Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes

Zavarez, Ludmilla Balbo; Utsunomiya, Yuri Tani; Carmo, Adriana Santana do; Neves, Haroldo Henrique de Rezende; Carvalheiro, Roberto; Ferenčaković, Maja; O'Brien, Ana M. Pérez; Čurik, Ino; Cole, J.B.; Tassell, C. P. van; Silva, Marcus Vinicius; Sonstegard, Tad S.; Sölkner, Johann; Garcia, José Fernando

doi:10.3389/fgene.2015.00005

Cited by 73 publications

(71 citation statements)

References 40 publications

(55 reference statements)

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“…The poor correlation reported in our study between F GRM and F ROH was according to other studies Zhang et al, 2015). Zavarez et al (2015) in a study on autozygosity using high-density SNPs, showed that the correlation between F GRM and F ROH decreased from 0.74 per ROH >0.5 Mb to 0.41 per ROH >16 Mb, probably due to the properties of the G matrix which is based on individual loci, whereas F ROH is based on chromosomal segments. A higher correlation between F MOL i and F ROH were reported by Gómez-Romano et al (2014) in Austrian Brown Swiss cattle (0.76) and Rodríguez-Ramilo et al (2015) in Spanish Holstein breed (0.88).…”

Section: Resultscontrasting

confidence: 62%

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

136

128

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In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient ( F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH ( F ROH ) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix ( F GRM ), based on the difference between observed v. expected number of homozygous genotypes ( F HOM ) and the genomic homozygosity of individual i ( F MOL i ). The molecular coancestry coefficient ( f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH , whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 ( F MOL i − F ROH ) in Cinisara to 0.17 ( F GRM − F ROH ) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.Keywords: genomic inbreeding, local cattle breeds, runs of homozygosity ImplicationsIn the local breeds with small population size, one of the most important problems is the increase of inbreeding that leads to different negative effects as a reduction in phenotypic values. The current study aims to quantify the genomic inbreeding derived from runs of homozygosity (ROH) (F ROH ) in three Italian local dairy cattle breeds. According to ROH results, recent inbreeding was well detected in the investigated local dairy cattle breeds. Our results showed the necessity of implementing co...

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Section: Resultscontrasting

confidence: 62%

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

136

128

View full text Add to dashboard Cite

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“…; Zavarez et al . ), given their high correlation with autozygosity (r ≈ 0.7) (McQuillan et al . ) and, consequently, the high accuracy with which autozygosity is detected (Keller et al .…”

Section: Introductionmentioning

confidence: 99%

Runs of homozygosity: current knowledge and applications in livestock

et al. 2016

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This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F ). The better results of F suggest that F can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

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“…The genomic-based inbreeding method correlated moderately or poorly with pedigree 319 data, showing values lower than 0.39 (Figure7 to 9). Similary weak or no correlation was 320 reported for cattle [24,45,47], whereas a moderate to strong positive correlation was 321 described by some authors [15,40,48,59]. An increase in the correlation between genomic-322 and pedigree-based inbreeding as the pedigree depth increases is expected [24].…”

Section: Inbreeding Coefficients Correlations 312mentioning

confidence: 63%

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

Yoshida

Cáceres

Marín-Nahuelpi

et al. 2020

Preprint

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AbstractThe characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon breeding nuclei, genotyped using a 200K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.

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Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes

Cited by 73 publications

References 40 publications

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Runs of homozygosity: current knowledge and applications in livestock

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

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