A genome-wide associate study reveals favorable alleles conferring apical and basal spikelet fertility in wheat (Triticum aestivum L.)

Kernel number per spike (KNPS) is one of the key factors affecting wheat yield, which can be significantly reduced by lower fertility or sterility of the apical and basal spikelets. In this study, the spikelet number per spike (SNPS), thousand kernel weight (TKW), KNPS, total grain numbers of the top three apical spikelets (GNAS), and total grain numbers of the bottom three basal spikelets (GNBS) of 212 wheat lines were recorded from five different environmental conditions. These 212 accessions were genotyped using the 9K iSelect SNP Beadchip. A total of 3269 SNP markers were used for genome-wide association analysis (GWAS). One hundred twelve significant marker-trait associations (MTAs) were identified. Twenty-two MTAs were identified in at least two environments and two of them showed association with two or more grain setting properties. Different loci showed an additive effect with both GNAS and GNBS being much higher in the lines with more favorite alleles. Two SNP loci, wsnp_Ex_c31799_40545376 and wsnp_BF293620A_Ta_2_3, showed the largest effects on increasing KNPS through improved fertility of apical and basal spikelets, respectively. These MTAs have the potential to be used in future marker-assisted selection.