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Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome. Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as tetraploid and diploid dosages, plus allele ratios) and SNP marker subsetting (all available SNPs, only genic regions, and only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used genotyping by sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and the onset of flowering, which were assessed in 143 genotyped plants from a genetically broad European reference population and their phenotyped half-sib progenies. Results: On average, the allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), while using all the SNPs offered an advantage compared with any specific SNP subsetting (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting achieved better performances. We also released Legpipe2, an SNP calling pipeline tailored for reduced representation (GBS, RAD) in medium-sized genotyping experiments. [ABSTRACT FROM AUTHOR]

Drought-resistant plants exhibit strong water retention capability. In this regard, the autotetraploid sour jujube leaves exhibit better water retention than diploid leaves. Morphological comparisons and physiological comparisons of diploid and autotetraploid leaves showed that the autotetraploid leaves had thicker leaf cuticles and more leaf wax accumulation than the diploid leaves, which could reduce cuticle permeability and improve the drought tolerance of leaves. In this study, the cuticular wax crystalloids on the adaxial and abaxial sides of young and mature jujube leaves were observed in the two ploidy types, and unique cuticular wax crystalloids covering a large area of the cuticle on autotetraploid sour jujube leaves may provide an advantage in reducing leaf non-stomata transpiration and improving plant drought tolerance. Based on the transcriptome, 115 differentially expressed genes between diploids and autotetraploids were further analyzed and found to be involved in the accumulation of cuticular wax components, including terpenoids, fatty acids, and lipids, as well as ABC transporter and wax biosynthetic process. Finally, 14 genes differentially expressed between glossy autotetraploid leaves and nonglossy diploid leaves, such as LOC107414787, LOC107411574 and LOC107413721, were screened as candidate genes by qRT-PCR analysis. This findings provided insights into how polyploidization improved drought tolerance. [ABSTRACT FROM AUTHOR]

Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano , M. janickei , and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano , which consists of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements. [ABSTRACT FROM AUTHOR]

Persian shallot has been propagated vegetatively through daughter bulbs and has a narrow genetic base. In the present study, to create genetic diversity in terms of ploidy level, the effects of in vitro polyploidization were investigated on morphological, physiological and phytochemical traits. Different colchicine treatments (0, 0.3%, 0.5% and 0.7% concentrations) for 24, 36 and 48 h and oryzalin treatments (0, 0.001%, 0.002% and 0.004% concentrations) for 4, 6 and 8 h were used. A sterile basal plate of bulbs was used for the induction of polyploidy in liquid and solid media. After obtaining plantlets, root tip chromosomes were counted for the determination of ploidy levels. Flow cytometry was performed to confirm the chromosome counting results. The regenerated diploid and tetraploid plantlets were transferred to ex vitro conditions. Colchicine and oryzalin were both successful in inducing polyploids and the polyploids induced were tetraploids and mixoploids. The highest induction of polyploidy was obtained in solid media using 0.5% (w/v) colchicine for 36 h (35.0% polyploidy induction) and in 0.001% (w/v) Oryzalin for 8 h (45.5% polyploidy induction). Differences in plantlet height and weight, bulblet weight, density, stomatal width and length, and chlorophyll content were observed between tetraploid and diploid plants. Chromosome duplication, as a result of tetraploid induction, significantly influenced the antioxidant content and enzyme activities. The results showed that total phenolic content, allicin, and antioxidant capacity were significantly higher in the tetraploid plantlets than that in the diploid plantlets. SRAP loci polymorphisms indicated that the 12 autotetraploid plants (with high allicin content) had different genotypes from the parental diploid plant. Besides, in vitro polyploidy induction not only duplicated chromosomes but also altered the DNA sequence in Allium hirtifolium. In vitro induction of tetraploids in A. hirtifolium can be a reliable way to obtain suitable plant material for breeding programs to generate new genotypic variations. [ABSTRACT FROM AUTHOR]

The mandarin is an important fruit crop worldwide, and 'Xinyu mandarin'—a local Citrus reticulata variety—is widely cultivated in Jiangxi Province, in China. Autopolyploidy has frequently been used for the improvement of crop varieties. In a previous study, we identified a tetraploid (4X) material of 'Xinyu mandarin' generated from its diploid (2X) mother seedling via a spontaneous mutation. However, the physiological and metabolic variations after polyploidy are not clear enough, which is not conducive to the early screening. In the present study, we analyzed the morphological, physiological, and metabolic differences between the tetraploid and diploid plants. The tetraploids had larger and thicker leaves, and the activities of key enzymes in photosynthesis, the total chlorophyll, phenolic, and proline contents, were all higher in tetraploids. In the non-targeted metabolomic profile, a total of 522 metabolites were identified, of which 61 were significantly different between diploids and tetraploids. The differential metabolites included similar proportions of primary and secondary metabolites, and most of these were up-regulated in tetraploids, especially stress-related metabolites such as phenolic acids, flavonoids, alkaloids, and so on, indicating that tetraploids may possess better stress tolerance ability and vigor. Therefore, the tetraploids of 'Xinyu mandarin' may serve as an excellent female parent for the improvement of citrus varieties. [ABSTRACT FROM AUTHOR]

Safflower (Carthamus tinctorius L.) is one of the important oilseed and bio-energy crops. All of the safflower cultivars in the world have diploid genomes (2n= 2x= 24). In this research, autotetraploidy induction in safflower was performed by colchicine treatments to the emerging shoot tips at the cotyledonary stage. As a result of flow cytometric analyses performed in the C2 progenies, autotetraploids (4x= 48) had DNA content of 4.88 pg 2C-1, while diploids (2x= 24) had 2.29 pg 2C-1. The autotetraploids in C2 generation exhibited bigger stomata size (33.40 μm to 46.90 μm in length) and a higher chloroplast number (9.5 to 17.2 in the guard cells), but less stomatal density (17.98% to 16.67% in index) compared to their diploid counterparts. However, autotetraploidy reduced the pollen viability from 80.24% to 16.20%, and seed set rate from 35.06% to 7.01% per capitula. As a result, autotetraploid plants were able to produce very few seeds despite the high unit seed size and weight in their heads. While oil content of the large-seeded autotetraploids was significantly lower, by two-fold, (26.37% to 13.23% in the whole seeds) than the small-seeded diploids, fatty acid composition was not significantly influenced by autopolyploidization. [ABSTRACT FROM AUTHOR]

Polyploidization is an important technique used in grape breeding to create new genetic resources and can be induced using some antimitotic agents, including colchicine. Plants with increased ploidy can gain better quality than their original diploids in some characteristics. In this study, which was carried out to obtain polyploid genotypes under in vivo conditions, the effects of six (1 g L-1, 2 g L-1, 3 g L-1, 4 g L-1, 5 g L-1, 6 g L-1) doses of colchicine were applied to the shoot tip meristem regions of the seedlings obtained from the seeds of grapevine cv. Ekşi Kara and cv. Trakya İlkeren, for three consecutive days and twice a day (at 08.30 and 18.00 h) were investigated. The effects of mutagen were evaluated by following the treated seedlings' morphological changes and comparing them with the 'Kyoho' (4x) by flow cytometry (FC) analysis. In surviving plants after treatment, stomatal characteristics differed to varying degrees from their original diploids, and stomatal density decreased inversely with the increase in stomatal size in polyploid genotypes. Among cv. Ekşi Kara seedlings, 1 tetraploid (5 g L-1), and cv. Trakya İlkeren seedlings, 1 mixoploid (2 g L-1), and 1 tetraploid (6 g L-1) genotypes were selected by stomatal characteristics, chloroplast numbers, and confirmed by FC analysis. It was determined that colchicine is an effective mutagen in the breeding of polyploid grapevine, and stomatal observations, chloroplast numbers, and FC analysis are useful methods for obtaining confirmed results in the selection of polyploid genotypes. [ABSTRACT FROM AUTHOR]

The mandarin is an important fruit crop worldwide, and ‘Xinyu mandarin’—a local Citrus reticulata variety—is widely cultivated in Jiangxi Province, in China. Autopolyploidy has frequently been used for the improvement of crop varieties. In a previous study, we identified a tetraploid (4X) material of ‘Xinyu mandarin’ generated from its diploid (2X) mother seedling via a spontaneous mutation. However, the physiological and metabolic variations after polyploidy are not clear enough, which is not conducive to the early screening. In the present study, we analyzed the morphological, physiological, and metabolic differences between the tetraploid and diploid plants. The tetraploids had larger and thicker leaves, and the activities of key enzymes in photosynthesis, the total chlorophyll, phenolic, and proline contents, were all higher in tetraploids. In the non-targeted metabolomic profile, a total of 522 metabolites were identified, of which 61 were significantly different between diploids and tetraploids. The differential metabolites included similar proportions of primary and secondary metabolites, and most of these were up-regulated in tetraploids, especially stress-related metabolites such as phenolic acids, flavonoids, alkaloids, and so on, indicating that tetraploids may possess better stress tolerance ability and vigor. Therefore, the tetraploids of ‘Xinyu mandarin’ may serve as an excellent female parent for the improvement of citrus varieties.

Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimized in an autotetraploid (within-species polyploid) to avoid missegregation. Here, we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara , 17 My diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodeling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara , suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organization, stress signaling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD. [ABSTRACT FROM AUTHOR]

Copyright of Anadolu Tarım Bilimleri Dergisi is the property of Ondokuz Mayis Universitesi, Ziraat Fakultesi 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.)

Polyploid plants often exhibit enhanced stress tolerance relative to their diploid counterparts, but the physiological and molecular mechanisms of this enhanced stress tolerance remain largely unknown. In this study, we showed that autotetraploid trifoliate orange (Poncirus trifoliata (L.) Raf.) exhibited enhanced salt tolerance in comparison with diploid progenitors. Global transcriptome profiling of diploid and tetraploid plants with or without salt stress by RNA-seq revealed that the autotetraploids displayed specific enrichment of differentially expressed genes. Interestingly, the leaves and roots of tetraploids exhibited different expression patterns of a variety of upregulated genes. Genes related to plant hormone signal transduction were enriched in tetraploid leaves, whereas those associated with starch and sucrose metabolism and proline biosynthesis were enriched in roots. In addition, genes encoding different antioxidant enzymes were upregulated in the leaves (POD) and roots (APX) of tetraploids under salt stress. Consistently, the tetraploids accumulated higher levels of soluble sugars and proline but less ROS under salt stress compared to the diploids. Moreover, several genes encoding transcription factors were induced specifically or to higher levels in the tetraploids under salt stress. Collectively, this study demonstrates that the activation of various multifaceted defense systems in leaves and roots contributes to the enhanced salt tolerance of autotetraploids. [ABSTRACT FROM AUTHOR]

A colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape. [ABSTRACT FROM AUTHOR]

Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

Highlights • The autotetraploid 'Riguang' displayed slower growth and dwarfing characteristics. • The 'Riguang' has bigger leaves, stomata, pollens, flowers and fruits than diploid. • The autotetraploid exhibited darker green leaves, higher chlorophyll content. • The autotetraploid exhibited higher photosynthetic efficiency. • The 'Riguang' has better quality fruits than its diploid. Abstract Polyploidization plays an important role in plant breeding because polyploid plants often show better agronomic characteristics related to growth, yield and quality. The autotetraploid Chinese jujube, 'Riguang', was induced from diploid 'Dongzao' by colchicine in 2004, but systematic comparative study on its characteristics has not been done. The morphological, cytological and nutritional differences between 'Riguang' and 'Dongzao' were comparatively analyzed. The autotetraploid displayed relatively slower growth and significant dwarfing characteristics as compared to the diploid counterpart. Compared with its diploid donor, 'Riguang' exhibited darker green leaves and much bigger stomata, pollens, flowers and fruits. The average fruit weight of 'Riguang' was 40.56% heavier; The contents of ascorbic acid, titratable acids, soluble sugar and cyclic adenosine monophosphate in 'Riguang' fruits were significantly higher than those in 'Dongzao' fruits. The significant higher chlorophyll content in 'Riguang' leaves led to the increased photosynthetic efficiency in the autotetraploid plants. In brief, the autotetraploid 'Riguang' exhibited some superior agronomic characteristics that include less vigor, but higher photosynthetic capacity, higher yield per tree, bigger and more nutritious fruit. This is the first systematic comparative study on the characters of autotetraploid and its diploid counterpart in Chinese jujube, which can provide reference for in-depth study of autotetraploid in fruit tree. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia 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.)

Background: Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data. Results: Our upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated. Conclusion: Our updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article. [ABSTRACT FROM AUTHOR]

Paspalum is a noteworthy grass genus due to the forage quality of most species, with approximately 330 species, and the high proportion of those that reproduce via apomixis. Harnessing apomictic reproduction and widening knowledge about the cytogenetic relationships among species are essential tools for plant breeding.We conducted cytogenetic analyses of inter‐ and intraspecific hybridisations involving a sexual, colchicine‐induced autotetraploid plant of P. plicatulum Michx. and five indigenous apomictic tetraploid (2n = 40) species: P. compressifolium Swallen, P. lenticulare Kunth, two accessions of P. nicorae Parodi, P. rojasii Hack. and two accessions of P. plicatulum. Fertility of the hybrids was investigated and their reproductive system was analysed considering the relative embryo:endosperm DNA content from flow cytometry. Morphological, nomenclatural and taxonomic issues were also analysed.Cytogenetic analysis suggested that all indigenous tetraploid accessions of five apomictic species are autotetraploid or segmental allotetraploid. If segmental allotetraploids, they probably originated through autoploidy followed by diploidisation processes. Autosyndetic male chromosome pairing observed in all hybrid families supported this assertion. Allosyndetic chromosome associations were also observed in all hybrid families. In the hybrids, the proportion of male parent chromosomes involved in allosyndesis per pollen mother cell varied from 5.5% to 35.0% and the maximum was between 25% and 60%. The apomictic condition of the indigenous male parents segregated in the hybrids.These results confirm a strong association between autoploidy and apomixis in Paspalum, and the existence of cytogenetic relationships between different species of the Plicatula group. Allosyndetic chromosome pairing and seed fertility of the hybrids suggest the feasibility of gene transfer among species. [ABSTRACT FROM AUTHOR]

Highlights • Our data showed that autotetraploids showed higher tolerance to drought stress than diploids. • Autopolyploid does not seem to undergo major changes of gene expression over long periods (2.84%) and under drought stress. • Genome duplication resulted in more differentially expressed drought-related genes in autopolyploid than in diploid. • Genome duplication also resulted in gain or loss of drought-related genes. Abstract The evolutionary mechanism where autopolyploid tolerate abiotic stresses better than its diploid ancestor is poorly known. Large-scale gene-expression changes were not observed in synthetic autopolyploids compared to their respective diploids. However, natural autopolyploids with longer evolutionary periods might have experienced major changes that resulted in greater adaptation of autopolyploids, which might contribute to gene expression in natural autopolyploid differently from that in synthetic autopolyploid, and explain why genome doubling can help plants develop a stronger ability to adapt to various environmental stresses. However, information on this is still lacking. Here, diploid and autotetraploid sea barley tolerance to drought stress were analyzed. Our data showed that autotetraploids showed higher tolerance to drought stress than diploids. The results of GO enrichment and KEGG pathway enrichment showed that diploid and tetraploid would alter their physiological and biochemical process, even morphology to respond to drought stress via different molecular mechanism. Genome duplication resulted in more differentially expressed drought-related genes and higher expression level of those genes in autopolyploid than in diploid, 186 drought-related genes with 97 genes up-regulated in comparison of DiH826Dr_vs_DiH826Ck, while 297 drought-related genes with 126 up-regulated in TetraH832Dr_vs_TetraH832Ck. Among these drought-related genes, 81 of them were specific significantly expressed in DiH826Dr_vs_DiH826Ck, 192 genes were specific significantly expressed in TetraH832Dr_vs_TetraH832Ck. Although our results indicated that the autopolyploid does not seem to undergo major changes of gene expression over long periods (2.84%) and under drought stress, more DEGs and more up-regulated DEGs between autotetraploid and diploid were observed than those in the CK. Furthermore, genome duplication also resulted in gain or loss of drought-related genes, which might offer potential for autopolyploid to survive better under drought environment. [ABSTRACT FROM AUTHOR]

Highlights • The morphological characteristics and reproductive potential of three autotetraploid kumquats were examined. • Tetraploid kumquats had the typical morphological characteristics of tetraploid Citrus plants. • The fruits of these tetraploid kumquats showed desirable traits for kumquats such as thicker pericarp and higher SSC. • When tetraploids were crossed with diploid kumquats, triploid progenies were obtained. Abstract Three Fortunella (kumquat) species, the Meiwa kumquat (F. crassifolia Swingle), the Round kumquat [ F. japonica (Thunb.) Swingle] and the Changshou kumquat (F. obovata hort. ex Tanaka), showing tetraploid, which had been induced by treating the seeds with colchicine, were examined for origin and horticultural characteristics (e. g. morphology of leaves, flowers, pollen and fruits). Additionally, these tetraploid kumquats were crossed to produce triploid kumquats. All of the tetraploids were confirmed to be derived from the nucellar embryo of each original kumquat by examining their chromosomal composition with chromomycin A 3 staining. All of the tetraploid kumquats had the typical morphological characteristics of tetraploid Citrus plants, such as round and thick leaves, and large flowers and pollen grains. On the other hand, the fruits of these tetraploid plants showed desirable traits for kumquats such as thicker pericarp and higher soluble solids content. Furthermore, when these tetraploids were crossed with some diploid cultivars, triploid progenies were obtained from almost all of the cross combinations. [ABSTRACT FROM AUTHOR]

Summary: Whole genome duplication is a key process in plant evolution and has direct phenotypic consequences. However, it remains unclear whether ploidy‐related phenotypic changes can significantly alter the fitness of polyploids in nature and thus contribute to establishment of new polyploid mutants in diploid populations.We addressed this question using a unique natural system encompassing a diploid and its sympatric locally established autotetraploid derivative. By setting a common garden experiment with two manipulated environmental factors (presence/absence of serpentine substrate and competition), we tested whether these two locally important factors differently shape the phenotypic response of the two ploidy levels.Tetraploids attained significantly higher values of both above‐ and below‐ground biomass, and root : shoot ratio compared to their diploid progenitors. Tetraploid superiority in vegetative fitness indicators was most prominent when they were cultivated together with a competitor in nutrient‐rich nonserpentine substrate.We show that even genetically very closely related diploids and tetraploids can respond differently to key environmental factors. Provided there are sufficient nutrients, tetraploids can be more successful in tolerating interspecific competition than their diploid progenitors. Such superior performance might have provided an adaptive advantage for the newly established tetraploid promoting colonisation of new (micro‐)habitats, which was indeed observed at the natural site. [ABSTRACT FROM AUTHOR]

Polyploidization is considered as the major force that drives plant species evolution and biodiversity. The leaves of Chinese cabbage, an important vegetable crop valued for its nutritional quality, constitute the main edible organ. In this study, we found that autotetraploid Chinese cabbage (Brassica rapa ssp. pekinensis) generated from a doubled haploid (DH) line via isolated microspore culture exhibits a dwarf phenotype, along with thick leaves and delayed flowering. Abscisic acid (ABA) and brassinosteroid (BR) levels were significantly lower in autotetraploids compared to DHs. Comparative transcriptome analysis was performed to examine the gene regulatory network. A total of 13,225 differentially expressed genes (DEGs) were detected. Further microRNA (miRNA) analysis identified 102 DEGs that correspond to 35 differentially expressed miRNAs (DEMs). Subsequent screening of these 102 genes identified 13 key genes with 12 corresponding differentially expressed miRNAs that are related to leaf development and dwarfism. These 13 genes are involved in the regulation of various processes, including BR synthesis (dwarfing), plant growth, flowering time delay, ABA pathway-related growth and metabolism, leaf morphology and development, and cell extension. Two dwarfing-related genes (BraA01000252 and BraA05004386) regulated by two miRNAs (novel_15 and novel_54) were determined to be downregulated, indicating their possible role in leaf thickness and dwarfism in autotetraploid plants. We also propose two possible miRNA-dependent regulatory pathways that contribute to trait formation in autotetraploid Chinese cabbage. These results provide a theoretical basis for further work involving Chinese cabbage varieties by inducing polyploidy. [ABSTRACT FROM AUTHOR]

Autotetraploid rice is a useful germplasm that has four chromosome sets and strong biological advantages; however, low fertility limits its commercial utilization. Little information is available about the DNA variation and differential gene expressions associated with low fertility in autotetraploid rice. In the present study, 81 SNPs and 182 InDels were identified in T449 (an autotetraploid rice line with low fertility) compared to E249 (diploid counterpart) by whole-genome re-sequencing. We detected only three non-synonymous SNPs and six large-effect InDels, which were associated with three and six genes, respectively. A total of 75 meiosis-related differentially expressed genes were detected during the meiosis stage by transcriptome analysis, including OsMTOPVIB, which is essential for meiotic DSB formation, and OsMOF, which takes part in homologous chromosome pairing and synapsis. Approximately 20.69% lagging chromosome at metaphase I and 4.65% abnormal tetrad were observed in T449. Moreover, transcriptome analysis revealed down-regulation of a sucrose transporter (OsSUT5) and two monosaccharide transporters (OsMST1 and OsMST8) in T449 at the single microspore stage, and their expression levels were verified by qRT-PCR. Cytological observation of saccharide distribution showed abnormal accumulation of saccharides in T449 and the contents of fructose and glucose were markedly higher in T449 than E249 at the single microspore stage. Our results suggested that polyploidy not only induces abrupt expression changes in the meiosis-related genes that lead to abnormal chromosome behavior, but also causes changes in the saccharide distribution and expression patterns of saccharide-related genes, which jointly causes sterility in the autotetraploid rice. [ABSTRACT FROM AUTHOR]

Autotetraploid fish (4n = 200, abbreviated as 4nRR), which reach sexual maturity at 1 year of age, were derived from the whole genome duplication of red crucian carp Carassius auratus red var. (RCC; 2n = 100) and possess four sets of chromosomes from RCC. The histological features of the gonads showed that the RCC and 4nRR both possessed normal gonadal structure and could arrive at maturation. To understand the expression characteristics of genes related to reproductive development in the autotetraploid fish, we analysed the nucleotide sequence and expression characteristics of the gnrh2, gthb and gthr genes, which are the pivotal genes of the hypothalamic–pituitary–gonadal (HPG) axis. We found that the gnrh2, gthb and gthr genes in 4nRR share remarkable homology with RCC, but there were obvious differences in expression levels between 4nRR and RCC. These results demonstrate that autotetraploidization can lead to gene expression changes. This study provides insights into the molecular mechanism underlying the reproductive development of autotetraploid fish and is expected to be of great significance for subsequent research on polyploidization. [ABSTRACT FROM AUTHOR]

Summary: Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits. We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies. We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL. The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered. [ABSTRACT FROM AUTHOR]

Autotetraploids fish (4nRR) (4n = 200, AAAA) were resulted from the whole-genome duplication of Carassius auratus red var. (RCC) (2n = 100, AA). Following activation by UV-irradiated Megalobrama amblycephala (BSB) sperm, the autodiploid eggs (2n = 100, AA) of 4nRR females developed into all-female autodiploid gynogenetic offspring (G 1 ) (2n = 100, AA) without chromosome doubling treatment, indicating an XXXX genotype of the female autotetraploids. Compared with 4nRR and RCC, G 1 individuals matured after 2 years, suggesting obviously delayed maturity. Tetraploid offspring (4nRG) (4n = 200) were also produced by crossing G 1 females with male autotetraploids, suggesting that G 1 individuals can produce unreduced eggs (2n = 100). After activation by UV-irradiated BSB sperm, the fertilized eggs of G 1 females developed into a second generation of autodiploid gynogenetic offspring (G 2 ) (2n = 100, AA) without chromosome doubling treatment. The diploid gametes are an important gamete source for the production of polyploid fish and the establishment of a diploid gynogenetic clone line, which will be useful for genetic analyses and breeding. [ABSTRACT FROM AUTHOR]

Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non‐equilibrium conditions following bottlenecks. We use stochastic individual‐based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo‐autotetraploids form from the union of unreduced gametes. With a ploidy‐independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy‐dependent effects for another reason–in some cases matings between close relatives temporarily increase inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo‐autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation‐selection‐drift balance, providing a transient period of permissive conditions favoring the evolution of selfing. [ABSTRACT FROM AUTHOR]

Abstract: We have developed the first comprehensive simulator for polyploid genomes (PolySim) and demonstrated its value by performing large‐scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating single nucleotide polymorphisms, minor allele frequency, heterozygosity, R2 and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent (MV) pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. MV formation can homogenize allotetraploid subgenomes, but this homogenization requires a higher MV rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations, which, in combination with quantitative genetics tools, can be used to investigate the power of genomewide association, genomic selection or breeding programme designs in these species. [ABSTRACT FROM AUTHOR]

Autotetraploid rice is a useful germplasm with high biomass production; however, low fertility is the main barrier in commercial utilization. In our previous study, differential expression of meiosis-related miRNAs was found to be involved in the pollen sterility of autotetraploid rice. However, genome-wide DNA variations and methylomes associated with low fertility of autotetraploid rice are still poorly understood. Here, we measured both global DNA variations and the methylome and compared them with the transcriptome during pollen development in autotetraploid rice by high-throughput sequencing. A total of 34416 SNPs, 6993 InDels, 1003 SVs and 25 CNVs were detected, and 11367 and 41117 differentially methylated regions showed hypermethylation and hypomethylation in 02428-4x. In total, 1110 genes displayed differentially expression in 02428-4x during meiosis, of these six harbored CNVs, including four upregulated genes with gain CNVs, such as LOC_Os11g38620. We identified 122 genes by comparing with the previous data that might be associated with low fertility during pollen development in 02428-4x. Of the 122 gens, 98 were displayed methylation and differential expression, including OsMADS98, CYP703A3 and OsABCG26. The downregulation of these three genes were confirmed by qPCR during meiosis of 02428-4x, which played pivotal roles in pollen fertility. These results indicate that the low fertility of autotetraploid rice is not only caused by the differential expression of genes involved in pollen development, but also by sequence variation and differential methylation, suggesting that the reason for pollen sterility in autotetraploid rice is complex and might be affected by multiple factors. [ABSTRACT FROM AUTHOR]

Elite parental lines are more likely to breed fine varieties, but knowledge about elite parents and their genetic backgrounds is limited. In this paper, we investigated the pedigree relationships of potato varieties bred worldwide and in China. Several elite parents were identified, and these parents were more frequently used as parents in breeding programs across different time periods and countries. We next used 2b-RAD, a reduced-representation sequencing method, to genotype the elite parent Mira and 24 of its offspring. These cultivars span 5 generations, making this lineage the longest continuous pedigree among Chinese bred potatoes. A total of 47,314 tetraploid single nucleotide polymorphisms (SNPs) identified by FreeBayes were used to trace the conserved segments of the Mira genome. The conserved segments had identical or similar allele-specific SNPs across the analyzed genotypes. In Mira, 3,788 segments comprising over 10,000 bp, or 20.8% of the genome, were defined as conserved segments. These segments contain genes involved in crucial biological processes that are of special interest to breeders. These regions, which have been conserved across generations of highly selective breeding, may be helpful for further breeding and performing genome-wide breeding by design. [ABSTRACT FROM AUTHOR]

Key message: A novel process for the production of transgenic alfalfa varieties.Abstract: Numerous species of legumes, including alfalfa, are critical factors for agroecosystems due to their ability to grow without nitrogen fertilizers derived from non-renewable fossil fuels, their contribution of organic nitrogen to the soil, and their increased nutritional value. Alfalfa is the main source of vegetable proteins in meat and milk production systems worldwide. Despite the economic and ecological importance of this autotetraploid and allogamous forage crop, little progress has been made in the incorporation of transgenic traits into commercial alfalfa. This is mainly due to the unusually strong transgene silencing and complex reproductive behavior of alfalfa, which limit the production of events with high transgene expression and the introgression of selected events within heterogeneous synthetic populations, respectively. In this report, we describe a novel procedure, called supertransgene process, where a glufosinate-tolerant alfalfa variety was developed using a single event containing the BAR transgene associated with an inversion. This approach can be used to maximize the expression of transgenic traits into elite alfalfa germplasm and to reduce the cost of production of transgenic alfalfa cultivars, contributing to the public improvement of this legume forage and other polyploid and outcrossing crop species. [ABSTRACT FROM AUTHOR]

Autopolyploid plants and their organs are larger than their corresponding diploid ancestors, and they attract considerable attention for plant breeding. Paulownia is a fast-growing tree. To identify genes related to the biological characteristics of tetraploid Paulownia, transcriptome and small RNA sequencing were used to identify the key gene expression regulation in tetraploid Paulownia fortunei and tetraploid P. tomentosa and their corresponding diploids. A total of 1977 common differentially expressed genes (DEGs) and 89 differentially expressed miRNAs (DEMs) (38 conserved and 51 novel) were obtained in tetraploid vs. diploid comparisons of the two Paulownia species, and 18 target genes were identified by target prediction. Finally, by analyzing the expression profiles of the DEGs and DEMs and their target genes, we discovered that Pau-miR169, Pau-miR408 and Pau-miR156 interacted with their target gene nuclear transcription factor Y subunit A-9 (NF-YA9), serine/threonine protein phosphatase (PP1) and s-adenosyl-methionine-sterol-c-methyltransfera--se (SAM:SMT) to regulate the abiotic stress tolerance and the timber quality of the tetraploid Paulownia. This study lays a molecular biology foundation for understanding autotetraploid Paulownia and will benefit future breeding work. [ABSTRACT FROM AUTHOR]

Background and aims: Understanding the consequences of polyploidization is a major step towards assessing the importance of this mode of speciation. Most previous studies comparing different cytotypes, however, did so only within a single environment and considered only one group of traits. To take a step further, we need to explore multiple environments and a wide range of traits. The aim of this study was to assess response of diploid and autotetraploid individuals of Knautia arvensis (Dipsacaceae) to two stress conditions, shade or drought. Methods: We studied eleven photosynthetic, morphological and fitness parameters of the plants over three years in a common garden under ambient conditions and two types of stress. Key results: The results indicate strong differences in performance and physiology between cytotypes in ambient conditions. Interestingly, higher fitness in diploids contrasted with more efficient photosynthesis in tetraploids in ambient conditions. However, stress, especially drought, strongly reduced fitness and disrupted function of the photosystems in both cytotypes reducing the between cytotype differences. The results indicate that drought stress reduced function of the photosynthetic processes in both cytotypes but particularly in tetraploids, while fitness reduction was stronger in diploids. Conclusions: The photosynthesis related traits show higher plasticity in polyploids as theoretically expected, while the fitness related traits show higher plasticity in diploids especially in response to drought. This suggests that between cytotype comparisons need to consider multiple traits and multiple environments to understand the breath of possible responses of different cytotypes to stress. They also show that integrating results based on different traits is not straightforward and call for better mechanistic understanding of the relationships between species photosynthetic activity and fitness. Still, considering multiple environments and multiple species traits is crucial for understanding the drivers of niche differentiation between cytotypes in future studies. [ABSTRACT FROM AUTHOR]

Artificial induction of polyploidy is an efficient technique for improving the biological properties and developing new varieties of many plants. Autotetraploid plants were generated through in vitro chromosome doubling of the ‘Hanfu’ apple cultivar ( Malus × domestica ) using colchicine treatment. In the present study, we analysed and compared the differences in the morphological and biological characteristics of diploid and autotetraploid ‘Hanfu’ apple cultivars from 2009 to 2014. We found that the autotetraploid plants flowered at 5 years of age, which was 2 years later than in the diploid plants. Compared with the diploid plants, the autotetraploid plants showed retarded growth and significant dwarfing characteristics before flowering, but their growth was restored after flowering. The stomata were larger and the leaves were not only larger and heavier but also darker green in the autotetraploid than in the diploid plants. The chlorophyll content of the leaves was significantly higher and the photosynthetic efficiency and fluorescence performance were increased in the autotetraploid plants. Additionally, the volume and size of the flowers, fruits and seeds were greater and the soluble solid contents were higher in the autotetraploid than its diploid counterparts. In this study, we provide the first detailed analysis of the morphological and biological characteristics associated with growth and development in diploid and autotetraploid ‘Hanfu’ apple, and the results will make a meaningful contribution to the breeding of polyploid apples. [ABSTRACT FROM AUTHOR]

Paulownia tomentosa is a fast-growing tree species with multiple uses. It is grown worldwide, but is native to China, where it is widely cultivated in saline regions. We previously confirmed that autotetraploid P. tomentosa plants are more stress-tolerant than the diploid plants. However, the molecular mechanism underlying P. tomentosa salinity tolerance has not been fully characterized. Using the complete Paulownia fortunei genome as a reference, we applied next-generation RNA-sequencing technology to analyze the effects of salt stress on diploid and autotetraploid P. tomentosa plants. We generated 175 million clean reads and identified 15,873 differentially expressed genes (DEGs) from four P. tomentosa libraries (two diploid and two autotetraploid). Functional annotations of the differentially expressed genes using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed that plant hormone signal transduction and photosynthetic activities are vital for plant responses to high-salt conditions. We also identified several transcription factors, including members of the AP2/EREBP, bHLH, MYB, and NAC families. Quantitative real-time PCR analysis validated the expression patterns of eight differentially expressed genes. Our findings and the generated transcriptome data may help to accelerate the genetic improvement of cultivated P. tomentosa and other plant species for enhanced growth in saline soils. [ABSTRACT FROM AUTHOR]

Key message : Autotetraploid Arabidopsis line esd and 4COL exhibit enhanced tolerance to Cu stress by enhancing activation of antioxidative defenses, altering expression of genes related to Cu transport, chelation, and ABA-responsive. Abstract: Autopolyploidy is ubiquitous among angiosperms and often results in better adaptation to stress conditions. Although copper (Cu) is an essential trace element, excess amounts can inhibit plant growth and even result in death. Here, we report that autotetraploid Arabidopsis thaliana esd and 4COL exhibit higher tolerance to Cu stress. Under such conditions, tetraploid plants had lower Cu contents and significantly more biomass compared with diploid plants. When exposed to excess Cu for 24 h, levels of superoxide anions, hydrogen peroxide, and malondialdehyde were lower in tetraploids than in diploids. Moreover, activities of the antioxidant enzymes superoxide dismutase and peroxidase were stimulated and glutathione content was maintained at a relative higher level in the tetraploids. The expression of genes related to Cu transport and chelation was altered in autotetraploid Arabidopsis under Cu stress, and several key genes involved in the response to abscisic acid (ABA) were significantly up-regulated. Our results indicate that tetraploid Arabidopsis esd and 4COL acquire improved tolerance to Cu stress through enhanced activation of antioxidative defense mechanisms, altered expression of genes related to Cu transport and chelation, and positive regulation of expression for ABA-responsive genes. [ABSTRACT FROM AUTHOR]

Polyploids are typically classified as autopolyploids or allopolyploids based on the origin of their chromosome sets. Autopolyploidy is much more common than traditionally believed. Allopolyploidization, accompanied by genomic and transcriptomic changes, has been well investigated. In this study, genetic, DNA methylation and gene expression changes in autotetraploid Brassica rapa were investigated. No genetic alteration was detected using an amplified fragment length polymorphism (AFLP) approach. Using a cDNA-AFLP approach, approximately 0.58% of fragments showed changes in gene expression in autotetraploid B. rapa. The methylation-sensitive amplification polymorphism (MSAP) analysis showed that approximately 1.7% of the fragments underwent DNA methylation changes upon genome doubling, with hypermethylation and demethylation changes equally affected. Fragments displaying changes in gene expression and methylation status were isolated and then sequenced and characterized, respectively. This study showed that variation in cytosine methylation is a major consequence of genome doubling in autotetraploid Brassica rapa. [ABSTRACT FROM AUTHOR]

Polyploidization can trigger rapid changes in morphology, ecology and genomics even in the absence of associated hybridization. However, disentangling the immediate biological consequences of genome duplication from the evolutionary change that subsequently accumulates in polyploid lineages requires the identification and analysis of recently formed polyploids. We investigated the incidence of polyploidization in introduced populations of Mimulus guttatus in the UK and report the discovery of a new mixed diploid-autopolyploid population in the Shetland Isles. We conducted a genetic analysis of six Shetland populations to investigate whether tetraploid individuals may have originated from local diploid plants and compared the morphology of tetraploids and local diploids to assess the phenotypic consequences of genome duplication. Autotetraploids are genetically close to sympatric diploids, suggesting that they have originated locally. Phenotypically, whole genome duplication has resulted in clear differences between ploidies, with tetraploids showing delayed phenology and larger flowers, leaves and stems than diploids. Our results support the hypothesis that novel evolutionary lineages can rapidly originate via polyploidization. The newly discovered autopolyploidization event in a non-native Mimulus population provides an opportunity to investigate the early causes and consequences of polyploidization in the wild. [ABSTRACT FROM AUTHOR]

Key message: A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium 8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. Abstract: Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population. B2721 consists of an IHN susceptible×resistant cross: Atlantic×B1829-5. We developed a next-generation SNP-based linkage map of this cross using the Infinium 8303 SNP array and conducted additional QTL analyses of IHN susceptibility in the B2721 population. Using SNP dosage sensitive markers, linkage maps for both parents were simultaneously analyzed. The linkage map contained 3427 SNPs and totaled 1397.68 cM. QTL were detected for IHN on chromosomes 1, 5, 9, and 12 using LOD permutation thresholds and colocation of high LOD scores across multiple years. Genetic effects were modeled for each putative QTL. Markers associated with a QTL were regressed in models of effects for IHN incidence and severity for all years. In the full model, the SNP markers were shown to have significant effects for IHN ( p < 0.0001), and explained 28.21% of the variation for incidence and 25.3% of the variation for severity. We were able to utilize SNP dosage information to identify and model the effects of putative QTL, and identify SNP loci associated with IHN resistance that need to be confirmed. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. [ABSTRACT FROM AUTHOR]

Paulownia australis has important economic and ecological values. In this study, the morphological and physiological changes of the leaves in diploid and autotetraploid P. australis under salt stress were analyzed. To detect related genes and gain a comprehensive perspective on the molecular mechanisms underlying salt tolerance in P. australis, transcriptome-wide gene expression profiling was conducted in the leaves of the diploid and autotetraploid P. australis under control and salinity conditions, respectively. Evaluation of the responses against salinity stress revealed the superiority of autotetraploid over diploid in terms of salinity tolerance. Changes in physiological parameters in diploid P. australis (PA2) and tetraploid P. australis (PA4) plants in response to salt stress were measured. Transcriptome data revealed that many of the common unigenes which were involved in accumulation of compatible solutes, oxidative stress detoxification, ion homeostasis, and signal transduction showed significant differences between the two accessions in response to salt stress. A number of salt-responsive unigenes were identified in two accessions of P. australis under salt stress. Furthermore, the differentially expressed unigenes found to be common in both accessions may be useful genetic resources for further genetic improvement of Paulownia using transgenic approaches. [ABSTRACT FROM AUTHOR]

Exposure to high salinity can trigger acclimation in many plants. Such an adaptative response is greatly advantageous for plants and involves extensive reprogramming at the molecular level. Acclimation allows plants to survive in environments that are prone to increasing salinity. In this study, diploid and autotetraploid Paulownia fortunei seedlings were used to detect alterations in leaf proteins in plants under salt stress. Up to 152 differentially abundant proteins were identified by Multiplex run iTRAQ-based quantitative proteomic and LC-MS/MS methods. Bioinformatics analysis suggested that P. fortunei leaves reacted to salt stress through a combination of common responses, such as induced metabolism, signal transduction, and regulation of transcription. This study offers a better understanding of the mechanisms of salt tolerance in P. fortunei and provides a list of potential target genes that could be engineered for salt acclimation in plants, especially trees. [ABSTRACT FROM AUTHOR]

Vicia cracca diploids and autotetraploids are highly parapatric in Europe; tetraploids reside in western and northern part, whereas diploids occupy much drier south-eastern part. They meet together in a Central European contact zone. This distribution pattern raised questions about a transformative effect of polyploidization on plant performance and environmental tolerances. We investigated plant survival, growth, and seed production in two water regimes in a common garden experiment using seeds collected from five localities in the Central European contact zone where diploids and tetraploids occur in sympatry. Obtained data imply that tetraploids of V. cracca are not generally superior in performance to diploids. Significantly larger seeds from tetraploid mother plants collected in the field were not correlated with greater stature of the seedlings. Nonetheless, tetraploids might have a potential to out-compete diploids in the long run due to the tetraploids' ability of greater growth which manifested in the second year of cultivation. Considering the response of diploids and tetraploids to water supply, drought stressed tetraploids but not diploids produced a higher proportion of aborted seeds than watered ones, which implies that tetraploids are more drought susceptible than diploids. On the other hand, decreased plant height in drought stresses tetraploids, which simultaneously increased total seed production, may suggest that tetraploids have a greater ability to avoid local extinction under unfavourable conditions by enhancing biomass allocation into production of seeds at the cost of lower growth. The significant interaction between ploidy level and locality in several traits suggests possible polyfyletic origin of tetraploids and the necessity to clarify the history of the tetraploids in Europe. [ABSTRACT FROM AUTHOR]

Background: Salmonids are ray-finned fishes which constitute 11 genera and at least 70 species including Atlantic salmon, whitefishes, graylings, rainbow trout, and char. The common ancestor of all Salmonidae experienced a whole genome duplication (WGD) ~80 million years ago, resulting in an autotetraploid genome. Genomic rediplodization is still going on in salmonid species, providing an unique system for studying evolutionary consequences of whole genome duplication. In recent years, high quality genome sequences of Atlantic salmon and Rainbow trout has been established, due to their scientific and commercial values. In this paper we introduce SalmoBase (http://www.salmobase.org/), a tool for making molecular resources for salmonids public available in a framework of visualizations and analytic tools. Results: SalmoBase has been developed as a part of the ELIXIR.NO project. Currently, SalmoBase contains molecular resources for Atlantic salmon and Rainbow trout. Data can be accessed through BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse) and Gene Expression Browser (GEBrowse). Conclusions: To the best of our knowledge, SalmoBase is the first database which integrates salmonids data and allow users to study salmonids in an integrated framework. The database and its tools (e.g., comparative genomics tools, synteny browsers) will be expanded as additional public resources describing other Salmonidae genomes become available. [ABSTRACT FROM AUTHOR]

Polyploidy is a key innovation in plant evolution that allows plants to adapt to various biotic stresses. Autotetraploid apple trees ( Malus × domestica ) perform better in the field than do diploid apple trees. Fungal diseases seriously affect the apple industry, and due to the long growth period of autopolyploid woody plants, little information is available on breeding disease-resistant artificially induced autotetraploid. The study aimed to evaluate the difference in disease resistance between autotetraploid and diploid apple plants and the difference in the expression levels of related genes that may be involved in disease resistance. Two autotetraploid apple cultivars, ‘Hanfu’ and ‘Gala’, perform better in response to Alternaria alternata and Colletotrichum gloeosporioides in that disease spot is smaller, infection is lighter and disease incidence is lower than those in the diploid. Real-time quantitative PCR analysis revealed that disease resistance-related genes were remarkably up-regulated in autotetraploid plants. These results could provide a theoretical basis for breeding disease-resistant autopolyploid apple plants. [ABSTRACT FROM AUTHOR]

Fertilization is a general feature of eukaryotic uni- and multicellular organisms to restore a diploid genome from female and male gamete haploid genomes. In angiosperms, polyploidization is a common phenomenon, and polyploidy would have played a major role in the long-term diversification and evolutionary success of plants. As for the mechanism of formation of autotetraploid plants, the triploid-bridge pathway, crossing between triploid and diploid plants, is considered as a major pathway. For the emergence of triploid plants, fusion of an unreduced gamete with a reduced gamete is generally accepted. In addition, the possibility of polyspermy has been proposed for maize, wheat and some orchids, although it has been regarded as an uncommon mechanism of triploid formation. One of the reasons why polyspermy is regarded as uncommon is because it is difficult to reproduce the polyspermy situation in zygotes and to analyze the developmental profiles of polyspermic triploid zygotes. Recently, polyspermic rice zygotes were successfully produced by electric fusion of an egg cell with two sperm cells, and their developmental profiles were monitored. Two sperm nuclei and an egg nucleus fused into a zygotic nucleus in the polyspermic zygote, and the triploid zygote divided into a two-celled embryo via mitotic division with a typical bipolar microtubule spindle. The two-celled proembryos further developed and regenerated into triploid plants. These suggest that polyspermic plant zygotes have the potential to form triploid embryos, and that polyspermy in angiosperms might be a pathway for the formation of triploid plants. [ABSTRACT FROM AUTHOR]

As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar's genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants. [ABSTRACT FROM AUTHOR]

Background: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. Results: A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during pollen and embryo sac development in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of DEM associated with embryo sac and pollen development revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development, while only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development in autotetraploid rice. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression patterns during pollen and embryo sac development. Of these DEM, osa-miR1436_L + 3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21 nt-phasiRNAs were detected during both pollen and embryo sac development, while 24 nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24 nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. Conclusion: The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-specific-24 nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice. [ABSTRACT FROM AUTHOR]

Cultivated potato ( Solanum tuberosum L.) is a highly heterozygous autotetraploid crop species, and this creates challenges for traditional line development and molecular breeding. Recent availability of a single-nucleotide polymorphism (SNP) array with 8303 features and software packages for linkage and association mapping in autotetraploid species present new opportunities for the identification of genomic regions that contribute to high-value traits in cultivated potato. A biparental tetraploid potato population was evaluated across three field seasons and storage trials in order to identify quantitative trait loci (QTL) for multiple tuber traits including fried chip color after 5.5-7.2 °C storage. Tetra-allelic dosage information was used to construct a genetic linkage map that covered 1041 cM and contained 2095 SNP markers with a median marker interval of 0.4 cM. A total of 41 QTL were identified for flower color, tuber yield, tuber number per plant, tuber weight, tuber size, and chip color after various storage regimes. Moderate effect QTL for chip color at 3 months were identified that co-localized with candidate genes vacuolar invertase ( VInv), invertase inhibitor ( INH2), and apoplastic invertase ( Inv -b). A separate QTL for chip color after 6 months of storage was identified in the short arm of chromosome 2, and this locus may contribute to variation in senescent sweetening resistance. QTL for tuber weight, length, and width co-localized with a known QTL for plant maturity on chromosome 5. Genome-wide association mapping using a polyploid model detected the tuber size QTL and identified a number of candidate SNPs, but was unable to detect markers significantly associated with chip color. [ABSTRACT FROM AUTHOR]

Verticillium wilt (VW) is a fungal disease that causes severe yield losses in alfalfa. The most effective method to control the disease is through the development and use of resistant varieties. The identification of marker loci linked to VW resistance can facilitate breeding for disease-resistant alfalfa. In the present investigation, we applied an integrated framework of genome-wide association with genotyping-by-sequencing (GBS) to identify VW resistance loci in a panel of elite alfalfa breeding lines. Phenotyping was performed by manual inoculation of the pathogen to healthy seedlings, and scoring for disease resistance was carried out according to the standard test of the North America Alfalfa Improvement Conference (NAAIC). Marker-trait association by linkage disequilibrium identified 10 single nucleotide polymorphism (SNP) markers significantly associated with VW resistance. Alignment of the SNP marker sequences to the M. truncatula genome revealed multiple quantitative trait loci (QTLs). Three, two, one and five markers were located on chromosomes 5, 6, 7 and 8, respectively. Resistance loci found on chromosomes 7 and 8 in the present study co-localized with the QTLs reported previously. A pairwise alignment ( blastn) using the flanking sequences of the resistance loci against the M. truncatula genome identified potential candidate genes with putative disease resistance function. With further investigation, these markers may be implemented into breeding programmes using marker-assisted selection, ultimately leading to improved VW resistance in alfalfa. [ABSTRACT FROM AUTHOR]