Key message A high-resolution genetic map combined with haplotype analyses identified a wheat ortholog of rice gene APO1 as the best candidate gene for a 7AL locus affecting spikelet number per spike. Abstract A better understanding of the genes controlling differences in wheat grain yield components can accelerate the improvements required to satisfy future food demands. In this study, we identified a promising candidate gene underlying a quantitative trait locus (QTL) on wheat chromosome arm 7AL regulating spikelet number per spike (SNS). We used large heterogeneous inbred families ( > 10,000 plants) from two crosses to map the 7AL QTL to an 87-kb region (674,019,191–674,106,327 bp, RefSeq v1.0) containing two complete and two partial genes. In this region, we found three major haplotypes that were designated as H1, H2 and H3. The H2 haplotype contributed the high-SNS allele in both H1 × H2 and H2 × H3 segregating populations. The ancestral H3 haplotype is frequent in wild emmer (48%) but rare (~ 1%) in cultivated wheats. By contrast, the H1 and H2 haplotypes became predominant in modern cultivated durum and common wheat, respectively. Among the four candidate genes, only TraesCS7A02G481600 showed a non-synonymous polymorphism that differentiated H2 from the other two haplotypes. This gene, designated here as WHEAT ORTHOLOG OF APO1 ( WAPO1 ), is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 ( APO1 ), which affects spikelet number. Taken together, the high-resolution genetic map, the association between polymorphisms in the different mapping populations with differences in SNS, and the known role of orthologous genes in other grass species suggest that WAPO-A1 is the most likely candidate gene for the 7AL SNS QTL among the four genes identified in the candidate gene region. Electronic supplementary material The online version of this article (10.1007/s00122-019-03382-5) contains supplementary material, which is available to authorized users.

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.

Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris L.) core collection of the USDA Western Regional Plant Introduction Station was one of the first collections to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a single nucleotide polymorphism (SNP) platform and new information about genetic diversity of the species, including phaseolin and seed type data. The SNP diversity was studied with a combination of STRUCTURE, principal coordinate analysis (PCoA), and neighbor-joining analysis (NJA). STRUCTURE analyses were conducted for K (number of subpopulations) = 3 and K = 7, based on the ad hoc statistic ΔK. The K = 3 analysis recognized the split between Andean and Mesoamerican domesticates and the subdivision of the Mesoamerican domesticates into high-(Durango/Jalisco) and low-altitude (Mesoamerica) ecogeographic races. The K = 7 analysis further subdivided the Andean group identified for K = 3, as well as the high-altitude group from the Mesoamerican gene pool. It also identified smaller groups consisting of Mesoamerican wild beans. The PCoA and NJA confirmed the STRUCTURE results and highlighted the existence of presumed hybridization among groups. Our results suggest that this core collection should be updated by adding domesticated categories, developing a separate wild common bean core collection, and developing cores for specific purposes.