;PERIPOLLI et al, 2019) Densidade de SNPs mínima permitida (SNPs/Kb):…”

“…• 1/50 (PURFIELD et al, 2012;KARIMI, 2013;WILLIAMS et al, 2015) • 1/100 (ZAVAREZ et al, 2015;MASTRANGELO et al, 2016) • 1/120 (PURFIELD et al, 2012;PERIPOLLI et al, 2019) • 1/500 (SUMREDDEE et al, 2018)…”