Genome-Wide Association Study Reveals Genetic Loci for Important Growth Traits of Gemetophyte in Neopyropia yezoensis

In order to address the paucity of genetic loci associated with growth traits in the genetic breeding studies of Neopyropia yezoensis, the genome-wide association study (GWAS) was conducted for 4 important growth traits in gametophytes of N. yezoensis. One hundred and thirty thalli of N. yezoensis with single genotype were cultured under the same environment. Four growth-related phenotypic values of thallus length, thallus width, fresh mass and dry mass were measured. Study revealed that the coefficient of variation of different growth traits of thalli ranged from 32.63% to 50.95%, and there were significant correlations among the four traits. The genotype of each individual were obtained by whole genome re-sequencing. After quality inspection of the re-sequencing data, a total of 405 999 high-quality SNPs were obtained, of which 53 077 sites were in the exon region, and the ratio of SNPs transitions to translocations was 1.23. Population structure analysis found that the population in this work could be divided into 4 subgroups, and there were obvious genetic differences between any two different subgroups. The subgroups division were not in accordance with geographical location. The relatively distant phylogenetic relationship among the individuals and the short range of LD decay distance indicated that the genetic variation was relatively rich in the population. The mixed linear model (Q+K) was used to screen the associated loci of traits. A total of 90 significant SNP markers were detected, of which 67 loci were correlated with thallus length, 17 loci were correlated with thallus width, 4 loci were correlated with fresh mass, and 2 loci were correlated with dry mass, which could explain 16.12% to 24.85% of the observed phenotypic variation. A total of 39 candidate genes were identified within a 20 kb range upstream and downstream of the SNP site with significant association. The gene functions involved cell proliferation, control of cell metabolic pathways, and regulation of plant growth and development. This study furnishes a set of candidate genetic markers and crucial evidence for molecular breeding of N. yezoensis.