Genome-wide association study and genome prediction of tallness trait in spinach tallness phenotyping

Plant height (tallness) is a crucial agronomic trait in spinach (Spinacia oleracea L.), affecting mechanical harvesting efficiency and overall yield. This study evaluated plant height variation in a panel of 307 USDA germplasm accessions, which were phenotyped for this trait and genotyped using 15,058 single-nucleotide polymorphisms (SNPs) from whole-genome resequencing. A genome-wide association study (GWAS) using GLM, MLM, FarmCPU, and BLINK in GAPIT3 identified six SNPs significantly associated with plant height: SOVchr2_68062488 (68,062,488 bp) on chromosome 2; SOVchr4_38323167 (38,323,167 bp) and SOVchr4_188084338 (188,084,338 bp) on chromosome 4; SOVchr5_70192260 (70,192,260 bp) on chromosome 5; and SOVchr6_8139833 (8,139,833 bp) and SOVchr6_91175684 (91,175,684 bp) on chromosome 6. Additionally, genomic prediction (GP) models estimated genomic estimated breeding values (GEBVs) for plant height, achieving r-values of 0.50 using GWAS-derived SNP markers in cross-population prediction. The integration of GWAS and GP provides valuable insights into the genetic architecture of plant height in spinach, supporting marker-assisted breeding strategies to enhance crop management and economic returns.