Inbreeding depression in Zebu cattle traits

Pereira, Rodrigo Junqueira; Júnior, Mário Luiz Santana; Ayres, Denise Rocha; Bignardi, Annaíza Braga; Menezes, G.R.O.; Silva, L.O.C.; Machado, Carlos Henrique; Josahkian, L. A.; Albuquerque, Lúcia Galvão de

doi:10.1111/jbg.12219

Cited by 33 publications

(32 citation statements)

References 26 publications

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“…The inbreed coefficient values considering only inbred animals were also similar, ranging from 12.75 to 13.02%. These results may cause important losses, because the animal's performance may be compromised by increasing inbreeding (Santana Jr. et al, 2010;Pereira et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Cavani

Silva

Carreño

et al. 2018

Pesq. agropec. bras.

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The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.

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Section: Resultsmentioning

confidence: 99%

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Cavani

Silva

Carreño

et al. 2018

Pesq. agropec. bras.

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“…Baes et al 14 and Marras et al 18 studied the interval from first insemination to calving, which is defined as the IFL plus the gestation length. However, Pereira et al 19 showed that increased inbreeding did not affect the gestation length, suggesting why the lengthening in first insemination to calving can www.nature.com/scientificreports www.nature.com/scientificreports/ be compared with that in IFL caused by the unfavourable genotype. Marras et al 18 found an effect of around 14 days for heifers and 23 days for first-parity cows.…”

Section: Discussionmentioning

confidence: 99%

Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle

Martikainen

Koivula

Uimari

2020

Sci Rep

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Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes. In dairy cattle breeding, genetic gain of economically important traits has been achieved by intensive selection. The downside of intensive selection is, however, increased levels of inbreeding and, thus, possible accumulation of recessive deleterious alleles. This, in turn, results in inbreeding depression, which is defined as a reduction in average phenotypic performance 1. Managing inbreeding is crucial to maintaining the profitability of dairy cattle production, since inbreeding depression has been linked with impairment in economically important traits such as fertility and milk production 2-5. With the availability of single-nucleotide polymorphism (SNP) marker panels, the effects of inbreeding can be investigated at the genomic level. Inbreeding gives rise to continuous segments of homozygous genotypes known as runs of homozygosity (ROH), which are present in an individual if both parents transmit identical haplotypes to their offspring 6. Since ROHs unlikely arise by chance, they are considered good estimates of inbreeding 7. Inbreeding depression is assumed to be mostly caused by homozygosity for deleterious recessive mutations, which occur typically at low frequency in a population 8. ROHs are enriched for these deleterious recessive alleles and can, therefore, be linked to inbreeding depression 9. Previous research has found an association between increased inbreeding based on ROH (F ROH) and reduced fertility or milk production. For example, a 1% increase in F ROH was associated with 1.72 days increase in days open and 20 kg decrease in 205-day milk yield 3 , and also with 0.4 days longer insemination interval in heifers 5. Since the patterns of inbreeding vary throughout the genome 10 , identification of genomic regions with associati...

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“…Inbreeding can be defined as the probability of an individual receiving, at a given locus, the same ancestral-allele from both parents (Wright, 1922). Several studies have reported the negative effects of inbreeding in sheep (e.g., Drobik and Martyniuk, 2016;Gholizadeh and Ghafouri-Kesbi, 2016), goats (Deroide et al, 2016;Mahmoudi et al, 2018), and cattle (Smith et al, 2010;Pereira et al, 2016;Reverter et al, 2017). Therefore, monitoring inbreeding is important to avoid inbreeding depression.…”

Section: Inbreedingmentioning

confidence: 99%

Genetic Connectedness Between Norwegian White Sheep and New Zealand Composite Sheep Populations With Similar Development History

Oliveira

McEwan

Jakobsen³

et al. 2020

Front. Genet.

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The Norwegian White sheep (NWS) and New Zealand Terminal Sire Composite (NZC) sheep breeds have been developed based on crossing of multiple breeds, mainly of Northern European origin. A close genetic relationship between these populations could enable across-country genomic evaluations. The main objectives of this study were to assess the genetic connectedness between Norwegian and New Zealand sheep populations and estimate numerous genetic diversity metrics for these two populations. A total of 792 NWS and 16,912 NZC animals were genotyped using a high-density Illumina SNP chip panel (∼606K SNPs). The NZC animals were grouped based on their breed composition as: Finn, Lamb Supreme, Primera, Texel, "Other Dual Purpose", and "Other Terminal Sire". The average level of linkage disequilibrium ranged from 0.156 (for Primera) to 0.231 (for Finn). The lowest consistency of gametic phase was estimated between NWS and Finn (0.397), and between NWS and Texel (0.443), respectively. Similar consistency of gametic phase was estimated between NWS and the other NZC populations (∼ 0.52). For all composite sheep populations analyzed in this study, the majority of runs of homozygosity (ROH) segments identified had short length (<2,500 kb), indicating ancient (instead of recent) inbreeding. The variation in the number of ROH segments observed in the NWS was similar to the variation observed in Primera and Lamb Supreme. There was no clear discrimination between NWS and NZC based on the first few principal components. In addition, based on admixture analyses, there seems to be a significant overlap of the ancestral populations that contributed to the development of both NWS and NZC. There were no evident signatures of selection in these populations, which might be due to recent crossbreeding. In conclusion, the NWS composite breed was shown to be moderately related to NZC populations, especially Primera and Lamb Supreme. The findings reported here indicate a promising opportunity for collaborative genomic analyses involving NWS and NZC sheep populations.

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Inbreeding depression in Zebu cattle traits

Cited by 33 publications

References 26 publications

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Genetic diversity of Brazilian Brahman cattle by pedigree analysis

Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle

Genetic Connectedness Between Norwegian White Sheep and New Zealand Composite Sheep Populations With Similar Development History

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