Genomic Characterization of Interspecific Hybrids between the Scallops Argopecten purpuratus and A. irradians irradians

The Peruvian scallop (Argopecten purpuratus) has been introduced to China and has successfully been hybridized with the bay scallop (A. irradians irradians). The F1 hybrids of these two scallops exhibited a large increase in production traits and some other interesting new characteristics. To understand the genetic basis of this heterosis, nuclear gene and partial mtDNA sequences, and genomic in situ hybridization (GISH) were employed to analyze the genomic organization of the hybrids. Amplification of the ribosomal DNA internal transcribed spacer (ITS) showed that the parental ITS sequences were present in all the hybrid individuals, illustrating that the hybrid offspring inherited nuclear DNA from both parents. Sequence analyses of the ITS region further confirmed that the hybrids harbored alleles from their parents; some recombinant variants were also detected, which revealed some alterations in the nuclear genetic material of the hybrids. The analysis of mitochondrial 16S rDNA showed that the hybrids possessed sequences that were identical to the 16S rDNA of the female parents, proving a matrilineal inheritance of mitochondrial genes in scallops. In addition, GISH clearly discriminated between the parental chromosomes and indicated a combination of haploid genomes of duplex parents in the hybrids. The genetic analyses in our study illustrated that the F1 hybrids inherited nuclear material from both parents and cytoplasmic genetic material maternally, and some variations occurred in the genome, which might contribute to a further understanding of crossbreeding and heterosis in scallop species.     

Genetic analysis of the near-infrared spectral phenome of a global Eucalyptus species

Understanding the genetic-based variability in plant phytochemical compounds provides insight into the evolutionary and ecological processes affecting those traits. In some cases, it is an advantage to quantify the holistic phytochemical profile of a sample rather than focus on individual compounds of known interest. Near-infrared (NIR) reflectance spectroscopy provides a means to rapidly characterise the holistic physicochemical profile of biological materials (known as the spectral phenome). To date, most studies examining differences in the spectral phenome between groups and species have not been conducted in such a way as to enable the quantitative genetic basis of the variation in the spectral phenome to be determined. Here, we investigate the genetic-based variation in the spectral phenome of eucalypts focussing on comparisons at multiple scales of the genetic hierarchy using a tree species of global economic importance, Eucalyptus globulus. Using foliage collected from common-environment field trials we were able to use the spectral phenome to accurately differentiate advanced generation inter-specific hybrids and their parents and examine the pattern of inheritance of the holistic chemical profile. We also found intra-specific variability in the spectral phenome at the race, sub-race and family within race levels, and could identify clear genomic positions influencing the spectral phenome. We have used Eucalyptus as a test system to demonstrate the general approach of using the spectral phenome in genetic-based analyses, an approach that is readily transferrable to other plant systems.     

Hybridization in the genusCarex with special reference to North America

The first reports ofCarex hybrids in North America appeared in the middle and late 1800’s. By the early 1900’s and up to the middle 1900’s there was disagreement among the influential North American botanists regarding the extent to which hybrids existed. Those who recognized hybridization inCarex have been largely supported by recent studies, but only a small proportion of the reported hybrids are well documented. An understanding of hybridization in the genus is very important to systematic research and routine identification, as well as to the study of evolution and ecology. A total of 253Carex hybrids have been reported from North America, the greatest number of hybrids occurring in the northeast, where recent glaciation and overlapping flowering periods are probably among the causal factors. Based on current reports, hybrids are much more prevalent in subgenusCarex than in subgenusVignea. Field studies and cultivation have proven useful in determining hybrid parentage and delimiting morphological variation, respectively. Both reproductive and vegetative characters as well as anatomical and micromorphological characters have proven taxonomically useful. Cytological studies have documented meiotic irregularities inCarex hybrids and intermediate chromosome numbers. Variation in the meiotic anomalies is apparently associated with the relationship of the parents and with differences in chromosome number.Carex hybrids are largely sterile but some restoration of fertility is evident in backcrosses. Experimental hybridization, flavonoid chromatography, enzyme electrophoresis, phenological characteristics, developmental anomalies and host-parasite relationships have all been underexploited in the characterization of hybrids. A cross-referenced list of North AmericanCarex hybrids is included, along with a list of hybrids not yet reported for North America involving circumpolar species.     

Introgressive hybridization between a native and an introduced species:Viola lutea subsp.Sudetica versusV. Tricolor

A hybrid swarm betweenViola lutea subsp.sudetica (2n=50, native species) andViola tricolor (2n=26, introduced species) originated in the 1970’s in the Krkono?e Mts. Analyses of chromosome numbers, reproductive biology, morphology, and ecology gave the following results: (1) Compared to the plants found in the 1970’s, the number of colour morphs have decreased and the types now prevailing in the field are morphologically closer toV. lutea subsp.sudetica, forming a continuum. (2) In the field, hybrids having approximately the same chromosome number as the primary hybrids are most common. Some plants of the hybrid swarm have certain characters unknown to their parents. (3) In the field, autogamous types similar toV. tricolor were found. (4) A limited number of plants from the field and culture have higher somatic chromosome numbers thanV. lutea subsp.sudetica; there was a tendency towards increasing chromosome numbers in their progeny (up to 2n=62). These plants have some new morphological characters (a small proportion of hexacolpate pollen) not found in the parents (nor in the other hybrids with prevailing tetracolpate and pentacolpate pollen grains) and higher pollen fertility in comparison to the other hybrids. These plants also have the highest germination rate. (5) There is a tendency for chromosome numbers to decline in the progeny of open pollinated hybrid plants in the lowland experimental graden. (6) The phenology of the plants in the mountain grasslands and the lowland garden is different; the parents behave in a totally contrasting manner. (7) In the field at least some hybrids extend outside the geographical and ecological ranges of the parental species, invading new communities. (8) Seeds ofV. tricolor do not show any dormancy and germinate in the year of production; most of theV. lutea subsp.sudetica seeds germinate during the spring of the following year. Hybrids with intermediate chromosome numbers had both types of germination strategy. The germination rate of intermediates with high chromosome numbers was even higher than that ofV. tricolor.     

Floral scent in natural hybrids of Ipomopsis (Polemoniaceae) and their parental species

Background and Aims

Floral traits, such as floral volatiles, can contribute to pre-zygotic reproductive isolation by promoting species-specific pollinator foraging. When hybrid zones form, floral traits could also influence post-zygotic isolation. This study examined floral volatiles in parental species and natural hybrids in order to explore potential scent mediation of pre-zygotic and post-zygotic isolation.

Methods

Floral bouquets were analysed for the sister species Ipomopsis aggregata and I. tenuituba and their natural hybrids at two contact sites differing in both hybridization rate and temporal foraging pattern of hawkmoth pollinators. Floral volatiles were quantified in diurnal and nocturnal scent samples using gas chromatography–mass spectrometry.

Key Results

The bouquets of parental species and hybrids showed qualitative overlap. All flowers emitted similar sets of monoterpenoid, sesquiterpenoid, aliphatic and benzenoid compounds, but separated into groups defined by multivariate analysis of quantitative emissions. The parental species differed most strikingly in the nitrogenous compound indole, which was found almost exclusively in nocturnal bouquets of I. tenuituba. Natural hybrid bouquets were highly variable, and showed emission rates of several compounds that appeared transgressive. However, indole emission rates were intermediate in the hybrids compared with rates in the parents. Volatile bouquets at the contact site with lower hybridization did not show greater species specificity in overall scent emission, but I. tenuituba presented a stronger indole signal during peak hawkmoth activity at that site.

Conclusions

The two species of Ipomopsis differed in patterns of floral bouquets, with indole emitted in nocturnal I. tenuituba, but not in I. aggregata. Natural hybrid bouquets were not consistently intermediate between the parents, although hybrids were intermediate in indole emission. The indole signal could potentially serve as a hawkmoth attractant that mediates reproductive isolation both before and after hybrid formation.     

Juncus x stuckeyi (Juncaceae), a natural hybrid from northern Ohio

Hybrids betweenJuncus alpinus andJ. torreyi (Juncaceae) have been discovered in abandoned limestone quarries and on sandy beaches of Lake Erie in Erie and Ottawa counties, Ohio. The plants are morphologically intermediate in height, inflorescence length, number of glomerules per inflorescence, and number of flowers per glomerule. Both parents are diploid, 2n= 40; the hybrid is also diploid, 2n= 40, but at metaphase I both univalents and unequal bivalents are present. Using starch gel electrophoresis, ten enzymes were studied. The parents show differences in the allozymes of malic dehydrogenase, esterase, and malic enzyme. At each of these loci, the hybrids exhibit both the parental allozymes. Morphological and chromosomal data, augmented by the flavonoid and electrophoretic studies, confirm the hybrid nature of the newly discovered plants. The new taxon is described and namedJuncus xstuckeyi.     

Phenolics of Pyrus interspecific hybrids

The leaf phenolics of a number of Pyrus interspecific hybrids (from controlled hand-crosses) and the parental individuals have been examined. In most instances it was found that the presence of certain phenolics in the hybrids is of diagnostic value in predicting the identities of one or both of the original parents. The flavone and flavonol glycosides appear to be inherited as simple dominant characters (whether inherited from male or female parents) but phenolics such as epicatechin, catechin, caffeoylcalleryanin and p-hydroxybenzoic acid did not always appear to show such simple dominance.     

Stable,fertile somatic hybrids between <Emphasis Type="Italic">Sinapis alba</Emphasis> and <Emphasis Type="Italic">Brassica juncea</Emphasis> show resistance to <Emphasis Type="Italic">Alternaria brassicae</Emphasis> and heat stress

Wild relatives of Brassica are a rich reservoir of genes that are invaluable for the improvement of cultivated species. Sinapis alba is a close relative of crop Brassicas that possesses several desirable traits such as tolerance to Alternaria black spot disease, heat stress, insect pests and nematodes. This study is aimed at developing and characterizing hybrids between Brassica juncea and S. alba with the ultimate goal of transferring genes for tolerance to Alternaria brassicae and heat stress, the traits that are lacking in cultivated Brassica. We generated three hybrids between B. juncea and S. alba through protoplast fusion. The hybridity was confirmed through cytology and molecular markers. While two of the hybrids were symmetric, the third one was asymmetric and had greater resemblance to B. juncea. Hybrids showed some characteristic features of the parents and were fully male and female fertile and also set seeds upon back crossing with the parent species. In vitro leaf assay and field inoculation studies revealed that the hybrids are highly resistant to A. brassicae. Besides, hybrids set seeds at temperature of >?38 °C when parents failed to produce seeds indicating that hybrids possess heat tolerance. These stable hybrids provide a reliable genetic resource for transfer of genes from S. alba into cultivated Brassica species.     

Maternal inheritance of mitochondrial genomes and complex inheritance of chloroplast genomes in Actinidia Lind.: evidences from interspecific crosses

The inheritance pattern of chloroplast and mitochondria is a critical determinant in studying plant phylogenetics, biogeography and hybridization. To better understand chloroplast and mitochondrial inheritance patterns in Actinidia (traditionally called kiwifruit), we performed 11 artificial interspecific crosses and studied the ploidy levels, morphology, and sequence polymorphisms of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) of parents and progenies. Sequence analysis showed that the mtDNA haplotypes of F1 hybrids entirely matched those of the female parents, indicating strictly maternal inheritance of Actinidia mtDNA. However, the cpDNA haplotypes of F1 hybrids, which were predominantly derived from the male parent (9 crosses), could also originate from the mother (1 cross) or both parents (1 cross), demonstrating paternal, maternal, and biparental inheritance of Actinidia cpDNA. The inheritance patterns of the cpDNA in Actinidia hybrids differed according to the species and genotypes chosen to be the parents, rather than the ploidy levels of the parent selected. The multiple inheritance modes of Actinidia cpDNA contradicted the strictly paternal inheritance patterns observed in previous studies, and provided new insights into the use of cpDNA markers in studies of phylogenetics, biogeography and introgression in Actinidia and other angiosperms.     

Intergeneric ethanol producing hybrids of thermotolerant Kluyveromyces and non-thermotolerant Saccharomyces cerevisiae

Intergeneric hybrids of an Arg auxotroph of Kluyveromyces marxianus able to grow up to 52¡C and Saccharomyces cerevisiae capable of growth up to 40¡C, have been constructed by protoplasmic fusion. The fusants resembled the former except that they were prototrophic and some produced ethanol in excess of 6% (v/v) both at 30 and 45¡C, an attribute otherwise lacking in the parents. The hybrids were stable during mitotic and meiotic growth. Genetic evidence leading to the retrieval of orthodox arg at a frequency of 6% from the prototrophic hybrids, confirmed their genuineness and the presence of S. cerevisiae-specific ARG in an integrative manner. The integration seemed to have occurred at a locus ~12 cM away from the orthodox arg which on the other side was found to be linked to MET. The order of three genes was, therefore, speculated to be either MET-arg-ARG or ARG-arg-MET.     

Bt maize and mycotoxins: the current state of research

The commercialisation of Bt (Bacillus thuringensis) maize expressing the Cry endotoxin specific for some types of Lepidopteran and Coleopteran pests has lead researchers to study the reduction in mycotoxin concentrations in Bt hybrids compared to the correspondent isogenic plants. Indeed, insect damage is one of the main inoculation pathways of mycotoxinogenic moulds. The present study aims to evaluate, according to the scientific literature published to date, the real efficiency of Bt maize hybrids in reducing the mycotoxin problem. The results obtained from the analysis of the literature do not show significant variations in the content of aflatoxins, zearalenone and trichothecenes, between Bt hybrids and corresponding isogenic control plants. The only mycotoxins where Bt hybrids have any effect are the fumonisin group, but even in this case studies in commercially planted fields have shown that their effect is mitigated by many biotic and abiotic factors.     

MicroRNA expression changes following synthesis of three full-sib <Emphasis Type="Italic">Populus</Emphasis> triploid populations with different heterozygosities

Key message

Through high-throughput sequencing, we compared the relative expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one diploid hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. In addition, unbalanced parental expression level dominance of miRNAs were found in the three allotriploid and interspecific hybrid populations, which may reprogram gene expression networks and contribute to the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among one diploid and three triploid hybrid populations, hinting that miRNA abundances do not increase with the genome content. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the slight decrease in miRNA regulation, suggesting an important molecular mechanism of polyploid advantage.

Abstract

Hybridization with three types of induced 2n gametes transmitted different parental heterozygosities has been proven as an efficient method for Populus triploid production. Several researches have shown that miRNA could be non-additively expressed in allopolyploids. However, it is still unclear whether the non-additively expressed miRNAs result from the effect of hybridization or polyploidization, and whether a dose response to the additional genomic content exists for the expression of miRNA. Toward this end, through high-throughput sequencing, we compared the expression levels of miRNA in three full-sib Populus triploid populations with that in their parents and one interspecific hybrid population. We found similar numbers of miRNAs differentially expressed between the parents and the four progeny hybrid populations. Unbalanced parental expression level dominance of miRNAs were found in the three triploid and diploid hybrid populations, which may reprogram gene expression networks and affect the growth of Populus hybrids. These results indicated that hybridization has a great impact on the miRNA expression variation in the newly synthesized Populus triploid and diploid hybrid populations. However, we also found no significant differences in miRNA expression among the three triploid populations and the diploid hybrid population. No dosage effect of miRNA expression could lead to dosage-dependent negative effects on target genes and their downstream pathway in polyploids. We speculate that polyploids may gain advantages from the decrease in miRNA negative regulation, suggesting an important molecular mechanism of polyploid advantage.

     

Artificial hybridization of the genera zinnia (Sect. Mendezia) and tragoceras (Compositae-Zinninae)

Morphological and cytological observations onZinnia-Tragoceras hybrids are presented. At the diploid level, the cytology of the artificial hybrids indicates thatZinnia sect.Mendezia andTragoceras share a common genomic background, and that the divergence of the two genera has been accompanied by reciprocal translocations involving nonhomologous chromosomes. Diakinesis associations in artificial tetraploids of the hybrids have been used to shed light on the extent of chromosome homology of the parents. As a result of this studyTragoceras has been merged intoZinnia as a new section.     

Flow cytometry confirms reticulate evolution and reveals triploidy in Central European Diphasiastrum taxa (Lycopodiaceae, Lycophyta)

Background and Aims

Interspecific Diphasiastrum hybrids have been assumed to be homoploid and to produce well-formed spores serving sexual reproduction. If this were the case, forms intermediate between hybrids and parents or hybrid swarms should be expected. The purpose of this study was: (1) to check whether homoploidy consistently applies to the three hybrids throughout their Central European range; (2) to examine whether their genome sizes confirm their parentage as assumed by morphology; and (3) to perform a screening for detection of ploidy levels other than diploid and variation in DNA content due to backcrossing.

Methods

Flow cytometry was used first to measure the relative DNA values [with 4′,6-diamidino-2-phenylindole (DAPI) staining] and ploidy level as a general screening, and secondly to determine the absolute DNA 2C values [with propidium iodide (PI) staining] in a number of selected samples with the main focus on the hybrids.

Key Results

A considerable variation of DNA 2C values (5·26–7·52 pg) was detected between the three European Diphasiastrum species. The values of the diploid hybrids are highly constant without significant variation between regions. They are also intermediate between their assumed parents and agree closely with those calculated from their putative parents. This confirms their hybrid origin, assumed parentage and homoploid status. Considerably higher DNA amounts (9·48–10·30 pg) were obtained for three populations, suggesting that these represent triploid hybrids, an interpretation that is strongly supported by their morphology.

Conclusions

Diploid hybrids have retained their genetic and morphological identites throughout their Central European range, and thus no indications for diploid backcrossing were found. The triploid hybrids have probably originated from backcrossing between a diploid gametophyte of a hybrid (derived from a diplospore) and a haploid gametophyte of a diploid parental species. By repeated crossing events, reticulate evolution patterns arise that are similar to those known for a number of ferns.     

Chloroplast evidence for the multiple origins of the hybrid Potamogeton × fluitans

Previous studies of Potamogeton × fluitans Roth. have supported the putative origin of this taxon as a result of hybridization between Potamogeton lucens L. and Potamogeton natans L. In the British Isles P. × fluitans is restricted to only a few sites, while both its parents are relatively common. Previous studies have shown that most of these hybrid populations are monomorphic, with the exception of the Moors River, in Hampshire and Dorset, where multiple genotypes have been identified. This is despite the fact that here the hybrid grows in the absence of one its parents, P. lucens. In this study, species-specific differences in the TrnL (UAA) chloroplast region, a maternally inherited marker, were used to identify the original seed-bearing parent of the hybrids within this river system. It was shown that both species have been maternal parents in the creation of this hybrid population.     

Rapid genomic DNA changes in allotetraploid fish hybrids

Rapid genomic change has been demonstrated in several allopolyploid plant systems; however, few studies focused on animals. We addressed this issue using an allotetraploid lineage (4nAT) of freshwater fish originally derived from the interspecific hybridization of red crucian carp (Carassius auratus red var., ♀, 2n=100) × common carp (Cyprinus carpio L., ♂, 2n=100). We constructed a bacterial artificial chromosome (BAC) library from allotetraploid hybrids in the 20th generation (F₂₀) and sequenced 14 BAC clones representing a total of 592.126 kb, identified 11 functional genes and estimated the guanine–cytosine content (37.10%) and the proportion of repetitive elements (17.46%). The analysis of intron evolution using nine orthologous genes across a number of selected fish species detected a gain of 39 introns and a loss of 30 introns in the 4nAT lineage. A comparative study based on seven functional genes among 4nAT, diploid F₁ hybrids (2nF₁) (first generation of hybrids) and their original parents revealed that both hybrid types (2nF₁ and 4nAT) not only inherited genomic DNA from their parents, but also demonstrated rapid genomic DNA changes (homoeologous recombination, parental DNA fragments loss and formation of novel genes). However, 4nAT presented more genomic variations compared with their parents than 2nF₁. Interestingly, novel gene fragments were found for the iqca1 gene in both hybrid types. This study provided a preliminary genomic characterization of allotetraploid F₂₀ hybrids and revealed evolutionary and functional genomic significance of allopolyploid animals.     

Reproductive isolation and hybridization in sympatric populations of three Dactylorhiza species (Orchidaceae) with different ploidy levels

Background and Aims

The potential for gene exchange between species with different ploidy levels has long been recognized, but only a few studies have tested this hypothesis in situ and most of them focused on not more than two co-occurring species. In this study, we examined hybridization patterns in two sites containing three species of the genus Dactylorhiza (diploid D. incarnata and D. fuchsii and their allotetraploid derivative D. praetermissa).

Methods

To compare the strength of reproductive barriers between diploid species, and between diploid and tetraploid species, crossing experiments were combined with morphometric and molecular analyses using amplified fragment length polymorphism markers, whereas flow cytometric analyses were used to verify the hybrid origin of putative hybrids.

Key Results

In both sites, extensive hybridization was observed, indicating that gene flow between species is possible within the investigated populations. Bayesian assignment analyses indicated that the majority of hybrids were F₁ hybrids, but in some cases triple hybrids (hybrids with three species as parents) were observed, suggesting secondary gene flow. Crossing experiments showed that only crosses between pure species yielded a high percentage of viable seeds. When hybrids were involved as either pollen-receptor or pollen-donor, almost no viable seeds were formed, indicating strong post-zygotic reproductive isolation and high sterility.

Conclusions

Strong post-mating reproductive barriers prevent local breakdown of species boundaries in Dactylorhiza despite frequent hybridization between parental species. However, the presence of triple hybrids indicates that in some cases hybridization may extend the F₁ generation.     

Determination of heterotic groups for tropical Indica hybrid rice germplasm

Key message

Two heterotic groups and four heterotic patterns were identified for IRRI hybrid rice germplasm to develop hybrid rice in the tropics based on SSR molecular data and field trials.

Abstract

Information on heterotic groups and patterns is a fundamental prerequisite for hybrid crop breeding; however, no such clear information is available for tropical hybrid rice breeding after more than 30 years of hybrid rice commercialization. Based on a study of genetic diversity using molecular markers, 18 parents representing hybrid rice populations historically developed at the International Rice Research Institute (IRRI) were selected to form diallel crosses of hybrids and were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the magnitude of yield heterosis among marker-based parental groups, (2) examining the consistency between marker-based group and heterotic performance of hybrids, and (3) identifying foundational hybrid parents in discrete germplasm pools to provide a reference for tropical indica hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. On average, the hybrids yielded 14.8 % higher than the parents. Results revealed that inter-group hybrids yielded higher, with higher yield heterosis than intra-group hybrids. Four heterotic patterns within two heterotic groups based on current IRRI B- and R-line germplasm were identified. Parents in two marker-based groups were identified with limited breeding value among current IRRI hybrid rice germplasm because of their lowest contribution to heterotic hybrids. Heterotic hybrids are significantly correlated with high-yielding parents. The efficiency of breeding heterotic hybrids could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful for exploiting those widely distributed IRRI hybrid rice parents.