Comparing Longitudinal Multi-Trait GWAS to Single-Trait GWAS for Yield and Forage Quality in Red Clover

Red clover is a major and highly important forage legume in Northern Europe. It is a perennial crop commonly grown together with grasses and harvested multiple times per season. With decreasing phenotypic stability of red clover due to various factors, mainly caused by climate change, breeders face increasing challenges when improving dry matter yield and forage quality. Marker-assisted selection using genetic markers can aid breeders in making quick decisions with higher accuracy. Candidate markers can be found through genome-wide association studies (GWAS). This study looked at the performance of longitudinal multi-trait (MT) and single-trait (ST) models for GWAS. A collection of 532 red clover accessions, both diploid and tetraploid, was phenotyped at multiple locations and genotyped using pool-seq. The target traits, dry matter yield, neutral detergent fiber (NDF), net energy for lactation (NEL) and crude protein content are highly quantitative traits that can be affected by the plant’s growth that are affected by plant development stages and growth conditions. Using a longitudinal MT model, markers associated with traits over time were identified. Genomic regions that appear to contain genes involved in the regulation of both dry matter yield and forage quality traits were also identified. Furthermore, the observed effects of significantly associated single nucleotide polymorphisms (SNPs) showed that there were considerable non-additive genetic effects in some traits. This study sets the foundation for longitudinal MT GWAS for red clover and suggests ways for further improvement to gain a deeper understanding of the genetic mechanisms underlying dry matter yield and forage quality.