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1.
An Acad Bras Cienc ; 91(3): e20180387, 2019 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-31432899

RESUMO

This study aimed to estimate genetic parameters and correlations between morphological, agronomic and root quality traits of cassava plants, as well as to study cause and effect relationships through path analysis. A total of 814 genotypes were evaluated from 2011 to 2015. The joint analysis of the data was performed by the mixed models approach. The predicted genetic values of the genotypes were used to estimate the genetic correlations among as well the path analysis. The estimates of heritability of the genotype means ranged from 0.31 (commercial fresh root yield - CRY) to 0.62 (plant height - PLH). The highest genetic correlation coefficient estimates were observed for starch yield (STY) × total fresh root yield (FRY) (0.97). The results of the path analysis showed that FRY had the highest direct effect on STY, but the indirect selection based on FRY was not efficient to improve the gain of STY.


Assuntos
Variação Genética/genética , Manihot/genética , Característica Quantitativa Herdável , Seleção Genética/genética , Genótipo
2.
Genet Sel Evol ; 51(1): 36, 2019 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-31382878

RESUMO

BACKGROUND: Recessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions. METHODS: Two beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0-100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping. RESULTS: With full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring (aa) as compared to indiscriminate selection against carrier parents (Aa). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses. CONCLUSIONS: Genotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding.


Assuntos
Cruzamento , Bovinos/genética , Genes Recessivos , Software , Alelos , Animais , Feminino , Fertilidade , Técnicas de Genotipagem/veterinária , Mutação com Perda de Função , Masculino , Seleção Genética
3.
Genet Sel Evol ; 51(1): 42, 2019 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-31387519

RESUMO

BACKGROUND: Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population. METHODS: Two aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method. RESULTS: Validation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations. CONCLUSIONS: Our results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations.


Assuntos
Cruzamento , Mapeamento Cromossômico , Doenças dos Peixes/genética , Infecções por Flavobacteriaceae/veterinária , Flavobacterium , Oncorhynchus mykiss/genética , Animais , Resistência à Doença/genética , Feminino , Pesqueiros , Infecções por Flavobacteriaceae/genética , Padrões de Herança , Masculino , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Seleção Genética
4.
BMC Plant Biol ; 19(1): 347, 2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395025

RESUMO

BACKGROUND: Flavonoid 3'-hydroxlase (F3'H) is an important enzyme in determining the B-ring hydroxylation pattern of flavonoids. In monocots, previous studies indicated the presence of two groups of F3'Hs with different enzyme activities. One F3'H in rice was found to display novel chrysoeriol-specific 5'-hydroxylase activity. However, the evolutionary history of monocot F3'Hs and the molecular basis for the observed catalytic difference remained elusive. RESULTS: We performed genome-wide survey of 12 common monocot plants, and identified a total of 44 putative F3'H genes. The results showed that F3'H gene family had underwent volatile lineage-specific gene duplication and gene loss events in monocots. The expansion of F3'H gene family was mainly attributed to dispersed gene duplication. Phylogenetic analyses showed that monocot F3'Hs have evolved into two independent lineages (Class I and Class II) after gene duplication in the common ancestor of monocot plants. Evolutionary dynamics analyses had detected positive natural selection in Class II F3'Hs, acting on 7 specific amino acid sites. Protein modelling showed these selected sites were mainly located in the catalytic cavity of F3'H. Sequence alignment revealed that Class I and Class II F3'Hs displayed amino acid substitutions at two critical sites previously found to be responsible for F3'H and flavonoid 3'5'-hydroxylase (F3'5'H) activities. In addition, transcriptional divergence was also observed for Class I and Class II F3'Hs in four monocot species. CONCLUSIONS: We concluded that monocot F3'Hs have evolved into two independent lineages (Mono_F3'H Class I and Class II), after gene duplication during the common ancestor of monocot plants. The functional divergence of monocot F3'H Class II has been affected by positive natural selection, which acted on specific amino acid sites only. Critical amino acid sites have been identified to have high possibility to affect the substrate specificity of Class II F3'Hs. Our study provided an evolutionary and protein structural explanation to the previously observed chrysoeriol-specific 5'-hydroxylation activity for CYP75B4 in rice, which may also be true for other Class II F3'Hs in monocots. Our study presented clear evidence of plant-environmental interaction at the gene evolutionary level, and would guide future functional characterization of F3'Hs in cereal plants.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Grão Comestível/genética , Proteínas de Plantas/genética , Sistema Enzimático do Citocromo P-450/química , Grão Comestível/enzimologia , Evolução Molecular , Duplicação Gênica , Modelos Moleculares , Filogenia , Proteínas de Plantas/química , Seleção Genética , Alinhamento de Sequência
5.
Genet Sel Evol ; 51(1): 41, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337334

RESUMO

BACKGROUND: This study aimed at estimating genetic parameters of sex-influenced production traits, evaluating the impact of genotype-by-sex interaction, and identifying the selection criteria that could be included in multiple-trait genetic evaluation to increase the rate of genetic improvement in both sexes. To achieve this goal, we used 10 male and 10 female phenotypes, which were measured in a population of 2111 Australian Brahman cattle genotyped at high-density. RESULTS: Heritability estimates ranged from very low (0.03 ± 0.03 for cows' days to calving at first calving opportunity, DC1), to moderate (0.33 ± 0.08 for cows' adult body weight, AWTc), and to high (0.95 ± 0.07 for cows' hip height, HHc). Genetic correlation (rg) estimates between male and female homologous traits were favorable and ranged from moderate to high values, which indicate that selection for any of the traits in one sex would lead to a correlated response with the equivalent phenotype in the other sex. However, the estimated direct response was greater than the indirect response. Moreover, Pearson correlations between estimated breeding values obtained from each sex separately and from female and male homologous traits combined into a single trait in univariate analysis ranged from 0.74 to 0.99, which indicate that small ranking variation might appear if male and female traits are included as single or separate phenotypes. Genetic correlations between male growth and female reproductive traits were not significant, ranging from - 0.07 ± 0.13 to 0.45 ± 0.65. However, selection to improve HHc and AWTc in cows may reduce the percentage of normal sperm at 24 months of age (PNS24), possibly due to correlated effects in the same traits in males, which are related to late maturing animals. CONCLUSIONS: Hip height in cows and PNS24, as well as blood insulin-like growth factor 1 (IGF1) concentration in bulls at 6 months of age are efficient selection criteria to improve male growth and female reproductive traits, simultaneously. In the presence of genotype-by-sex interactions, selection for traits in each sex results in high rates of genetic improvement, however, for the identification of animals with the highest breeding value, data for males and females may be considered a single trait.


Assuntos
Cruzamento , Bovinos/genética , Seleção Genética , Animais , Peso Corporal/genética , Bovinos/crescimento & desenvolvimento , Feminino , Variação Genética , Fator de Crescimento Insulin-Like I/metabolismo , Masculino , Reprodução/genética
6.
Gene ; 713: 143975, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31302167

RESUMO

Hair is one of the defining characteristics of mammals. The hair shaft has a two-layer structure comprising the cortex, which is the inner layer and is composed of cortical cells, and the cuticle, which is the outermost layer. S100 calcium-binding protein A3 (S100A3) is expressed at high levels in the human hair cuticle. Arginine 51 of S100A3 protein is citrullinated specifically by peptidylarginine deiminase 3 (PAD3), and this citrullination is related to maturation of the cuticle. However, the detailed evolutionary processes of S100A3 and PAD3 during mammalian evolution are unknown. Here, we show that nonsynonymous changes in S100A3 accelerated in the common ancestral branch of mammals, probably as a result of positive selection that returned after the acquisition of hair cuticle-specific function in mammals. Later, pseudogenisation or nonfunctionalisation of S100A3 and PAD3 occurred in some species, such as the cetaceans. Our results show that positive selection and relaxation of the functional constraints of genes played important roles in the evolution of mammalian hair.


Assuntos
Evolução Molecular , Cabelo/química , Mamíferos/genética , Desiminases de Arginina em Proteínas/genética , Proteínas S100/genética , Seleção Genética , Sequência de Aminoácidos , Animais , Filogenia , Homologia de Sequência
7.
World J Microbiol Biotechnol ; 35(8): 118, 2019 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-31332540

RESUMO

The fungal genus Ustilago consists of intimidating pathogens associated with disease manifestations in plants of agricultural importance and gravity. Rapid progress of genome sequencing has opened the floodgates for biological research. Availability of Ustilago genomes provides a scope to explore complex codon and amino acid usage patterns in the genus. An extensive scrutiny of the factors underlying the complex modalities of codon and amino acid usage in Ustilago has been executed in the present analysis. Multivariate statistical analysis revealed a dominant effect of natural selection pressure, aimed at translational accuracy, to be operative on the codon usage behavior. Subtle impact of GC compositional constraint was also evident on the codon usage patterns. Gene expressivity was inferred to be the most crucial determinant governing observed codon usage variations. Amino acid usage patterns were found to be significantly governed by aromatic and hydrophobic characters of the encoded proteins. GC content and length of protein coding sequences also had considerable influence on the amino acid usage signatures. Extensive analysis of codon context variations revealed that UpA dinucleotides were strictly avoided at the codon-codon junctions (cP3-cA1) which might be attributed to reduce the risk of nonsense mutations and subsequently, improve translational finesse. Identification of the optimal codons, employed preferentially among the genes with high expressivity, and estimation of preferred and avoided codon pairs in Ustilago promises to be useful pertaining to mutational experiments at the codonic level, targeted to thwart the growth of Ustilago and combat associated pathogenesis.


Assuntos
Perfilação da Expressão Gênica , Ustilago/genética , Aminoácidos/metabolismo , Composição de Bases/genética , Códon , Seleção Genética/genética , Ustilago/metabolismo , Sequenciamento Completo do Genoma
8.
Yi Chuan ; 41(6): 486-493, 2019 Jun 20.
Artigo em Chinês | MEDLINE | ID: mdl-31257197

RESUMO

Genomic selection (GS) is a powerful tool which can be used to estimate the breeding value of individual animals by using the molecular markers of the animal's entire genome. GS improves the accuracy and intensity of selection, reduces the interval of generation, and realizes the effects of early accuracy selection contributing to a significant evolution in animal breeding. In the past decade, GS was successfully applied in the genetic improvement of dairy animals with improved selection accuracy and genetic gain of breeding animals. However, GS focuses on the genetic gain of target traits while it ignores the genetic relationship between mating pairs such that it ignores long term genetic merits such as an increase in inbreeding coefficient of offspring population, a decrease of genetic diversity and the homozygous presentation of harmful genes. In 2016, genomic mating (GM) was proposed as a sustainable genetic selection method using genomic information of the breeding candidate individuals to optimize selection and mating with resultant control of the growth rate of population inbreeding coefficient and achieving long-term and sustainable genetic progress. Therefore, GM is more suitable for modern animal breeding than GS, especially for the genetic improvement of indigenous species. In this review, we summarize the basic concepts, methods, and applications of GM, and then present examples comparing the effects of six simulated mating schemes. This review serves as a valuable reference for the applications of animal breeding methods.


Assuntos
Cruzamento , Genômica , Seleção Genética , Animais , Endogamia
9.
Arch Virol ; 164(10): 2459-2467, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31286220

RESUMO

Tobacco vein banding mosaic virus (TVBMV) is of increasing importance in tobacco production. Knowledge of the genetic structure and variability of the virus population is vital for developing sustainable management. In this study, 24 new TVBMV isolates from Sichuan Province together with 46 previous isolates were studied based on their coat protein sequences. Two distinguishable clades were supported by phylogenetic analysis. The summary statistics PS, AI and MC showed a strong TVBMV-geography association between the isolates from Southwest China (SW) and Mainland China (MC). Further analysis indicated that the spatial genetic structure of TVBMV populations is likely to have been caused by natural selection. Phylogeographic analysis provided strong support for spatial diffusion pathways between the Southwest and Northwest tobacco-producing regions. The TVBMV CP gene was found to be under negative selection, and no significant positive selection of amino acids was detected in the SW group; however, the isolates of the MC group experienced significant positive selection pressure at the first and third amino acid sites of CP. This study suggests that natural selection and habitat heterogeneity are important evolutionary mechanisms affecting the genetic structure of the TVBMV population.


Assuntos
Variação Genética , Doenças das Plantas/virologia , Potyvirus/classificação , Potyvirus/genética , Tabaco/virologia , Proteínas do Capsídeo/genética , China , Filogeografia , Potyvirus/isolamento & purificação , Seleção Genética , Análise de Sequência de DNA
10.
BMC Evol Biol ; 19(1): 141, 2019 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-31296160

RESUMO

BACKGROUND: The LysM receptor-like kinases (LysM-RLKs) are important to both plant defense and symbiosis. Previous studies described three clades of LysM-RLKs: LysM-I/LYKs (10+ exons per gene and containing conserved kinase residues), LysM-II/LYRs (1-5 exons per gene, lacking conserved kinase residues), and LysM-III (two exons per gene, with a kinase unlike other LysM-RLK kinases and restricted to legumes). LysM-II gene products are presumably not functional as conventional receptor kinases, but several are known to operate in complexes with other LysM-RLKs. One aim of our study was to take advantage of recently mapped wild tomato transcriptomes to evaluate the evolutionary history of LysM-RLKs within and between species. The second aim was to place these results into a broader phylogenetic context by integrating them into a sequence analysis of LysM-RLKs from other functionally well-characterized model plant species. Furthermore, we sought to assess whether the Group III LysM-RLKs were restricted to the legumes or found more broadly across Angiosperms. RESULTS: Purifying selection was found to be the prevailing form of natural selection within species at LysM-RLKs. No signatures of balancing selection were found in species-wide samples of two wild tomato species. Most genes showed a greater extent of purifying selection in their intracellular domains, with the exception of SlLYK3 which showed strong purifying selection in both the extracellular and intracellular domains in wild tomato species. The phylogenetic analysis did not reveal a clustering of microbe/functional specificity to groups of closely related proteins. We also discovered new putative LysM-III genes in a range of Rosid species, including Eucalyptus grandis. CONCLUSIONS: The LysM-III genes likely originated before the divergence of E. grandis from other Rosids via a fusion of a Group II LysM triplet and a kinase from another RLK family. SlLYK3 emerges as an especially interesting candidate for further study due to the high protein sequence conservation within species, its position in a clade of LysM-RLKs with distinct LysM domains, and its close evolutionary relationship with LYK3 from Arabidopsis thaliana.


Assuntos
Evolução Molecular , Lycopersicon esculentum/enzimologia , Lycopersicon esculentum/genética , Proteínas Serina-Treonina Quinases/genética , Sequência de Aminoácidos , Filogenia , Domínios Proteicos , Proteínas Serina-Treonina Quinases/química , Proteínas Serina-Treonina Quinases/metabolismo , Seleção Genética , Transcriptoma
11.
Phys Rev Lett ; 122(23): 238101, 2019 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-31298905

RESUMO

Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to date unproven, hypothesis is that this disadvantage is equal to the fractional cost relative to the total resting metabolic expenditure. We validate this result from physical principles through a general growth model and show it holds to excellent approximation for experimental parameters drawn from a wide range of species.


Assuntos
Metabolismo Energético , Crescimento , Modelos Biológicos , Seleção Genética
12.
Genet Sel Evol ; 51(1): 40, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311493

RESUMO

BACKGROUND: In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme's wider dairy population. These features of a breeding programme contribute in different ways to the rate of genetic gain for the wider industry. METHODS: A deterministic recursive gene flow model across subpopulations of animals in a dairy industry was created to predict the commercial performance of replacement heifers and future artificial insemination bulls. Various breeding strategies were assessed by varying the reliability of breeding values, the genetic contributions from subpopulations, and the genetic trend and merit of the foreign subpopulation. RESULTS: A higher response in the true breeding goal measured in standard deviations (SD) of true merit (G) after 20 years of selection can be achieved when genetic contributions shift towards higher merit alternatives compared to keeping them fixed. A foreign annual genetic trend of 0.08 SD of the breeding goal, while the domestic genetic trend is 0.10 SD, results in the overall net present value of genetic gain increasing by 1.2, 2.3, and 3.4% after 20 years as the reliability of GS in the domestic population increased from 0.3 to 0.45, 0.60 and 0.75. With a foreign genetic trend of 0.10 SD, these increases are more modest; 0.9, 1.7, and 2.4%. Increasing the foreign genetic trend so that it is higher than the domestic trend erodes the benefits of increasing the reliability of domestic GS further. CONCLUSIONS: Having a foreign source of genetic material with a high rate of genetic progress contributes substantially to the benefits of domestic genetic progress while at the same time reducing the expected returns from investments to improve the accuracy of genomic prediction in the home country.


Assuntos
Bovinos/genética , Indústria de Laticínios , Modelos Genéticos , Seleção Genética , Seleção Artificial , Animais , Feminino , Fluxo Gênico , Masculino
13.
Genet Sel Evol ; 51(1): 24, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146682

RESUMO

BACKGROUND: In settings with social interactions, the phenotype of an individual is affected by the direct genetic effect (DGE) of the individual itself and by indirect genetic effects (IGE) of its group mates. In the presence of IGE, heritable variance and response to selection depend on size of the interaction group (group size), which can be modelled via a 'dilution' parameter (d) that measures the magnitude of IGE as a function of group size. However, little is known about the estimability of d and the precision of its estimate. Our aim was to investigate how precisely d can be estimated and what determines this precision. METHODS: We simulated data with different group sizes and estimated d using a mixed model that included IGE and d. Schemes included various average group sizes (4, 6, and 8), variation in group size (coefficient of variation (CV) ranging from 0.125 to 1.010), and three values of d (0, 0.5, and 1). A design in which individuals were randomly allocated to groups was used for all schemes and a design with two families per group was used for some schemes. Parameters were estimated using restricted maximum likelihood (REML). Bias and precision of estimates were used to assess their statistical quality. RESULTS: The dilution parameter of IGE can be estimated for simulated data with variation in group size. For all schemes, the length of confidence intervals ranged from 0.114 to 0.927 for d, from 0.149 to 0.198 for variance of DGE, from 0.011 to 0.086 for variance of IGE, and from 0.310 to 0.557 for genetic correlation between DGE and IGE. To estimate d, schemes with groups composed of two families performed slightly better than schemes with randomly composed groups. CONCLUSIONS: Dilution of IGE was estimable, and in general its estimation was more precise when CV of group size was larger. All estimated parameters were unbiased. Estimation of dilution of IGE allows the contribution of direct and indirect variance components to heritable variance to be quantified in relation to group size and, thus, it could improve prediction of the expected response to selection in environments with group sizes that differ from the average size.


Assuntos
Variação Genética , Gado/genética , Modelos Genéticos , Animais , Feminino , Masculino , Fenótipo , Tamanho da Amostra , Seleção Genética , Comportamento Social
14.
Nat Commun ; 10(1): 2472, 2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-31171781

RESUMO

The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. Here we show how interference impacts systems biology by constraining genetic and phenotypic complexity. Our analysis uses biophysically grounded evolutionary models for molecular phenotypes, such as fold stability and enzymatic activity of genes. We find a generic mode of phenotypic interference that couples the function of individual genes and the population's global evolutionary dynamics. Biological implications of phenotypic interference include rapid collateral system degradation in adaptation experiments and long-term selection against genome complexity: each additional gene carries a cost proportional to the total number of genes. Recombination above a threshold rate can eliminate this cost, which establishes a universal, biophysically grounded scenario for the evolution of sex. In a broader context, our analysis suggests that the systems biology of microbes is strongly intertwined with their mode of evolution.


Assuntos
Bactérias/genética , Evolução Biológica , Dobramento de Proteína , Estabilidade Proteica , Vírus/genética , Bactérias/metabolismo , Evolução Molecular , Aptidão Genética , Fenótipo , Recombinação Genética , Seleção Genética , Biologia de Sistemas , Vírus/metabolismo
15.
Genet Sel Evol ; 51(1): 27, 2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31195962

RESUMO

BACKGROUND: Selection of mice for decreased environmental variability of birth weight has achieved higher survivability and larger litter size as a correlated response to canalized selection, which suggests higher welfare and robustness, and animals that are more homogeneous. However, in these studies, animals were not exposed to an environmental challenge. To demonstrate the advantages of this mouse line with a low environmental variability of birth weight, animals from two divergent lines (high and low variability of birth weight) were subjected to feed restriction. The objective of this study was to use these divergent lines to compare their response in terms of robustness against an environmental challenge. At weaning, 120 females, i.e. four full-sib females from 10 random litters of three consecutive generations of selection, were chosen from these divergent lines. The total number of females was divided into four groups, which were subjected to a feeding regimen by imposing different levels of feed restriction (i.e. 75, 90 and 85% of full ad libitum feed across three generations, respectively) in different combinations during the growth and reproduction periods. RESULTS: Animals from the "low" line were less sensitive to a change in feed level than those from the "high" line. Regarding reproduction, the "low" line performed better in terms of number of females having parturitions, number of parturitions, and litter size. Imposing a feed restriction on female mice during their growth period did not affect the birth weight of their pups. The "low" line was preferred because of its higher reproductive efficiency and survival under an environmental challenge. CONCLUSIONS: Selection for decreased environmental variability of birth weight produces animals that are less sensitive to environmental conditions, which can be interpreted as having greater robustness.


Assuntos
Variação Biológica da População , Peso ao Nascer , Restrição Calórica , Seleção Genética , Animais , Meio Ambiente , Feminino , Especiação Genética , Masculino , Camundongos , Seleção Artificial
16.
Nat Commun ; 10(1): 2645, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201315

RESUMO

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.


Assuntos
Núcleo Celular/genética , Interações Hospedeiro-Patógeno/genética , Alface/microbiologia , Oomicetos/genética , Doenças das Plantas/microbiologia , Núcleo Celular/efeitos dos fármacos , Resistência à Doença/genética , Fungicidas Industriais/farmacologia , Genômica , Alface/genética , Oomicetos/citologia , Oomicetos/patogenicidade , Seleção Genética/efeitos dos fármacos , Transcriptoma/efeitos dos fármacos , Transcriptoma/genética , Virulência/genética
17.
Vet Parasitol ; 270: 49-55, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31213241

RESUMO

Variation in the timing of development of immunity to gastro-intestinal nematode parasites was assessed in resistant and resilient Romney selection lines exposed to mixed natural infection. From weaning, at mean 92 days-of-age, animals (n = 53) were sampled for faecal egg count (FEC) expressed as eggs per gram of faeces (epg), saliva for immunoglobulin (IgG and IgA) determination and fasted live weight (LW) every 10 days until 351 days-of-age. Overall, mean back-transformed FEC were consistently low for resistant animals (<200 epg) whereas resilient counterparts' FEC increased with time to reach a peak of 1400 epg at day 230 for females and 1800 epg for males at day 280 before declining to less than 500 epg by day 300, respectively (P < 0.001). Resistant lambs reached a threshold for Trichostrongylus colubriformis L3-specific IgG which was indicative of the presence of immunity earlier at 220.6 ± 8.8 days-of-age compared with resilient-line animals which reach this threshold 40 days later at 263.4 ± 6.9 days-of-age (P < 0.001). In addition, resistant females reached sexual maturity earlier compared with their resilient counterparts viz. 263.5 ± 3.7 c.f. 274.4 ± 3.4 days-of-age, respectively, (P = 0.048). Mean fasted live weight (LW) showed a selection line by time interaction (P < 0.001) which reflected greater LW in the early phase of the study in resilient males but increasing for all groups until day 280 before declining and being similar for all groups from day 330. In summary, differences appear to exist in the timing of immune development between these Romney lines, with resistant animals developing immunity earlier and these resistant-line animals also appear to be more physiologically mature at the same chronological age than resilient animals. These observations have implications on the timing of identification and selection of resistant animals.


Assuntos
Cruzamento , Resistência à Doença/imunologia , Doenças dos Ovinos/imunologia , Tricostrongilose/veterinária , Animais , Feminino , Masculino , Seleção Genética , Maturidade Sexual , Ovinos , Tricostrongilose/imunologia
18.
Genome Biol ; 20(1): 126, 2019 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-31227026

RESUMO

BACKGROUND: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. RESULTS: Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. CONCLUSIONS: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.


Assuntos
Brassicaceae/genética , Genoma de Planta , Polimorfismo Genético , Seleção Genética , Resistência à Doença/genética
19.
Nat Commun ; 10(1): 2017, 2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31043615

RESUMO

Sexual selection has manifold ecological and evolutionary consequences, making its net effect on population fitness difficult to predict. A powerful empirical test is to experimentally manipulate sexual selection and then determine how population fitness evolves. Here, we synthesise 459 effect sizes from 65 experimental evolution studies using meta-analysis. We find that sexual selection on males tends to elevate the mean and reduce the variance for many fitness traits, especially in females and in populations evolving under stressful conditions. Sexual selection had weaker effects on direct measures of population fitness such as extinction rate and proportion of viable offspring, relative to traits that are less closely linked to population fitness. Overall, we conclude that the beneficial population-level consequences of sexual selection typically outweigh the harmful ones and that the effects of sexual selection can differ between sexes and environments. We discuss the implications of these results for conservation and evolutionary biology.


Assuntos
Evolução Biológica , Aptidão Genética/fisiologia , Preferência de Acasalamento Animal/fisiologia , Seleção Genética/fisiologia , Animais , Conservação dos Recursos Naturais/métodos , Feminino , Masculino
20.
BMC Genomics ; 20(1): 354, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072350

RESUMO

BACKGROUND: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. RESULTS: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. CONCLUSIONS: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates.


Assuntos
Proteínas de Anfíbios/genética , Anfíbios/genética , Evolução Molecular , Efeitos da Radiação , Seleção Genética , Proteínas de Anfíbios/efeitos da radiação , Anfíbios/classificação , Animais , Genoma , Anotação de Sequência Molecular , Fenótipo , Filogenia
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