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Summary: Allopolyploid Brassica juncea crops in Brassicaceae are becoming increasingly revitalized as vegetables and oilseeds owing to wide adaptability and significant economic values. However, the genomic differentiation of diversified vegetables and oilseed B. juncea and the genetic basis underlying glucosinolates accumulation have yet to be elucidated. To address this knowledge gap, we report the sequencing of pairwise genomes of vegetable and oilseed B. juncea at chromosome scale. Comparative genomics analysis unveils panoramic structural variation footprints, particularly the genetic loci of HSP20 and TGA1 associated with abiotic and biotic stresses responses between oilseed and vegetable subgroups. We anchored two major loci of MYB28 (HAG1) orthologues caused by copy number variations on A02 and A09 chromosomes using scored genomic SNPs‐based GWAS that are responsible for seed oil quality‐determining glucosinolates biosynthesis. These findings will provide valuable repertories of polyploidy genomic information enabling polyploidy genome evolution studies and precise genomic selections for crucial traits like functional components of glucosinolates in B. juncea crops and beyond. [ABSTRACT FROM AUTHOR]

Abstract Background Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes. Results In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging. Conclusions These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.

Abstract Background Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations. Results By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge. Conclusion This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

The Adriatic sturgeon, Acipenser naccarii (Bonaparte, 1836), is a critically endangered tetraploid endemism of the Adriatic region; it has been targeted, over the last 20 years, by different conservation programs based on controlled reproduction of captive breeders followed by the release of their juvenile offspring; its preservation would greatly benefit from the correct and coordinated management of the residual genetic variability available in the different captive stocks. In this sense, the setup of an efficient parental allocation procedure would allow identifying familiar groups and establishing informed breeding plans, effectively preserving genetic variation. However, being the species tetraploid, the analyses often deal with complex genome architecture and a preliminary evaluation of allele segregation patterns at different chromosomes is necessary to assess whether the species can be considered a pure tetraploid, as previously observed at some loci, or if a more complex situation is present. Here we study the segregation at 14 microsatellites loci in 12 familiar groups. Results support in different families the tetrasomic segregation pattern at 11 markers and the disomic segregation at three markers. The Adriatic sturgeon thus shows a mixed inheritance modality. In this species, and likely in other sturgeons, accurate knowledge of the loci used for paternity analysis is therefore required.

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

Lineage recombination is an important source of genetic and morphological variation in species-rich groups of plants. Tetraploids that are intermediate in morphology and ecology with respect to sympatric diploids are regularly hypothesized to be the products of hybridization. Arctostaphylos mewukka is one such intermediate tetraploid long regarded as the result of hybridization and genome duplication among divergent and geographically overlapping diploids widely distributed across the western slope of the Sierra Nevada. Here we set out to test this hypothesis leveraging the notion that allopolyploids arise repetitively and may show signs of reciprocal organellar exchange among species between maternal and paternal progenitors. We compared nuclear ribosomal and plastid sequence data acquired from samples within and outside this target species complex. Molecular sequence data show striking patterns indicative of widespread reticulation and chloroplast capture events across the genus Arctostaphylos. Results support the notion that outcrossing, long-lived woody plant species such as members of the genus Arctostaphylos can retain a secured morphological identity despite ongoing influence of interspecific gene flow that would otherwise render species boundaries vulnerable to dissolution. [ABSTRACT FROM AUTHOR]

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus , the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages. [ABSTRACT FROM AUTHOR]

Summary: Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine‐scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing.We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally.These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats. [ABSTRACT FROM AUTHOR]

Summary: Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well‐established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing.We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide‐based haplotype‐specific chromosome painting.We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation.We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids. [ABSTRACT FROM AUTHOR]

Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids. [ABSTRACT FROM AUTHOR]

Allopolyploidization usually causes prominent genomic and transcriptional changes, and consequently, promotes the occurrence of phenotypic modifications and/or novelties. The tetraploid Achillea alpina L. species complex in the daisy family has been clearly studied concerning genetic variations and parentage. Population genetic data point to their progenitors as the diploid A. acuminata (Ledeb.) Sch. Bip. and A. asiatica Serg., and show that they have kept two distinct parental genomes relatively intact. Phenotypically, this complex displays a range of leaf form variation between the parental species. To better understand the source of variation at the transcriptional level of the allotetraploid species, we undertook morphological and gene expression analyses with regard to leaf dissection patterns. Morphometrics of leaf traits were carried out on two members of the tetraploid complex, A. alpina and A. wilsoniana Heimerl ex Hand.‐Mazz. and their diploid progenitor species, A. acuminata and A. asiatica. In parallel, the expression patterns of a dozen leaf dissection‐related genes were detected using reverse transcription real‐time quantitative polymerase chain reaction (RT‐qPCR) method. In the allotetraploid species, important leaf dissection‐related genes, such as NAM and PIN, were expressed at the intermediate level between the two diploid species. In general, most of the genes examined in the allotetraploids were expressed at mid‐parent levels or close to one of the parental species. Considering the relative contribution of parental homeologs to the allotetraploids, there is no consistent pattern among the genes analyzed. Overall, lack of transgressive expression of leaf dissection‐related genes could be correlated with the intermediate leaf phenotypes of the allotetraploids A. alpina and A. wilsoniana between their parental species. [ABSTRACT FROM AUTHOR]

Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A-C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors were non-uniformly distributed across the genome in resynthesized B. napus, and in particular homoeologs sharing synteny along their entire length exhibited multivalents at diakinesis and polysomic inheritance at telophase I. Natural B. napus appeared to resolve meiotic errors mainly by suppressing homoeologous pairing, resolving nonhomologous centromere associations and 45S rDNA associations before diakinesis, and reducing homoeologous crossovers [ABSTRACT FROM AUTHOR]

We investigated whether six microsatellite (MS) markers previously developed for two marine crop species, Neopyropia yezoensis and Neopyropia tenera (formerly Pyropia yezoensis and Pyropia tenera, respectively), are useful for molecular analysis of gametophytic blades resulting from a cross between Neopyropia yezoensis and Neopyropia sp. 2, a cryptic species of the N. yezoensis complex. Three (Pye1, Pye13, and Pye38) of the six MS markers could be used to genotype the cryptic species Neopyropia sp. 2. Using these three MS markers, we evaluated whether the F1 gametophytic blades resulting from the cross between N. yezoensis and the cryptic species Neopyropia sp. 2 are allodiploid in the haploid gametophytic phase. The F1 blades that developed from both conchospore and archeospore exhibited heterozygous genotypes at two MS loci (Pye13 and Pye38). The MS marker analyses clearly showed that the F1 blades were allodiploid, strongly supporting the findings of a previous study that was based on a single CAPS marker. In addition, the MS markers employed in this study could serve as useful tools for studies on allopolyploidy in and sympatric speciation of the marine alga Neopyropia.

Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.

Contemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, Cardamine amara and Cardamine rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis -homeolog of C. insueta , but not in C. amara. Moreover, some amara -homeologs of these genes were also upregulated in the triploid, suggesting trans -regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient. [ABSTRACT FROM AUTHOR]

Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America. [ABSTRACT FROM AUTHOR]

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision. [ABSTRACT FROM AUTHOR]

Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs. [ABSTRACT FROM AUTHOR]

Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability. [Display omitted] • Compared the protein expression pattern of G. barbadense and G. hirsutum during their seed germination. • In the initial state, proteins in two cotton involved similar bioprocess. G. hirsutum expressed more superoxide dismutase after germination. • Single-copy orthogroups indicate proteins in G. hirsutum were associated with stress response, and some protein functions only found in G. hirsutum. • Identified 349 putative non-canonical peptides in G. hirsutum by proteogenomic analysis. [ABSTRACT FROM AUTHOR]

We investigated the distribution of allopolyploids of the red algal genus Neopyropia (referred to as nori) in natural populations of eastern Japan and compared the growth characteristics of allopolyploids and ancestral species under laboratory culture. To detect hybrids between Neopyropia yezoensis and Neopyropia tenera , 99 samples collected from 7 localities were examined by sequence analysis of the chloroplast RUBISCO spacer region and DNA marker analyses of two nuclear genes. The results indicated that 20 samples were hybrids derived from interspecific hybridization between the two species. Using 5 conchocelis strains among the hybrids, the blades that developed from both conchospores and archeospores were obtained under laboratory culture and were examined by nuclear DNA marker analyses to confirm allopolyploidy. As a result, the five strains were confirmed as allopolyploids derived from interspecific hybridization between N. yezoensis as the maternal strain and N. tenera as the paternal strain. Furthermore, from two of the five strains, the allopolyploid strains TUYTA-7 and TUYTA-8 were established via self-fertilization of the blade from an archeospore, and the blade growth and photosynthetic pigments of the two strains were compared with those of the strain UM-T55 of the ancestral species N. tenera collected from the same origin site as the two strains. In the allopolyploid strains, the TUYTA-8 blades exhibited superior characteristics, such as a long and linear shape, rapid elongation, low fertility and high pigment content. These results imply the importance of exploring and isolating more allopolyploid strains in bladed Bangiales. Moreover, it is possible that polyploid breeding due to interspecific hybridization in the bladed Bangiales will become more popular as a practical method for developing new cultivars of nori. • Hybrids between N. yezoensis and N. tenera were detected in natural populations of eastern Japan. • Most of the hybrids were inferred to be allopolyploids based on culture experiments and molecular analyses. • One of the allopolyploid strains exhibited superior characteristics, such as rapid blade elongation and low fertility. • Polyploid breeding in the marine crop will become more popular as a practical method to develop the new cultivars. [ABSTRACT FROM AUTHOR]

Intergeneric crosses between Brassica species and Raphanus sativus have produced crops with prominent shoot and root systems of Brassica and R. sativus, respectively. It is necessary to discriminate donor genomes when studying cytogenetic stability in distant crosses to identify homologous chromosome pairing, and microsatellite repeats have been used to discriminate subgenomes in allopolyploids. To identify genome-specific microsatellites, we explored the microsatellite content in three Brassica species (B. rapa, AA, B. oleracea, CC, and B. nigra, BB) and R. sativus (RR) genomes, and validated their genome specificity by fluorescence in situ hybridization. We identified three microsatellites showing A, C, and B/R genome specificity. ACBR_msat14 and ACBR_msat20 were detected in the A and C chromosomes, respectively, and ACBR_msat01 was detected in B and R genomes. However, we did not find a microsatellite that discriminated the B and R genomes. The localization of ACBR_msat20 in the 45S rDNA array in ×Brassicoraphanus 977 corroborated the association of the 45S rDNA array with genome rearrangement. Along with the rDNA and telomeric repeat probes, these microsatellites enabled the easy identification of homologous chromosomes. These data demonstrate the utility of microsatellites as probes in identifying subgenomes within closely related Brassica and Raphanus species for the analysis of genetic stability of new synthetic polyploids of these genomes.

Abstract Background Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry. Results Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry ‘Reiko’ were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F. × ananassa, and the diploid strawberry, F. vesca. The 144 samples were classified into seven pseudo-molecules of F. vesca. The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%. Conclusion We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes.

Genome polyploidy has been revealed to result in evolutionary advantages and novelties, and therefore, polyploid aquatic animals may possess excellent traits of economic interest including rapid growth, extensive adaptability and disease resistance. For this reason, numerous species of natural polyploid fishes, such as common carp, gibel carp, crucian carp, salmon, and sturgeon, were chosen as important target species for aquaculture. Many artificial polyploids have been commercially utilized for aquaculture and most of them were created from natural polyploid fishes of the Cyprinidae and Salmonidae. Thanks to the easy mass production and better economic traits in growth and flesh quality, the synthetized autopolyploids or allopolyploids from natural polyploid species in cyprinid fishes have been extensively applied to aquaculture throughout China. This review outlines polyploidy advantages and innovative opportunities, lists natural polyploid species used in aquaculture, and summarizes artificial polyploids that have been induced or synthetized, and used in aquaculture. Moreover, some main research trends on polyploid utilization and ploidy manipulation of aquaculture animals are also introduced and discussed in the review.

Allopolyploid organisms can be formed by hybridization between closely related plant species with similar genomes. It is believed that many plant species have passed through allopolyploidization, which played a significant role in the formation of a huge diversity of plants, as well as their high adaptive capacity. Thanks to the whole genome sequencing of a wide range of angiosperm species and comparative analysis of genome structure, the sequence of events that formed the genomes of modern plant taxa was restored. These studies have shown that many diploid species have passed through more than one cycle of polyploidization-diploidization. The purpose of this review is to summarize the estimates of what proportion of genes is undergoing changes due to allopoly-ploidization and to illustrate the variety of mechanisms underlying the functional divergence of homoeologous copies (orthologous genes in allopolyploid subgenomes). Changes of individual copies can be associated with epigenetic features of the gene organization (the methylation status of the promoter region or the presence of copy-specific small interfering RNA) or can affect structure of the coding or regulatory regions of the gene. Studies on artificial allopolyploid plants showed widespread transcriptional dominance and change of the transcription level as compared with the genes of diploid parental forms. The study of the transcription of certain homoeologous gene copies allowed estimating the extent of the complete suppression of certain homoeologous genes in newly synthesized (0.4–5.0 %) and natural (30 %) allopolyploids. One the whole, full or partial suppression affects up to 49% of the wheat genes.

Establishing the whole set of aneuploids, for one naturally evolved allopolyploid species, provides a unique opportunity to elucidate the transcriptomic response of the constituent subgenomes to serial aneuploidy. Previously, the whole set of monosomic alien addition lines (MAALs, C1-C9) with each of the nine C subgenome chromosomes, added to the extracted A subgenome, was developed in the context of the allotetraploid Brassica napus donor “Oro,” after the restitution of the ancestral B. rapa (RBR Oro) was realized. Herein, transcriptomic analysis using high-throughput technology was conducted to detect gene expression alterations in these MAALs and RBR. Compared to diploid RBR, the genes of all of the MAALs showed various degrees of dysregulated expressions that resulted from cis effects and more prevailing trans effects. In addition, the trans-effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes, instead of gene numbers of extra chromosomes. A total of 10 trans-effect dysregulated genes, among all pairwise comparisons, were mainly involved in the function of transporter activity. Furthermore, highly expressed genes were more prone to downregulation and vice-versa, suggesting a common trend for transcriptional pattern responses to aneuploidy. These results provided a comprehensive insight of the impact of gene expression of individual chromosomes, in one subgenome, on another intact subgenome for one allopolyploid with a long evolutionary history.

Polyploidy is a major factor in the evolution of plants, yet we know little about the origin and evolution of polyploidy in intertidal species. This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus Acanthus distributed in the Indo-West Pacific region. For this purpose, we took an integrative approach that combined data on morphology, cytology, climatic niche, phylogeny, and biogeography of 493 samples from 42 geographic sites. Our results show that the Acanthus ilicifolius lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype, which is morphologically distinct from that of the lineage on the west side. The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes, one each from A. ilicifolius and A . ebracteatus , the paternal and maternal parents, respectively. Population structure analysis also supports the hybrid speciation history of the new tetraploid species. The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene. Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids, but also expanded into novel environments. Our findings suggest that A. ilicifolius species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species, A . tetraploideus , followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species.A. ilicifolius and A. ebracteatus , followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species., Competing Interests: The authors have no conflict of interest., (© 2024 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.)

Since the 1970s, an apomictic tetraploid beech fern (genus Phegopteris (C. Presl) Fée) has been known in northeastern North America. Previously published isozyme data suggest that this lineage is of allopolyploid origin involving long beech fern (P. connectilis (Michx.) Watt.) but not broad beech fern (P. hexagonoptera (Michx.) Fée), as originally hypothesized. Its second progenitor remains unknown. We performed a principal components analysis of the apomict and its North American congeners to elucidate morphological differences between them. We recognize the apomictic tetraploid at specific rank as P. excelsior N. R. Patel & A. V. Gilman and provide an illustration, a range map, a list of exsiccatae, and a key to Phegopteris species of North America. [ABSTRACT FROM AUTHOR]

Summary: Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large‐scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double‐low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double‐low and double‐high), accompanied by an increase in genetic load in the double‐low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra‐ and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop. [ABSTRACT FROM AUTHOR]

Reticulate evolution, in which phylogenetic relationships are not strictly bifurcating (tree-like), is a common feature of fern evolution. Ferns are prone to hybridization and whole genome duplication, two processes that can make untangling phylogenetic relationships among species challenging. Next-generation sequencing technologies have greatly increased the amount of data available for analyzing various aspects of evolutionary history, and here we test the ability of one next-generation sequencing approach to identify the progenitors of allopolyploids. We produced and analyzed double-digest restriction-site-associated DNA (ddRAD) sequences from six species of North American Dryopteris, including two allopolyploids and their respective diploid parents. The relationships of these species have been confidently established in previous studies, and our goal was to determine the extent to which RAD data are capable of identifying these known relationships. Analyses of the genetic structure in our samples reliably separated the diploids from one other, but in general each polyploid sample resembled one or the other of its progenitors, or had genetic variation unassignable to either parent. None of the polyploid samples had unambiguous genetic contributions from both known parents, as we had expected. These results may have been influenced by small overall sample size, different numbers of samples from the two diploid parents in each pair, and the large divergence times between the diploids. These are all potentially important issues to consider when designing similar studies, and our results therefore have useful implications for researchers interested in using a RAD approach to study polyploid complexes. [ABSTRACT FROM AUTHOR]

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ∼21 nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives. [ABSTRACT FROM AUTHOR]

Establishing the whole set of aneuploids, for one naturally evolved allopolyploid species, provides a unique opportunity to elucidate the transcriptomic response of the constituent subgenomes to serial aneuploidy. Previously, the whole set of monosomic alien addition lines (MAALs, C1-C9) with each of the nine C subgenome chromosomes, added to the extracted A subgenome, was developed in the context of the allotetraploid Brassica napus donor "Oro," after the restitution of the ancestral B. rapa (RBR Oro) was realized. Herein, transcriptomic analysis using high-throughput technology was conducted to detect gene expression alterations in these MAALs and RBR. Compared to diploid RBR, the genes of all of the MAALs showed various degrees of dysregulated expressions that resulted from cis effects and more prevailing trans effects. In addition, the trans -effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes, instead of gene numbers of extra chromosomes. A total of 10 trans -effect dysregulated genes, among all pairwise comparisons, were mainly involved in the function of transporter activity. Furthermore, highly expressed genes were more prone to downregulation and vice-versa, suggesting a common trend for transcriptional pattern responses to aneuploidy. These results provided a comprehensive insight of the impact of gene expression of individual chromosomes, in one subgenome, on another intact subgenome for one allopolyploid with a long evolutionary history. [ABSTRACT FROM AUTHOR]

How polyploids become established is a long-debated question, especially for autopolyploids that seem to have no evolutionary advantage over their progenitors. The Centaurea aspera polyploid complex includes diploid C. aspera and two related tetraploids C. seridis and C. gentilii. Our purpose was to study the mating system among these three taxa and to analyze its influence on polyploid establishment. The distribution and ploidy level of the Moroccan populations, and forced intra- and inter-specific crosses were assessed. Allotetraploid C. seridis produced more cypselae per capitulum in the intra-specific crosses. It is a bigger plant and autogamous, and previous studies indicated that selfing forces the asymmetric formation of sterile hybrids. All these characteristics help C. seridis to avoid the minority-cytotype-exclusion effect and become established. Inter-specific hybridization was possible between C. aspera and C. gentilii, and with the symmetric formation of hybrids. However, 49% of the hybrid cypselae were empty, which probably reveals postzygotic barriers. Autotetraploid C. gentilii produced the same number of cypselae per capitulum as those of the diploid parental, has an indistinguishable field phenotype, is allogamous, and symmetrically produces hybrids. Therefore, C. gentilii does not seem to have the same competitive advantages as those of C. seridis.

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.

Allopolyploidization often leads to disruptive conflicts among more than two sets of subgenomes, leading to genomic modifications and changes in gene expression. Although the evolutionary trajectories of subgenomes in allopolyploids have been studied intensely in angiosperms, the dynamics of subgenome evolution remain poorly understood in ferns, despite the prevalence of allopolyploidization. In this study, we have focused on an allotetraploid fern- Phegopteris decursivepinnata -and its diploid parental species, P. koreana ( K ) and P. taiwaniana ( T ). Using RNA-seq analyses, we have compared the gene expression profiles for 9,540 genes among parental species, synthetic F 1 hybrids, and natural allotetraploids. The changes in gene expression patterns were traced from the F 1 hybrids to the natural allopolyploids. This study has revealed that the expression patterns observed in most genes in the F 1 hybrids are largely conserved in the allopolyploids; however, there were substantial differences in certain genes between these groups. In the allopolyploids compared with the F 1 hybrids, the number of genes showing a transgressive pattern in total expression levels was increased. There was a slight reduction in T -dominance and a slight increase in K -dominance, in terms of expression level dominance. Interestingly, there is no obvious bias toward the T - or K -subgenomes in the number and expression levels overall, showing the absence of subgenome dominance. These findings demonstrated the impacts of the substantial transcriptome change after hybridization and the moderate modification during allopolyploid establishment on gene expression in ferns and provided important insights into subgenome evolution in polyploid ferns., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Katayama, Yamamoto, Aiuchi, Watano and Fujiwara.)

Premise of the Study: The traditional approach used in analyses of population genetic data for historical inference is to average across multiple marker loci, but averaging conflates the different evolutionary signals provided by stable vs. labile markers. Methods: We used a battery of microsatellites with a wide range of mutation/substitution rates, grouping them into two sets (stable and hypervariable) to provide a more nuanced reconstruction of the population genetics and evolutionary history of the allotriploid peat moss Sphagnum × falcatulum across three disjunct regions. Key Results: Shannon diversity translation analyses show that the relative apportionment of total within‐species allelic diversity (∆WS) within and among strata ranges widely, both between the two sets and within and among regions. The majority of diversity in the stable set was inherited directly from the ancestors of this genetically complex allopolyploid, but most of the diversity in the hypervariable set has developed post‐hybrid‐origin. Conclusions: It is useful to group markers into sets having similar evolutionary lability, with each set being analyzed separately, particularly for allopolyploids. A methodology for determining how to group markers into such sets is presented, which can be applied to the requirements of other studies. Within‐individual allelic diversity (ΔWI) should be addressed in genetic studies on allopolyploids. Allotriploid haplotypes based on a set of nine highly stable microsatellites appear to serve as a clonal‐detection set for S. × falcatulum. An additive "allele‐metric" diversity approach is introduced, which facilitates a direct comparison of within‐ and among‐stratum diversity components at all levels of diversity. [ABSTRACT FROM AUTHOR]

Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood. We describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogon mirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome. [ABSTRACT FROM AUTHOR]

Summary: Common wheat is an allohexaploid (BBAADD) that originated from the hybridization and polyploidization of the diploid Aegilops tauschii (DD) with the allotetraploid Triticum turgidum (BBAA). Phenotypic changes often arise with the formation and evolution of allopolyploid wheat, but little is known about the evolution of root traits in different wheat species with varying ploidy levels. Here, we reported that the lateral root number on the primary root (LRNPR) of synthetic and natural allohexaploid wheats (BBAADD) is significantly higher than that of their allotetraploid (BBAA) and diploid (AA and SS) progenitors, but is much lower than that of their diploid (DD) progenitors. The expression of the wheat gene TaLBD16, an ortholog of the Arabidopsis LATERAL ORGAN BOUNDARIES‐DOMAIN16/ASYMMETRIC LEAVES2‐LIKE18 (LBD16), which is involved in lateral root development in Arabidopsis, was positively correlated with the LRNPR in diploid and allopolyploid wheats. In natural and synthetic allohexaploid wheats, the transcript of the TaLBD16 from the D genome (TaLBD16‐D) was relatively more abundant compared with TaLBD16‐A and TaLBD16‐B. Consistent with the observed variation in LRNPR, the divergence in the expression of TaLBD16 homoeologous genes occurred before the formation of polyploidy wheat. Collectively, our observations indicate that the D genome played a crucial role in the increased lateral root number of allohexaploid wheats compared with their allotetraploid progenitors, and that TaLBD16‐D was one of the key genes involved in the formation of lateral root number during wheat evolution. [ABSTRACT FROM AUTHOR]

Summary: Cotton cultivars have evolved to produce extensive, long, seed‐born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix‐loop‐helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A‐homoeologous biased in allotetraploid cultivars. Transgenic studies demonstrated that PRE1 is a positive regulator of fiber elongation. We determined that the natural variation of the canonical TATA‐box, a regulatory element commonly found in many eukaryotic core promoters, is necessary for subgenome‐biased PRE1 expression, representing a mechanism underlying the selection of homoeologous genes. Thus, variations in the promoter of the cell elongation regulator gene PRE1 have contributed to spinnable fiber formation in cotton. Overexpression of GhPRE1 in transgenic cotton yields longer fibers with improved quality parameters, indicating that this bHLH gene is useful for improving cotton fiber quality. [ABSTRACT FROM AUTHOR]

Premise of the Study: Recurrent formation of polyploid taxa is a common observation in many plant groups. Haploid, cytoplasmic genomes like the plastid genome can be used to overcome the problem of homeologous genes and recombination in polyploid taxa. Fragaria (Rosaceae) contains several octo‐ and decaploid species. We use plastome sequences to infer the plastid ancestry of these taxa with special focus on the decaploid Fragaria cascadensis. Methods: We used genome skimming of 96 polyploid Fragaria samples on a single Illumina HiSeq 3000 lane to obtain whole plastome sequences. These sequences were used for phylogenetic reconstructions and dating analyses. Ploidy of all samples was inferred with flow cytometry, and plastid inheritance was examined in a controlled cross of F. cascadensis. Key Results: The plastid genome phylogeny shows that only the octoploid F. chiloensis is monophyletic, all other polyploid taxa were supported to be para‐ or polyphyletic. The decaploid Fragaria cascadensis has biparental plastid inheritance and four different plastid donors. Diversification of the F. cascadensis clades occurred in the last 230,000 years. The southern part of its distribution range harbors considerably higher genetic diversity, suggestive of a potential refugium. Conclusions: Fragaria cascadensis had at least four independent origins from parents with different plastomes. In contrast, para‐ and polyphyletic taxa of the octoploid Fragaria species are best explained by incomplete lineage sorting and/or hybridization. Biogeographic patterns in F. cascadensis are probably a result of range shift during the last glacial maximum. [ABSTRACT FROM AUTHOR]

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive. [ABSTRACT FROM AUTHOR]

Polyploidy is one of the most important events in plant evolution: the evidence suggests that more than 70% of the angiosperms underwent some event of genomic duplication during their diversification. In potato, the third more important crop worldwide, the effects of autopolyploidization at morphological, physiological and molecular levels have been explored and no evident phenotypic superiority of polyploid lines respect to the parental diploid lines has been found. On the other hand, the consequences of allopolyploidization have not been analysed so far in potato from a molecular point of view. In this work we study the variability induced by whole genome duplication in potato auto and allotetraploids obtained by chromosomal duplication of a S. kurtzianum genotype (autopolyploid model) and by chromosomal duplication of a diploid interspecific hybrid between S. tuberosum and S. kurtzianum (allopolyploid model). Polyploid lines in both models showed a tendency to increase the vigor in phenotypic characters compared with diploid parent they derived from. AFLP analysis showed no polymorphism between parental diploid and derived polyploids lines. However, there were DNA methylation changes between diploids and polyploids, indicating that polyploidization alters the epigenetic patterns in potato. It is possible that the superiority of the tetraploid can be explained as a heterotic response dependent on the presence of heterozygous loci and epistatic interactions inducing alterations in the gene regulation of the polyploid genomes. [ABSTRACT FROM AUTHOR]

Polyploidization has played an important role in the speciation and diversification of plant species. However, genetic analyses of polyploids are challenging because the vast majority of the model species are diploids. The allotetraploid Arabidopsiskamchatica, which originated through the hybridization of the diploid Arabidopsis halleri and Arabidopsis lyrata, is an emerging model system for studying various aspects of polyploidy. However, a transgenic method that allows the insertion of a gene of interest into A. kamchatica is still lacking. In this study, we investigated the early development of pistils in A. kamchatica and confirmed the formation of open pistils in young flower buds (stages 8–9), which is important for allowing Agrobacterium to access female reproductive tissues. We established a simple Agrobacterium-mediated floral dip transformation method to transform a gene of interest into A. kamchatica by dipping A. kamchatica inflorescences bearing many young flower buds into a 5% sucrose solution containing 0.05% Silwet L-77 and Agrobacterium harboring the gene of interest. We showed that a screenable marker comprising fluorescence-accumulating seed technology with green fluorescent protein was useful for screening the transgenic seeds of two accessions of A. kamchatica subsp. kamchatica and an accession of A. kamchatica subsp. kawasakiana. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Oil Crop Sciences is the property of Oil Crops Research Institute of Chinese Academy of Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Chinese Journal of Oil Crop Sciences is the property of Oil Crops Research Institute of Chinese Academy of Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared with its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormone (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines. We also found evidence for decreased expression divergence of the homoeologous gene pairs in the allopolyploid F1 hybrids and suggest that high-parental expression-level dominance plays an important role in heterosis. Small RNA and methylation studies aimed at examining the epigenetic effect of the changes in gene expression level in the F1 hybrids showed that the majority of the small interfering RNA (si RNA) clusters had a higher expression level in the F1 hybrids than in the parents, and that there was an increase in genome-wide DNA methylation in the F1 hybrid. Transposable elements associated with si RNA clusters had a higher level of methylation and a lower expression level in the F1 hybrid, implying that the non-additively expressed si RNA clusters resulted in lower activity of the transposable elements through DNA methylation in the hybrid. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms contribute to heterosis during early flower development in allopolyploid B. napus. [ABSTRACT FROM AUTHOR]