Biology subjects

Marty-Rivera, M.

Publications and source records attributed to Marty-Rivera, M..

4 recordsLinked to original sources

bioRxiv2022

Genomic selection in organisms with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study

Sugar kelp (Saccharina latissima) has a biphasic life cycle, allowing selection on both the diploid sporophytes (SPs) and haploid gametophytes (GPs). We trained a genomic selection (GS) model from farm-tested SP phenotypic data and used a mixed-ploidy additive relationship matrix to predict GP breeding values. Top-ranked GPs were used to make crosses for further farm evaluation. The relationship matrix included 866 individuals: a) founder SPs sampled from the wild; b) progeny GPs from founders; c) Farm-tested SPs crossed from b); and d) progeny GPs from farm-tested SPs. The complete pedigree-based relationship matrix was estimated for all individuals. A subset of founder SPs (n = 58) and GPs (n = 276) were genotyped with Diversity Array Technology and whole genome sequencing, respectively. We evaluated GS prediction accuracy via cross validation on farm-tested SPs in two years using a basic GBLUP model. We also estimated the general combining ability (GCA) and specific combining ability (SCA) variances of parental GPs. A total of 11 yield-related and morphology traits were evaluated. The cross validation accuracies for dry weight per meter (r ranged from 0.16 to 0.35) and wet weight per meter (r ranged 0.19 to 0.35) were comparable to GS accuracy for yield traits in terrestrial crops. For morphology traits, cross validation accuracy exceeded 0.18 in all scenarios except for blade thickness in the second year. Accuracy in a third validation year for dry weight per meter over a confirmation set of 87 individuals was 0.31.

genetics↗

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↗

bioRxiv2020

Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers

An assessment of genetic diversity of marine populations is critical not only for the understanding and preservation of natural biodiversity but also for its economic potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea surface temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp species, Saccharina latissima and putative species, Saccharina angustissima. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, Fst, admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is moderately more heterogeneous than SNE. While admixture was observed between regions, these results confirm that Cape Cod acts as a biogeographic barrier for sugar kelp gene flow. We detected one significant SNP (P-value=2.03x10-7) associated with stipe length, and 243 SNPs with higher-than-neutral differentiation. The findings of this study provide fundamental knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for cultivation and bioenergy production.

genetics↗

bioRxiv2018

Mitigation of coral bleaching by antioxidants

Coral bleaching, loss of symbiotic dinoflagellate algae from the coral holobiont, is a complex phenomenon that can result in coral death and reef degradation. Reactive oxygen species (ROS) have been suggested as a possible mechanism underlying this event. To determine if antioxidants can be used to reduce ROS production and coral bleaching, we tested the effects of thermal stress in Aiptasia pallida a model system for coral bleaching studies, and the scleractinian coral, Porites astreoides. We analyzed host ROS levels, symbiont dark-adapted quantum yield of photosystem II, and symbiont loss in the presence or absence of antioxidants. We found that a single dose of the antioxidant catechin, significantly reduced ROS levels in the hosts, mitigated the degradation of the symbionts quantum yield and reduced the loss of symbionts from thermally stressed P. astreoides but not from A. pallida. Taken together, these results support a key role of ROS and that antioxidants can prevent symbiont degradation and loss during thermally-induced bleaching in P. astreoides.

ecology↗