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1.
BMC Genomics ; 22(1): 650, 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34496767

RESUMO

BACKGROUND: Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive. RESULTS: Heterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone. CONCLUSION: More alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.


Assuntos
Gastrópodes , Vigor Híbrido , Animais , Gastrópodes/genética , Perfilação da Expressão Gênica , Vigor Híbrido/genética , Hibridização Genética , Melhoramento Vegetal , Transcriptoma
2.
Commun Biol ; 4(1): 952, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376793

RESUMO

Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.


Assuntos
Evolução Biológica , Domesticação , Evolução Molecular , Genoma de Planta , Oryza/genética , Plantas Daninhas/genética , Hibridização Genética
3.
An Acad Bras Cienc ; 93(suppl 3): e20201649, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34378636

RESUMO

The objective of the present work was the molecular characterization of 11 parents and 101 hybrid progenies of conilon coffee, obtained through diallel crosses from the breeding program of the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (Incaper, ES, Brazil). The analyses were performed with 18 Simple Sequence Repeat (SSR) molecular markers, obtaining a total of 32 alleles. SSR markers were classified as moderately informative (PIC = 0.37), being efficient in characterizing individuals. High genetic diversity was verified in the 112 genotypes, based on the greater values of observed heterozygosity about to the expected heterozygosity (0.55 and 0.44, respectively), negative values for the fixation index (F) (-0.14), and the formation of distinct groups by UPGMA. These results indicate high genetic variability among the conilon coffee genitors, which remained similar and persisting in the progenies. The average dissimilarity between parents was 0.29 and between progenies 0.34. The progenies 38 and 40 and the parent P11 were considered the most divergent in the study. The genetic variability found can be explored in the genetic breeding of the conilon coffee and guide crossings between diversified and compatible genetic materials, for the composition of novel cultivars for the state of Espírito Santo.


Assuntos
Coffea/genética , Variação Genética , Genótipo , Hibridização Genética , Repetições de Microssatélites , Melhoramento Vegetal
4.
Int J Mol Sci ; 22(15)2021 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-34360921

RESUMO

Hybrid varieties can provide the boost needed to increase stagnant wheat yields through heterosis. The lack of an efficient hybridization system, which can lower the cost of goods of hybrid seed production, has been a major impediment to commercialization of hybrid wheat varieties. In this review, we discuss the progress made in characterization of nuclear genetic male sterility (NGMS) in wheat and its advantages over two widely referenced hybridization systems, i.e., chemical hybridizing agents (CHAs) and cytoplasmic male sterility (CMS). We have characterized four wheat genes, i.e., Ms1, Ms5, TaMs26 and TaMs45, that sporophytically contribute to male fertility and yield recessive male sterility when mutated. While Ms1 and Ms5 are Triticeae specific genes, analysis of TaMs26 and TaMs45 demonstrated conservation of function across plant species. The main features of each of these genes is discussed with respect to the functional contribution of three sub-genomes and requirements for complementation of their respective mutants. Three seed production systems based on three genes, MS1, TaMS26 and TaMS45, were developed and a proof of concept was demonstrated for each system. The Tams26 and ms1 mutants were maintained through a TDNA cassette in a Seed Production Technology-like system, whereas Tams45 male sterility was maintained through creation of a telosome addition line. These genes represent different options for hybridization systems utilizing NGMS in wheat, which can potentially be utilized for commercial-scale hybrid seed production.


Assuntos
Hibridização Genética , Melhoramento Vegetal , Infertilidade das Plantas/genética , Proteínas de Plantas/genética , Pólen/genética , Triticum , Triticum/genética , Triticum/crescimento & desenvolvimento
5.
J Anim Sci ; 99(8)2021 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-34343280

RESUMO

It is of interest to evaluate crossbred pigs for hot carcass weight (HCW) and birth weight (BW); however, obtaining a HCW record is dependent on livability (LIV) and retained tag (RT). The purpose of this study is to analyze how HCW evaluations are affected when herd removal and missing identification are included in the model and examine if accounting for the reasons for missing traits improves the accuracy of predicting breeding values. Pedigree information was available for 1,965,077 purebred and crossbred animals. Records for 503,716 commercial three-way crossbred terminal animals from 2014 to 2019 were provided by Smithfield Premium Genetics. Two pedigree-based models were compared; model 1 (M1) was a threshold-linear model with all four traits (BW, HCW, RT, and LIV), and model 2 (M2) was a linear model including only BW and HCW. The fixed effects used in the model were contemporary group, sex, age at harvest (for HCW only), and dam parity. The random effects included direct additive genetic and random litter effects. Accuracy, dispersion, bias, and Pearson correlations were estimated using the linear regression method. The heritabilities were 0.11, 0.07, 0.02, and 0.04 for BW, HCW, RT, and LIV, respectively, with standard errors less than 0.01. No difference was observed in heritabilities or accuracies for BW and HCW between M1 and M2. Accuracies were 0.33, 0.37, 0.19, and 0.23 for BW, HCW, RT, and LIV, respectively. The genetic correlation between BW and RT was 0.34 ± 0.03, and between BW and LIV was 0.56 ± 0.03. Similarly, the genetic correlation between HCW and RT was 0.26 ± 0.04, and between HCW and LIV was 0.09 ± 0.05, respectively. The positive and moderate genetic correlations between BW and other traits imply a heavier BW resulted in a higher probability of surviving to harvest. Genetic correlations between HCW and other traits were lower due to the large quantity of missing records. Despite the heritable and correlated aspects of RT and LIV, results imply no major differences between M1 and M2; hence, it is unnecessary to include these traits in classical models for BW and HCW.


Assuntos
Hibridização Genética , Modelos Genéticos , Animais , Peso ao Nascer , Peso Corporal , Feminino , Paridade , Linhagem , Fenótipo , Gravidez , Suínos/genética
6.
Methods Mol Biol ; 2287: 267-279, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270036

RESUMO

The intergeneric hybridization of wheat (Triticum aestivum L.) with maize (Zea mays L.) enables the production of doubled haploids (DHs) of wheat from all wheat hybrids with high efficiencies. Wheat and maize donor plants are raised in environmentally controlled greenhouses until crossing. Before anthesis, wheat spikes are emasculated and then pollinated with maize. Auxin is applied to each individual wheat floret 1 day after pollination. About 2 weeks after crossing, in vitro embryo culture is performed, enabling the regeneration of haploid wheat plantlets after maize chromosome elimination. Haploid plantlets are transferred to the greenhouse and after recovery, their genome is doubled with colchicine. Haploid plantlets can be sampled for DNA extractions and molecular analyses to aid the rapid discard of undesirable plantlets. Doubled haploid plants are raised in a greenhouse until maturity. Seeds of each fertile DH are harvested and often sown the same year. Several cycles of multiplication and evaluation in replicated plot trials and different geographical locations are then done to select the best candidate(s) for varietal registration.


Assuntos
Hibridização Genética , Melhoramento Vegetal/métodos , Triticum/crescimento & desenvolvimento , Triticum/genética , Zea mays/crescimento & desenvolvimento , Zea mays/genética , Cruzamentos Genéticos , Haploidia , Sementes/genética , Sementes/crescimento & desenvolvimento
7.
Methods Mol Biol ; 2289: 3-22, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270060

RESUMO

Haploid production is of great importance in plant breeding programs. Doubled haploid technology accelerates the generation of inbred lines with homozygosity in all loci in a single year. Haploids can be induced in vitro via cultivating the haploid gametes or in vivo through inter- and intraspecific hybridization. Haploid induction through centromere engineering is a novel system that is theoretically applicable to many plant species. The present review chapter discusses the proposed molecular mechanisms of selective chromosome elimination in early embryogenesis and the effects of kinetochore component modifications on proper chromosome segregation. Finally, the advantages and limitations of the CENH3-mediated haploidization approach and its applications are highlighted.


Assuntos
Centrômero/genética , Plantas/genética , Animais , Produtos Agrícolas/genética , Genoma de Planta/genética , Haploidia , Humanos , Hibridização Genética/genética , Cinetocoros/fisiologia , Melhoramento Vegetal/métodos
8.
Methods Mol Biol ; 2289: 167-178, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270070

RESUMO

Doubled haploids have a high impact on the improvement of heterozygous crops through hybridization. Anther culture is a doubled haploid technique for producing homozygous lines. In coconut, a tree species reported to be recalcitrant for tissue culture, a successful doubled haploid protocol was established through anther culture. All the factors affecting androgenesis induction have been optimized. In this chapter, a stepwise protocol, from doubled haploid induction including palm selection, anther isolation, pretreatment, and culture initiation, up to plant regeneration and thereafter acclimatization of the regenerated plants, is described. Furthermore, the protocol for testing the anther-derived plants for the ploidy level is also presented.


Assuntos
Cocos/genética , Flores/genética , Haploidia , Hibridização Genética/genética
9.
Genet Sel Evol ; 53(1): 62, 2021 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-34284721

RESUMO

BACKGROUND: Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. While there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Using imputed whole-genome sequence for 38,085 mixed-breed New Zealand dairy cattle, we conducted GWAS on 895 individual FT-MIR wavenumber phenotypes, and assessed the value of these direct phenotypes for identifying candidate causal genes and variants, and improving our understanding of the physico-chemical properties of milk. RESULTS: Separate GWAS conducted for each of 895 individual FT-MIR wavenumber phenotypes, identified 450 1-Mbp genomic regions with significant FT-MIR wavenumber QTL, compared to 246 1-Mbp genomic regions with QTL identified for FT-MIR predicted milk composition traits. Use of mammary RNA-seq data and gene annotation information identified 38 co-localized and co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in the ABO gene that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, we examined the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum. This revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk. CONCLUSIONS: This study demonstrates the utility of FT-MIR wavenumber phenotypes for improving our understanding of milk composition, presenting a larger number of QTL and putative causative genes and variants than found from FT-MIR predicted composition traits. Examining patterns of significance across the mid-infrared spectrum for loci of interest further highlighted commonalities of association, which likely reflects the physico-chemical properties of milk constituents.


Assuntos
Bovinos/genética , Leite/química , Locos de Características Quantitativas , Animais , Estudo de Associação Genômica Ampla , Hibridização Genética , Leite/normas , Oligossacarídeos/análise , Espectroscopia de Infravermelho com Transformada de Fourier
10.
Nat Commun ; 12(1): 4377, 2021 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-34312382

RESUMO

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.


Assuntos
Apomixia/genética , Citrus/genética , Frutas/genética , Genoma de Planta/genética , Alelos , Citrus/classificação , Extremo Oriente , Frequência do Gene , Genética Populacional , Genótipo , Geografia , Haplótipos , Hibridização Genética , Filogenia , Especificidade da Espécie
12.
Methods Mol Biol ; 2287: 323-332, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34270040

RESUMO

Wide hybridization is one of the haploid-inducing techniques that can accelerate the breeding process. Obtaining new cultivars is crucial to solve the problem of the constantly growing world population and global increase in demand for food, feed and renewable energy under changing environmental conditions. Here, we present a detailed protocol for obtaining oat (Avena sativa L.) doubled haploids (DHs) by pollination with maize (Zea mays L.). After fertilization, not only oat homozygotes, but also oat × maize hybrid zygotes can be formed, and during early embryo development, maize chromosomes are preferentially eliminated, which ultimately results in haploid plant formation. This chapter describes a method to produce oat DHs by crossing oat with maize, covering all steps from crossings to haploid plant regeneration and chromosome doubling.


Assuntos
Avena/genética , Hibridização Genética/genética , Zea mays/genética , Avena/crescimento & desenvolvimento , Cromossomos de Plantas/genética , Flores/crescimento & desenvolvimento , Engenharia Genética/métodos , Genótipo , Haploidia , Hibridização de Ácido Nucleico/métodos , Melhoramento Vegetal/métodos , Polinização , Sementes/genética , Zea mays/crescimento & desenvolvimento
13.
Mol Ecol ; 30(17): 4245-4258, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34219316

RESUMO

When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.


Assuntos
Genoma , Isolamento Reprodutivo , Animais , Genética Populacional , Humanos , Hibridização Genética , Sigmodontinae/genética
14.
J Genet ; 1002021.
Artigo em Inglês | MEDLINE | ID: mdl-34282737

RESUMO

Eucalyptus breeding programme mainly aims at increasing productivity associated with wood property traits which are suitable for different end uses. The principal challenge in this endeavor is to combine productivity with industrially relevant wood traits. In the present study, 23 hybrid clones derived from a biparental mapping population of Eucalyptus camaldulensis × E. tereticornis was assessed for six wood property traits across two sites in Tamil Nadu, India. The mean of most of the traits evaluated was consistently higher in Muthupettai, indicating significant site effect. Combined and location-wise analysis indicated additive genetic control of assessed traits. The stability of acoustic velocity in study sites, negligible G × E interaction and significant correlation with dynamic modulus of elasticity (DMoE) implies its use in selecting trees/logs for solid wood properties. Combined analysis of locations revealed low to moderate heritability (0.294-0.439) for all the traits with H2 being highest for cellulose per cent (0.439) followed by acoustic velocity (0.416). Genetic advance was calculated and was the highest for diameter (10.47%) followed by DMoE (9.19%). The two major chemical constituents of wood, namely total lignin and cellulose per cent showed 7.13% and 7.53% advancement in the hybrids. The out-performance of several hybrid clones when compared to the parents for different wood traits reiterates the use of Eucalyptus hybrids in plantation programmes to improve quality of raw material suitable for industrial application.


Assuntos
Eucalyptus/química , Hibridização Genética , Locos de Características Quantitativas/genética , Madeira/genética , Eucalyptus/genética , Índia , Fenótipo , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único/genética , Madeira/química
15.
J Genet ; 1002021.
Artigo em Inglês | MEDLINE | ID: mdl-34282738

RESUMO

Grain yield is a complex polygenic trait representing a multiplicative end product of contributing yield attributes governed by simple to complex gene interactions. Deciphering the genetics and inheritance of traits/genes influencing yield is a prerequisite to harness the yield potential in any crop species. The objective of the present investigation was to estimate genetic variance components and type of gene action controlling yield and its component traits using six populations (P1, P2, F1, F2, BC1 and BC2) of the three bread wheat crosses. Cross I (25th HRWSN 2105 × WH 1080), cross II (22ndSAWYT323 × RSP 561) and cross III (22ndSAWYT333 × WH 1080) involving elite stripe rust resistant wheat genetic stocks in combination with commercial check varieties were used for analysis. A combination of morpho-physiological, biochemical and disease influencing traits were evaluated, thus exploring the possibility of multi-trait integration in future. Results revealed that the estimated mean effects (m) were highly significant for all the traits in all crosses, indicating that selected traits were quantitatively inherited. The estimate of dominant gene effect was highly significant for plant height, number of tillers per plant in all the three crosses. Grain yield per plant was highly significant in the cross II while total protein content was highly significant in both crosses II and III. Glycine betaine content showed significant additive genes effect. Duplicate epistasis was the most significant for traits like plant height, total protein content and grain yield per plant. Dominance gene effect was more important than additive gene effects in the inheritance of grain yield and most other traits studied. The magnitude of additive X additive gene effects was high and positively significant whereas dominance × dominance was negatively significant for most of the traits studied in the three crosses. Additive × dominance gene effects was of minor significance, thus indicating that selection for grain yield and its components should be delayed to later generations of breeding.


Assuntos
Grão Comestível/genética , Epistasia Genética , Melhoramento Vegetal , Triticum/genética , Pão/normas , Mapeamento Cromossômico , Cruzamentos Genéticos , Humanos , Hibridização Genética , Herança Multifatorial/genética , Fenótipo , Locos de Características Quantitativas , Triticum/classificação , Triticum/crescimento & desenvolvimento
16.
Genes (Basel) ; 12(5)2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-34068148

RESUMO

Breeding programs in ornamentals can be facilitated by integrating knowledge of phylogenetic relatedness of potential parents along with other genomic information. Using AFLP, genetic distances were determined for 59 Geranium genotypes, comprising 55 commercial cultivars of the three subgenera of a total collection of 61 Geranium genotypes. A subgroup of 45 genotypes, including intragroup and intergroup hybrids, were selected and further characterized for genome sizes and chromosome numbers. The variation in genome size ranged from 1.51 ± 0.01 pg/2C to 12.94 ± 0.07 pg/2C. The chromosome numbers ranged from 26 to 108-110 with some hybrids showing an aberrant number of chromosomes based on their parents' constitution. All chromosome numbers of Geranium are an even number, which presumes that unreduced gametes occur in some cross combinations. Overall, parental difference in genome size and chromosome number were not limiting for cross compatibility. Good crossing compatibility was correlated to a Jaccard similarity coefficient as parameter for parental relatedness of about 0.5. Additionally, parent combinations with high differences in the DNA/chromosome value could not result in a successful cross. We expect that our results will enable breeding programs to overcome crossing barriers and support further breeding initiatives.


Assuntos
Cromossomos de Plantas/genética , Tamanho do Genoma , Geranium/genética , Melhoramento Vegetal/métodos , Polimorfismo Genético , Hibridização Genética
17.
Mol Ecol ; 30(16): 4077-4089, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34097806

RESUMO

A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment.


Assuntos
Besouros , Genoma de Inseto , Genoma Mitocondrial , Animais , Temperatura Baixa , Besouros/genética , Genoma Mitocondrial/genética , Hibridização Genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
18.
Mol Ecol ; 30(16): 4090-4102, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34101940

RESUMO

Contact zones between recently diverged taxa provide opportunities to examine the causes of reproductive isolation and the processes that determine whether two species can coexist over a broad region. The Pacific wren (Troglodytes pacificus) and winter wren (Troglodytes hiemalis) are two morphologically similar songbirds that started diverging about 4 million years ago, older than most sister species pairs of temperate songbirds. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct. To assess evidence for differentiation, hybridization and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genome. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals, two first-generation hybrids (i.e., F1 's) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or other evidence of recent breeding success of F1 's, indicating very low or zero fitness of F1  hybrids. Examination of genomic variation shows evidence for only a single backcrossing event many generations ago. The moderate rate of hybridization combined with very low F1  hybrid fitness is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species.


Assuntos
Aptidão Genética , Hibridização Genética , Isolamento Reprodutivo , Aves Canoras , Animais , Genoma , Genômica , Aves Canoras/genética
19.
Mol Ecol ; 30(16): 4103-4117, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34145663

RESUMO

The green odorous frog (Odorrana margaretae) displays a circular distribution around the Sichuan Basin of western China and possesses multiple replicate hybrid zones between lineages with high levels of divergence. To gain an understanding of the speciation process, we obtained 1540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: the West, North & South, and East groups. Demographic inference showed that they were initially isolated at ~2 million years ago, and subsequent post-glacial expansion produced the current circular distribution with four secondary contact zones. Hybridization in those zones involved lineages with various levels of divergence and produced greatly different patterns of introgression. Contact zones between the East and North & South groups (E-S and E-N) had contrast admixture levels but both showed a general lack of potential barrier loci. Meanwhile, the reconnection of the West and North & South groups produced two contact zones along the rim of the Basin. The S-W zone had extensive admixture while the N-W zone had limited admixture within a narrow geographic distance. Both showed substantial barrier effects, and a large number of potential barrier loci were shared. We also detected strong coupling among these loci. The N-W hybrid zone involved two highly-diverged lineages (FST = 0.704) and many loci have reached fixation around the hybrid zone. This study system offers a unique opportunity to understand the dynamics of introgression in contact zones and the architecture of reproductive isolation at different stages of speciation.


Assuntos
Genética Populacional , Rana clamitans , Animais , China , DNA Mitocondrial/genética , Fluxo Gênico , Especiação Genética , Hibridização Genética , Isolamento Reprodutivo
20.
Genet Sel Evol ; 53(1): 46, 2021 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-34058971

RESUMO

BACKGROUND: In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires from different pure breeds, and the genetic composition of crossbred animals is an admixture of the breeds included in the rotation. How to use the data of such individuals in genomic evaluations is still an open question. In this study, we aimed at providing methodologies for the use of data from crossbred individuals with an admixed genetic background together with data from multiple pure breeds, for the purpose of genomic evaluations for both purebred and crossbred animals. A three-breed rotational crossbreeding system was mimicked using simulations based on animals genotyped with the 50 K single nucleotide polymorphism (SNP) chip. RESULTS: For purebred populations, within-breed genomic predictions generally led to higher accuracies than those from multi-breed predictions using combined data of pure breeds. Adding admixed population's (MIX) data to the combined pure breed data considering MIX as a different breed led to higher accuracies. When prediction models were able to account for breed origin of alleles, accuracies were generally higher than those from combining all available data, depending on the correlation of quantitative trait loci (QTL) effects between the breeds. Accuracies varied when using SNP effects from any of the pure breeds to predict the breeding values of MIX. Using those breed-specific SNP effects that were estimated separately in each pure breed, while accounting for breed origin of alleles for the selection candidates of MIX, generally improved the accuracies. Models that are able to accommodate MIX data with the breed origin of alleles approach generally led to higher accuracies than models without breed origin of alleles, depending on the correlation of QTL effects between the breeds. CONCLUSIONS: Combining all available data, pure breeds' and admixed population's data, in a multi-breed reference population is beneficial for the estimation of breeding values for pure breeds with a small reference population. For MIX, such an approach can lead to higher accuracies than considering breed origin of alleles for the selection candidates, and using breed-specific SNP effects estimated separately in each pure breed. Including MIX data in the reference population of multiple breeds by considering the breed origin of alleles, accuracies can be further improved. Our findings are relevant for breeding programs in which crossbreeding is systematically applied, and also for populations that involve different subpopulations and between which exchange of genetic material is routine practice.


Assuntos
Bovinos/genética , Hibridização Genética , Polimorfismo de Nucleotídeo Único , Animais , Estudo de Associação Genômica Ampla/métodos , Estudo de Associação Genômica Ampla/normas , Endogamia , Modelos Genéticos , Locos de Características Quantitativas , Padrões de Referência , Seleção Artificial
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