TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite European hexaploid winter wheat (Triticum aestivum L.) varieties

Abstract

We dissected the genetic basis of total spikelet number (TSN) along with other traits, viz. spike length (SL) and flowering time (FT) in a panel of 518 elite European winter wheat varieties. Genome-wide association studies (GWAS) based on 39,908 SNP markers revealed highly significant quantitative trait loci (QTL) for TSN on chromosomes 2D, 7A, and 7B, for SL on 5A, and FT on 2D, with 2D-QTL being the functional marker for the gene Ppd-D1. The physical region of the 7A-QTL for TSN revealed the presence of a wheat ortholog (TaAPO-A1) to APO1–a rice gene that positively controls the spikelet number on the panicles. Interspecific analyses of the TaAPO-A1 orthologs showed that it is a highly conserved gene important for floral development and present in a wide range of terrestrial plants. Intraspecific studies of the TaAPO-A1 across wheat genotypes revealed a polymorphism in the conserved F-box domain, defining two haplotypes. A KASP marker developed on the polymorphic site showed a highly significant association of TaAPO-A1 with TSN, explaining 23.2% of the total genotypic variance. Also, the TaAPO-A1 alleles showed weak but significant differences for SL and grain yield. Our results demonstrate the importance of wheat sequence resources to identify candidate genes for important traits based on genetic analyses.

Prospects of GWAS and predictive breeding for European winter wheat’s grain protein content, grain starch content, and grain hardness

“…To analyze the two physical regions, we used a similar strategy, as described in Muqaddasi et al 50 . More specifically, ~ 2-Mb (1-Mb upstream and downstream) wheat reference genomic sequence around the most significant markers was retrieved to characterize the QTL physical region.…”

“…As previously used to investigate the genetic basis of total spikelet number 50 and suggested by Borril et al 58 , the availability of high-quality assemblies of cultivars makes it possible to explore the physical regions associated with the MTA. We analyzed the haplotype structure and the nucleotide diversity of high-confidence genes annotated in an interval of 2-Mb around the most significant markers of QGpc.ipk-2B and QGpc.ipk-6A .…”

Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A

“…Ultimately, grain yield represents the culmination of many genetic, developmental, and environmental interactions with the coordination of plant growth and development across the growing season, and is under complex genetic control—although it can often show high heritability (e.g. Muqaddasi et al 2019 ). Yield can be largely partitioned into three major components: grain weight/size and shape, grain number per spike and spike number per unit area (Gegas et al 2010 ).…”

“…For example, numerous natural genetic variants controlling yield components have been map-based cloned in the diploid cereal crop rice ( Oryza sativa L.) (for a review of rice grain size genes, see Li et al 2018a ), and these tend to account for ~ 10–40% of the phenotypic variation. In contrast, while exceptions do exist, most notably a locus on chromosome 7A controlling spikelet number per ear (Muqaddasi et al 2019 ; Kuzay et al 2019 ; Voss-Fels et al 2019 ), natural variation at wheat genetic loci controlling yield and yield component traits in bread wheat typically control just ~ 2–10% of the variation (reviewed by Brinton and Uauy, 2019 ). This observation is likely due to the compensatory effects of homoeologous genes in polyploid wheat.…”

Molecular Insights into Inflorescence Meristem Specification for Yield Potential in Cereal Crops

“…Recently, it has been reported that APO1 and APO2 physically associate with an E3 ubiquitin ligase, LARGE2, to regulate panicle size and grain number, suggesting a promising module of LARGE2-APO1/APO2 for yield improvement in crops (Figure 3) [131]. Wheat TaAPO-A1, an ortholog of rice APO1, is crucial for the total spikelet number determination, suggesting the conserved nature of this gene across grass species [132]. Rice TAW1 (TAWAWA1) encodes a nuclear protein and acts the upstream of SVP MADS-box genes to fine-tune the timing when meristems acquire the determinant spikelet phase.…”