A Duplicated Copy of the Meiotic Gene ZIP4 Preserves up to 50% Pollen Viability and Grain Number in Polyploid Wheat.
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ABSTRACT:
SUBMITTER: Alabdullah AK
PROVIDER: S-EPMC8065865 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Of the many processes that generate gene duplications, polyploidy is unique in that entire genomes are duplicated. This process has been important in the evolution of many eukaryotic groups, and it occurs with high frequency in plants. Recent evidence suggests that polyploidization may be accompanied by rapid genomic changes, but the evolutionary fate of discrete loci recently doubled by polyploidy (homoeologues) has not been studied. Here we use locus-specific isolation techniques with comparative mapping to characterize the evolution of homoeologous loci in allopolyploid cotton (Gossypium hirsutum) and in species representing its diploid progenitors. We isolated and sequenced 16 loci from both genomes of the allopolyploid, from both progenitor diploid genomes and appropriate outgroups. Phylogenetic analysis of the resulting 73.5 kb of sequence data demonstrated that for all 16 loci (14.7 kb/genome), the topology expected from organismal history was recovered. In contrast to observations involving repetitive DNAs in cotton, there was no evidence of interaction among duplicated genes in the allopolyploid. Polyploidy was not accompanied by an obvious increase in mutations indicative of pseudogene formation. Additionally, differences in rates of divergence among homoeologues in polyploids and orthologues in diploids were indistinguishable across loci, with significant rate deviation restricted to two putative pseudogenes. Our results indicate that most duplicated genes in allopolyploid cotton evolve independently of each other and at the same rate as those of their diploid progenitors. These indications of genic stasis accompanying polyploidization provide a sharp contrast to recent examples of rapid genomic evolution in allopolyploids.
| S-EPMC24449 | biostudies-literature
Project description:Meiotic recombination is triggered by programmed double-strand breaks (DSBs), a subset of these being repaired as crossovers, promoted by eight evolutionarily conserved proteins, named ZMM. Crossover formation is functionally linked to synaptonemal complex (SC) assembly between homologous chromosomes, but the underlying mechanism is unknown. Here we show that Ecm11, a SC central element protein, localizes on both DSB sites and sites that attach chromatin loops to the chromosome axis, which are the starting points of SC formation, in a way that strictly requires the ZMM protein Zip4. Furthermore, Zip4 directly interacts with Ecm11, and point mutants that specifically abolish this interaction lose Ecm11 binding to chromosomes and exhibit defective SC assembly. This can be partially rescued by artificially tethering interaction-defective Ecm11 to Zip4. Mechanistically, this direct connection ensuring SC assembly from CO sites could be a way for the meiotic cell to shut down further DSB formation once enough recombination sites have been selected for crossovers, thereby preventing excess crossovers. Finally, the mammalian ortholog of Zip4, TEX11, also interacts with the SC central element TEX12, suggesting a general mechanism.
| S-EPMC8763056 | biostudies-literature
Project description:Background and aimsLeymus chinensis is an economically and ecologically important grass that is widely distributed across eastern areas of the Eurasian steppe. A major problem facing its propagation by man is its low sexual reproductivity. The causes of low fecundity are uncertain, largely because many aspects of the reproductive biology of this species remained unknown or incomplete. This study aims to address some of these issues.MethodsPollen dispersion, pollen viability, pollen longevity and pistil receptivity were studied in a representative, natural population of L. chinensis growing in Inner Mongolia.Key resultsFlowering of L. chinensis occurred at the end of June and lasted for 5 d. Pollination peaked between 1600 h and 1700 h, and about 56.1 % of the total pollen grains were released at this time. Pollen density was highest towards the middle of flowering spikes and lowest at the bottom over the 5 d measurement period. Pollen viability (62.4 %) assessed using TTC was more accurate than using IKI (85.6 %); 50 % of pollen arriving on stigmas germinated. Pollen remained viable for only 3 h and the pollen : ovule ratio was 79 333 : 1. Pistil receptivity lasted for only 3 h and, overall, 86.7 % of pistils were pollinated. Within the spike, the relative fecundity of different positions was middle > lower > upper throughout the period of pollination; daily variation of fecundity was similar to that of the pollen flow. The spikes that opened on the day of highest pollen density exhibited the highest fecundity (36.0 %). No seeds were produced by self-pollination.ConclusionsThe data suggest that low pollen viability, short pollen longevity and short pistil receptivity all appear to contribute to the low seed production typical of this important forage crop.
| S-EPMC4242205 | biostudies-literature
Project description:Wheat sheds tricellular short-lived pollen at maturity. The identification of viable pollen required for high seed set is important for breeders and conservators. The present study aims to evaluate and improve pollen viability tests and to identify factors influencing viability of pollen. In fresh wheat pollen, sucrose was the most abundant soluble sugar (90%). Raffinose was present in minor amounts. However, the analyses of pollen tube growth on 112 liquid and 45 solid media revealed that solid medium with 594 mM raffinose, 0.81 mM H3BO3, 2.04 mM CaCl2 at pH5.8 showed highest pollen germination. Partly or complete substitution of raffinose by sucrose, maltose, or sorbitol reduced in vitro germination of the pollen assuming a higher metabolic efficiency or antioxidant activity of raffinose. In vitro pollen germination varied between 26 lines (P < 0.001); between winter (15.3 ± 8.5%) and spring types (30.2 ± 13.3%) and was highest for the spring wheat TRI 2443 (50.1 ± 20.0%). Alexander staining failed to discriminate between viable, fresh pollen, and non-viable pollen inactivated by ambient storage for >60 min. Viability of fresh wheat pollen assessed by fluorescein diacetate (FDA) staining and impedance flow (IF) cytometry was 79.2 ± 4.2% and 88.1 ± 2.7%, respectively; and, when non-viable, stored pollen was additionally tested, it correlated at r = 0.54 (P < 0.05) and r = 0.67 (P < 0.001) with in vitro germination, respectively. When fresh pollen was used to assess the pollen viability of 19 wheat, 25 rye, 11 barley, and 4 maize lines, correlations were absent and in vitro germination was lower for rye (11.7 ± 8.5%), barley (6.8 ± 4.3%), and maize (2.1 ± 1.8%) pollen compared to wheat. Concluding, FDA staining and IF cytometry are used for a range of pollen species, whereas media for in vitro pollen germination require specific adaptations; in wheat, a solid medium with raffinose was chosen. On adapted media, the pollen tube growth can be exactly analyzed whereas results achieved by FDA staining and IF cytometry are higher and may overestimate pollen tube growth. Hence, as the exact viability and fertilization potential of a larger pollen batch remains elusive, a combination of pollen viability tests may provide reasonable indications of the ability of pollen to germinate and grow.
| S-EPMC6987437 | biostudies-literature
Project description:Control over cell viability is a fundamental property underlying numerous physiological processes. Cell spreading on a substrate was previously demonstrated to be a major factor in determining the viability of individual cells. In multicellular organisms, cell-cell contact is likely to play a significant role in regulating cell vitality, but its function is easily masked by cell-substrate interactions, thus remains incompletely characterized. In this study, we show that suspended immortalized human keratinocyte sheets with persisting intercellular contacts exhibited significant contraction, junctional actin localization, and reinforcement of cell-cell adhesion strength. Further, cells within these sheets remain viable, in contrast to trypsinized cells suspended without either cell-cell or cell-substrate contact, which underwent apoptosis at high rates. Suppression of plakoglobin weakened cell-cell adhesion in cell sheets and suppressed apoptosis in suspended, trypsinized cells. These results demonstrate that cell-cell contact may be a fundamental control mechanism governing cell viability and that the junctional protein plakoglobin is a key regulator of this process. Given the near-ubiquity of plakoglobin in multicellular organisms, these findings could have significant implications for understanding cell adhesion, modeling disease progression, developing therapeutics and improving the viability of tissue engineering protocols.
| S-EPMC3203941 | biostudies-literature
Project description:Pollen quality is important for growers and breeders. This study was carried out to determine in vitro pollen viability and pollen germination in seven genotypes of cherry laurel (Prunus laurocerasus L.). Two pollen viability tests, TTC (2,3,5-triphenyl tetrazolium chloride) and IKI (iodine potassium iodide), were used. Pollen traits of genotypes were studied using an in vitro medium containing 0%, 5%, 10%, 15%, and 20% sucrose to determine the best sucrose concentrations for germination. In the second step, the germinated pollen was counted 1, 4, 6, 10, 12, 24, and 48 hours later until there was no further germination. The viability rates were different according to genotypes and tests used. The IKI and TTC staining tests and pollen germination had low correlation (r(2) = 0.0614 and r(2) = 0.0015, resp.). Painted pollen rate was higher and pollen was well-stained with IKI test and pollen viability estimated with TTC staining test was better than that estimated with the IKI staining test. 15% sucrose gave the best germination rates in most of the genotypes. Pollen germination rates were recorded periodically from one hour to 48 hours in 15% sucrose and the results showed that pollen germination rates increased after 6 hours of being placed in culture media.
| S-EPMC4227381 | biostudies-other
Project description:Evolutionary fates of duplicated genes have been widely investigated in many polyploid plants and animals, but research is scarce in recurrent polyploids. In this study, we focused on foxl2, a central player in ovary, and elaborated the functional divergence in gibel carp (Carassius gibelio), a recurrent auto-allo-hexaploid fish. First, we identified three divergent foxl2 homeologs (Cgfoxl2a-B, Cgfoxl2b-A, and Cgfoxl2b-B), each of them possessing three highly conserved alleles and revealed their biased retention/loss. Then, their abundant sexual dimorphism and biased expression were uncovered in hypothalamic-pituitary-gonadal axis. Significantly, granulosa cells and three subpopulations of thecal cells were distinguished by cellular localization of CgFoxl2a and CgFoxl2b, and the functional roles and the involved process were traced in folliculogenesis. Finally, we successfully edited multiple foxl2 homeologs and/or alleles by using CRISPR/Cas9. Cgfoxl2a-B deficiency led to ovary development arrest or complete sex reversal, whereas complete disruption of Cgfoxl2b-A and Cgfoxl2b-B resulted in the depletion of germ cells. Taken together, the detailed cellular localization and functional differences indicate that Cgfoxl2a and Cgfoxl2b have subfunctionalized and cooperated to regulate folliculogenesis and gonad differentiation, and Cgfoxl2b has evolved a new function in oogenesis. Therefore, the current study provides a typical case of homeolog/allele diversification, retention/loss, biased expression, and sub-/neofunctionalization in the evolution of duplicated genes driven by polyploidy and subsequent diploidization from the recurrent polyploid fish.
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Project description:Bee-pollinated plants face a dilemma in that bees both passively transport pollen grains among conspecific flowers and actively collect pollen to feed their larvae. Therefore, mechanisms that reduce pollen collection by bees have evolved in melittophilous plants. Malvaceae pollen is uncollectable for corbiculate bees which has previously been ascribed to pollen size, spines, and pollenkitt. We analysed the influence of pollen grain properties (diameter, spine length, spine density) on the collectability of echinate (spiny) pollen by bumble bees (Bombus terrestris). Workers individually foraging on one of eight plant species from six families performed significantly less pollen foraging on plants which have large, echinate pollen grains. Nevertheless, neither pollen grain size, spine length, nor spine density prove to be an absolute disqualifier for collectability. While pollen foragers did not shift to nectar collection but seized visiting flowers with uncollectable pollen, nectar foragers performed regular foraging bouts on these plants. Pollen that is uncollectable for corbiculate bees limits pollen depletion by generalist bumble bees and probably also honey bees while maintaining them as pollinators, which is an effective solution to the pollen dilemma. As previous assumptions about the impact of pollen morphology on its collectability are disproved, potentially determining factors are discussed.
| S-EPMC6423004 | biostudies-literature
Project description:Pollen identification is an important task for the botanical certification of honey. It is performed via thorough microscopic examination of the pollen present in honey; a process called melissopalynology. However, manual examination of the images is hard, time-consuming and subject to inter- and intra-observer variability. In this study, we investigated the applicability of deep learning models for the classification of pollen-grain images into 20 pollen types, based on the Cretan Pollen Dataset. In particular, we applied transfer and ensemble learning methods to achieve an accuracy of 97.5%, a sensitivity of 96.9%, a precision of 97%, an F1 score of 96.89% and an AUC of 0.9995. However, in a preliminary case study, when we applied the best-performing model on honey-based pollen-grain images, we found that it performed poorly; only 0.02 better than random guessing (i.e., an AUC of 0.52). This indicates that the model should be further fine-tuned on honey-based pollen-grain images to increase its effectiveness on such data.
| S-EPMC9002917 | biostudies-literature
Project description:Genomic sequence duplication is an important mechanism for genome evolution, often resulting in large sequence variations with implications for disease progression. Although paired-end sequencing technologies are commonly used for structural variation discovery, the discovery of novel duplicated sequences remains an unmet challenge. We analyze duplicons starting from identified high-copy number variants. Given paired-end mapped reads, and a candidate high-copy region, our tool, Reprever, identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon. Reprever resolves ambiguous mapping signatures from existing homologs, repetitive elements and sequencing errors to identify breakpoint. At each breakpoint, Reprever reconstructs the inserted sequence using profile hidden Markov model (PHMM)-based guided assembly. In a test on 1000 artificial genomes with simulated duplication, Reprever could identify novel duplicates up to 97% of genomes within 3 bp positional and 1% sequence errors. Validation on 680 fosmid sequences identified and reconstructed eight duplicated sequences with high accuracy. We applied Reprever to reanalyzing a re-sequenced data set from the African individual NA18507 to identify >800 novel duplicates, including insertions in genes and insertions with additional variation. polymerase chain reaction followed by capillary sequencing validated both the insertion locations of the strongest predictions and their predicted sequence.
| S-EPMC3695505 | biostudies-literature