Application of machine learning to explore the genomic prediction accuracy of fall dormancy in autotetraploid alfalfa

11Citations
Citations of this article
9Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Fall dormancy (FD) is an essential trait to overcome winter damage and for alfalfa (Medicago sativa) cultivar selection. The plant regrowth height after autumn clipping is an indirect way to evaluate FD. Transcriptomics, proteomics, and quantitative trait locus mapping have revealed crucial genes correlated with FD; however, these genes cannot predict alfalfa FD very well. Here, we conducted genomic prediction of FD using whole-genome SNP markers based on machine learning-related methods, including support vector machine (SVM) regression, and regularization-related methods, such as Lasso and ridge regression. The results showed that using SVM regression with linear kernel and the top 3000 genome-wide association study (GWAS)-associated markers achieved the highest prediction accuracy for FD of 64.1%. For plant regrowth height, the prediction accuracy was 59.0% using the 3000 GWAS-associated markers and the SVM linear model. This was better than the results using whole-genome markers (25.0%). Therefore, the method we explored for alfalfa FD prediction outperformed the other models, such as Lasso and ElasticNet. The study suggests the feasibility of using machine learning to predict FD with GWAS-associated markers, and the GWAS-associated markers combined with machine learning would benefit FD-related traits as well. Application of the methodology may provide potential targets for FD selection, which would accelerate genetic research and molecular breeding of alfalfa with optimized FD.

Cite

CITATION STYLE

APA

Zhang, F., Kang, J., Long, R., Li, M., Sun, Y., He, F., … Yang, Q. (2023). Application of machine learning to explore the genomic prediction accuracy of fall dormancy in autotetraploid alfalfa. Horticulture Research, 10(1). https://doi.org/10.1093/hr/uhac225

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free