How Cold Shock Affects Ploidy Level and Early Ontogenetic Development of the Sterlet, A. ruthenus L.

The objective of the present research was to study the effect of cold shock (3 °C and 6 °C) on fertilized eggs of the sterlet, Acipenser ruthenus L. Cold shock was applied for various durations (30, 60 and 90 min) and the ploidy levels, survival, and genotypes of the treated embryos/larvae were recorded. Analysis of ploidy levels confirmed the presence of diploid, triploid, and mosaic (1n/2n, 2n/3n, and 1n/2n/3n) genotypes in experimental groups, while it was strictly diploid in control groups. Microsatellite genotyping confirmed both the incidence of polyspermy and retention of the 2nd polar body in experimental groups. However, patterns of inheritance in all diploid offspring in experimental and control groups revealed classical Mendelian disomic inheritance. Interestingly, the observed mosaic sterlets had normal morphology and were alive. However, some larvae had abnormal morphology which may be due to haploid syndrome. In all treatment groups (treatments: 3 °C–30 min; 3 °C–60 min; 3 °C–90 min; 6 °C–60 min), where the percentage of polyploid/mosaic larvae were high, the mortality was also high. Whereas, in the control groups (where there were only diploid (2n) larvae), the mortality was relatively low.

Evidence for hexasomic inheritance in Chrysanthemum morifolium Ramat. based on analysis of EST-SSR markers

Chrysanthemums (Chrysanthemum morifolium Ramat.) are ornamental flowers, which are famous worldwide. The mode of inheritance has great implications for the genetic analysis of polyploid species. However, genetic analysis of chrysanthemum has been hampered because of its controversial inheritance mode (disomic or hexasomic). To classify the inheritance mode of chrysanthemums, an analysis of three approaches was carried out in an F1 progeny of 192 offspring using 223 expressed sequence tag-simple sequence repeat (EST-SSR) markers. The analysis included segregation analysis, the ratio of simplex marker alleles linked in coupling to repulsion, as well as the transmission and segregation patterns of EST-SSR marker alleles. After segregation analysis, 204 marker alleles fit hexasomic inheritance and 150 marker alleles fit disomic inheritance, showing that marker alleles were inherited predominantly in a hexasomic manner. Furthermore, the results of the analysis of allele configuration and segregation behavior of five EST-SSR markers also suggested random pairing of chromosomes. Additionally, the ratio of simplex marker alleles linked in coupling to repulsion was 1:0, further supporting hexasomic inheritance. Therefore, it could be inferred that chrysanthemum is a complete or near-complete hexasome.

Patterns and Processes of Diploidization in Land Plants

Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing, disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

AllCoPol: inferring allele co-ancestry in polyploids

Background Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835–849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable. Results We present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition. Conclusions AllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.

Switchgrass as a bioenergy feedstock: advances in breeding and genomics research

Switchgrass (Panicum virgatum L), a native perennial of the North American prairie, possesses high biomass yield potential in marginal environments with limited input. It is an outcrossing tetraploid (2n = 4x = 36) with disomic inheritance. Previous research on cultivar improvement was focused primarily on herbage yield and forage digestibility. The decision of the U.S. Department of Energy Biomass Feedstock Development Program (NFDP) to develop switchgrass as a lignocellulosic bioenergy feedstock in the USA in the 1990s prompted a growing motivation for breeding and genomics research. The species is in early stages of domestication and current cultivars include mostly early releases for forage use that were selected directly from collected strains. Recent releases specifically for biomass feedstock have undergone one or two cycles of selection. As an outcrossing self-incompatible species, switchgrass possesses ample genetic diversity both between and within native populations. Conventional population improvement approaches such as recurrent restricted phenotypic selection (RRPS) are effective in improving forage yield and digestibility. Hybrids between different populations also demonstrated heterosis for key feedstock traits. However, genetic gains per year from selection using conventional approaches are low due to perennial growth habit and low heritability of important traits. Genomic approaches could be helpful in improving selection gain. Significant efforts have been placed in developing genomics resources. Genetic linkage maps were published and a large number of DNA-based markers were developed. Whole-genome sequencing is near completion, and the genetic bases of inheritance of key feedstock traits are being investigated. New insights into the molecular mechanisms will enable tailoring more efficient cultivar breeding approaches in the future.

Observation of the Disomic Inheritance of Four Allelic Pairs in the Octoploid Cultivated Strawberry

Although recent genetic studies suggest that octoploid cultivated strawberry, Fragaria ×ananassa Duch., is highly diploidized, there have been no reports that directly and clearly described the behavior of four allelic pairs. In this study, we demonstrated the disomic inheritance of four allelic pairs in F. ×ananassa by using two highly polymorphic simple sequence repeat markers. By genotyping the offspring of ‘Summer-princess’ (containing eight distinct alleles of marker FxaHGA02P13) × ‘Dekoruju’ (containing another four distinct alleles for this marker), four allelic pairs could be identified in ‘Summer-princess’. In a similar way, four allelic pairs could be identified for cultivar Ohishi-shikinari and marker EMFvi136. The results of this study provide direct evidence that at least part of the octoploid strawberry genome is fully diploidized and that the genome composition hypothesis AAA′A′BBB′B′ is possible as suggested by other recent genetic studies.