Biology subjects

Janninck, J.-L.

Publications and source records attributed to Janninck, J.-L..

4 recordsLinked to original sources

bioRxiv2021

Generalizable approaches for genomic prediction of metabolites in plants

Plant metabolites are important for plant breeders to improve nutrition and agronomic performance, yet integrating selection for metabolomic traits is limited by phenotyping expense and limited genetic characterization, especially of uncommon metabolites. As such, developing biologically-based and generalizable genomic selection methods for metabolites that are transferable across plant populations would benefit plant breeding programs. We tested genomic prediction accuracy for more than 600 metabolites measured by GC-MS and LC-MS in oat (Avena sativa L.) seed. Using a discovery germplasm panel, we conducted metabolite GWAS (mGWAS) and selected loci to use in multi-kernel models that encompassed metabolome-wide mGWAS results, or mGWAS from specific metabolite structures or biosynthetic pathways. Metabolite kernels developed from LC-MS metabolites in the discovery panel improved prediction accuracy of LC-MS metabolite traits in the validation panel, consisting of more advanced breeding lines. No approach, however, improved prediction accuracy for GC-MS metabolites. We tested if similar metabolites had consistent model ranks and found that, while different metrics of similarity had different results, using annotation-free methods to group metabolites led to consistent within-group model rankings. Overall, testing biological rationales for developing kernels for genomic prediction across populations, contributes to developing frameworks for plant breeding for metabolite traits.

genomics↗

bioRxiv2021

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Ugandan for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8,820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant-pathogen interaction pathway, several previously identified CMD resistance genes and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.

genomics↗

bioRxiv2021

Selection for seed size has indirectly shaped specialized metabolite abundance in oat (Avena sativa L.)

Plant breeding strategies to optimize metabolite profiles are necessary to develop health-promoting food crops. In oats (Avena sativa L.), seed metabolites are of interest for their antioxidant properties and their agronomic role in mitigating disease severity, yet have not been a direct target of selection in breeding. In a diverse oat germplasm panel spanning a century of breeding, we investigated the degree of variation of these specialized metabolites and how it has been molded by selection for other traits, like yield components. We also ask if these patterns of variation persist in modern breeding pools. Integrating genomic, transcriptomic, metabolomic and phenotypic analyses for three types of seed specialized metabolites - avenanthramides, avenacins, and avenacosides - we found reduced genetic variation in modern germplasm compared to diverse germplasm, in part due to increased seed size associated with more intensive breeding. Specifically, we found that abundance of avenanthramides increases with seed size, but additional variation is attributable to expression of biosynthetic enzymes, but avenacoside abundance decreases with seed size and plant breeding intensity. Overall, we show that increased seed size associated with plant breeding has uneven effects on the seed metabolome, and broadly contributes to understanding how selection shapes plant specialized metabolism.

plant biology↗

bioRxiv2021

Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to prioritize accelerated research gains

The domestication process of sugar kelp in the Northeast U.S. was initiated by selective breeding two years ago. In this study, we will demonstrate how obstacles for accelerated genetic gain can be assessed using simulation approaches that inform resource allocation decisions in our research. Thus far, we have used 140 wild sporophytes (SPs) that were sampled from the northern Gulf of Maine (GOM) to southern New England (SNE). From these SPs, we sampled gametophytes (GPs) and made and evaluated over 600 progeny SPs from crosses among the GPs. The biphasic life cycle of kelp gives a great advantage in selective breeding as we can potentially select both on the SPs and GPs. However, several obstacles exist, such as the amount of time it takes to complete a breeding cycle, the number of GPs that can be maintained in the lab, and whether positive selection can be conducted on farm tested SPs. Using the GOM population characteristics for heritability and effective population size, we simulated a founder population of 1000 individuals and evaluated the impact of overcoming these obstacles on genetic gain. Our results showed that key factors to improve current genetic gain rely mainly on our ability to induce reproduction of the best farm-tested SPs, and to accelerate the clonal vegetative growth of released GPs so that enough GP biomass is ready for making crosses by the next growing season. Overcoming these challenges could improve rates of genetic gain more than two-fold. Future research should focus on conditions favorable for inducing spring and early summer reproduction, and increasing the amount of GP tissue available in time to make fall crosses.

genetics↗