Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to accelerate genetic gains

Authors: HUANG, MAO - Cornell University; ROBBINS, KELLY - Cornell University; LI, YAOGUANG - University Of Connecticut; UMANZOR, SCHERY - University Of Connecticut; MARTY-RIVERA, MICHAEL - University Of Connecticut; BAILEY, DAVID - Woods Hole Oceanographic Institute (WHOI); YARISH, CHARLES - University Of Connecticut; LINDELL, SCOTT - Woods Hole Oceanographic Institute (WHOI); Jannink, Jean-Luc

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2021
Publication Date: 1/19/2022
Citation: Huang, M., Robbins, K.R., Li, Y., Umanzor, S., Marty-Rivera, M., Bailey, D., Yarish, C., Lindell, S., Jannink, J. 2022. Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to accelerate genetic gains. Genes, Genomes, Genetics. 12(3). https://doi.org/10.1093/g3journal/jkac186.
DOI: https://doi.org/10.1093/g3journal/jkac186

Interpretive Summary: Though Saccharina japonica cultivation has been established for many decades in East Asian countries, the domestication process of sugar kelp (Saccharina latissima) in the Northeast United States is still in its infancy. Best practices to accelerate improvement in sugar kelp for farming need to be established. Using data from our breeding experience, we demonstrate how obstacles for accelerated genetic gain can be assessed using simulation. Simulation results can help inform breeding practices that will generate the most gain. We have used 140 wild kelp that were sampled in 2018 from the northern Gulf of Maine to southern New England. From these sampled kelp, we evaluated over 600 progeny in 2019 and 2020. Several breeding obstacles exist, such as the amount of time it takes to complete a breeding cycle, the number of progeny that can be maintained in the laboratory, and whether positive selection can be conducted on farm-tested kelp. Using the Gulf of Maine population characteristics for heritability and effective population size, we simulated a founder population of 1,000 individuals and evaluated the impact of overcoming these obstacles on the rate of genetic gain. Our results showed that key factors to improve genetic gain rely mainly on our ability to induce reproduction of the best farm-tested kelp, and to accelerate the clonal vegetative growth of their progeny to enable the to be crossed by the next growing season. Overcoming these challenges could improve rates of genetic gain more than 2-fold. Future research should focus on conditions favorable for inducing reproduction, and on increasing the amount of clonal tissue available in time to make fall crosses in the same year.

Technical Abstract: Though Saccharina japonica cultivation has been established for many decades in East Asian countries, the domestication process of sugar kelp (Saccharina latissima) in the Northeast United States is still at its infancy. In this study, by using data from our breeding experience, we will demonstrate how obstacles for accelerated genetic gain can be assessed using simulation approaches that inform resource allocation decisions. Thus far, we have used 140 wild sporophytes that were sampled in 2018 from the northern Gulf of Maine to southern New England. From these sporophytes, we sampled gametophytes and made and evaluated over 600 progeny sporophytes from crosses among the gametophytes in 2019 and 2020. The biphasic life cycle of kelp gives a great advantage in selective breeding as we can potentially select both on the sporophytes and gametophytes. However, several obstacles exist, such as the amount of time it takes to complete a breeding cycle, the number of gametophytes that can be maintained in the laboratory, and whether positive selection can be conducted on farm-tested sporophytes. Using the Gulf of Maine population characteristics for heritability and effective population size, we simulated a founder population of 1,000 individuals and evaluated the impact of overcoming these obstacles on rate of 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 sporophytes, and to accelerate the clonal vegetative growth of released gametophytes so that enough gametophyte biomass is ready for making crosses by the next growing season. Overcoming these challenges could improve rates of genetic gain more than 2-fold. Future research should focus on conditions favorable for inducing spring reproduction, and on increasing the amount of gametophyte tissue available in time to make fall crosses in the same year.