Evaluation of Bermudagrass [Cynodon (L.) Rich] Accessions with Different Ploidy Levels

AbstractKinesins play important roles in the progression and development of cancer. Kinesin family member C1 (KIFC1), a minus end-directed motor protein, is a novel Kinesin involved in the clustering of excess centrosomes found in cancer cells. Recently KIFC1 has shown to play a role in the progression of many different cancers, however, the involvement of KIFC1 in the progression of prostate cancer (PCa) is still not well understood. This study investigated the expression and clinical significance of KIFC1 in PCa by utilizing multiple publicly available datasets to analyze KIFC1 expression in patient samples. High KIFC1 expression was found to be associated with high Gleason score, high tumor stage, metastatic lesions, high ploidy levels, and lower recurrence-free survival. These results reveal that high KIFC1 levels are associated with a poor prognosis for PCa patients and could act as a prognostic indicator for PCa patients as well.

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Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex

BMC Plant Biology ◽

10.1186/s12870-021-03099-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhi Wang ◽

Caihong Zhong ◽

Dawei Li ◽

Chunlin Yan ◽

Xiaohong Yao ◽

...

Keyword(s):

Environmental Changes ◽

Demographic History ◽

Wide Distribution ◽

Historical Demography ◽

Actinidia Chinensis ◽

Ecological Niche Models ◽

Subtropical China ◽

Modeling Tools ◽

Climatic Fluctuations ◽

Ploidy Levels

Abstract Background Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. Results The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties’ ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). Conclusions Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.

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Applying RGB- and Thermal-Based Vegetation Indices from UAVs for High-Throughput Field Phenotyping of Drought Tolerance in Forage Grasses

Remote Sensing ◽

10.3390/rs13010147 ◽

2021 ◽

Vol 13 (1) ◽

pp. 147

Author(s):

Tom De Swaef ◽

Wouter H. Maes ◽

Jonas Aper ◽

Joost Baert ◽

Mathias Cougnon ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Lolium Perenne ◽

High Throughput ◽

Festuca Arundinacea ◽

Stress Index ◽

Forage Grasses ◽

Crop Water Stress Index ◽

Ploidy Levels ◽

Field Phenotyping

The persistence and productivity of forage grasses, important sources for feed production, are threatened by climate change-induced drought. Breeding programs are in search of new drought tolerant forage grass varieties, but those programs still rely on time-consuming and less consistent visual scoring by breeders. In this study, we evaluate whether Unmanned Aerial Vehicle (UAV) based remote sensing can complement or replace this visual breeder score. A field experiment was set up to test the drought tolerance of genotypes from three common forage types of two different species: Festuca arundinacea, diploid Lolium perenne and tetraploid Lolium perenne. Drought stress was imposed by using mobile rainout shelters. UAV flights with RGB and thermal sensors were conducted at five time points during the experiment. Visual-based indices from different colour spaces were selected that were closely correlated to the breeder score. Furthermore, several indices, in particular H and NDLab, from the HSV (Hue Saturation Value) and CIELab (Commission Internationale de l’éclairage) colour space, respectively, displayed a broad-sense heritability that was as high or higher than the visual breeder score, making these indices highly suited for high-throughput field phenotyping applications that can complement or even replace the breeder score. The thermal-based Crop Water Stress Index CWSI provided complementary information to visual-based indices, enabling the analysis of differences in ecophysiological mechanisms for coping with reduced water availability between species and ploidy levels. All species/types displayed variation in drought stress tolerance, which confirms that there is sufficient variation for selection within these groups of grasses. Our results confirmed the better drought tolerance potential of Festuca arundinacea, but also showed which Lolium perenne genotypes are more tolerant.

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Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels

Genetics ◽

10.1093/genetics/iyaa048 ◽

2021 ◽

Vol 217 (2) ◽

Author(s):

L E Puhl ◽

J Crossa ◽

S Munilla ◽

P Pérez-Rodríguez ◽

R J C Cantet

Keyword(s):

Hexaploid Wheat ◽

Variance Components ◽

Bayesian Model ◽

Synthetic Hexaploid Wheat ◽

Data Sets ◽

Hierarchical Bayesian Model ◽

Additive Variance ◽

Ploidy Levels ◽

Breeding Values ◽

Synthetic Hexaploid

Abstract Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii—T. aestivum and T. turgidum—T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.

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Three founding ancestral genomes involved in the origin of sugarcane

Annals of Botany ◽

10.1093/aob/mcab008 ◽

2021 ◽

Author(s):

Nicolas Pompidor ◽

Carine Charron ◽

Catherine Hervouet ◽

Stéphanie Bocs ◽

Gaëtan Droc ◽

...

Keyword(s):

Evolutionary Model ◽

Saccharum Officinarum ◽

Modern Cultivar ◽

Ploidy Levels ◽

Saccharum Spp ◽

Bac Clones ◽

B Genome ◽

A Genome ◽

Genomic Regions ◽

Complex Genome

Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

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Autotetraploid Emergence via Somatic Embryogenesis in Vitis vinifera Induces Marked Morphological Changes in Shoots, Mature Leaves, and Stomata

Cells ◽

10.3390/cells10061336 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1336

Author(s):

Caterina Catalano ◽

Loredana Abbate ◽

Antonio Motisi ◽

Dalila Crucitti ◽

Vincenzo Cangelosi ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Morphological Changes ◽

Ploidy Levels ◽

Dna Profile ◽

Morphological Alterations ◽

Cell Pair ◽

Mature Leaves ◽

Induction Process ◽

Ploidy Changes ◽

Dna Profiles

Polyploidy plays an important role in plant adaptation to biotic and abiotic stresses. Alterations of the ploidy in grapevine plants regenerated via somatic embryogenesis (SE) may provide a source of genetic variability useful for the improvement of agronomic characteristics of crops. In the grapevine, the SE induction process may cause ploidy changes without alterations in DNA profile. In the present research, tetraploid plants were observed for 9.3% of ‘Frappato’ grapevine somatic embryos regenerated in medium supplemented with the growth regulators β-naphthoxyacetic acid (10 µM) and N6-benzylaminopurine (4.4 µM). Autotetraploid plants regenerated via SE without detectable changes in the DNA profiles were transferred in field conditions to analyze the effect of polyploidization. Different ploidy levels induced several anatomical and morphological changes of the shoots and mature leaves. Alterations have been also observed in stomata. The length and width of stomata of tetraploid leaves were 39.9 and 18.6% higher than diploids, respectively. The chloroplast number per guard cell pair was higher (5.2%) in tetraploid leaves. On the contrary, the stomatal index was markedly decreased (12%) in tetraploid leaves. The observed morphological alterations might be useful traits for breeding of grapevine varieties in a changing environment.

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Male meiosis and pollen morphology in diploid Indonesian wild bananas and cultivars

The Nucleus ◽

10.1007/s13237-021-00350-7 ◽

2021 ◽

Author(s):

Fajarudin Ahmad ◽

Yuyu S. Poerba ◽

Gert H. J. Kema ◽

Hans de Jong

Keyword(s):

Hybrid Sterility ◽

Pollen Grains ◽

Chromosome Analysis ◽

Male Meiosis ◽

Enzyme Treatment ◽

Unreduced Gamete ◽

Ploidy Levels ◽

Scientific Disciplines ◽

Sterile Pollen ◽

Mother Cells

AbstractBreeding of banana is hampered by its genetic complexity, structural chromosome rearrangements and different ploidy levels. Various scientific disciplines, including cytogenetics, linkage mapping, and bioinformatics, are helpful tools in characterising cultivars and wild relatives used in crossing programs. Chromosome analysis still plays a pivotal role in studying hybrid sterility and structural and numerical variants. In this study, we describe the optimisation of the chromosome spreading protocol of pollen mother cells focusing on the effects of standard fixation methods, duration of the pectolytic enzyme treatment and advantages of fluorescence microscopy of DAPI stained cell spreads. We demonstrate the benefits of this protocol on meiotic features of five wild diploid Musa acuminata bananas and a diploid (AA) cultivar banana “Rejang”, with particular attention on pairing configurations and chromosome transmission that may be indicative for translocations and inversions. Pollen slides demonstrate regular-shaped spores except “Rejang”, which shows fertile pollen grains of different size and sterile pollen grains, suggesting partial sterility and unreduced gamete formation that likely resulted from restitutional meiotic divisions.

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Effect of Seasonal Drought on the Agronomic Performance of Four Banana Genotypes (Musa spp.) in the East African Highlands

Agronomy ◽

10.3390/agronomy11010004 ◽

2020 ◽

Vol 11 (1) ◽

pp. 4

Author(s):

Brigitte Uwimana ◽

Yasmín Zorrilla-Fontanesi ◽

Jelle van Wesemael ◽

Hassan Mduma ◽

Allan Brown ◽

...

Keyword(s):

Yield Traits ◽

East African ◽

Ploidy Levels ◽

Early Effect ◽

Seasonal Drought ◽

Musa Spp ◽

Drought Tolerant ◽

Genome Group ◽

African Highlands ◽

East African Highlands

Banana (Musa spp.), a perennial (sub-)tropical crop, suffers from seasonal droughts, which are typical of rain-fed agriculture. This study aimed at understanding the effect of seasonal drought on early growth, flowering and yield traits in bananas grown in the East African highlands. A field experiment was set up in North Tanzania using four genotypes from different geographical origins and two different ploidy levels. The treatments considered were exclusively rain-fed versus rain supplemented with irrigation. Growth in plant girth and leaf area were promising traits to detect the early effect of water deficit. Seasonal drought slowed down vegetative growth, thus significantly decreasing plant girth, plant height and the number of suckers produced when compared to irrigated plants. It also delayed flowering time and bunch maturity and had a negative effect on yield traits. However, the results depended on the genotype and crop cycle and their interaction with the treatments. “Nakitengwa”, an East African highland banana (EAHB; AAA genome group), which is adapted to the region, showed sensitivity to drought in terms of reduced bunch weight and expected yield, while “Cachaco” (ABB genome group) showed less sensitivity to drought but had a poorer yield than “Nakitengwa”. Our study confirms that seasonal drought has a negative impact on banana production in East Africa, where EAHBs are the most predominant type of bananas grown in the region. We also show that a drought-tolerant cultivar not adapted to the East African highlands had a low performance in terms of yield. We recommend a large-scale screening of diploid bananas to identify drought-tolerant genotypes to be used in the improvement of locally adapted and accepted varieties.

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Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

Genes ◽

10.3390/genes12070957 ◽

2021 ◽

Vol 12 (7) ◽

pp. 957

Author(s):

Paulina Tomaszewska ◽

Till K. Pellny ◽

Luis M. Hernández ◽

Rowan A. C. Mitchell ◽

Valheria Castiblanco ◽

...

Keyword(s):

Flow Cytometry ◽

Germplasm Collection ◽

Forage Grass ◽

Breeding Programs ◽

Robust Identification ◽

Ploidy Levels ◽

Sustainable Improvement ◽

Tropical Forage ◽

Relative Differences

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the ’brizantha’ and ’humidicola’ agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.

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