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Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria × ananassa) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested-broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1 DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.

This research aimed to determine the mitotic abnormalities, changes in the number of chromosomes, mitotic index, and the number and length of kepok abu banana plantlet roots due to administration of 0.1% colchicine in tissue culture media. This research was performed at the Botanical Laboratory of the Biology Department, Faculty of Mathematics and Natural Sciences, UNILA. This research compared the cytology by employing the Squash method between root tip cells of kepok abu banana plantlets after administering 0.1% colchicine and the control group. The researchers analyzed the data descriptively and presented them in tables and bar charts. The results showed that the administration of 0.1% colchicine resulted in mitotic abnormalities. It also increased the number of chromosomes in the controls 2n=3x and 2n=3x+4. The mitotic index decreased, and the average number of roots was lower. However, the size was longer compared to the control group.

Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na+/H+ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops.

Background: Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. Results: We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. Conclusions: Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution. [ABSTRACT FROM AUTHOR]

Crossbreeding within narrow genetic resources increases the homozygosity of the offspring. Resultant inbreeding depression can reduce the yield potential of the offspring. Slow progress in breeding programs because of inbreeding has been suggested in persimmon (Diospyros kaki Thunb.), but quantitative evidence has been limited. Here we assessed how inbreeding affects a population's yield-related traits by using sequence-based genotyping. To find a reliable inbreeding estimation method that considers persimmon's hexaploidy, we screened nine marker-based inbreeding estimators (FM) and various read-depth thresholds for genotype calling; the results suggested that the Loiselle–Huang (LH) FM and a read-depth threshold of 10 were optimal. After validating 11,379 variant sites selected under the optimal read-depth threshold, we calculated the LH FM of 97 breeding populations by using the dosage genotypes of 47 cross parents. In these populations, LH FM successfully identified the less inbred populations and confirmed that the inbreeding level was significantly reduced by a pseudo-backcross strategy designed to widen the genetic diversity of the breeding population. In regression analyses using mean phenotypic value and LH FM of the 97 populations as response and explanatory variables, respectively, we detected significant reductions of fruit weight, yield, and tree vigor at the first fruit-bearing age, and delay of the first fruit-bearing age itself as inbreeding progressed; the other eight FM showed similar trends. These results indicate that inbreeding depression occurs in yield-related traits in persimmon and that employing FM would help breeders increase the chance of developing less inbred cultivars with higher yield potential. [ABSTRACT FROM AUTHOR]

Polyploidization is one of the important driving forces of speciation and crop domestication. Polyploidization is widely employed in the research and application of crops because it can greatly enrich the diversity in a very short period of time. Crop improvement using polyploidization has been successful in watermelon, cucumber, melon and other important Cucurbitaceae crops. Recent studies have shown that polyploids often have distinct environmental fitness advantages. With the increasingly serious of climate problems nowadays, improving the environmental adaptability of Cucurbitaceae crops via polyploidy has become one of the essential contents of Cucurbitaceae crop breeding. According to the genome composition, polyploids are divided into autopolyploids and allopolyploids. Most of the previous studies on Cucurbitaceae crops only focused on autopolyploid, and the understanding and research on allopolyploid were obviously lacking, which needed further development and utilization. Meanwhile, along with the advancement of genome sequencing technology and the rapid development of various omics and molecular biology technologies, many important progresses have been made in plant polyploidy research, which provides unprecedented opportunity for research on polyploidy-related mechanisms in Cucurbitaceae crops. This paper systematically reviewed the recent research and application on polyploidy in Cucurbitaceae crops, aiming to explore the development and future of polyploidy in the breeding of Cucurbitaceae crops, and providing a reference for the genetic breeding of cucurbit and other crops. [ABSTRACT FROM AUTHOR]

Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei vary tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in their life cycle), the germline micronucleus is transcriptionally inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively fragmented gene‐sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes. [ABSTRACT FROM AUTHOR]

Premise: The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species or by range shifts during climate oscillations. However, few studies have considered both of these factors simultaneously. We resolved the origin of a tetraploid fern, Lepisorus yamaokae, and explored a pattern of niche differentiation among the allotetraploid and parental species in past and current climates. Methods: We reconstructed phylogenetic trees based on plastid marker and single‐copy nuclear genes to resolve the allopolyploid origin of L. yamaokae. We also evaluated climatic niche differentiation among L. yamaokae and its two parental species using species distribution models in geographic space and principal component analysis. Results: We infer that L. yamaokae had a single allotetraploid origin from L. annuifrons and L. uchiyamae. Climatic niche analyses show that the parental species currently occupy different niche spaces. The predicted distribution of the parental species at the Last Glacial Maximum (LGM) suggests more opportunities for hybridization during the LGM or during other recent temporary range shifts. Lepisorus yamaokae has a narrower niche than the additive niche of the parental species. We also observed niche conservatism in L. yamaokae. Conclusions: Range shifts of the parental species during climatic oscillations in the Quaternary likely facilitated the formation and establishment of L. yamaokae. Further, the genetic intermediacy of L. yamaokae may have enabled a niche shift in its microenvironment, resulting in its successful establishment without a macroclimatic niche shift in L. yamaokae. [ABSTRACT FROM AUTHOR]

SUMMARY: Polyploidy is a major force shaping eukaryote evolution but poses challenges for meiotic chromosome segregation. As a result, first‐generation polyploids often suffer from more meiotic errors and lower fertility than established wild polyploid populations. How established polyploids adapt their meiotic behaviour to ensure genome stability and accurate chromosome segregation remains an active research question. We present here a cytological description of meiosis in the model allopolyploid species Arabidopsis suecica (2n = 4x = 26). In large part meiosis in A. suecica is diploid‐like, with normal synaptic progression and no evidence of synaptic partner exchanges. Some abnormalities were seen at low frequency, including univalents at metaphase I, anaphase bridges and aneuploidy at metaphase II; however, we saw no evidence of crossover formation occurring between non‐homologous chromosomes. The crossover number in A. suecica is similar to the combined number reported from its diploid parents Arabidopsis thaliana (2n = 2x = 10) and Arabidopsis arenosa (2n = 2x = 16), with an average of approximately 1.75 crossovers per chromosome pair. This contrasts with naturally evolved autotetraploid A. arenosa, where accurate chromosome segregation is achieved by restricting crossovers to approximately 1 per chromosome pair. Although an autotetraploid donor is hypothesized to have contributed the A. arenosa subgenome to A. suecica, A. suecica harbours diploid A. arenosa variants of key meiotic genes. These multiple lines of evidence suggest that meiosis in the recently evolved allopolyploid A. suecica is essentially diploid like, with meiotic adaptation following a very different trajectory to that described for autotetraploid A. arenosa. Significance Statement: In this manuscript we describe meiosis in the allopolyploid model species Arabidopsis suecica, showing that meiosis, and the genes controlling it, are essentially diploid‐like. Meiotic adaptation in allopolyploid A. suecica therefore follows a very different route to that previously described for autotetraploid A. arenosa. [ABSTRACT FROM AUTHOR]

When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it. [ABSTRACT FROM AUTHOR]

Golden 2-Like (GLK) transcription factors play a crucial role in chloroplast development and chlorophyll synthesis in many plant taxa. To date, no systematic analysis of GLK transcription factors in tree species has been conducted. In this study, 40 EgrGLK genes in the Eucalyptus grandis genome were identified and divided into seven groups based on the gene structure and motif composition. The EgrGLK genes were mapped to 11 chromosomes and the distribution of genes on chromosome was uneven. Phylogenetic analysis of GLK proteins between E. grandis and other species provided information for the high evolutionary conservation of GLK genes among different species. Prediction of cis-regulatory elements indicated that the EgrGLK genes were involved in development, light response, and hormone response. Based on the finding that the content of chlorophyll in mature leaves was the highest, and leaf chlorophyll content of triploid Eucalyptus urophylla was higher than that of the diploid control, EgrGLK expression pattern in leaves of triploid and diploid E. urophylla was examined by means of transcriptome analysis. Differential expression of EgrGLK genes in leaves of E. urophylla of different ploidies was consistent with the trend in chlorophyll content. To further explore the relationship between EgrGLK expression and chlorophyll synthesis, coexpression networks were generated, which indicated that EgrGLK genes may have a positive regulatory relationship with chlorophyll synthesis. In addition, three EgrGLK genes that may play an important role in chlorophyll synthesis were identified in the co-expression networks. And the prediction of miRNAs targeting EgrGLK genes showed that miRNAs might play an important role in the regulation of EgrGLK gene expression. This research provides valuable information for further functional characterization of GLK genes in Eucalyptus. [ABSTRACT FROM AUTHOR]

Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs. This redundancy is more extensive in recently formed polyploids such as wheat, which can now benefit from the deployment of useful recessive mutations previously identified in its diploid relatives. Sequenced mutant populations and genome editing have changed the paradigm of what is possible in functional genetic analysis of wheat.

Abstract Background Ploidy manipulation is effective in seedless loquat breeding, in which flesh color is a key agronomic and economic trait. Few techniques are currently available for detecting the genotypes of polyploids in plants, but this ability is essential for most genetic research and molecular breeding. Results We developed a system for genotyping by quantitative PCR (qPCR) that allowed flesh color genotyping in multiple tetraploid and triploid loquat varieties (lines). The analysis of 13 different ratios of DNA mixtures between two homozygous diploids (AA and aa) showed that the proportion of allele A has a high correlation (R2 = 0.9992) with parameter b [b = a1/(a1 + a2)], which is derived from the two normalized allele signals (a1 and a2) provided by qPCR. Cluster analysis and variance analysis from simulating triploid and tetraploid hybrids provided completely correct allelic configurations. Four genotypes (AAA, AAa, Aaa, aaa) were found in triploid loquats, and four (AAAA, AAAa, AAaa, Aaaa; absence of aaaa homozygotes) were found in tetraploid loquats. DNA markers analysis showed that the segregation of flesh color in all F1 hybrids conformed to Mendel's law. When tetraploid B431 was the female parent, more white-fleshed triploids occurred among the progeny. Conclusions qPCR can detect the flesh color genotypes of loquat polyploids and provides an alternative method for analyzing polyploid genotype and breeding, dose effects and allele-specific expression.

This study was conducted with the aim of gaining the outcomes of polyploidy induction by soaking black sesame seeds, Sesamum indicum Linn, in 0.0%, 0.1%, 0.2%, 0.3% and 0.4% colchicine for 24 hours. When checking the characteristics of polyploidy using the fifteen days old seedlings’ abnormalities as indicators. The abnormal seedlings grew very slowly. The stems were short containing only cotyledon leaves and the first pair of unifoliate leaves. Their hypocotyls were swollen, fat and short while epicotyls did not extended but stunted. However, these hypocotyls could be extended or grew longer but they would take more time. The examination revealed that the sesame seedlings which were not treated by using colchicine could grow normally. In contrast, those, which were treated by using colchicine, yielded abnormal seedlings. The higher percentage of the concentrations of colchicine, the more abnormal seedlings were obtained as the following.

Polyploid plants, an important source for the selection of ornamental plants for their advantages of faster growth, higher yields, and stronger adaptability to an adverse environment, play an essential role in the development of economic plants for agricultural stress. The methodology has been improved to decrease blindness and increase the efficiency of ornamental plants’ polyploid breeding in the long term. The progress of research on ornamental plants related to natural polyploidy, chromosome doubling, the 2n gametes pathway, and plant ploidy identification are reviewed in this paper. The main routes in polyploid breeding are chromosome doubling and sexual hybridization. Screening of suitable induction methods and plant material should be enhanced in chromosome doubling to improve induction efficiency. Regarding polyploid breeding, the utilization and research on 2n gametes produced by natural conditions or artificial induction should be strengthened to shorten the breeding years. Therefore, further research should strengthen the combination of chromosome doubling and sexual hybridization to improve breeding efficiency and strengthen the research and application of polyploid plants. This thesis review provides some reference value for polyploid breeding in ornamental plants.

Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.

Polyploidy plays a crucial role in plant evolution and speciation. The development of male and female gametes is essential to the reproductive capacity of polyploids, but their gene expression pattern has not been fully explored in newly established polyploids. The present study aimed to reveal a detailed atlas of gene expression for gamete development in newly synthetic Brassica allohexaploids that are not naturally existing species. Comparative transcriptome profiling between developing anthers (staged from meiosis to mature pollen) and ovules (staged from meiosis to mature embryo sac) was performed using RNA-Seq analysis. A total of 8676, 9775 and 4553 upregulated differentially expressed genes (DEGs) were identified for the development of both gametes, for male-only, and for female-only gamete development, respectively, in the synthetic Brassica allohexaploids. By combining gene ontology (GO) biological process analysis and data from the published literature, we identified 37 candidate genes for DNA double-strand break formation, synapsis and the crossover of homologous recombination during male and female meiosis and 51 candidate genes for tapetum development, sporopollenin biosynthesis and pollen wall development in male gamete development. Furthermore, 23 candidate genes for mitotic progression, nuclear positioning and cell specification and development were enriched in female gamete development. This study lays a good foundation for revealing the molecular regulation of genes related to male and female gamete development in Brassica allohexaploids and provides more resourceful genetic information on the reproductive biology of Brassica polyploid breeding. [ABSTRACT FROM AUTHOR]

Tumor heterogeneity plays a key role in cancer relapse and metastasis, however, the distinct cellular behaviors and kinetics of interactions among different cancer cell subclones and the tumor microenvironment are poorly understood. By profiling an isogenic model that resembles spontaneous human ovarian cancer metastasis with an highly metastatic (HM) and non‐metastatic (NM) tumor cell pair, one finds an upregulation of Wnt/β‐catenin signaling uniquely in HM. Using humanized immunocompetent mice, one shows for the first time that activated β‐catenin acts nonautonomously to modulate the immune microenvironment by enhancing infiltrating tumor‐associated macrophages (TAM) at the metastatic site. Single‐cell time‐lapse microscopy further reveals that upon contact with macrophages, a significant subset of HM, but not NM, becomes polyploid, a phenotype pivotal for tumor aggressiveness and therapy resistance. Moreover, HM, but not NM, polarizes macrophages to a TAM phenotype. Mechanistically, β‐catenin upregulates cancer cell surface metadherin, which communicates through CEACAM1 expressed on macrophages to produce CCL3. Tumor xenografts in humanized mice and clinical patient samples both corroborate the relevance of enhanced metastasis, TAM activation, and polyploidy in vivo. The results thus suggest that targeting the β‐catenin‐metadherin/CEACAM1‐CCL3 positive feedback cascade holds great therapeutic potential to disrupt polyploidization of the cancer subclones that drive metastasis. [ABSTRACT FROM AUTHOR]

Cell division is a necessity of life which can be either mitotic or amitotic. While both are fundamental, amitosis is sometimes considered a relic of little importance in biology. Nevertheless, eukaryotes often have polyploid cells, including cancer cells, which may divide amitotically. To understand how amitosis ensures the completion of cell division, we turn to the macronuclei of ciliates. The grand scheme governing the proliferation of the macronuclei of ciliate cells, which involves chromosomal replication and amitosis, is currently unknown, which is crucial for developing population genetics model of ciliate populations. Using a novel model that encompasses a wide range of mechanisms together with experimental data of the composition of mating types at different stages derived from a single karyonide of Tetrahymena thermophila , we show that the chromosomal replication of the macronucleus has a strong head-start effect, with only about five copies of chromosomes replicated at a time and persistent reuse of the chromosomes involved in the early replication. Furthermore the fission of a fully grown macronucleus is non-random with regard to chromosome composition, with a strong tendency to push chromosomes and their replications to the same daughter cell. [ABSTRACT FROM AUTHOR]

The seasonal production of Allium cepa var. ascalonicum causes a rise in its demand during the offseason. Consumers mostly prefer onion cultivars like the 'Super Philip', because of their high productivity, large and round bulbs, shiny appearance, and less spicy taste. In plant breeding, polyploidy induction through mutagens is a technique often used to produce shallot cultivars of better quality. Bio-Catharantin from the leaf extract of Catharanthus roseus L. is used as a polyploid induction agent instead of colchicine. The latest study aimed to determine the effect of Bio-Catharantin concentration (0.2% and 0.4%) on phenotypic traits (plant height, bulb mass, and the number of bulbs), and the chromosome number to determine the minimum concentration that could cause polyploidization in shallots. The research was conducted from December 2020 to February 2021 in a greenhouse in Madurejo, Prambanan, and the Laboratory of Genetics and Breeding, Faculty of Biology, Gadjah Mada University, Indonesia. Bio-Catharantin concentration did not affect plant height which was comparable with the control. Both treatments caused an increase in bulb mass up to 37.7 and 41.76 g at the concentrations of 0.2% and 0.4%, respectively, compared with the control (31.47 g). The number of bulbs increased up to 10.6 and 9.8 g for 0.2% and 0.4% concentrations, respectively, compared with 8.8 in the control. The ploidy level of cells was increased from 2n (16) to 3n (24) at 2% and 4n (32) at 4% Bio-Catharantin. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) technology is used to obtain homozygous lines in a single generation, a technique that significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but this technique is limited by species and genotype recalcitrance. In vivo haploid induction (HI) through seed is widely and efficiently used in maize and was recently extended to several other crops. Here we show that in vivo HI can be triggered by mutation of DMP maternal haploid inducer genes in allopolyploid (allotetraploid) Brassica napus and Nicotiana tabacum. We developed a pipeline for selection of DMP orthologs for clustered regularly interspaced palindromic repeats mutagenesis and demonstrated average amphihaploid induction rates of 2.4% and 1.2% in multiple B. napus and N. tabacum genotypes, respectively. These results further confirmed the HI ability of DMP gene in polyploid dicot crops. The DMP‐HI system offers a novel DH technology to facilitate breeding in these crops. The success of this approach and the conservation of DMP genes in dicots suggest the broad applicability of this technique in other dicot crops. [ABSTRACT FROM AUTHOR]

Buddleja lindleyana Fort. is a garden ornamental plant with great potential for development and also a commonly used medicinal plant. To enrich its germplasm resources, the seeds of B. lindleyana were treated with colchicine solution with concentration gradients of 0.5%, 1.0%, 1.5%, 2.0% and 3.0% for 12-, 24- and 48-h respectively, and the water treatment was set as the control group. The purpose was to explore the effects of colchicine on the germination and mutagenic effect of B. lindleyana seeds at different concentrations and different times, to screen the appropriate combination of mutagenic concentration and time, to provide guidance for the construction of B. lindleyana mutation population in future research. The results were as follows: (1) Colchicine had an inhibitory effect on seed germination and seedling height of B. lindleyana seeds, and the higher the concentration, the more obvious the inhibitory effect. (2) After colchicine treatment, 30 mutant plants showed morphological variations such as leaf malformation, leaf color macular, early leaf bud germination, uneven leaf surface and leaf hyperplasia, among which 3.0% + 48-h treatment group had great potential to produce yellow-leaf plants. (3) Detection and analysis by flow cytometry revealed that among the 30 morphologically variant plants, there were 22 diploid plants, 3 tetraploid plants, and 5 chimera plants. Among them, tetraploids were mainly from colchicine concentration of 3.0% (2 plants) and 1.5% (1 plant), chimeras were mainly from colchicine concentration of 1.0% (2 plants), 1.5% (1 plant) and 3.0% (2 plants), and the seed soaking time was 48-h. (4) The length and width of guard cells and stomata were significantly different between diploid and tetraploid, and there were significant differences in leaf width and leaf shape index between tetraploid and diploid, but there were no significant differences in leaf length among diploid, tetraploid and chimera. In short, we got tetraploids and chimeras materials which were potentially useful cultivars of B. lindleyana and provided an effective identification method for polyploids of B. lindleyana. Key message: The appropriate combination of mutagenesis concentration and time was screened, and tetraploid B. lindleyana plants were successfully mutagenized, which provided technical support for the breeding research of B. lindleyana polyploidy. [ABSTRACT FROM AUTHOR]

Vaccinium meridionale (section Pyxothamnus), a tetraploid species native to higher-altitude locations in Jamaica, Colombia, and Venezuela, is of interest to Vaccinium breeders for its profuse, concentrated flowering, vigor, and monopodial plant structure, all of which may be useful in breeding for mechanical harvest in blueberry. In this study, tetraploid V. meridionale was successfully hybridized as both female and male with 2x Vaccinium vitis-idaea (section Vitis-idaea, lingonberry). The resultant F1 hybrids with lingonberry were both 3x and 4x, respectively. These hybrids were intermediate in morphology and notably vigorous. Most appear to be evergreen, with small, red-colored fruit. The 4x F1 hybrids displayed good fertility as females in backcrosses to both lingonberry and V. meridionale. Pollen production and quality were evaluated as an indicator of male fertility. Most clones had good pollen shed and high frequencies of well-formed tetrads. The overall fertility suggests that these hybrids, despite being derived from intersectional crosses, might be conventionally used for breeding without substantial difficulty. [ABSTRACT FROM AUTHOR]

The yeast Saccharomyces cerevisiae is widely used for ethanol production. In the production of alcoholic beverages, flavours are affected mainly by yeast metabolism in the fermentation process. To increase the contents of initial scented fruity flavours, such as isoamyl alcohol and isoamyl acetate, leucine accumulation in yeast cells is induced by a decrease of leucine feedback inhibition in the l‐leucine synthetic pathway using conventional mutagenesis. Diploid strains are commonly used in sake brewing because of better fermentation performance, such as vitality and endurance, compared with those of haploid strains. Heterozygous mutations are mostly detected in target genes of brewing yeasts generated through mutation breeding. Here we describe that an allele of the LEU4 gene, LEU4G516S, dominantly induced leucine accumulation even in triploid and tetraploid yeasts as with in diploid yeasts. Importantly, we demonstrated that there is no difference in the intracellular amount of branched‐chain amino acids between LEU4G516S/LEU4 heterozygous diploids and LEU4G516S/LEU4G516S homozygous diploids. The approach to increase isoamyl alcohol and isoamyl acetate by intracellular leucine accumulation can potentially be applied to a variety of yeast strains, including aneuploid and polyploid yeasts. Take away: The LEU4 mutant allele dominantly induced leucine accumulation in polyploids.There is no difference in the productivity of branched‐chain amino acids between diploid mutants.These modifications are available regardless of their ploidy and aneuploidy. [ABSTRACT FROM AUTHOR]

Chromosome numbers (2n) for 12 alien species (Apiaceae, Asteraceae, Brassicaceae, Campanulaceae, Fabaceae, Lamiaceae, Malvaceae, Onagraceae, Poaceae, Polygonaceae) from the Novosibirsk Region are given. For the first time for Russia, the number of chromosomes of Xanthogalum purpurascens (2n = 22) is given, for Siberia – Nepeta cataria (2n = 34), Malva pusilla (2n = 42) and Koenigia weyrichii subsp. weyrichii (2n = 20). For all studied species, short information on the general distribution and dispersal in the Novosibirsk Region, literature data on the number of chromosomes from the territory of Russia are presented.

Abstract Background Artificial synthesis of octoploid rapeseed double haploid (DH) induction lines Y3380 and Y3560 was made possible by interspecific hybridization and genome doubling techniques. Production of pure lines by DH induction provides a new way to achieve homozygosity earlier in B.napus. Previously, the mechanism of induction, and whether the induction has obvious maternal genotypic differences or not, are not known so far. Results In this study, different karyogene and cytoplasmic genotype of B.napus were pollinated with the previously reported DH inducers e.g. Y3380 and Y3560. Our study presents a fine comparison of different cytoplasmic genotypes hybridization to unravel the mechanism of DH induction. Ploidy identification, fertility and SSR marker analysis of induced F1 generation, revealed that ploidy and phenotype of the induced F1 plants were consistent with that type of maternal, rather than paternal parent. The SNP chip analysis revealed that induction efficiency of DH inducers were affected by the karyogene when the maternal cytoplasmic genotypes were the same. However, DH induction efficiency was also affected by cytoplasmic genotype when the karyogenes were same, and the offspring of the ogura cytoplasm showed high frequency inducer gene hybridization or low-frequency infiltration. Conclusion The induction effect is influenced by the interaction between maternal karyogene and cytoplasmic genotype, and the results from the partial hybridization of progeny chromosomes indicate that the induction process may be attributed to the selective elimination of paternal chromosome. This study provides a basis for exploring the mechanism of DH inducer in B.napus, and provides new insights for utilization of inducers in molecular breeding.

Abstract While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. We developed nPhase, a ploidy agnostic tool that leverages long reads and accurate short reads to solve alignment-based phasing for samples of unspecified ploidy ( https://github.com/OmarOakheart/nPhase ). nPhase is validated by tests on simulated and real polyploids. nPhase obtains on average over 95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover more than 90% of each chromosome (heterozygosity rate ≥ 0.5%). nPhase allows population genomics and hybrid studies of polyploids.

Abstract Tumor heterogeneity plays a key role in cancer relapse and metastasis, however, the distinct cellular behaviors and kinetics of interactions among different cancer cell subclones and the tumor microenvironment are poorly understood. By profiling an isogenic model that resembles spontaneous human ovarian cancer metastasis with an highly metastatic (HM) and non‐metastatic (NM) tumor cell pair, one finds an upregulation of Wnt/β‐catenin signaling uniquely in HM. Using humanized immunocompetent mice, one shows for the first time that activated β‐catenin acts nonautonomously to modulate the immune microenvironment by enhancing infiltrating tumor‐associated macrophages (TAM) at the metastatic site. Single‐cell time‐lapse microscopy further reveals that upon contact with macrophages, a significant subset of HM, but not NM, becomes polyploid, a phenotype pivotal for tumor aggressiveness and therapy resistance. Moreover, HM, but not NM, polarizes macrophages to a TAM phenotype. Mechanistically, β‐catenin upregulates cancer cell surface metadherin, which communicates through CEACAM1 expressed on macrophages to produce CCL3. Tumor xenografts in humanized mice and clinical patient samples both corroborate the relevance of enhanced metastasis, TAM activation, and polyploidy in vivo. The results thus suggest that targeting the β‐catenin‐metadherin/CEACAM1‐CCL3 positive feedback cascade holds great therapeutic potential to disrupt polyploidization of the cancer subclones that drive metastasis.

Cold stress (CS) affects the survivability, geographical distribution, and yield stability of crops. Suitable management and agronomic practices can minimize the crop losses associated with cooler environments. However, agronomic practices alone can't support plants adequately to withstand the harsh cold. Therefore, exploring plants cold stress-responsive factors such as genetic, epigenetic, physiological, and cellular is crucial. This report discusses on cold stress effect, signal perception, signal transduction, gene expression, and associated molecular phenomena in plants. Three cold acclimation response pathways: Ca2+ mediated ICE1- CBF/ DREB1, hormonal, and reactive oxygen species (ROS), are elucidated. Also, this report summarizes the latest research work on genetics and genomics of forage species from the perspectives of cold tolerance improvement. In several instances, our hypotheses have been supported by a recent research output from our genetic analysis experiment on alfalfa (Medicago sativa L.) cold tolerance. We further review the importance of high-throughput genomics and phenomics for cold tolerance improvement in forage species and recommended implementing widely recognized techniques such as genomic selection (GS) and genome-wide association studies (GWAS) to develop climate-resilient cultivars. The transgenics and genome-edited cold-tolerant forage cultivars with low or no yield penalty must be the goals of future research.

Abstract Background Polyploidy is very common in plants and can be seen as one of the key drivers in the domestication of crops and the establishment of important agronomic traits. It can be the main source of genomic repatterning and introduces gene duplications, affecting gene expression and alternative splicing. Since fully sequenced genomes are not yet available for many plant species including crops, de novo transcriptome assembly is the basis to understand molecular and functional mechanisms. However, in complex polyploid plants, de novo transcriptome assembly is challenging, leading to increased rates of fused or redundant transcripts. Since assemblers were developed mainly for diploid organisms, they may not well suited for polyploids. Also, comparative evaluations of these tools on higher polyploid plants are extremely rare. Thus, our aim was to fill this gap and to provide a basic guideline for choosing the optimal de novo assembly strategy focusing on autotetraploids, as the scientific interest in this type of polyploidy is steadily increasing. Results We present a comparison of two common (SOAPdenovo-Trans, Trinity) and one recently published transcriptome assembler (TransLiG) on diploid and autotetraploid species of the genera Acer and Vaccinium using Arabidopsis thaliana as a reference. The number of assembled transcripts was up to 11 and 14 times higher with an increased number of short transcripts for Acer and Vaccinium, respectively, compared to A. thaliana. In diploid samples, Trinity and TransLiG performed similarly good while in autotetraploids, TransLiG assembled most complete transcriptomes with an average of 1916 assembled BUSCOs vs. 1705 BUSCOs for Trinity. Of all three assemblers, SOAPdenovo-Trans performed worst (1133 complete BUSCOs). Conclusion All three assembly tools produced complete assemblies when dealing with the model organism A. thaliana, independently of its ploidy level, but their performances differed extremely when it comes to non-model autotetraploids, where specifically TransLiG and Trinity produced a high number of redundant transcripts. The recently published assembler TransLiG has not been tested yet on any plant organism but showed highest completeness and full-length transcriptomes, especially in autotetraploids. Including such species during the development and testing of new assembly tools is highly appreciated and recommended as many important crops are polyploid.

The Pacific oyster, Crassostrea gigas , is a commercially important species, which is widely cultured in the world. In recent years, triploid cultivation of C. gigas has gradually emerged due to the advantages of poor fertility and rapid growth in China. However, the adaptation of triploid and tetraploid larvae to temperature, salinity and rearing density has not been studied. A central composite design and a response surface method were used to analyze the combined effects of temperature, salinity and rearing density on growth and survival of triploid and tetraploid larvae. Temperature, salinity and rearing density exerted significant effects on larvae growth and survival of triploid and tetraploid. Rearing density was identified as the most significant negative factor affecting the growth and survival of three populations. The reliable models on accumulated growth rate (AGR) and survival rate (SR) of three populations were obtained. The optimal conditions for larval development in the three populations were achieved by simultaneously maximizing growth and survival models. In diploids, the maximum AGR of 13.92 μm day−1 and the maximum SR of 65.73 were achieved at 23.66 °C / 28.47 psu / 2.23 ind.ml−1 with a value of desirability being 100%. In triploids, the maximum AGR of 15.82 μm day−1 and the maximum SR of 69.26 were achieved at 23.16 °C / 30.67 psu / 2.15 ind.ml−1 with a value of desirability being 100%. In tetraploids, the maximum AGR of 10.75 μm day−1 and the maximum SR of 46.29 were achieved at the 25.48 °C / 28.94 psu / 2.00 ind.ml−1 with a value of desirability being 95%. This study provides valuable new insights into refining the production efficiency of C. gigas larvae of different ploidy. • The adaptation of triploid and tetraploid larvae of Crassostrea gigas to temperature, salinity and rearing density was evaluated for the first time. • The relationship of accumulated growth rate (AGR) and survival rate (SR) to temperature, salinity and rearing density was modeled. • The optimal temperature-salinity-rearing density combination for three populations was determined with desirability value as 95% (tetraploid) and 100% (diploid and triploid). [ABSTRACT FROM AUTHOR]

As a cancer type potentially dominated by copy number variations, ovarian cancer shows hyperploid karyotypes and large-scale chromosome alterations, which might be promising biomarkers correlated with tumor metastasis and chemoresistance. Experimental studies have provided more information about the roles of aneuploids and polyploids in ovarian cancer. However, ploidy evaluation of ovarian cancer cell lines is still limited, even in some ploidy-related research. Herein, the ploidy landscape of 51 ovarian cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were analyzed, and the ploidy statuses of 13 human ovarian cancer cell lines and 2 murine cell lines were evaluated using G-banding and flow cytometry. Most human ovarian cancer cell lines were aneuploid, with modal numbers of 52–86 and numerical complexity ranging from 5 to 12. A2780, COV434 and TOV21G were screened as diploid cell lines, with a modal number of 46, a low aneuploid score and a near-diploid ploidy value. Two murine cell lines, both OV2944-HM1 and ID-8, were near-tetraploid. Integrated information on karyotypes, aneuploid score and ploidy value supplied references for a nondiploid model construction and a parallel analysis of diploid versus aneuploid. Moreover, the gene expression profiles were compared between diploid and aneuploid cell lines. The functions of differentially expressed genes were mainly enriched in terms of protein function regulation, TGF-β signaling and cell adhesion molecules. Genes downregulated in the aneuploid group were mainly related to metabolism and protein function regulation, and genes upregulated in the aneuploid group were mainly involved in immune regulation. Differentially expressed genes were randomly distributed on all chromosomes, while chromosome 1 alteration might contribute to immune-related alterations in aneuploid cell lines. Chromosome 19 alteration might be potentially significant for aneuploid ovarian cancer cell lines and patients, which needs further verification in ploidy research.

The NODULE-INCEPTION-like protein (NLP) is a plant-specific transcription factor (TF) family that plays an important role in both signal transduction and nitrate assimilation. However, the NLP gene family in Chinese cabbage (Brassica rapa) has yet to be studied. Here we identified 17, 16, and 32 NLP genes in Chinese cabbage, Brassica oleracea , and Brassica napus , respectively. We found that duplication of those NLP genes almost always originated from genome-wide duplication events. Further analysis (using Arabidopsis as a reference) revealed that the NLP family in Chinese cabbage and B. oleracea was characterized by direct expansion caused by whole-genome duplication. By contrast, indirect expansion characterized B. napus , which arose from hybridization and fusion of the two species. In addition, phylogenetic and homology analyses showed that the Brassica NLP gene family has been highly conserved in evolution. Finally, we also identified optimal codons for four studied species. Altogether, through comparative genome analysis methods, we presented compelling evidence that triplication is the main driving force for the NLP TF family's evolution in Chinese cabbage and related Brassica plants, a process evidently highly conserved. This work will help in better understanding the impact of genome-wide duplication on gene families of plants. • Biological systems can be recombined at many levels, from molecules to swarms. • Genome-wide duplication is the driving force behind the NLP gene familys' expansion. • NLP family evolution is a highly conserved process. • There has been some divergence in the NLP structure of Brassica crops. • The codon bias of NLP family genes in Brassicaceae plants is generally weak. [ABSTRACT FROM AUTHOR]

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids. Cultivated potato is an autotetraploid species with a highly heterogeneous genome. Knowledge of the complexity of the potato genome will be important for breeding. This study reports genome assemblies of six potato cultivars and the construction of potato pan-genome. Comparative genomic analyses reveal extensive allelic diversity in cultivated potato cultivars, including altered coding and transcript sequences, preferential allele expression, structural variation, and pan-genome variation. [ABSTRACT FROM AUTHOR]

Amana Honda (Liliaceae), known as 'east Asian tulips', is a spring ephemeral genus endemic to Sino-Japanese Floristic Subregion, mainly distributed in eastern and central China, Japan and the Korean peninsula. Chromosome numbers are reported here for the first time from 89 populations of Amana (representing all seven accepted species, two new species about to be published, and two suspected new species). Three ploidy levels are found in this genus. These are diploid (2n = 2x = 24) and tetraploid (2n = 4x = 48) in the widespread A. edulis, while all the narrow endemics are diploid, except for one population of A. tianmuensis, which is triploid (2n = 3x = 36). The northernmost and southernmost populations of A. edulis are diploid and tetraploid, respectively, while diploids and tetraploids coexist in between, with gradual transition to diploids as the latitude increases. This may indicate polyploids have an advantage in tolerance of environmental stress and are more adaptable to high-temperature environment in subtropical regions than diploids. The species and cytotype distributions in Amana are complex, and these results provide hypotheses about the origins of the genus and the polyploid cytotypes. [ABSTRACT FROM AUTHOR]

The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. The 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, of which many are imperiled and of high conservation concern. Until now, no genomic resources were available for this genus, which may serve as a model system for understanding the evolutionary genomics of explosive plant diversification. Here, we present a high-quality reference genome for the Hawaiʻi Island endemic species B. hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences generated on a Pacific Biosciences Sequel II System. The haplotype-aware, draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the holoploid genome size estimate of 7.56 Gb (±0.44 SD) determined by flow cytometry. After removal of alternate haplotigs and contaminant filtering, the consensus haploid reference genome was comprised of 15 904 contigs containing ~3.48 Gb, with a contig N50 value of 422 594. The high interspersed repeat content of the genome, approximately 74%, along with hexaploid status, contributed to assembly fragmentation. Both the haplotype-aware and consensus haploid assemblies recovered >96% of Benchmarking Universal Single-Copy Orthologs. Yet, the removal of alternate haplotigs did not substantially reduce the proportion of duplicated benchmarking genes (~79% vs. ~68%). This reference genome will support future work on the speciation process during adaptive radiation, including resolving evolutionary relationships, determining the genomic basis of trait evolution, and supporting ongoing conservation efforts. [ABSTRACT FROM AUTHOR]

While adult zebrafish and newborn mice possess a robust capacity to regenerate their hearts, this ability is generally lost in adult mammals. The logic behind the diversity of cardiac regenerative capacity across the animal kingdom is not well understood. We have recently reported that animal metabolism is inversely correlated to the abundance of mononucleated diploid cardiomyocytes in the heart, which retain proliferative and regenerative potential. Thyroid hormones are classical regulators of animal metabolism, mitochondrial function, and thermogenesis, and a growing body of scientific evidence demonstrates that these hormonal regulators also have direct effects on cardiomyocyte proliferation and maturation. We propose that thyroid hormones dually control animal metabolism and cardiac regenerative potential through distinct mechanisms, which may represent an evolutionary tradeoff for the acquisition of endothermy and loss of heart regenerative capacity. In this review, we describe the effects of thyroid hormones on animal metabolism and cardiomyocyte regeneration and highlight recent reports linking the loss of mammalian cardiac regenerative capacity to metabolic shifts occurring after birth. [ABSTRACT FROM AUTHOR]

The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis , both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica , microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history. [ABSTRACT FROM AUTHOR]

In most plant species, DNA repeated elements such as satellites and retrotransposons are composing the majority of their genomes. Saccharum officinarum (2 n = 8 x = 80) and S. spontaneum (2 n = 40–128) are the two fundamental donors of modern sugarcane cultivars. These two species are polyploids with large genome sizes and are enriched in repetitive elements. In this work, we adopted a de novo strategy to isolate highly repetitive and abundant sequences in S. officinarum LA Purple and S. spontaneum SES208. The findings obtained from alignment to the genome assemblies revealed that the vast majority of the repeats (97.9% in LA Purple and 96.5% in SES208) were dispersed in the respective genomes. Fluorescence in situ hybridization assays were performed on 27 representative repeats to investigate their distributions and abundances. The results showed that the copies of some highly repeated sequences, including rDNA and centromeric or telomeric repeats, were underestimated in current genome assemblies. The analysis of the raw read mapping strategy showed more copy numbers for all studied repeats, suggesting that copy number underestimation is common for highly repeated sequences in current genome assemblies of LA Purple and SES208. In addition, the data showed that the centromeric retrotransposons in all SES208 centromeres were absent in certain S. spontaneum clones with different ploidies. This rapid turnover of centromeric DNA in sugarcane provides new clues regarding the pattern of centromeric retrotransposon formation and accumulation. [ABSTRACT FROM AUTHOR]

Bread wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), which accounts for most of the cultivated wheat crop worldwide, is a typical allohexaploid with a genome derived from three diploid wild ancestors. Bread wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of domestication. Today, cultivated allohexaploid bread wheat has numerous advantageous traits, including adaptive plasticity, favorable yield traits, and extended end‐use quality, which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food crop. In the past decade, rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid crop. Here, we summarize recent advances in characterizing major genetic factors underlying the origin, evolution, and improvement of polyploid wheats. We end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding. [ABSTRACT FROM AUTHOR]

Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment‐based methods are fundamentally limited in their applicability to polyploids, alignment‐free methods bypass most of these limits. We investigated the use of Mash, a k‐mer analysis tool that uses the MinHash method to reduce complexity in large genomic data sets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short‐read sequences with various levels of missing data. Mash‐based estimates of genetic distance were comparable to alignment‐based estimates, and were less impacted by missing data. We also used Mash to analyse publicly available short‐read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment‐based methods, though we found that Mash genetic distance estimates could be biased by per‐sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment‐based results and for basic population genetics in reference‐free systems or those with only poor‐quality sequence data available. [ABSTRACT FROM AUTHOR]

Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem. We introduce two new mathematical formulations of polyploid haplotype phasing: (1) the min-sum max tree partition problem, which is a more flexible graphical metric compared with the standard minimum error correction (MEC) model in the polyploid setting, and (2) the uniform probabilistic error minimization model, which is a probabilistic analogue of the MEC model. We incorporate both formulations into a long-read based polyploid haplotype phasing method called flopp. We show that flopp compares favorably with state-of-the-art algorithms—up to 30 times faster with 2 times fewer switch errors on 6 × ploidy simulated data. Further, we show using real nanopore data that flopp can quickly reveal reasonable haplotype structures from the autotetraploid Solanum tuberosum (potato). [ABSTRACT FROM AUTHOR]

A comparison of diploid, neo-tetraploid, and evolved tetraploid plants (67 species) shows that, in many cases, cellular traits that are consistently affected by genome duplication (i.e., differ between diploids and neo-tetraploids), are ultimately not dramatically different when comparing diploids and evolved autopolyploids, suggesting that over evolutionary time they return to a diploid-like state (Bomblies, 2020). Thus, the signatures of selection on meiotic genes in tetraploids likely reflect a response to novel challenges caused by genome duplication, rather than diploid and tetraploid I A. arenosa i having distinct optima. Keywords: adaptive evolution; evolution; evolutionary cell biology; genome scan; meiosis; polyploid; protein evolution; trait maintenance EN adaptive evolution evolution evolutionary cell biology genome scan meiosis polyploid protein evolution trait maintenance 189 192 4 03/03/22 20220201 NES 220201 Like many evolutionary geneticists, I am fascinated by genes underlying potentially adaptive traits that differentiate populations. Many cellular traits are altered immediately by genome duplication, particularly cell size, which affects a wide range of physiological traits (Doyle and Coate, 2019). [Extracted from the article]

Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor , has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes. [ABSTRACT FROM AUTHOR]

Testing Hardy-Weinberg equilibrium (HWE) is a fundamental approach for inferring population diversity and evolution, but its application to octoploids containing eight chromosome sets has not well been justified. We derive a mathematical model to trace how genotype frequencies transmit from parental to offspring generations in the natural populations of autooctoploids. We find that octoploids, including autooctolpoids undergoing double reduction, attach asymptotic HWE (aHWE) after 15 generations of random mating, in a contrast to diploids where one generation can assure exact equilibrium and, also, different from tetraploids that use 5 generations to reach aHWE. We develop a statistical procedure for testing aHWE in octoploids and apply it to analyze a real data set from octoploid switchgrass distributed in two ecologically different regions, demonstrating the usefulness of the test procedure. Our model provides a tool for studying the population genetic diversity of octoploids, inferring their evolutionary history, and identifying the ecological relationship of octoploid-genome structure with environmental adaptation. [ABSTRACT FROM AUTHOR]

Summary: The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution. [ABSTRACT FROM AUTHOR]

Keywords: blood cells; grass carp; haemolysis; larvae; polyploid EN blood cells grass carp haemolysis larvae polyploid 325 330 6 12/20/21 20220101 NES 220101 INTRODUCTION Artificially induced, functionally sterile triploid grass carp I (Ctenopharyngodon idella i , Valenciennes, 1844) are used globally to control populations of aquatic macrophytes (Chilton & Muoneke, 1992; Wittmann et al., 2014), avoiding ecological risk (Fraser et al., 2012), and diploids serve as a major food source globally, as well (FAO, 2020). States within the U.S. utilizing triploid grass carp can monitor diploid contamination in the triploid supply chain (Kinter et al., 2018) and in natural water bodies (Clemens et al., 2016) by determining ploidy level of these individuals. Grass carp (a), common carp (b) and European catfish (c) phase-contrast microscopy and PI DNA fluorescence intensity histogram profile detected on the FL3 fluorescence Lin channel are represented. [Extracted from the article]