Refining Bulk Segregant Analyses: Ontology-Mediated Discovery of Flowering Time Genes in Brassica oleracea

Bulk segregant analysis (BSA) can help identify quantitative trait loci (QTLs), but this may result in substantial bycatch of functionally irrelevant genes. Here we develop a Gene Ontology-mediated approach to zoom in on specific markers implicated in flowering time from among QTLs identified by BSA of the giant woody Jersey kale phenotyped in four bulks of flowering onset. Our BSA yielded tens of thousands of candidate genes. We reduced this by two orders of magnitude by focusing on genes annotated with terms contained within relevant subgraphs of the Gene Ontology. A further enrichment test led to the pathway for circadian rhythm in plants. The genes that enriched this pathway are attested from previous research as regulating flowering time. Some of these genes were also identified as having functionally significant variation compared to Arabidopsis. We validated and confirmed our ontology-mediated results through a more targeted, homology-based approach. However, our ontology-mediated approach produced additional genes of putative importance, showing that the approach aids in exploration and discovery. We view our method as potentially applicable to the study of other complex traits and therefore make our workflows available as open-source code and a reusable Docker container.

Overexpression of SHORT VEGETATIVE PHASE-LIKE (SVL) in Populus delays onset and reduces abundance of flowering in field-grown trees

The spread of transgenes and exotic germplasm from planted crops into wild or feral species is a difficult problem for public and regulatory acceptance of genetically engineered plants, particularly for wind-pollinated trees such as poplar. We report that overexpression of a poplar homolog of the floral repressor SHORT VEGETATIVE PHASE-LIKE (SVL), a homolog of the Arabidopsis MADS-box repressor SHORT VEGETATIVE PHASE (SVP), delayed the onset of flowering several years in three genotypes of field-grown transgenic poplars. Higher expression of SVL correlated with a delay in flowering onset and lower floral abundance, and did not cause morphologically obvious or statistically significant effects on leaf characteristics, tree form, or stem volume. Overexpression effects on reproductive and vegetative phenology in spring was modest and genotype-specific. Our results suggest that use of SVL and related floral repressors can be useful tools to enable a high level of containment for vegetatively propagated short-rotation woody energy or pulp crops.

Flowering Phenology Adjustment and Flower Longevity in a South American Alpine Species

Delayed flowering due to later snowmelt and colder temperatures at higher elevations in the alpine are expected to lead to flowering phenological adjustment to prevent decoupling of peak flowering from the warmest time of the year, thereby favoring pollination. However, even if flowering is brought forward in the season at higher elevations, an elevational temperature gap is likely to remain between the high- and low-elevation populations of a species at the time these reach peak flowering on account of the atmospheric reduction in temperature with increasing elevation. The negative effect of this temperature gap on pollination could be compensated by plastically-prolonged flower life spans at higher elevations, increasing the probability of pollination. In a tightly temperature-controlled study, the flowering phenology adjustment and flower longevity compensation hypotheses were investigated in an alpine species in the Andes of central Chile. The snow free period varied from 7 to 8.2 months over 810 m elevation. Temperatures were suitable for growth on 82–98% of the snow free days. Flowering onset was temporally displaced at the rate of 4.6 d per 100 m increase in elevation and flowering was more synchronous at higher elevations. Flowering phenology was adjusted over elevation. The latter was manifest in thermal sums tending to decrease with elevation for population flowering onset, 50% flowering, and peak flowering when the lower thermal limit for growth (TBASE) was held constant over elevation. For TBASE graded over elevation so as to reflect the growing season temperature decline, thermal sums did not vary with elevation, opening the door to a possible elevational decline in the thermal temperature threshold for growth. Potential flower longevity was reduced by passive warming and was more prolonged in natural populations when temperatures were lower, indicating a plastic trait. Pollination rates, as evaluated with the Relative Pollination Rate index (RPR), when weighted for differences in floral abundance over the flowering season, declined with elevation as did fruit set. Contrary to expectation, the life-spans of flowers at higher elevations were not more prolonged and failed to compensate for the elevational decrease in pollination rates. Although strong evidence for phenological adjustment was forthcoming, flower longevity compensation did not occur over Oxalis squamata’s elevational range. Thus, flower longevity compensation is not applicable in all alpine species. Comparison with work conducted several decades ago on the same species in the same area provides valuable clues regarding the effects of climate change on flowering phenology and fitness in the central Chilean alpine where temperatures have been increasing and winter snow accumulation has been declining.

General and specific combining abilities in a lulo diallel cross (Solanum quitoense Lam.)

Lulo (Solanum quitoense) is a promising agro-industry fruit tree, not only because of its nutritional value, taste, and appearance but also because it provides an alternative production system in mild and moderately cold climate zones. Lulo crop yield and production in the Department of Nariño (Colombia) has decreased in recent years when compared to other producing regions in Colombia. Therefore, the objective of this study was to estimate the effects of the general combining ability (GCA) and the specific combining ability (SCA) in a diallel cross of 10 promising parents in four growing regions of the Department of Nariño for use in breeding programs. A total of 45 hybrid combinations were obtained and assessed with Griffing method 4. The following variables were assessed: days to flowering onset (DFO), number of clusters per branch (NCB), fruit weight (FW), polar axis (PA) of the fruit, and yield (Y). The analysis of variance showed statistical differences for most variables in response to single-cross hybrid effects and locations, except for NCB and Y. Moreover, significant differences were found for the interactions between the GCA and SCA and the hybrids and locations, respectively, meaning that environment must be considered when selecting parents with specific adaptability. The effects of the GCA and SCA promoted higher positive values for the FW and Y in parents 4, 6, and 8 and their combinations. Therefore, these parental genotypes are promising for lulo genetic improvement programs since their additive effects and genetic dominance favor fruit weight and yield.

Earlier onset of flowering and increased reproductive allocation of an annual invasive plant in the north of its novel range

Background and Aims It remains unclear whether invasive species can maintain both high biomass and reproductive output across their invaded range. Along latitudinal gradients, allocation theory predicts that faster flowering onset at high latitudes results in maturation at smaller size and thus reduced reproductive output. For annual invasive plants, more favourable environmental conditions at low latitudes probably result in stronger competition of co-occurring species, potentially driving selection for higher investment in vegetative biomass, while harsher climatic conditions and associated reproductive uncertainty at higher latitudes could reduce selection for vegetative biomass and increased selection for high reproductive investment (stress-gradient hypothesis). Combined, these drivers could result in increased or constant reproductive allocation with increasing latitude. Methods We quantified life-history traits in the invasive annual plant Impatiens glandulifera along a latitudinal gradient in Europe. By growing two successive glasshouse generations, we assessed genetic differentiation in vegetative growth and reproductive output across six populations, and tested whether onset of flowering drives this divergence. Key Results Trait variation was mainly caused by genetic differentiation. As expected, flowering onset was progressively earlier in populations from higher latitudes. Plant height and vegetative biomass also decreased in populations from higher latitudes, as predicted by allocation theory, but their variation was independent of the variation in flowering onset. Reproductive output remained constant across latitudes, resulting in increased reproductive allocation towards higher latitudes, supporting the stress-gradient hypothesis. We also observed trait genetic differentiation among populations that was independent of latitude. Conclusions We show that an annual invasive plant evolved several life-history traits across its invaded range in ~150 years. The evolution of vegetative and reproductive traits seems unconstrained by evolution of flowering onset. This genetic decoupling between vegetative and reproductive traits possibly contributes to the invasion success of this species.

COMPARATIVE PHARMACOGNOSTIC RESEARCH OF CENTAUREA SCABIOSA L. WILD-GROWING AND CULTI-VATED IN THE CONDITIONS OF TOMSK

The purpose of this study is: on the basis of a comparative study of the biological characteristics and chemical composition of Centaurea scabiosa L. wild-growing and cultivated, to assess the prospects for its introduction into culture as an additional source of raw materials for the anthelmintic drug development. It has been established that the Centaurea scabiosa L. cultivated under the conditions of the Tomsk city in terms of developmental phenology is close to a wild-growing plant. The vegetative organs ratios of wild-growing and cultivated plants were determined: leaves constitute 10% and 24%; baskets – 37% and 24%; stems up to 0.5 cm of thick –18% and 20%; stems with a thickness of more than 0.5 cm – 34% and 31%, respectively (beginning of flowering phase). The cultivated Centaurea scabiosa L. is comparable to a wild-growing plant according to the sesquiterpene lactones content in separated organs. The sesquiterpene lactones maximum amount accumulates in the budding phase, decreases slightly at the beginning of flowering, and significantly decreases at the mass flowering phase. The Centaurea scabiosa L. harvesting periods (the leafiest shoots with a stem diameter of not more than 0.5 cm) are experimentally substantiated – the phase of flowering onset.

Weed Functional Diversity as Affected by Agroecological Service Crops and No-Till in a Mediterranean Organic Vegetable System

This paper explores the effect of agroecological service crops (ASCs), i.e., crops included in the crop rotation for their ecosystem services, terminated with an in-line tillage roller crimper (ILRC) on weed community composition and their functional traits in comparison to a tilled control without ASC. A two-year study was performed in a long-term experiment with vegetables under organic management. Four different cereal crops were introduced as ASCs. Weed abundance and richness and the functional traits were assessed at three different stages, i.e., before and after ASC termination and before harvest of the following crop, melon. All the ASCs showed strong weed suppression, with few differences between the cereals tested. Weed communities with ASCs had later flowering onset and wider flowering span compared to the control, which positively affects weed dispersal and attraction of beneficial insects. However, weed communities with ASCs had higher values for traits related to competition (specific leaf area, seed weight and more perennials). A trade-off between weed suppression and selection of more competitive weed communities by the introduction of ASCs managed with the ILRC should be evaluated in the long-run. The use of the ILRC alternating with other soil management practices seems the more effective strategy to benefit from the minimal soil tillage while avoiding the selection of disservice-related traits in the weed community.

Opportunistically collected photographs can be used to estimate large-scale phenological trends

ABSTRACTPremiseResearch on large-scale patterns of phenology have utilized multiple sources of data to analyze the timing of events such as flowering, fruiting, and leaf out. In-situ observations from standardized surveys are ideal, but remain spatially sparse. Herbarium records and phenology-focused citizen science programs provide a source of historic data and spatial replication, but the sample sizes for any one season are still relatively low. A novel and rapidly growing source of broad-scale phenology data are photographs from the iNaturalist platform, but methods utilizing these data must generalize to a range of different species with varying season lengths and occurring across heterogenous areas. They must also be robust to different sample sizes and potential biases toward well travelled areas such as roads and towns.Methods/ResultsWe developed a spatially explicit model, the Weibull Grid, to estimate flowering onset across large-scales, and utilized a simulation framework to test the approach using different phenology and sampling scenarios. We found that the model is ideal when the underlying phenology is non-linear across space. We then use the Weibull Grid model to estimate flowering onset of two species using iNaturalist photographs, and compare those estimates with independent observations of greenup from the Phenocam network. The Weibull Grid model estimate consistently aligned with Phenocam greenup across four years and broad latitudes.ConclusioniNaturalist observations can considerably increase the amount of phenology observations and also provide needed spatial coverage. We showed here they can accurately describe large-scale trends as long as phenological and sampling processes are considered.