Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland

Szmatoła, Tomasz; Gurgul, Artur; Ropka‐Molik, Katarzyna; Jasielczuk, Igor; Ząbek, Tomasz; Bugno‐Poniewierska, Monika

doi:10.1016/j.livsci.2016.04.006

Cited by 75 publications

(105 citation statements)

References 48 publications

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“…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).…”

Section: Distribution Of Rohsupporting

confidence: 87%

“…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.…”

Section: Resultsmentioning

confidence: 71%

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

Peripolli

Stafuzza

Amorim

et al. 2019

J Animal Breeding Genetics

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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.

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Section: Distribution Of Rohsupporting

confidence: 87%

Section: Resultsmentioning

confidence: 71%

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

Peripolli

Stafuzza

Amorim

et al. 2019

J Animal Breeding Genetics

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“…The most frequent ROH islands in the Bp population were located on BTA6 and BTA17. These regions have also been described by Szmatoła et al () in the Simmental breed, by Sölkner et al () in the Angus breed and by Mastrangelo et al () in the Italian Reggiana breed. In the Dp population, ROH islands were most frequently identified on BTA11 and BTA26.…”

Section: Discussionsupporting

confidence: 68%

“…In the Dp population, ROH islands were most frequently identified on BTA11 and BTA26. These islands were also reported in Simmental and Limousine breeds (Szmatoła et al, ) and in the Italian Holstein breed (Gaspa et al, ; Mastrangelo et al, ).…”

Section: Discussionsupporting

confidence: 61%

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Ospina

Faria

Filho

et al. 2020

Reprod Domestic Animals

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Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1‐2 Mb) were observed between the two populations, while the number of long ROH (ROH>16 Mb) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

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“…The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH (Szmatola et al . ; Purfield et al . ).…”

Section: Methodsmentioning

confidence: 99%

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

et al. 2018

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Summary 18The availability of dense single-nucleotide polymorphism (SNP) assays allows for the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 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 F o r P e e r R e v i e wThe abundance of single-nucleotide polymorphisms (SNPs) throughout the genome and the 44 availability of dense SNP assays, makes these markers particularly suitable for the detection of 45 genomic regions where a reduction in heterozygosity occurred (Kim et al. 2013). Runs of 46 homozygosity (ROH) are contiguous segments of homozygous genotypes that are present in an 47 individual due to parents transmitting identical haplotypes to their offspring (Gibson et al. 2006). 48In animal genetics, ROH are used as predictors of whole genome inbreeding levels (Purfield et 49 al. 2012; Marras et al. 2015; Mastrangelo et al. 2016), to characterize the genomic distribution of 50 inbreeding depression on a phenotype (Biscarini et al. 2014; Pryce et al. 2014), and to identify 51 genes associated with traits of economic interest present in these regions (Zhang et al. 2015; 52 Szmatola et al. 2016; Purfield et al. 2017). Selection pressure and mating schemes can be 53 disentangled by ROH; therefore, ROH detection can also be used to minimize inbreeding and to 54 improve mating systems (Bosse et al. 2012; Zhang et al. 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 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 Runs of homozygosity definition 106Runs of homozygosity were estimated for each animal using PLINK (Purcell et al. 2007). No where L ROH is the total length of all ROH in the genome of an individual, and L aut the specified 118 length of the autosomal genome covered by SNPs on the chip (2 452.06 Mb). 119Each ROH was categorized based on its physical length into 1 to <5 Mb, 5 to <10 Mb, 10 to <15 and averaging this per breed. 123The genomic inbreeding coefficient based on the difference between observed vs. expected 124 number of homozygous genotypes (F HOM ) was also estimated using PLINK (Purcell et al. 2007). 125Pearson's correlation between the two measures of inbreeding was calculated. 127Detection of common runs of homozygosity 128To identify the genomic regions most commonly associated with ROH for the meta-population, 129and for groups on the basis of production purposes (milk, meat, wool and "milk and meat"), the 136Genomic coordinates for all the identified ROH islands were used for the annotation of genes 137 that were fully or partially contained within each selected region using the UCSC Genome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 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...

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Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland

Cited by 75 publications

References 48 publications

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

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

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

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Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland

Cited by 75 publications

References 48 publications

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

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

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Runs of homozygosity reveal genome‐wide autozygosity in Italian sheep breeds

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

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