WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

Abstract

Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study, show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.

Genes Impacting Grain Weight and Number in Wheat (Triticum aestivum L. ssp. aestivum)

“…The Wheat Aberrant Panicle Organization 1 (WAPO1) gene codes for an F-Box protein [44]. In wheat, the F-box proteins function as a component of the Skp1-Cullin1-F-box (SCF) complex that recognizes substrates to be ubiquitin tagged for degradation [75].…”

“…At higher levels of WAPO1 expression, more spikelets were observed; however, the percent of infertile spikelets increased with the expression, such that the plants with the highest expression of WAPO1 were associated with a decrease in yield. WAPO1 contains two exons and one small intron, spanning approximately 1460 base pairs, and is predicted to translate into a 440 amino acid protein [44]. A single copy of WAPO1 exists on each of the three chromosomes from set seven with a relatively even, but low expression across all three genomes (Figure 5).…”

Genetic Incorporation of the Favorable Alleles for Three Genes Associated With Spikelet Development in Wheat

“…WAPO1 on wheat chromosome arm 7AL was identified as the best candidate gene regulating spikelet number per spike based on a fine genetic map, a genome-wide association analysis, and the known functions of the orthologous APO1 gene in rice ( Kuzay et al, 2019 ; Voss-Fels et al, 2019 ). Since then, more robust evidence from numerous materials with various genetic backgrounds that were tested under different environments and from mutants and transgenic wheat ( Ma et al, 2019 ; Ding et al, 2021 ; Jones et al, 2021 ; Kuzay et al, 2022 ) has demonstrated that WAPO-A1 is the causal gene for the previously reported QTLs. WAPO-A1b in haplotypes such as Berkut had more than threefold higher transcript levels than WAPO-A1a with the 115-bp deletion and three SNPs in the promoter in haplotypes such as RAC875, suggesting that the reduced transcript level of WAPO-A1a was due to the 115-bp deletion and three SNPs ( Kuzay et al, 2019 ; Voss-Fels et al, 2019 ).…”

Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat

“…This would explain the low SPS observed for Soissons, carrying the early PPD-D1a allele, despite having the high-SPS WAPO-A1b allele, an observation mirrored for Fielder in comparison to Yitpi. WAPO-A1 native alleles on the other hand have not been reported to cause large changes in flowering time in field trials 25,45 and while transgenic expression delayed flowering, CRISPR and EMS mutants had no significant effects 27 . However, the WAPO-A1b allele has a larger effect on the number of SPS in the winter wheat NIAB MAGIC population (+2.1 SPS) compared to the spring wheat CSIRO MAGIC population (+1.1 SPS) and an epistatic interaction between WAPO-A1, VRN-D3, PPD-B1 and Qsn.csu-6B has been described 45 .…”

“…The WAPO-A1 gene has been proposed as the candidate gene for a major QTL for SPS on 7AL mapped in several populations [22][23][24][25][26] and the WAPO-B1 gene as a candidate for a smaller QTL for SPS on 7BL 22 . Recently, 27 Kuzay et al, 2022 demonstrated, using CRISPR-generated mutants and transgenic plants, the role of WAPO-A1 and WAPO-B1 in determining SPS in tetraploid wheat.…”