Epsilon Archive for Student Projects

Abstract

Timothy grass (Phleum pratense L.) is a cool-season perennial forage valued for its high herbage yield, nutritional quality, and good digestibility. Despite its agricultural importance, the genetic architecture underlying tiller-related traits remains poorly understood. This study aimed to identify genomic regions and candidate genes associated with tiller composition and biomass-related traits using genome-wide association analysis (GWAS). Previously generated phenotypic data from a diverse panel of domesticated (cultivars, landraces, and breeding lines) and non-domesticated (wild and semi-wild) timothy accessions were utilized. Brief assessment confirmed substantial variation among traits, with vegetative tillers accounted for the majority of total tillers (86.61%), while elongated and generative tillers represented smaller proportions (9.51% and 3.88%, respectively). The lowest variability was recorded for vegetative tillers (16.83%), whereas generative tillers exhibited extremely high variability (191.01%). Several traits, including the proportion of generative tillers (H² = 0.623), vegetative tillers (H² = 0.592), and generative tiller length (H² = 0.546), showed moderate heritability, indicating partial genetic control. A total of approximately 29,000 single nucleotide polymorphisms (SNPs) were used for the GWAS. No significant marker–trait associations (MTAs) were detected for total tiller number (TTN) or total dry weight (TDW) at the Bonferroni threshold, whereas six MTAs were identified at a lower suggestive threshold (−log10(P) ≥ 4), mainly on chromosome 2PpB.This suggests strong environmental influence on TTN and TDW. However, multiple MTAs were identified for tiller composition (the percentage of vegetative, elongating, and generative tillers) and their dry matter across different significance thresholds. Of these, 10 MTAs exceeded the Bonferroni threshold and were mainly located on chromosomes 1PpC and 2PpB. Functional annotation of genes located near significant SNPs revealed candidate genes involved in protein binding, transport, transcriptional regulation, photosynthesis, and protein turnover. Additional annotations, including ABC transporters and UDP-glycosyltransferases, indicate involvement in metabolite transport, detoxification, and cellular homeostasis. For dry matter traits, candidate genes included those related to pectinesterase activity, DNA recombination, transmembrane transport, and F-box proteins involved in protein degradation and stress responses. A candidate gene associated with elongated tiller dry weight was identified near a significant SNP on chromosome 7PpB, suggesting a potential locus influencing biomass accumulation. Overall, this study provides new insights into the genetic basis of tiller-related traits in timothy grass and highlights genomic regions that may support future research and breeding efforts aimed at improving biomass production and adaptation.