Rice yield is a complex trait affected by many related traits.  Traditional single-trait genome-wide association studies (GWAS) have limitations when studying complex traits, as they cannot account for the genetic relationships among multiple traits.  Multi-trait GWAS can consider the relationships among multiple traits and identify pleiotropic loci, so it is more suitable for complex traits such as rice yield than single-trait GWAS.  In this study, we conducted a multi-trait GWAS on 11 two-trait combinations of yield and yield-related traits with 575 hybrid rice varieties across two environments.  All these yield-related traits showed significant genetic correlations with yield (YD), including filled grains per panicle (FGPP), 1,000-grain weight (KGW), tillers per plant (TP), primary branch number (PB), secondary branch number (SB), and main panicle length (MPL).  In total, we identified 44 pleiotropic quantitative trait loci (pQTLs), including 29 new pQTLs not found in a single-trait GWAS.  We then screened 23 pQTLs showing common effects in two traits as key pQTLs.  These key pQTLs were subsequently analyzed by haplotype analysis, which identified 13 pleiotropic candidate genes.  Finally, we identified two optimal yield-enhancing allele combinations by pyramiding the superior haplotypes: GS3-GL3.1-OsCIPK17 for the YD-KGW combination and GNP12 for the YD-FGPP and YD-SB combinations.  This study provides pleiotropic candidate genes and allele combinations that exhibit superior differences in both yield and yield-related traits, offering valuable information for future high-yielding rice breeding.

High-throughput single nucleotide polymorphism (SNP) arrays have emerged as essential genotyping tools, significantly accelerating breeding programs and advancing basic research.  In this study, a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing (GBTS), featuring 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with key economic traits.  To demonstrate its utility, genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.  The results revealed that greater genetic distance was associated with higher middle parent heterosis (MPH) for single fruit weight.  Furthermore, 56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.  Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively indicated that these cultivars fall into two major groups.  Group I, comprising black or dark green skinned wax gourds, exhibited lower genetic diversity than Group II, which includes green or light green skinned varieties, reflecting shorter genetic distances within Group I.  Finally, 60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.  As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.