Rubin, M. J. | bioRxiv Science

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↗