Biology subjects

Rubin, M. J.

Publications and source records attributed to Rubin, M. J..

9 recordsLinked to original sources

bioRxiv2025

Watering regime affects aboveground and belowground trait covariation in a hybrid Silphium population

Premise of the studyPerennial, herbaceous members of the sunflower family (Asteraceae) can provide valuable agronomic products from aboveground biomass, as well as ecosystem services belowground. Aboveground and belowground trait covariation can be affected by environmental conditions such as the location of available water. Here, we investigated the effects of watering regime on trait covariation in Silphium (Asteraceae), an emerging perennial oilseed crop. MethodsSilphium integrifolium Michx. and S. perfoliatum L. are native North American species adapted to well-drained and moist soils, respectively. Using a backcrossed F1 hybrid S. integrifolium x S. perfoliatum population, we conducted a greenhouse experiment where plants were either watered at the soil line ("top-watered") or from below using watering trays ("bottom-watered"). Aboveground biomass, root distribution, and root morphology (e.g., specific root length) were measured destructively. Key resultsCompared to top-watered plants, bottom-watered plants were smaller aboveground and belowground, with a higher proportion of roots in the upper portions of the pots and higher specific root length. Negative relationships between aboveground biomass and specific root length were steeper for bottom-watered than top-watered plants. ConclusionsThe location of available water impacts aboveground biomass, the distribution and morphology of the root system, and relationships between aboveground and belowground plant structures. This work suggests that resource allocation depends in part on the location of available water, and has relevance for ongoing efforts aimed at developing perennial, herbaceous species that offer both economically viable products as well as ecosystem services.

plant biology↗

bioRxiv2025

Leveraging High-dimensional Seed Colorspace in Phenomic Selection Models for Herbaceous Perennial Crops

Herbaceous perennial crops, which only recently entered the domestication pipeline, offer the potential of ecological benefits in agricultural systems but remain underdeveloped, partly due to slow breeding cycles. Early-stage phenomic selection, the process of using high-dimensional secondary traits to predict target traits, may accelerate improvement. We evaluated whether seed traits derived from image scans could be used to predict germination traits in three perennial crop candidate species: sainfoin (Onobrychis viciifolia), intermediate wheatgrass (Thinopyrum intermedium), and silflower (Silphium integrifolium). Over 20,000 seeds were scanned, and PlantCV was used to extract 692 hue, saturation, and value (HSV) color features along with five morphological traits. We demonstrated that seed color, morphology, and germination traits were all influenced by maternal family, but patterns of correlation between germination traits and color and morphology traits are complex. To enable prediction from high-dimensional seed traits, we constructed relationship matrices from combinations of HSV and morphology features for use in phenomic selection models to predict germination proportion and timing. Model performance varied by trait, species, and cohort, and in many cases, predictions were significantly better than chance. HSV features, when combined with morphology, often yielded the most accurate predictions, with performance reaching a maximum of r = 0.33. These results demonstrate the potential of low-cost, image-based phenomic data to inform early-stage selection and support the development of sustainable perennial crops. Plain language summaryMany of the worlds most important crops (e.g., wheat, maize, soy) live for less than one year, leaving soil bare for many months and subject to erosion. Longer-lived (perennial) alternatives to these crops have the potential to support a more sustainable agricultural system by improving soil health and reducing the need for chemical inputs. However, perennial herbaceous plants were not domesticated by early farmers, and now lag behind annual crops in development. They take longer to breed and often lack the genetic resources needed for modern breeding approaches. In this study, we tested whether simple seed images derived from color scanners could be used to predict key traits like germination proportion and timing in emerging perennial crops. We found that seed color and shape varied by maternal family and that color, especially when combined with seed size and shape, could help predict germination performance. These predictions were significantly better than chance. This work shows that low-cost, image-based seed data can support early-stage selection in breeding programs, especially for undeveloped perennial crops, helping save time, reduce cost, and accelerate progress toward more sustainable agriculture.

plant biology↗

bioRxiv2025

A leaf phenomics approach to estimating below-ground traits in North American Licorice

Premise of the studyThousands of years of selective breeding has prioritized above-ground yield, with little regard for changes happening below-ground. Despite their central role in plant success and resilience, our knowledge of roots lags behind above-ground structures. Accurately phenotyping root traits is often labor-intensive, expensive, and destructive. In order to advance understanding of the fundamental biology underlying root systems, and to integrate hard-to-measure root traits into breeding programs, high-throughput non-destructive methods are required. MethodsThis study uses American licorice (Glycyrrhiza lepidota Pursh.), a perennial legume with a rich ethnobotanical history, as a model to investigate root system phenotypes. We assess root traits across multiple populations, analyze relationships between above- and below-ground phenotypes, and test the use of multidimensional leaf traits, including spectral reflectance, in predicting root traits. Key resultsAmerican licorice displays significant variation in root traits across source populations and strong correlations between above- and below-ground traits. Leaf spectral reflectance and elemental composition show promise in modeling below-ground traits, though the isometric relationship between plant size and root traits complicates model accuracy. ConclusionsThese findings demonstrate the use of high-dimensional leaf traits as a proxy for root traits, with potential applications for understanding foundational questions in plant biology and in breeding programs targeting the below-ground structures of perennial herbaceous species. Further optimization and larger studies are needed to improve predictive models.

plant biology↗

bioRxiv2021

Comparative population genomics in two sympatric species of Strophostyles (Fabaceae) with contrasting life histories

PREMISE OF THE STUDYLife history is an important predictor of population genetic variation, although this link remains unexplored in numerous important plant lineages. One such lineage is the legume genus Strophostyles, which contains both annual and herbaceous perennial vines native to eastern North America. Specifically, it remains to be determined whether Strophostyles species with different life histories show different patterns of genetic differentiation and diversity, as well as if these species hybridize across their range. METHODSHere we sampled the perennial Strophostyles helvola and annual S. leiosperma in five sites across a latitudinal transect in the central United States, including three sites where the species occur in sympatry. Using genotyping-by-sequencing, we identified 5556 polymorphic SNPs across 166 individuals. KEY RESULTSThere is no evidence that Strophostyles helvola and S. leiosperma hybridize in the populations examined. Within species, Strophostyles helvola (perennial) displays admixture among populations, while S. leiosperma (annual) does not, although both species show more genetic diversity among rather than within populations. Patterns of genetic diversity are varied across populations of both species, with both heterozygote excess and deficiency. CONCLUSIONSThe complex patterns of genetic differentiation and diversity warrant further investigation of life history and population dynamics in Strophostyles, particularly mating system and modes of gene flow. This study exemplifies the diversity of population genetic patterns even within a small genus, and it reinforces the need to characterize such diversity in non-model systems to gain a more complete understanding of how life history contributes to population genetics.

plant biology↗

bioRxiv2021

The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia (Fabaceae)

PREMISE OF THE STUDYAnnual and perennial life history transitions are abundant among angiosperms, and understanding the phenotypic variation underlying life span shifts is a key endeavor of plant evolutionary biology. Comparative analyses of trait variation and correlation networks among annual and perennial plants is increasingly important as new perennial crops are being developed in a predominately annual-based agricultural setting. However, it remains unclear how seed to vegetative growth trait relationships may correlate with life span. METHODSWe measured 29 annual and perennial congeneric species of three herbaceous legume genera (Lathyrus, Phaseolus, and Vicia) for seed size and shape, germination proportion, and early vegetative height and leaf growth over three months in order to assess relative roles of genus and life span in predicting phenotypic variation and correlation. KEY RESULTSGenus was the greatest predictor of seed size and shape variation, while life span consistently predicted static vegetative growth traits. Correlation networks revealed that annual species had significant associations between seed traits and vegetative traits, while perennials had no significant seed-vegetative associations. Each genus also differed in the extent of integration between seed and vegetative traits, as well as within-vegetative trait correlation patterns. CONCLUSIONSGenus and life span were important for predicting aspects of early life stage phenotypic variation and trait relationships. Differences in phenotypic correlation may indicate selection on seed size traits will impact vegetative growth differently depending on life span, which has important implications for nascent perennial breeding programs.

plant biology↗

bioRxiv2019

Comparative analysis of seed size, germination, and vegetative allocation in annual and herbaceous perennial crops and their wild relatives in Lupinus and Phaseolus (Fabaceae)

Herbaceous perennial species are receiving increased attention for their potential to provide both edible products and ecosystem services in agricultural systems. Many legumes (Fabaceae Lindl.) are of special interest due to nitrogen fixation carried out by bacteria in their roots and their production of protein-rich, edible seeds. However, herbaceous perennial legumes have yet to enter widespread use as pulse crops, and the response of wild, herbaceous, perennial species to artificial selection for increased seed yield remains under investigation. Here we compare cultivated and wild accessions of congeneric annual and herbaceous perennial legume species to investigate associations of lifespan and cultivation with seed size, germination, and first year vegetative growth patterns, and to characterize covariation among traits. We use \"cultivated\" to describe accessions with a history of human planting and use, which encompasses a continuum of domestication. Analyses focused on three annual and eight perennial Lupinus species, and three annual and four perennial Phaseolus species. We found a significant association of both lifespan and cultivation status with seed size (weight, area, length), germination proportion, node number, stem diameter, shoot dry mass, and root dry mass. Wild seed size was greater in annuals for Lupinus and greater for perennials in Phaseolus. Germination was lower in wild perennials than wild annuals in both genera, and vegetative allocation was roughly equivalent across lifespans in wild Phaseolus. Relative to wild forms, both cultivated annual and cultivated perennial accessions exhibited greater seed size, lower germination proportion, and larger overall plant size. Seed size traits were positively correlated with vegetative growth traits, and all biomass traits examined here were positively correlated. This study highlights some basic similarities and differences between annual and herbaceous perennial legumes, and provides insights into how perennial legumes might respond to artificial selection compared to annual species.

plant biology↗

bioRxiv2019

An ethnobotanical study of the genus Elymus

Grains of domesticated grasses (Poaceae) have long been a global food source and constitute the bulk of calories in the human diet. Recent efforts to establish more sustainable agricultural systems have focused in part on the development of herbaceous, perennial crops. Perennial plants have extensive root systems that stabilize soil and absorb water and nutrients at greater rates than their annual counterparts; consequently, perennial grasses are important potential candidates for grain domestication. While most contemporary grass domesticates consumed by humans are annual plants, there are over 7,000 perennial grass species that remain largely unexplored for domestication purposes. Documenting ethnobotanical uses of wild perennial grasses could aid in the evaluation of candidate species for de novo crop development. The objectives of this study are 1) to provide an ethnobotanical survey of the grass genus Elymus; and 2) to investigate floret size variation in species used by people. Elymus includes approximately 150 perennial species distributed in temperate and subtropical regions, of which at least 21 taxa have recorded nutritional, medicinal, and/or material uses. Elymus species used for food by humans warrant pre-breeding and future analyses to assess potential utility in perennial agricultural systems.

plant biology↗

bioRxiv2019

Comparative analysis of perennial and annual Phaseolus seed nutrient concentrations

Malnutrition is a global public health concern and identifying mechanisms to elevate the nutrient output of crops may minimize nutrient deficiencies. Perennial grains within an agroforestry context offers one solution. The development and integration of perennial crops for food has critically influenced dialogue on the ecological intensification of agriculture and agroforestry. However, the nutrient compositions of wild, perennial, herbaceous species, such as those related to the common bean (Phaseolus vulgaris) are not well known. In this study, seed amino acid and ion concentrations of perennial and annual Phaseolus species were quantified using ionomics and mass spectrometry. No statistical difference was observed for Zn, toxic ions (e.g. As) or essential amino acid concentrations (except threonine) between perennial and annual Phaseolus species. However, differences were observed for some nutritionally important ions among and within lifespan groups. Ca, Cu, Fe, Mg, Mn, and P concentrations were higher in annual species. Intraspecific variability in ion concentrations and amino acids was observed within species; further, ion concentrations and amino acids differ among annual species and among perennial species. Ion and amino acid concentration appear to be largely independent of each other. These results suggest variability in ion and amino acid concentrations exist in nature. As new crop candidates are considered for ecological services, nutritional quality should be optimized to maximize nutrient output of sustainable food crops.

plant biology↗

bioRxiv2019

Integrating transcriptomic network reconstruction and QTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development

Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use a hierarchical Bayesian Function-Valued Trait (FVT) approach to estimate Brassica rapa growth curves throughout ontogeny, across two treatments and in two growing seasons. We find that the shape of growth curves is relatively plastic across environments compared to final height, and that there are trade-offs between growth rate and duration. We determined that combining FVT Quantitative Trait Loci (QTL) and genes/eigengene expression identified via transcriptomic co-expression network reconstructions best characterized phenotypic variation. Further, targeted eQTL analyses identified regulatory hotspots that colocalized with FVT QTL and co-expression network identified genes and mechanistically link FVT QTL with structural trait variation throughout development in agroecologically relevant field settings.

genomics↗