Identification of candidate genes related to two economic traits using GWAS in Gracilariopsis lemaneiformis (Rhodophyta)

Abstract

The lack of systematic methods to measure traits and phenotypic data, along with limited research on genes regulating economic traits, has slowed down the variety improvement and breeding process of industrialized alga Gracilariopsis lemaneiformis (Gp. lemaneiformis). Here, we developed a unified, reliable and stable method for linear growth rate (VL) and branch measurement based on tip culture in Gp. lemaneiformis. Genome-wide association study (GWAS) including 174 haploid strains based on the phenotypic data measured by this trait assessment method was conducted, and 483,670 single nucleotide polymorphisms (SNPs) were identified through re-sequencing. There were 68 and 12 SNPs significantly associated with VL and branch respectively, and 79 and 16 genes related to VL and branch respectively within the flanking 20 kb region of these SNPs were screened. Validation of SNPs loci Chr3–969,142 and Chr13–2,948,547 confirmed their polymorphism and potential involvement in regulating VL and branch traits, respectively. Further analysis revealed a positive correlation between VL and genes LXC001292 (cell division cycle protein 20-like), LXC001293 (transcription factor-like protein DPB), and LXC001294 (unnamed protein product), indicating their potential role in VL regulation through cell cycle, ubiquitin, and RB-E2F regulatory pathways. Additionally, LXC004673 (Auxin transport protein BIG) was associated with Branch, suggesting that the gene and polar auxin transport might play a role on branch morphology of Gp. lemaneiformis. This study provides fundamental data and important gene resources for genetic and breeding studies of Gp. lemaneiformis.