Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 5.987
Filtrar
1.
Ecol Lett ; 23(10): 1460-1467, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32779837

RESUMO

In some animal species, individuals regularly breed with relatives, including siblings and parents. Given the high fitness costs of inbreeding, evolutionary biologists have found it challenging to understand the persistence of these inbred societies in nature. One appealing but untested explanation is that early life care may create a benign environment that offsets inbreeding depression, allowing inbred societies to evolve. We test this possibility using 21 years of data from a wild cooperatively breeding mammal, the banded mongoose, a species where almost one in ten young result from close inbreeding. We show that care provided by parents and alloparents mitigates inbreeding depression for early survival. However, as adults, inbred individuals provide less care, reducing the amount of help available to the next generation. Our results suggest that inbred cooperative societies are rare in nature partly because the protective care that enables elevated levels of inbreeding can be reduced by inbreeding depression.


Assuntos
Depressão por Endogamia , Endogamia , Altruísmo , Animais , Evolução Biológica , Cruzamento
2.
PLoS One ; 15(8): e0237765, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32804960

RESUMO

The failure of the maternal immune system to recognize fetal antigens and vice versa due to MHC similarity between the foal and its dam might result in the lack of placental separation during parturition in mares. The aim of the study was to investigate the influence of MHC similarity between a mare and a foal on the incidence of retained fetal membranes (RFM) in post-partum mares. DNA was sampled from 43 draft mares and their foals. Mares which failed to expel fetal membranes within three hours after foal expulsion were considered the RFM group (n = 14) and mares that expelled fetal membranes during the above period were the control group (n = 29). Nine MHC microsatellites of MHC I and MHC II were amplified for all mares and foals. MHC compatibility and MHC genetic similarity between mares and their foals was determined based on MHC microsatellites. The inbreeding coefficient was also calculated for all horses. The incidence of RFM in the studied population was 33%. Compatibility in MHC I and MHC II did not increase the risk of RFM in the studied population of draft mares (P>0.05). Differences in MHC similarity at the genetic level were not observed between mare-foal pairs in RFM and control group (P>0.05). We suspect that RFM in draft mares may not be associated with MHC similarity between a foal and its dam. Despite the above, draft horses could be genetically predisposed to the disease.


Assuntos
Doenças dos Cavalos/imunologia , Cavalos/imunologia , Endogamia , Complexo Principal de Histocompatibilidade/imunologia , Placenta Retida/veterinária , Animais , Estudos Transversais , Feminino , Técnicas de Genotipagem , Doenças dos Cavalos/epidemiologia , Cavalos/genética , Incidência , Complexo Principal de Histocompatibilidade/genética , Repetições de Microssatélites/genética , Repetições de Microssatélites/imunologia , Placenta Retida/epidemiologia , Placenta Retida/imunologia , Período Pós-Parto , Gravidez
3.
PLoS One ; 15(8): e0236629, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32797113

RESUMO

An important economic reason for the loss of local breeds is that they tend to be less productive, and hence having less market value than commercial breeds. Nevertheless, local breeds often have irreplaceable values, genetically and sociologically. In the breeding programs with local breeds, it is crucial to balance the selection for genetic gain and the maintaining of genetic diversity. These two objectives are often conflicting, and finding the optimal point of the trade-off has been a challenge for breeders. Genomic selection (GS) provides a revolutionary tool for the genetic improvement of farm animals. At the same time, it can increase inbreeding and produce a more rapid depletion of genetic variability of the selected traits in future generations. Optimum-contribution selection (OCS) represents an approach to maximize genetic gain while constraining inbreeding within a targeted range. In the present study, 515 Ningxiang pigs were genotyped with the Illumina Porcine SNP60 array or the GeneSeek Genomic Profiler Porcine 50K array. The Ningxiang pigs were found to be highly inbred at the genomic level. Average locus-wise inbreeding coefficients were 0.41 and 0.37 for the two SNP arrays used, whereas genomic inbreeding coefficients based on runs of homozygosity were 0.24 and 0.25, respectively. Simulated phenotypic data were used to assess the utility of genomic OCS (GOCS) in comparison with GS without inbreeding control. GOCS was conducted under two scenarios, selecting sires only (GOCS_S) or selecting sires and dams (GOCS_SD), while kinships were constrained on selected parents. The genetic gain for average daily body weight gain (ADG) per generation was between 18.99 and 20.55 g with GOCS_S, and between 23.20 and 28.92 with GOCS_SD, and it varied from 25.38 to 48.38 g under GS without controlling inbreeding. While the rate of genetic gain per generation obtained using GS was substantially larger than that obtained by the two scenarios of genomic OCS in the beginning generations of selection, the difference in the genetic gain of ADG between GS and GOCS reduced quickly in latter generations. At generation ten, the difference in the realized rates of genetic gain between GS and GOCS_SD diminished and ended up with even a slightly higher genetic gain with GOCS_SD, due to the rapid loss of genetic variance with GS and fixation of causative genes. The rate of inbreeding was mostly maintained below 5% per generation with genomic OCS, whereas it increased to between 10.5% and 15.3% per generation with GS. Therefore, genomic OCS appears to be a sustainable strategy for the genetic improvement of local breeds such as Ningxiang pigs, but keeping mind that a variety of GOCS methods exist and the optimal forms remain to be exploited further.


Assuntos
Endogamia , Seleção Genética , Suínos/genética , Animais , Feminino , Genômica , Homozigoto , Masculino , Fenótipo
4.
PLoS One ; 15(8): e0236717, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32797056

RESUMO

Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.


Assuntos
Búfalos/genética , Variação Genética , Endogamia , Filogenia , África Austral , Animais , Búfalos/fisiologia , Feminino , Masculino
5.
Proc Natl Acad Sci U S A ; 117(30): 18091-18098, 2020 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-32661148

RESUMO

The frequent mutations recovered recently from the pollen of select maize lines resulted from the meiotic mobilization of specific low-copy number long-terminal repeat (LTR) retrotransposons, which differ among lines. Mutations that arise at male meiosis produce kernels with concordant mutant phenotypes in both endosperm and embryo because the two sperms that participate in double fertilization are genetically identical. Those are in a majority. However, a small minority of kernels with a mutant endosperm carry a nonconcordant normal embryo, pointing to a postmeiotic or microgametophytic origin. In this study, we have identified the basis for those nonconcordant mutations. We find that all are produced by transposition of a defective LTR retrotransposon that we have termed dRemp (defective retroelement mobile in pollen). This element has several unique properties. Unlike the mutagenic LTR retrotransposons identified previously, dRemp is present in hundreds of copies in all sequenced lines. It seems to transpose only at the second pollen mitosis because all dRemp insertion mutants are nonconcordant yet recoverable in either the endosperm or the embryo. Although it does not move in most lines, dRemp is highly mobile in the Corn Belt inbred M14, identified earlier by breeders as being highly unstable. Lastly, it can be recovered in an array of structures, ranging from solo LTRs to tandem dRemp repeats containing several internal LTRs, suggestive of extensive recombination during retrotransposition. These results shed further light on the spontaneous mutation process and on the possible basis for inbred instability in maize.


Assuntos
Mitose , Mutação , Pólen , Retroelementos , Zea mays/fisiologia , Evolução Molecular , Mutação em Linhagem Germinativa , Endogamia , Fenótipo , Melhoramento Vegetal
6.
PLoS One ; 15(7): e0236647, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730350

RESUMO

The Great-billed Seed-finch (Sporophila maximiliani) is an endangered South American bird that has suffered from trafficking and the destruction of its natural habitat. In contrast, there are over 180,000 Great-billed Seed-finches legally raised in captivity in Brazil. The interest as a pet for Great-billed Seed-finches is due to their exceptional ability to sing. In the present research, the unknown genetic structure of the Great-billed Seed-finch captive population was investigated by quantitative analysis of 6,226 pedigree records. Additionally, 7,671 phenotypic records were available to estimate genetic parameters such as heritability and evolvability of a song-related trait of these birds for competitions. The captive Great-billed Seed-Finch population faces many of the problems commonly encountered in domestic animal populations such as a high level of inbreeding (average of 8.26%, 70.47% of birds were inbred), pedigree bottlenecks, unbalanced contribution of breeding animals and structuring (equivalent number of subpopulations of 2.91). Despite this, most genetic diversity remains preserved within aviaries. The high generation interval (5.74 years) found for this population should help to prevent a rapid increase in inbreeding and genetic drift. These results should serve as strong motivation and support for urgent actions to manage the genetic diversity of captive Great-billed Seed-Finches. From the viewpoint of genetic improvement for singing time in tournaments (STT), this trait presents sufficient variability to allow response to artificial selection given the heritability of 18.7% and evolvability of 2,447%. In contrast, inbreeding and high generation interval appear to be the most considerable barriers that may limit the genetic gain for STT. Widespread adoption of techniques such as optimal genetic contribution selection and implementation of routine genetic diversity monitoring via pedigree analysis and molecular tools can be crucial both in terms of breeding and conservation of genetic diversity of captive Great-billed Seed-Finches.


Assuntos
Variação Genética , Passeriformes/genética , Animais , Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Feminino , Endogamia , Masculino , Linhagem , Fenótipo , Vocalização Animal
7.
Proc Natl Acad Sci U S A ; 117(26): 15132-15136, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32546518

RESUMO

We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.


Assuntos
Genoma , Homem de Neandertal/genética , Animais , Evolução Biológica , Feminino , Fósseis , Regulação da Expressão Gênica , Variação Genética , Humanos , Endogamia , Densidade Demográfica , Federação Russa
8.
Proc Natl Acad Sci U S A ; 117(27): 15724-15730, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32571952

RESUMO

Inbreeding is often avoided in natural populations by passive processes such as sex-biased dispersal. But, in many social animals, opposite-sexed adult relatives are spatially clustered, generating a risk of incest and hence selection for active inbreeding avoidance. Here we show that, in long-tailed tits (Aegithalos caudatus), a cooperative breeder that risks inbreeding by living alongside opposite-sex relatives, inbreeding carries fitness costs and is avoided by active kin discrimination during mate choice. First, we identified a positive association between heterozygosity and fitness, indicating that inbreeding is costly. We then compared relatedness within breeding pairs to that expected under multiple mate-choice models, finding that pair relatedness is consistent with avoidance of first-order kin as partners. Finally, we show that the similarity of vocal cues offers a plausible mechanism for discrimination against first-order kin during mate choice. Long-tailed tits are known to discriminate between the calls of close kin and nonkin, and they favor first-order kin in cooperative contexts, so we conclude that long-tailed tits use the same kin discrimination rule to avoid inbreeding as they do to direct help toward kin.


Assuntos
Cruzamento/métodos , Passeriformes/crescimento & desenvolvimento , Reprodução/genética , Aves Canoras/crescimento & desenvolvimento , Animais , Feminino , Heterozigoto , Endogamia , Masculino , Passeriformes/genética , Comportamento Sexual Animal/fisiologia , Aves Canoras/genética
9.
Nat Commun ; 11(1): 2819, 2020 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-32499482

RESUMO

Increased grain yield will be critical to meet the growing demand for food, and could be achieved by delaying crop senescence. Here, via quantitative trait locus (QTL) mapping, we uncover the genetic basis underlying distinct life cycles and senescence patterns of two rice subspecies, indica and japonica. Promoter variations in the Stay-Green (OsSGR) gene encoding the chlorophyll-degrading Mg++-dechelatase were found to trigger higher and earlier induction of OsSGR in indica, which accelerated senescence of indica rice cultivars. The indica-type promoter is present in a progenitor subspecies O. nivara and thus was acquired early during the evolution of rapid cycling trait in rice subspecies. Japonica OsSGR alleles introgressed into indica-type cultivars in Korean rice fields lead to delayed senescence, with increased grain yield and enhanced photosynthetic competence. Taken together, these data establish that naturally occurring OsSGR promoter and related lifespan variations can be exploited in breeding programs to augment rice yield.


Assuntos
Genes de Plantas , Variação Genética , Oryza/crescimento & desenvolvimento , Oryza/genética , Regiões Promotoras Genéticas/genética , Alelos , Sequência de Bases , Regulação da Expressão Gênica de Plantas , Endogamia , Fenótipo , Polimorfismo Genético , Locos de Características Quantitativas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
10.
Proc Biol Sci ; 287(1927): 20200097, 2020 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-32429806

RESUMO

In polyandrous species, sexual selection extends beyond mating competition to selection for egg fertilization. As a result, the degree to which factors influencing mating success impact overall reproductive success becomes variable. Here, we used a longitudinal behavioural and genetic dataset for a population of eastern water dragons (Intellagama lesueurii) to investigate the degree to which male dominance, a pre-mating selection trait, influences overall reproductive success, measured as the number of surviving offspring. Moreover, we examine the interactive effects with a genetic trait, individual inbreeding, known to influence the reproductive success of males in this species. We found fitness benefits of male dominance, measured as body size and frequency of dominance behaviours displayed. However, individuals' propensity to display dominance behaviours had mixed effects, depending on the degree of inbreeding. While inbred males benefited from frequent displays, highly outbred males exhibited better reproductive outputs when displaying to a lesser extent. Given that outbred males have enhanced reproductive success in this species, the costs of displaying dominance behaviours may outweigh the benefits. Overall, our results demonstrate the fitness benefits of dominance in a polyandrous lizard, and suggest that these are modulated by an independent genetic trait. Our results may contribute to explaining the presence of alternative mating tactics in this species, owing to the variability in net fitness benefits of dominance. Our findings also reveal the challenges associated with investigating fitness traits in isolation, which may undermine the validity of results when important interactions are ignored.


Assuntos
Lagartos , Comportamento Sexual Animal , Animais , Feminino , Endogamia , Masculino , Preferência de Acasalamento Animal
11.
Yi Chuan ; 42(5): 493-505, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32431300

RESUMO

Xinjiang inbred cattle is a population which has been highly inbred for 45 years. However, the breed origin of this population cannot be traced back due to the lack of original records. To demonstrate the genetic background of Xinjiang inbred cattle, we analysed the worldwide genomic information of 16 cattle breeds using principal components analysis, and Admixture method. Furthermore, the shared SNP markers of Xinjiang inbred cattle, local Kazakh cattle, Holstein cattle, and Xinjiang Brown cattle were extracted to calculate population genetic parameters and genomic inbreeding indicators in order to evaluate the magnitude of inbreeding in each population. We also evaluated the relationship between inbreeding indicators and body size in the Xinjiang inbred population. Finally, the high frequency runs of homozygosity (ROH) regions for Xinjiang inbred cattle and local Kazakh population were selected for genes and QTL annotations. These results demonstrate that the ancestry proportions of inbreeding breed are similar to those of Kazakh cattle. The genomic homozygosity of Xinjiang inbred cattle is significantly higher than other populations; the inbreeding depression is observed in body size to a certain extent because body size decreased when corresponding homozygosity increased. Totally, six basic bio-pathways and 32 QTL regions that related to bovine economical traits were annotated. Our results provide the insights into breeding strategies, future protection, and utilization plan design for this special genetic material-Xinjiang inbred cattle.


Assuntos
Cruzamento , Bovinos/genética , Homozigoto , Polimorfismo de Nucleotídeo Único , Animais , Patrimônio Genético , Genômica , Endogamia
12.
Nat Commun ; 11(1): 2288, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32385271

RESUMO

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Endogamia , Zea mays/genética , Sequência de Bases , Elementos de DNA Transponíveis/genética , Genoma de Planta , Sequências Repetitivas de Ácido Nucleico/genética
13.
Am Nat ; 195(5): 753-771, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32364783

RESUMO

The time taken for a selectively favorable allele to spread through a single population was investigated early in the history of population genetics. The resulting formulas are based on deterministic dynamics, leading to inaccuracies at allele frequencies close to 0 or 1. To remedy this problem, the properties of the stochastic phases at either end point of allele frequency need to be analyzed. This article uses a heuristic approach to determining the expected times spent in the stochastic and deterministic phases of allele frequency trajectories, for a model of weak selection at a single locus that is valid for inbreeding populations and for autosomal and sex-linked inheritance. The net fixation time is surprisingly insensitive to the level of dominance of a favorable mutation, even with random mating. Approximate expressions for the variance of the net fixation time are also obtained, which imply that there can be substantial stochastic effects even in very large populations. The accuracy of the approximations was evaluated by comparisons with computer simulations. The results reveal some areas that need further investigation if a full understanding of selective sweeps is to be obtained, notably the possibility that fixations of slightly deleterious mutations may be affecting variability at closely linked sites.


Assuntos
Frequência do Gene , Mutação , Seleção Genética , Endogamia , Modelos Genéticos , Processos Estocásticos
14.
PLoS One ; 15(4): e0231809, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32310990

RESUMO

Genetic factors are often overlooked in conservation planning, despite their importance in small isolated populations. We used mitochondrial and microsatellite markers to investigate population genetics of the adder (Vipera berus) in southern Britain, where numbers are declining. We found no evidence for loss of heterozygosity in any of the populations studied. Genetic diversity was comparable across sites, in line with published levels for mainland Europe. However, further analysis revealed a striking level of relatedness. Genetic networks constructed from inferred first degree relationships suggested a high proportion of individuals to be related at a level equivalent to that of half-siblings, with rare inferred full-sib dyads. These patterns of relatedness can be attributed to the high philopatry and low vagility of adders, which creates high local relatedness, in combination with the polyandrous breeding system in the adder, which may offset the risk of inbreeding in closed populations. We suggest that reliance on standard genetic indicators of inbreeding and diversity may underestimate demographic and genetic factors that make adder populations vulnerable to extirpation. We stress the importance of an integrated genetic and demographic approach in the conservation of adders, and other taxa of similar ecology.


Assuntos
Endogamia , Viperidae/genética , Animais , Feminino , Variação Genética , Genética Populacional , Perda de Heterozigosidade , Masculino , Repetições de Microssatélites , Mitocôndrias/genética , Reino Unido , Viperidae/fisiologia
15.
J Dairy Sci ; 103(6): 5215-5226, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32253040

RESUMO

Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (pedigree-based methodologies, single SNP-based approach (homozygosity) and runs of homozygosity-based method) to analyze the evolution of genetic diversity measured as inbreeding or as coancestry of 3 selected populations of Latxa dairy sheep (Latxa Cara Rubia and Latxa Cara Negra from Euskadi and Navarre). Genomic data came from 972 artificial insemination rams genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) whose genealogy consisted of 4,484 animals. Inbreeding estimates based on molecular data were more similar between them than compared with those based on pedigree information. However, the SNP-based approach estimations of effective population size differed more, reflecting the sensitivity of effective population size to small changes in the evolution of inbreeding. The 2 Latxa Cara Negra populations showed increases of inbreeding rates with time and effective population sizes between 64 and 103 animals, depending on breed and methodology used. The Latxa Cara Rubia population did not show an increase in inbreeding rate, mainly due to semen importation from the related French population of Manech Tête Rousse. The effective size estimates based on coancestry increase show a higher variability and they are more sensitive to the source of information and the data structure considered. Realized effective population size based on individual increase in inbreeding were in agreement with the previous estimates. Coancestry evolution analysis based on DNA information showed an increase on coancestry during the last 10 yr in all breeds, as a consequence of the selection process. Moreover, the increase on coancestry between Latxa Cara Rubia and Manech Tête Rousse was more noticeable between than within each of those breeds.


Assuntos
Genoma/genética , Endogamia , Ovinos/fisiologia , Animais , Cruzamento , Genômica , Genótipo , Homozigoto , Masculino , Linhagem , Polimorfismo de Nucleotídeo Único/genética , Densidade Demográfica , Ovinos/genética
16.
J Dairy Sci ; 103(6): 5183-5199, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32278553

RESUMO

Genetic diversity in livestock populations is a significant contributor to the sustainability of animal production. Also, genetic diversity allows animal production to become more responsive to environmental changes and market demands. The loss of genetic diversity can result in a plateau in production and may also result in loss of fitness or viability in animal production. In this study, we investigated the rate of inbreeding (ΔF), rate of coancestry (Δf), and effective population size (Ne) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in North American Holstein and Jersey dairy cattle. To estimate the rate of inbreeding and coancestry, inbreeding and coancestry coefficients were calculated using the traditional pedigree method and genomic methods estimated from segment- and marker-based approaches. Furthermore, we estimated Ne from the rate of inbreeding and coancestry and extent of linkage disequilibrium. A total of 205,755 and 89,238 pedigreed and genotyped animals born between 1990 and 2018 inclusively were available for Holsteins and Jerseys, respectively. The estimated average pedigree inbreeding coefficients were 7.74 and 7.20% for Holsteins and Jerseys, respectively. The corresponding values for the segment and marker-by-marker genomic inbreeding coefficients were 13.61, 15.64, and 31.40% for Holsteins and 21.16, 22.54, and 42.62% for Jerseys, respectively. The average coancestry coefficients were 8.33 and 15.84% for Holsteins and 9.23 and 23.46% for Jerseys with pedigree and genomic measures, respectively. Generation interval for the whole 29-yr time period averaged approximately 5 yr for all selection pathways combined. The ΔF per generation based on pedigree, segment, and marker-by-marker genomic measures for the entire 29-yr period was estimated to be 0.75, 1.10, 1.16, and 1.02% for Holstein animals and 0.67, 0.62, 0.63, and 0.59% for Jersey animals, respectively. The Δf was estimated to be 0.98 and 0.98% for Holsteins and 0.73 and 0.78% for Jerseys with pedigree and genomic measures, respectively. These ΔF and Δf translated to an Ne that ranged from 43 to 66 animals for Holsteins and 64 to 85 animals for Jerseys. In addition, the Ne based on linkage disequilibrium was 58 and 120 for Holsteins and Jerseys, respectively. The 10-yr period that involved the application of genomic selection resulted in an increased ΔF per generation with ranges from 1.19 to 2.06% for pedigree and genomic measures in Holsteins. Given the rate at which inbreeding is increasing after the implementation of genomic selection, there is a need to implement measures and means for controlling the rate of inbreeding per year, which will help to manage and maintain farm animal genetic resources.


Assuntos
Bovinos/genética , Variação Genética , Genoma/genética , Genômica , Animais , Bovinos/fisiologia , Feminino , Genótipo , Endogamia , Desequilíbrio de Ligação , Parto , Linhagem , Densidade Demográfica , Gravidez
17.
J Dairy Sci ; 103(6): 5302-5313, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32331889

RESUMO

The advent of genomic selection paved the way for an unprecedented acceleration in genetic progress. The increased ability to select superior individuals has been coupled with a drastic reduction in the generation interval for most dairy populations, representing both an opportunity and a challenge. Homozygosity is now rapidly accumulating in dairy populations. Currently, inbreeding depression is managed mostly by culling at the farm level and by controlling the overall accumulation of homozygosity at the population level. A better understanding of how homozygosity and recessive load are related will guarantee continued genetic improvement while curtailing the accumulation of harmful recessives and maintaining enough genetic variability to ensure the possibility of selection in the face of changing environmental conditions. In this review, we present a snapshot of the current dairy selection structure as it relates to response to selection and accumulation of homozygosity, briefly outline the main approaches currently used to manage inbreeding and overall variability, and present some approaches that can be used in the short term to control accumulation of harmful recessives while maintaining sustained selection pressure.


Assuntos
Criação de Animais Domésticos , Cruzamento , Bovinos/genética , Seleção Genética , Animais , Genômica , Homozigoto , Endogamia
18.
PLoS One ; 15(4): e0229167, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32343700

RESUMO

Perennial habit and floral scent are major traits that distinguish domesticated cowpeas from their wild relatives. However, the genetic basis of these two important traits remains largely unknown in cowpea. Plant longevity, a perenniality-related trait, and floral scent, an outcrossing trait, were investigated using a RIL population derived from a cross between a domesticated and a wild cowpea. QTL analysis revealed three significant loci, one on chromosome 8 associated with plant longevity and two, on chromosomes 1 and 11, for floral scent. Genes within the QTL regions were identified. Genes encoding an F-box protein (Vigun08g215300) and two kinases (Vigun08g217000, Vigun08g217800), and involved in physiological processes including regulation of flowering time and plant longevity, were identified within the perenniality QTL region. A cluster of O-methyltransferase genes (Vigun11g096800, Vigun11g096900, Vigun11g097000, Vigun11g097600, and Vigun11g097800) was identified within the floral scent QTL region. These O-methyltransferase cowpea genes are orthologs of the Arabidopsis N-acetylserotonin O-methyltransferase (ASMT) gene, which is involved in the biosynthesis of melatonin. Melatonin is an indole derivative, which is an essential molecule for plant interactions with pollinators. These findings lay the foundation for further exploration of the genetic mechanisms of perenniality and floral scent in cowpea. Knowledge from this study can help in the development of new extended-growth cycle lines with increased yield or lines with increased outcrossing for population breeding.


Assuntos
Flores/genética , Odorantes/análise , Locos de Características Quantitativas/genética , Vigna/genética , Cromossomos de Plantas/química , Estudos de Associação Genética , Genética Populacional , Endogamia , Modelos Lineares , Melatonina/biossíntese , Fenótipo
19.
Proc Biol Sci ; 287(1922): 20192613, 2020 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-32126957

RESUMO

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.


Assuntos
Variação Genética , Passeriformes/genética , Animais , Espécies em Perigo de Extinção , Genética Populacional , Genoma , Haplótipos , Humanos , Endogamia , Densidade Demográfica , Cromossomos Sexuais
20.
Proc Biol Sci ; 287(1922): 20200195, 2020 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-32156218

RESUMO

The impact of inbreeding on fitness has been widely studied and provides consequential inference about adaptive potential and the impact on survival for reduced and fragmented natural populations. Correlations between heterozygosity and fitness are common in the literature, but they rarely inform about the likely mechanisms. Here, we investigate a pathology with a clear impact on health in striped dolphin hosts (a nematode infection that compromises lung function). Dolphins varied with respect to their parasite burden of this highly pathogenic lung nematode (Skrjabinalius guevarai). Genetic diversity revealed by high-resolution restriction-associated DNA (43 018 RADseq single nucleotide polymorphisms) analyses showed a clear association between heterozygosity and pathogen load, but only for female dolphins, for which the more heterozygous individuals had lower Sk. guevarai burden. One locus identified by RADseq was a strong outlier in association with parasite load (heterozygous in all uninfected females, homozygous for 94% of infected females), found in an intron of the citron rho-interacting serine/threonine kinase locus (associated with milk production in mammals). Allelic variation at the Class II major histocompatability complex DQB locus was also assessed and found to be associated with both regional variation and with pathogen load. Both sex specificity and the identification of associating functional loci provide insight into the mechanisms by which more inbred individuals may be more susceptible to the infection of this parasite. This provides important insight towards our understanding of the impact of inbreeding in natural populations, relevant to both evolutionary and practical conservation considerations.


Assuntos
Stenella/parasitologia , Animais , Evolução Biológica , Feminino , Aptidão Genética , Heterozigoto , Antígenos de Histocompatibilidade Classe II , Endogamia/estatística & dados numéricos , Masculino , Infecções por Nematoides/veterinária , Seleção Genética , Stenella/fisiologia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA