Genome-Wide Estimates of Coancestry and Inbreeding in a Closed Herd of Ancient Iberian Pigs

Saura, María; Fernández, Almudena; Rodríguez, M. C.; Toro, M. Á.; Barragán, C.; Fernández, Ana; Villanueva, Beatriz

doi:10.1371/journal.pone.0078314

Cited by 40 publications

(50 citation statements)

References 31 publications

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“…The average molecular F and f coefficients were 0.68 ± 0.024 and 0.67 ± 0.03 in CIN and 0.69 ± 0.020 and 0.70 ± 0.03 in MOD, respectively (Table 1). Similar results were reported by Saura et al (2013) in a study on genome-wide estimates of F and f coefficients in an endangered strain of Iberian pigs. High values of F and f coefficients in local breeds with low population size, such as CIN and MOD, can compromise the viability of the populations.…”

Section: Inbreeding and Coancestry Molecular Coefficients Rates Of Isupporting

confidence: 89%

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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ABSTRACT:Genomic technologies, such as highthroughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of N e were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r 2 in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

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Section: Inbreeding and Coancestry Molecular Coefficients Rates Of Isupporting

confidence: 89%

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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“…In the four breeds, the highest N e (estimated five generation ago) was observed in Cinisara (94.58), whereas the lowest one was observed in Modicana (59.84) ( Table 4). For Sicilian breeds, the N e estimates based on LD were substantially higher than those reported in a previous study (Mastrangelo et al, 2014) calculated from the rates of F and f. Different estimates for N e were also reported in Iberian pigs with complete and accurate pedigree records, where N e calculated from the rates of molecular F and f were 17 and 10, respectively (Saura et al, 2013), whereas N e estimate using information from LD and recombination rate was 36 . Therefore, the discrepancies were due to the different used methods.…”

Section: Resultscontrasting

confidence: 70%

“…In all breeds, f MOL ij and F MOL i values were much higher than the other coefficients because these two methods (that are obtained on a SNP-by-SNP basis) do not discriminate alleles that are IBD or identical by status (IBS) (Rodríguez-Ramilo et al, 2015). However, these estimates computed from SNP array data were strongly correlated with genealogical estimates, represent a useful alternative to genealogical information for measuring and maintaining genetic diversity and are very accurate in predicting genealogical coancestry (Gómez-Romano et al, 2013;Saura et al, 2013). Spearman's rank correlation between F ROH and the other genomic inbreeding estimated measures was calculated (Table 6).…”

Section: Resultsmentioning

confidence: 99%

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

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

130

126

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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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“…The choice of 4 Mb for the minimum length permitted for defining a ROH was based on the results of Ferenčaković et al [26] who showed that F ROH based on shorter segments systematically overestimates autozygosity when using the Illumina BovineSNP50 BeadChip.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Rodríguez‐Ramilo¹,

Fernández²,

Toro

et al. 2015

PLoS ONE

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Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

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Genome-Wide Estimates of Coancestry and Inbreeding in a Closed Herd of Ancient Iberian Pigs

Cited by 40 publications

References 31 publications

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

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

Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

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