Chromosome segment detection for seed size and shape traits using an improved population of wild soybean chromosome segment substitution lines

Size and shape of soybean seeds are closely related to seed yield and market value. Annual wild soybeans have the potential to improve cultivated soybeans, but their inferior seed characteristics should be excluded. To detect quantitative trait loci (QTLs)/segments of seed size and shape traits in annual wild soybean, its chromosome segment substitution lines (CSSLs) derived from NN1138-2 (recurrent parent, Glycine max) and N24852 (donor parent, Glycine soja) and then modified 2 iterations (coded SojaCSSLP3) were improved further to contain more lines (diagonal segments) and less heterozygous and missing portions. The new population (SojaCSSLP4) composed of 195 CSSLs was evaluated under four environments, and 11, 13, 7, 15 and 14 QTLs/segments were detected for seed length (SL), seed width (SW), seed roundness (SR), seed perimeter (SP) and seed cross section area (SA), respectively, with all 60 wild allele effects negative. Among them, 16 QTLs/segments were shared by 2–5 traits, respectively, but 0–3 segments for each of the 5 traits were independent. The non-shared Satt274 and shared Satt305, Satt540 and Satt239 were major segments, along with other segments composed of two different but related sets of genetic systems for SR and the other 4 traits, respectively. Compared with the literature, 7 SL, 5 SW and 2 SR QTLs/segments were also detected in cultivated soybeans; allele distinction took place between cultivated and wild soybeans, and also among cultivated parents. The present mapping is understood as macro-segment mapping, the segments may be further dissected into smaller segments as well as corresponding QTLs/genes.     

Correlations between chromosome segments and fitness in Drosophila melanogaster. IV. Fecundity, viability and the third chromosome

Unmarked segments within the third chromosome of three different Drosophila melanogaster lines were assessed for their effects on egg production and egg viability. By making a series of crosses among original and derived recombinant lines, it was possible to estimate parameters representing additive, dominance (for egg production), and interaction effects of the segments. Each segment influences both traits, but to extend which are dependent on the genetic background provided by an adjacent segment. There is no clear pattern, however, with respect to the segments' joint effects on the two characters. Unlike in the previous study involving the X chromosome, the majority of the derived recombinant lines were superior in fitness to their original lines. The agricultural implications of this result with respect to the manipulation of chromosomal segments in order to achieve higher yields are discussed.     

Latitudinal variation in seeds characteristics of Acer platanoides and A. pseudoplatanus

Climate change will likely affect population dynamics of numerous plant species by modifying several aspects of the life cycle. Because plant regeneration from seeds may be particularly vulnerable, here we assess the possible effects of climate change on seed characteristics and present an integrated analysis of seven seed traits (nutrient concentrations, samara mass, seed mass, wing length, seed viability, germination percentage, and seedling biomass) of Acer platanoides and A. pseudoplatanus seeds collected along a wide latitudinal gradient from Italy to Norway. Seed traits were analyzed in relation to the environmental conditions experienced by the mother trees along the latitudinal gradient. We found that seed traits of A. platanoides were more influenced by the climatic conditions than those of A. pseudoplatanus. Additionally, seed viability, germination percentage, and seedling biomass of A. platanoides were strongly related to the seed mass and nutrient concentration. While A. platanoides seeds were more influenced by the environmental conditions (generally negatively affected by rising temperatures), compared to A. pseudoplatanus, A. platanoides still showed higher germination percentage and seedling biomass than A. pseudoplatanus. Thus, further research on subsequent life-history stages of both species is needed. The variation in seed quality observed along the climatic gradient highlights the importance of studying the possible impact of climate change on seed production and species demography.     

Homozygous and Hemizygous Viability Variation on the X Chromosome of DROSOPHILA MELANOGASTER

We report here a study of viability inbreeding depression associated with the X chromosome of Drosophila melanogaster. Fifty wild chromosomes from Mt. Sinai, New York, and 90 wild chromosomes from Death Valley, California, were extracted using the marked FM6 balancer chromosome and viabilities measured for homozygous and heterozygous females, and for hemizygous males, relative to FM6 males as a standard genotype. No statistically significant female genetic load was observed for either chromosome set, although a 95% confidence limit estimated the total load <0.046 for the samples pooled. About 10% of the Death Valley chromosomes appear to be "supervital" as homozygotes. There is little evidence for a pervasive sex-limited detrimental load on the X chromosome; the evidence indicates nearly identical viability effects in males and homozygous females excluding the supervital chromosomes. The average degree of dominance for viability polygenes is estimated between 0.23 to 0.36, which is consistent with autosomal variation and implies near additivity. We conclude that there is little genetic load associated with viability variation on the X chromosome and that the substantial reduction in total fitness observed for chromosome homozygosity in an earlier study may be due largely to sex-limited fertility in females.     

Parental Influences on Pathogen Resistance in Brown Trout Embryos and Effects of Outcrossing within a River Network

Phenotypic plasticity can increase tolerance to heterogeneous environments but the elevations and slopes of reaction norms are often population specific. Disruption of locally adapted reaction norms through outcrossing can lower individual viability. Here, we sampled five genetically distinct populations of brown trout (Salmo trutta) from within a river network, crossed them in a full-factorial design, and challenged the embryos with the opportunistic pathogen Pseudomonas fluorescens. By virtue of our design, we were able to disentangle effects of genetic crossing distance from sire and dam effects on early life-history traits. While pathogen infection did not increase mortality, it was associated with delayed hatching of smaller larvae with reduced yolk sac reserves. We found no evidence of a relationship between genetic distance (W, F_ST) and the expression of early-life history traits. Moreover, hybrids did not differ in phenotypic means or reaction norms in comparison to offspring from within-population crosses. Heritable variation in early life-history traits was found to remain stable across the control and pathogen environments. Our findings show that outcrossing within a rather narrow geographical scale can have neutral effects on F₁ hybrid viability at the embryonic stage, i.e. at a stage when environmental and genetic effects on phenotypes are usually large.     

Analysis of the functional significance of linkage group conservation in Drosophila

Linkage groups, as defined by chromosome arms in Drosophila melanogaster, appear to have remained largely intact within the genus Drosophila and, possibly, within the higher Diptera per se. We hypothesized that linkage group conservation might have a functional basis (possibly related to interphase chromosome arrangement). To test this hypothesis, a series of autosomal 2–3 translocations were synthesized, creating many new linkage groups. A total of 167 2–3 translocations were recovered, cytologically analyzed to determine their polytene chromosome breakpoints, and tested for homozygous viability and fertility. The breakpoints associated with homozygous viable translocations were randomly distributed throughout the genome, indicating that the linear continuity of the linkage groups could be disrupted quite extensively. Inter se complementation crosses between homozygous lethal translocations having similar breakpoints further confirmed this result, documenting that, at least with respect to homozygous viability, the linear integrity of the autosomal linkage groups was not of major functional significance. Fertility analysis of the homozygous translocations also indicated that sterility could not be a single major factor. Having concluded that linkage group conservation is not based on important functional interactions between specific linked chromosomal segments, or due principally to the sterility of new linkages, the problem of linkage group conservation remains unsolved. Several possible selective factors are discussed, principally segregational load and inbreeding depression, which may contribute to the elimination of new linkage rearrangements.     

A Comparison of Inbreeding Depression in Tropical and Widespread Drosophila Species

The evolutionary history of widespread and specialized species is likely to cause a different genetic architecture of key ecological traits in the two species groups. This may affect how these two groups respond to inbreeding. Here we investigate inbreeding effects in traits related to performance in 5 widespread and 5 tropical restricted species of Drosophila with the aim of testing whether the two species groups suffered differently from inbreeding depression. The traits investigated were egg-to-adult viability, developmental time and resistance to heat, cold and desiccation. Our results showed that levels of inbreeding depression were species and trait specific and did not differ between the species groups for stress resistance traits. However, for the life history traits developmental time and egg-to adult viability, more inbreeding depression was observed in the tropical species. The results reported suggest that for life history traits tropical species of Drosophila will suffer more from inbreeding depression than widespread species in case of increases in the rate of inbreeding e.g. due to declines in population sizes.     

Differential Sensitivities and the Target of Heat-Induced Recombination at the Base of the X Chromosome of DROSOPHILA MELANOGASTER

The effect of heat on two small adjacent segments at the base of the X chromosome was examined. Recombination in the two segments delimited by recessive lethals was measured after treatment with 30° and 34°.Both segments were sensitive at 30°, while only the proximal one responded to 34° treatment. When the same segments were studied in structural heterozygotes (for deletions) the relative increase in recombination was greater, suggesting that heat exerts its effect on the "pairing" rather than the "exchange" components of crossing over. The effect of c (3) G/+ on the same segments in both homozygous and heterozygous structurals was studied. The results indicate that this meiotic mutant mediates its effect on a step different than that affected by heat.     

A comparison of partial dehydration and hydrated storage-induced changes in viability,reactive oxygen species production,and glutathione metabolism in two contrasting recalcitrant-seeded species

This study compared the responses of Avicennia marina and Trichilia dregeana seeds, both of which are recalcitrant, to partial dehydration and storage. Seeds of A. marina exhibited a faster rate of water and viability loss (± 50% viability loss in 4 days) during partial dehydration, compared with T. dregeana (± 50% viability loss in 14 days). In A. marina embryonic axes, reactive oxygen species (ROS) production peaked on 4 days of dehydration and was accompanied by an increase in the GSH:GSSG ratio; it appears that the glutathione system alone could not overcome dehydration-induced oxidative stress in this species. In A. marina, ROS and axis water content levels increased during hydrated storage and were accompanied by a decline in the GSH:GSSG ratio and rapid viability loss. In T. dregeana embryonic axes, ROS production (particularly hydrogen peroxide) initially increased and thereafter decreased during both partial dehydration and hydrated storage. Unlike in A. marina embryonic axes, this reduced ROS production was accompanied by a decline in the GSH:GSSG ratio. While T. dregeana seeds may have incurred some oxidative stress during storage, a delay in and/or suppression of the ROS-based trigger for germination may account for their significantly longer storage longevity compared with A. marina. Mechanisms of desiccation-induced seed viability loss may differ across recalcitrant-seeded species based on the rate and extent to which they lose water during partial drying and storage. While recalcitrant seed desiccation sensitivity and, by implication, storage longevity are modulated by redox metabolism, the specific ROS and antioxidants that contribute to this control may differ across species.     

A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Key message

A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits.

Abstract

Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar ‘Zhongyou 821’ (ZY821) as the recipient and a re-synthesized line ‘No.2127’ as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC₅F₄ were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56?×?of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.

     

The genetic covariance between life cycle stages separated by metamorphosis

Metamorphosis is common in animals, yet the genetic associations between life cycle stages are poorly understood. Given the radical changes that occur at metamorphosis, selection may differ before and after metamorphosis, and the extent that genetic associations between pre- and post-metamorphic traits constrain evolutionary change is a subject of considerable interest. In some instances, metamorphosis may allow the genetic decoupling of life cycle stages, whereas in others, metamorphosis could allow complementary responses to selection across the life cycle. Using a diallel breeding design, we measured viability at four ontogenetic stages (embryo, larval, juvenile and adult viability), in the ascidian Ciona intestinalis and examined the orientation of additive genetic variation with respect to the metamorphic boundary. We found support for one eigenvector of G (g_obsmax), which contrasted larval viability against embryo viability and juvenile viability. Target matrix rotation confirmed that while g_obsmax shows genetic associations can extend beyond metamorphosis, there is still considerable scope for decoupled phenotypic evolution. Therefore, although genetic associations across metamorphosis could limit that range of phenotypes that are attainable, traits on either side of the metamorphic boundary are capable of some independent evolutionary change in response to the divergent conditions encountered during each life cycle stage.     

Decrease of sexual organ reciprocity between heterostylous primrose species,with possible functional and evolutionary implications

Background and Aims

Heterostyly is a floral polymorphism that has fascinated evolutionary biologists since Darwin''s seminal studies on primroses. The main morphological characteristic of heterostyly is the reciprocal placement of anthers and stigmas in two distinct (distyly) floral morphs. Variation in the degree of intermorph sexual reciprocity is relatively common and known to affect patterns of pollen transfer within species. However, the partitioning of sexual organ reciprocity within and between closely related species remains unknown. This study aimed at testing whether intermorph sexual reciprocity differs within vs. between primrose species that hybridize in nature and whether the positions of sexual organs are correlated with other floral traits.

Methods

Six floral traits were measured in both floral morphs of 15 allopatric populations of Primula elatior, P. veris and P. vulgaris, and anther–stigma reciprocity was estimated within and between species. A combination of univariate and multivariate approaches was used to test whether positions of reproductive organs were less reciprocal between than within species, to assess correlations between sexual organ positions and other corolla traits, and to quantify differences between morphs and species.

Key Results

The three species were morphologically well differentiated in most floral traits, except that P. veris and P. vulgaris did not differ significantly in sexual organ positions. Overall, lower interspecific than intraspecific sexual organ reciprocity was detected. This decrease was marked between P. elatior and P. vulgaris, intermediate and variable between P. elatior and P. veris, but negligible between P. veris and P. vulgaris.

Conclusions

Differences in anther and stigma heights between the analysed primrose species were of the same magnitude or larger than intraspecific differences that altered pollen flow within other heterostylous systems. Therefore, it is possible to suggest that considerable reductions of sexual organ reciprocity between species may lower interspecific pollen flow, with potential effects on reproductive isolation.     

Temperature-Dependent Modulation of Chromosome Segregation in msh4 Mutants of Budding Yeast

Background

In many organisms, homologous chromosomes rely upon recombination-mediated linkages, termed crossovers, to promote their accurate segregation at meiosis I. In budding yeast, the evolutionarily conserved mismatch-repair paralogues, Msh4 and Msh5, promote crossover formation in conjunction with several other proteins, collectively termed the Synapsis Initiation Complex (SIC) proteins or ‘ZMM’s (Zip1-Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3). zmm mutants show decreased levels of crossovers and increased chromosome missegregation, which is thought to cause decreased spore viability.

Principal Findings

In contrast to other ZMM mutants, msh4 and msh5 mutants show improved spore viability and chromosome segregation in response to elevated temperature (23°C versus 33°C). Crossover frequencies in the population of viable spores in msh4 and msh5 mutants are similar at both temperatures, suggesting that temperature-mediated chromosome segregation does not occur by increasing crossover frequencies. Furthermore, meiotic progression defects at elevated temperature do not select for a subpopulation of cells with improved segregation. Instead, another ZMM protein, Zip1, is important for the temperature-dependent improvement in spore viability.

Conclusions

Our data demonstrate interactions between genetic (zmm status) and environmental factors in determining chromosome segregation.     

Ion Fluxes and Phytochrome Protons in Mung Bean Hypocotyl Segments: II. Fluxes of Chloride, Protons, and Orthophosphate in Apical and Subhook Segments

The active form of phytochrome (Pfr) decreased CI⁻ uptake by subhypocotyl hook segments of Phaseolus aureus Roxb. and increased uptake by apical segments. Pfr had similar effects on Pi [³²Pi] uptake. Modulations of Pi [³²Pi] uptake were detectable 10 minutes following photoconversion. Pfr may modulate Pi influx across the plasmalemma. Pfr inhibited H⁺ extrusion by subhook segments and enhanced extrusion by apical hook segments. No rapid effects on H⁺ extrusion were found. Phytochrome may regulate a K⁺ -H⁺ exchange process. The differential responses of the two regions of the hypocotyl are discussed with respect to Pfr-mediated changes in growth and development.     

Effect of Immunosuppressive Agents on Hepatocyte Apoptosis Post-Liver Transplantation

Introduction

Immunosuppressants are used ubiquitously post-liver transplantation to prevent allograft rejection. However their effects on hepatocytes are unknown. Experimental data from non-liver cells indicate that immunosuppressants may promote cell death thereby driving an inflammatory response that promotes fibrosis and raises concerns that a similar effect may occur within the liver. We evaluated apoptosis within the liver tissue of post-liver transplant patients and correlated these findings with in vitro experiments investigating the effects of immunosuppressants on apoptosis in primary hepatocytes.

Methods

Hepatocyte apoptosis was assessed using immunohistochemistry for M30 CytoDEATH and cleaved PARP in human liver tissue. Primary mouse hepatocytes were treated with various combinations of cyclosporine, tacrolimus, sirolimus, or MMF. Cell viability and apoptosis were evaluated using crystal violet assays and Western immunoblots probed for cleaved PARP and cleaved caspase 3.

Results

Post-liver transplant patients had a 4.9-fold and 1.7-fold increase in M30 CytoDEATH and cleaved PARP compared to normal subjects. Cyclosporine and tacrolimus at therapeutic concentrations did not affect hepatocyte apoptosis, however when they were combined with MMF, cell death was significantly enhanced. Cell viability was reduced by 46% and 41%, cleaved PARP was increased 2.6-fold and 2.2-fold, and cleaved caspase 3 increased 2.2-fold and 1.8-fold following treatment with Cyclosporine/MMF and Tacrolimus/MMF respectively. By contrast, the sirolimus/MMF combination did not significantly reduce hepatocyte viability or promote apoptosis.

Conclusion

Commonly used immunosuppressive drug regimens employed after liver transplantation enhance hepatocyte cell death and may thus contribute to the increased liver fibrosis that occurs in a proportion of liver transplant recipients.     

Effects of inter-subspecies hybridization of non-native <Emphasis Type="Italic">Monochamus alternatus alternatus</Emphasis> and native <Emphasis Type="Italic">M. a. endai</Emphasis> (Coleoptera: Cerambycidae) on the induction of larval diapause and adult body size

To evaluate the effects of Taiwanese Monochamus alternatus alternatus (Coleoptera: Cerambycidae) (T) on native M. a. endai populations (J) and pine wilt disease epidemics in Japan, the biological traits of reciprocally crossed lines between two subspecies were compared with parental lines. No significant differences were observed in egg viability among four crosses in the F1 generation. Hybridized lines had greater survival rates than inbred lines of the J × J cross. The incidence of larval diapause was lower in the inbred lines of M. a. alternatus (0.176 and 0.361) than in the inbred lines of M. a. endai (1.000). Hybridized lines showed a high diapause incidence of 0.896–1.000 in the F1 and F2 generations, indicating that diapause induction was dominant over nondiapause induction. Large numbers of ovarioles dominated over small numbers of ovarioles. Hybridized lines revealed greater adult body sizes than the inbred lines of parental subspecies in the F1 generation (heterosis), but not in the F2 generation. Heterosis in adult body size may contribute to pine wilt disease epidemics because of the greater oviposition rate and initial load of pathogenic nematodes. Two unlinked loci are estimated to control diapause induction. Gene introgression and the dynamics of nondiapause-inducing alleles are discussed.     

Correlations between Chromosome Segments and Fitness in DROSOPHILA MELANOGASTER. I. the X Chromosome and Egg Production

Unmarked segments within the X chromosomes of four different Drosophila melanogaster isogenic lines were assessed with respect to egg production. By making a series of crosses among original and derived recombinant lines, it was possible to estimate parameters representing additive, dominance and interaction effects of the segments. It was shown that whereas most of the segments were additive for egg production when homozygous, they all displayed dominance in the heterozygous condition. Two of the strains were characterized by intersegmental interaction. A possible position effect was detected for these same two strains, with flies in the coupling phase laying more eggs than those in the repulsion configuration. There was no apparent relationship between the number of eggs laid and the amount of heterozygosity within the X chromosome.     

The developmental high wire: Balancing resource investment in immunity and reproduction

The strategic allocation of resources into immunity poses a unique challenge for individuals, where infection at different stages of development may result in unique trade‐offs with concurrent physiological processes or future fitness‐enhancing traits. Here, we experimentally induced an immune challenge in female Gryllus firmus crickets to test whether illness at discrete life stages differentially impacts fitness. We injected heat‐killed Serratia marcescens bacteria into antepenultimate juveniles, penultimate juveniles, sexually immature adults, and sexually mature adults, and then measured body growth, instar duration, mating rate, viability of stored sperm, egg production, oviposition rate, and egg viability. Immune activation significantly impacted reproductive traits, where females that were immune challenged as adults had decreased mating success and decreased egg viability compared to healthy individuals or females that were immune challenged as juveniles. Although there was no effect of an immune challenge on the other traits measured, the stress of handling resulted in reduced mass gain and smaller adult body size in females from the juvenile treatments, and females in the adult treatments suffered from reduced viability of sperm stored within their spermatheca. In summary, we found that an immune challenge does have negative impacts on reproduction, but also that even minor acute stressors can have significant impacts on fitness‐enhancing traits. These findings highlight that the factors affecting fitness can be complex and at times unpredictable, and that the consequences of illness are specific to when during an individual''s life an immune challenge is induced.     

Short- and long-term freezing effects in a coastal (Lobaria virens) versus a widespread lichen (L. pulmonaria)

Lichens are considered freezing tolerant, although few species have been tested. Growth, a robust measure of fitness integrating processes in all partners of a lichen thallus, has not yet been used as a viability measure after freezing. We compared relative growth rates (RGR) after freezing with short-term viability measures of photo- and mycobiont functions in the coastal Lobaria virens and the widespread L. pulmonaria to test the hypothesis that low temperature shapes the coastal distribution of L. virens. Hydrated thalli from sympatric populations were subjected to freezing at −10, −20 and −40 °C for 5 h. The rate of cooling and subsequent warming was 5 °C h⁻¹. Short-term viability measures of photobiont (maximal photosystem II efficiency, effective PSII yield) and mycobiont viability (conductivity index), as well as subsequent RGR, were assessed. The exotherms showed that L. virens froze at −3 °C; L. pulmonaria, at −4 °C. Freezing significantly impaired short-term viability measures of both photo- and mycobiont, particularly in the coastal species. Lobaria pulmonaria grew 2.1 times faster than L. virens, but the short-term damage after one freezing event did not affect the long-term RGR in any species. Thereby, short-term responses were impaired by freezing, long-term responses were not. While the lacking RGR-responses to freezing suggest that freezing tolerance does not shape the coastal distribution of L. virens, the significant reported adverse short-term effects in L. virens may be aggravated by repeated freezing-thawing cycles in cold winters. In such a perspective, repeated freezing may eventually lead to reduced long-term fitness in L. virens.