Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat.

Background: Grain number (GN) is one of the key yield contributing factors in modern wheat (Triticum aestivum) varieties. Fruiting efficiency (FE) is a key trait for increasing GN by making more spike assimilates available to reproductive structures. Thousand grain weight (TGW) is also an important component of grain yield. To understand the genetic architecture of FE and TGW, we performed a genome-wide association study (GWAS) in a panel of 236 US soft facultative wheats that were phenotyped in three experiments at two locations in Florida and genotyped with 20,706 single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing (GBS).

Results: FE showed significant positive associations with GN, grain yield (GY), and harvest index (HI). Likewise, TGW mostly had a positive correlation with GY and HI, but a negative correlation with GN. Eighteen marker-trait associations (MTAs) for FE and TGW were identified on 11 chromosomes, with nine MTAs within genes. Several MTAs associated with other traits were found within genes with different biological and metabolic functions including nuclear pore complex protein, F-box protein, oligopeptide transporter, and glycoside vacuolar protein. Two KASP markers showed significant mean differences for FE and TGW traits in a validation population.

Conclusions: KASP marker development and validation demonstrated the utility of these markers for improving FE and TGW in breeding programs. The results suggest that optimizing intra-spike partitioning and utilizing marker-assisted selection (MAS) can enhance GY and HI.