The genetic architecture of soybean photothermal adaptation to high latitudes.

Soybean is a major plant protein source for both human food and animal feed, but to meet global demands as well as a trend towards regional production, soybean cultivation needs to be expanded to higher latitudes. In this study, we developed a large diversity panel consisting of 1503 early-maturing soybean lines and used genome-wide association mapping to dissect the genetic architecture underlying two crucial adaptation traits, flowering time and maturity. This revealed several known maturity loci, E1, E2, E3, and E4, and the growth habit locus Dt2 as causal candidate loci, and also a novel putative causal locus, GmFRL1, encoding a homolog of the vernalization pathway gene FRIGIDA-like 1. In addition, the scan for quantitative trait locus (QTL)-by-environment interactions identified GmAPETALA1d as a candidate gene for a QTL with environment-dependent reversed allelic effects. The polymorphisms of these candidate genes were identified using whole-genome resequencing data of 338 soybeans, which also revealed a novel E4 variant, e4-par, carried by 11 lines, with nine of them originating from Central Europe. Collectively, our results illustrate how combinations of QTL and their interactions with the environment facilitate the photothermal adaptation of soybean to regions far beyond its center of origin.

The performance of phenomic selection depends on the genetic architecture of the target trait.

KEY MESSAGE: The phenomic predictive ability depends on the genetic architecture of the target trait, being high for complex traits and low for traits with major QTL. Genomic selection is a powerful tool to assist breeding of complex traits, but a limitation is the costs required for genotyping. Recently, phenomic selection has been suggested, which uses spectral data instead of molecular markers as predictors. It was shown to be competitive with genomic prediction, as it achieved predictive abilities as high or even higher than its genomic counterpart. The objective of this study was to evaluate the performance of phenomic prediction for triticale and the dependency of the predictive ability on the genetic architecture of the target trait. We found that for traits with a complex genetic architecture, like grain yield, phenomic prediction with NIRS data as predictors achieved high predictive abilities and performed better than genomic prediction. By contrast, for mono- or oligogenic traits, for example, yellow rust, marker-based approaches achieved high predictive abilities, while those of phenomic prediction were very low. Compared with molecular markers, the predictive ability obtained using NIRS data was more robust to varying degrees of genetic relatedness between the training and prediction set. Moreover, for grain yield, smaller training sets were required to achieve a similar predictive ability for phenomic prediction than for genomic prediction. In addition, our results illustrate the potential of using field-based spectral data for phenomic prediction. Overall, our result confirmed phenomic prediction as an efficient approach to improve the selection gain for complex traits in plant breeding.

High-resolution association mapping with libraries of immortalized lines from ancestral landraces.

KEY MESSAGE: Association mapping with immortalized lines of landraces offers several advantages including a high mapping resolution, as demonstrated here in maize by identifying the causal variants underlying QTL for oil content and the metabolite allantoin. Landraces are traditional varieties of crops that present a valuable yet largely untapped reservoir of genetic variation to meet future challenges of agriculture. Here, we performed association mapping in a panel comprising 358 immortalized maize lines from six European Flint landraces. Linkage disequilibrium decayed much faster in the landraces than in the elite lines included for comparison, permitting a high mapping resolution. We demonstrate this by fine-mapping a quantitative trait locus (QTL) for oil content down to the phenylalanine insertion F469 in DGAT1-2 as the causal variant. For the metabolite allantoin, related to abiotic stress response, we identified promoter polymorphisms and differential expression of an allantoinase as putative cause of variation. Our results demonstrate the power of this approach to dissect QTL potentially down to the causal variants, toward the utilization of natural or engineered alleles in breeding. Moreover, we provide guidelines for studies using ancestral landraces for crop genetic research and breeding.

Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum.

BACKGROUND: Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus. RESULTS: In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (pG), however, four SNPs were associated with major quantitative trait loci (QTLs) with pG ranging from 12 to 48%. The QTL with the highest pG was involved in DON production and associated with a SNP most probably located within the Tri4 gene. CONCLUSIONS: The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding.

Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors.

KEY MESSAGE: Wheat cultivars largely differ in the content and composition of ATI proteins, but heritability was quite low for six out of eight ATIs. The genetic architecture of ATI proteins is built up of few major and numerous small effect QTL. Amylase trypsin inhibitors (ATIs) are important allergens in baker's asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.

Genetic Dissection of Phosphorus Use Efficiency in a Maize Association Population under Two P Levels in the Field.

Phosphorus (P) deficiency is an important challenge the world faces while having to increase crop yields. It is therefore necessary to select maize (Zea may L.) genotypes with high phosphorus use efficiency (PUE). Here, we extensively analyzed the biomass, grain yield, and PUE-related traits of 359 maize inbred lines grown under both low-P and normal-P conditions. A significant decrease in grain yield per plant and biomass, an increase in PUE under low-P condition, as well as significant correlations between the two treatments were observed. In a genome-wide association study, 49, 53, and 48 candidate genes were identified for eleven traits under low-P, normal-P conditions, and in low-P tolerance index (phenotype under low-P divided by phenotype under normal-P condition) datasets, respectively. Several gene ontology pathways were enriched for the genes identified under low-P condition. In addition, seven key genes related to phosphate transporter or stress response were molecularly characterized. Further analyses uncovered the favorable haplotype for several core genes, which is less prevalent in modern lines but often enriched in a specific subpopulation. Collectively, our research provides progress in the genetic dissection and molecular characterization of PUE in maize.

Misexpression of a transcriptional repressor candidate provides a molecular mechanism for the suppression of awns by Tipped 1 in wheat.

Awns are bristle-like structures formed at the tip of the lemma on the florets of some cereal grasses. Wild-type wheat is awned, but awnletted and awnless variants have been selected and nowadays all forms are cultivated. In this study, we dissected the genetic control underlying variation of this characteristic feature by association mapping in a large panel of 1110 winter wheat cultivars of worldwide origin. We identified the B1 (Tipped 1) locus on chromosome 5A as the major determinant of awnlessness globally. Using a combination of fine-mapping and expression analysis, we identified a putative C2H2 zinc finger protein with an EAR domain, characteristic of transcriptional repressors, as a likely candidate for Tipped 1. This gene was found to be up-regulated in awnless B1 compared with awned b1 plants, indicating that misexpression of this transcriptional regulator may contribute to the reduction of awn length in B1 plants. Taken together, our study provides an entry point towards a better molecular understanding of the evolution of morphological features in cereals through selection and breeding.

Speed breeding short-day crops by LED-controlled light schemes.

KEY MESSAGE: A simple and rapid speed breeding system was developed for short-day crops that enables up to five generations per year using LED lighting systems that allow very specific adjustments regarding light intensity and quality. Plant breeding is a key element for future agricultural production that needs to cope with a growing human population and climate change. However, the process of developing suitable cultivars is time-consuming, not least because of the long generation times of crops. Recently, speed breeding has been introduced for long-day crops, but a similar protocol for short-day crops is lacking to date. In this study, we present a speed breeding protocol based on light-emitting diodes (LEDs) that allow to modify light quality, and exemplarily demonstrate its effectiveness for the short-day crops soybean (Glycine max), rice (Oryza sativa) and amaranth (Amaranthus spp.). Adjusting the photoperiod to 10 h and using a blue-light enriched, far-red-deprived light spectrum facilitated the growth of short and sturdy soybean plants that flowered ~ 23 days after sowing and matured within 77 days, thus allowing up to five generations per year. In rice and amaranth, flowering was achieved ~ 60 and ~ 35 days after sowing, respectively. Interestingly, the use of far-red light advanced flowering by 10 and 20 days in some amaranth and rice genotypes, respectively, but had no impact on flowering in soybeans, highlighting the importance of light quality for speed breeding protocols. Taken together, our short-day crops' speed breeding protocol enables several generations per year using crop-specific LED-based lighting regimes, without the need of tissue culture tools such as embryo rescue. Moreover, this approach can be readily applied to a multi-storey 96-cell tray-based system to integrate speed breeding with genomics, toward a higher improvement rate in breeding.

Refining the genetic architecture of flag leaf glaucousness in wheat.

KEY MESSAGE: The cuticle is the plant's barrier against abiotic and biotic stresses, and the deposition of epicuticular wax crystals results in the scattering of light, an effect termed glaucousness. Here, we dissect the genetic architecture of flag leaf glaucousness in wheat toward a future targeted design of the cuticle. The cuticle serves as a barrier that protects plants against abiotic and biotic stresses. Differences in cuticle composition can be detected by the scattering of light on epicuticular wax crystals, which causes a phenotype termed glaucousness. In this study, we dissected the genetic architecture of flag leaf glaucousness in a panel of 1106 wheat cultivars of global origin. We observed a large genotypic variation, but the geographic pattern suggests that other wax layer characteristics besides glaucousness may be important in conferring tolerance to abiotic stresses such as heat and drought. Genome-wide association mapping identified two major quantitative trait loci (QTL) on chromosomes 3A and 2B. The latter corresponds to the W1 locus, but further characterization revealed that it is likely to contain additional QTL. The same holds true for the major QTL on 3A, which was also found to show an epistatic interaction with another locus located a few centiMorgan distal to it. Genome-wide prediction and the identification of a few additional putative QTL revealed that small-effect QTL also contribute to the trait. Collectively, our results illustrate the complexity of the genetic control of flag leaf glaucousness, with additive effects and epistasis, and lay the foundation for the cloning of the underlying genes toward a more targeted design of the cuticle by plant breeding.

Evaluation of the genetic architecture and the potential of genomics-assisted breeding of quality traits in two large panels of durum wheat.

KEY MESSAGE: New QTL for important quality traits in durum were identified, but for most QTL their effect varies depending on the investigated germplasm. Most of the global durum wheat (Triticum turgidum ssp. durum) production is used for human consumption via pasta and to a lower extent couscous and bulgur. Therefore, durum wheat varieties have to fulfill high demands regarding quality traits. In this study, we evaluated the quality traits protein content, sedimentation volume, falling number, vitreousity and thousand kernel weight in a Central European (CP) and a Southern and Western European panel (SP) with 183 and 159 durum lines, respectively, and investigated their genetic architecture by genome-wide association mapping. Except for protein content, we identified QTL explaining a large proportion of the genotypic variance for different traits. However, most of them were identified only in one panel. Nevertheless, for sedimentation volume a genomic region on chromosome 1B appeared important in both durum panels and a BLAST search against the emmer and bread wheat reference genomes points toward the candidate gene Glu-B3. This was further supported by the protein subunit banding pattern via SDS-PAGE gel electrophoresis. For vitreousity, genomic regions on chromosome 7A explained a larger proportion of the genotypic variance in both panels, whereas one QTL, possibly related to the Pinb-2 locus, also slightly influenced the protein content. Within each panel, high prediction abilities for genomic selection were obtained, which, however, dropped considerably when predicting across both panels. Nevertheless, the across-panel prediction ability was still larger than 0.4 for protein content and sedimentation volume, underlining the potential for genomics-aided durum breeding, if laboratory and logistical facilities are available.

The soybean experiment '1000 Gardens': a case study of citizen science for research, education, and beyond.

KEY MESSAGE: Citizen science, an approach that includes normal citizens in scientific research, holds great potential also for plant sciences and breeding and can be a powerful research tool to complement traditional approaches. Citizen science is an approach that includes normal citizens in scientific research, but has so far not been exploited by the various disciplines in plant sciences. Moreover, global threats challenge human well-being and science can provide solutions, but needs to leave the ivory tower in the mind of the broader public. In 2016, we performed the '1000 Gardens-the soybean experiment' citizen science project, that aimed at finding citizens in Germany who would grow soybean lines in their own gardens and evaluate them for a range of traits related to adaptation and agronomic performance. Here, we describe details of this project, i.e. the recruitment, performance, and compliance of the citizen scientists. A total of 2492 citizen scientists volunteered for the project, but through the high media coverage a much broader audience than just the participants was reached. Our 1000 Gardens project was successful in collecting a scientifically unique data set with heritabilities ranging up to 0.60 for maturity date or 0.69 for plant height. Our results suggest that the citizen science approach holds great potential also for plant sciences and can be a powerful research tool to complement traditional approaches. Our project was also successful in raising public awareness about the importance of plant breeding and in communicating key messages on the manifold benefits of legumes for a sustainable agriculture to a broader public. Thus, citizen science appears as a promising avenue to demonstrate the value of breeding and science to the general public by including normal citizens in scientific research.

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat.

BACKGROUND: Heading time is an important adaptive trait in durum wheat. In hexaploid wheat, Photoperiod-1 (Ppd) loci are essential regulators of heading time, with Ppd-B1 conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome Ppd-D1 locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat. RESULTS: In this study, we employed a panel of 328 diverse European durum genotypes that were evaluated for heading time at five environments. Genome-wide association mapping identified six putative QTL, with a major QTL on chromosome 2B explaining 26.2% of the genotypic variance. This QTL was shown to correspond to copy number variation at Ppd-B1, for which two copy number variants appear to be present. The higher copy number confers earlier heading and was more frequent in the heat and drought prone countries of lower latitude. In addition, two other QTL, corresponding to Vrn-B3 (TaFT) and Ppd-A1, were found to explain 9.5 and 5.3% of the genotypic variance, respectively. CONCLUSIONS: Our results revealed the yet unknown role of copy number variation of Ppd-B1 as the major source underlying the variation in heading time in European durum wheat. The observed geographic patterns underline the adaptive value of this polymorphism and suggest that it is already used in durum breeding to tailor cultivars to specific target environments. In a broader context our findings provide further support for a more widespread role of copy number variation in mediating abiotic and biotic stress tolerance in plants.

A modern Green Revolution gene for reduced height in wheat.

Increases in the yield of wheat during the Green Revolution of the late 20th century were achieved through the introduction of Reduced height (Rht) dwarfing genes. The Rht-B1 and Rht-D1 loci ensured short stature by limiting the response to the growth-promoting hormone gibberellin, and are now widespread through international breeding programs. Despite this advantage, interference with the plant's response to gibberellin also triggers adverse effects for a range of important agronomic traits, and consequently modern Green Revolution genes are urgently required. In this study, we revisited the genetic control of wheat height using an association mapping approach and a large panel of 1110 worldwide winter wheat cultivars. This led to the identification of a major Rht locus on chromosome 6A, Rht24, which substantially reduces plant height alone as well as in combination with Rht-1b alleles. Remarkably, behind Rht-D1, Rht24 was the second most important locus for reduced height, explaining 15.0% of the genotypic variance and exerting an allele substitution effect of -8.8 cm. Unlike the two Rht-1b alleles, plants carrying Rht24 remain sensitive to gibberellic acid treatment. Rht24 appears in breeding programs from all countries of origin investigated, with increased frequency over the last decades, indicating that wheat breeders have actively selected for this locus. Taken together, this study reveals Rht24 as an important Rht gene of commercial relevance in worldwide wheat breeding.

Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat.

Winter hardiness is important for the adaptation of wheat to the harsh winter conditions in temperate regions and is thus also an important breeding goal. Here, we employed a panel of 407 European winter wheat cultivars to dissect the genetic architecture of winter hardiness. We show that copy number variation (CNV) of CBF (C-repeat Binding Factor) genes at the Fr-A2 locus is the essential component for winter survival, with CBF-A14 CNV being the most likely causal polymorphism, accounting for 24.3% of the genotypic variance. Genome-wide association mapping identified several markers in the Fr-A2 chromosomal region, which even after accounting for the effects of CBF-A14 copy number explained approximately 15% of the genotypic variance. This suggests that additional, as yet undiscovered, polymorphisms are present at the Fr-A2 locus. Furthermore, CNV of Vrn-A1 explained an additional 3.0% of the genotypic variance. The allele frequencies of all loci associated with winter hardiness were found to show geographic patterns consistent with their role in adaptation. Collectively, our results from the candidate gene analysis, association mapping and genome-wide prediction show that winter hardiness in wheat is a quantitative trait, but with a major contribution of the Fr-A2 locus.

Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map.

BACKGROUND: Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf). RESULTS: A high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F2 mapping population and genotyping-by-sequencing (GBS). The parents of this cross were 'ICMA 02777' and 'ICMR 08888', which segregate for the A4 Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus. CONCLUSION: This study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A4 male-fertility restoration and male-sterility maintenance in pearl millet.

A three-component system incorporating Ppd-D1, copy number variation at Ppd-B1, and numerous small-effect quantitative trait loci facilitates adaptation of heading time in winter wheat cultivars of worldwide origin.

The broad adaptability of heading time has contributed to the global success of wheat in a diverse array of climatic conditions. Here, we investigated the genetic architecture underlying heading time in a large panel of 1,110 winter wheat cultivars of worldwide origin. Genome-wide association mapping, in combination with the analysis of major phenology loci, revealed a three-component system that facilitates the adaptation of heading time in winter wheat. The photoperiod sensitivity locus Ppd-D1 was found to account for almost half of the genotypic variance in this panel and can advance or delay heading by many days. In addition, copy number variation at Ppd-B1 was the second most important source of variation in heading, explaining 8.3% of the genotypic variance. Results from association mapping and genomic prediction indicated that the remaining variation is attributed to numerous small-effect quantitative trait loci that facilitate fine-tuning of heading to the local climatic conditions. Collectively, our results underpin the importance of the two Ppd-1 loci for the adaptation of heading time in winter wheat and illustrate how the three components have been exploited for wheat breeding globally.

Assessing the variation and genetic architecture of asparagine content in wheat: What can plant breeding contribute to a reduction in the acrylamide precursor?

KEY MESSAGE: A large genetic variation, moderately high heritability, and promising prediction ability for genomic selection show that wheat breeding can substantially reduce the acrylamide forming potential in bread wheat by a reduction in its precursor asparagine. Acrylamide is a potentially carcinogenic substance that is formed in baked products of wheat via the Maillard reaction from carbonyl sources and asparagine. In bread, the acrylamide content increases almost linearly with the asparagine content of the wheat grains. Our objective was, therefore, to investigate the potential of wheat breeding to contribute to a reduction in acrylamide by decreasing the asparagine content in wheat grains. To this end, we evaluated 149 wheat varieties from Central Europe at three locations for asparagine content, as well as for sulfur content, and five important quality traits regularly assessed in bread wheat breeding. The mean asparagine content ranged from 143.25 to 392.75 mg/kg for the different wheat varieties, thus underlining the possibility to reduce the acrylamide content of baked wheat products considerably by selecting appropriate varieties. Furthermore, a moderately high heritability of 0.65 and no negative correlations with quality traits like protein content, sedimentation volume and falling number show that breeding of quality wheat with low asparagine content is feasible. Genome-wide association mapping identified few QTL for asparagine content, the largest explaining 18% of the genotypic variance. Combining these QTL with a genome-wide prediction approach yielded a mean cross-validated prediction ability of 0.62. As we observed a high genotype-by-environment interaction for asparagine content, we recommend the costly and slow laboratory analysis only for late breeding generations, while selection in early generations could be based on marker-assisted or genomic selection.

Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components.

KEY MESSAGE: Phenotypic and genetic analysis of six spike and kernel characteristics in wheat revealed geographic patterns as well as long-term trends arising from breeding progress, particularly in regard to spikelet fertility, i.e. the number of kernels per spikelet, a grain yield component that appears to underlie the increase in the number of kernels per spike. Wheat is a staple crop of global relevance that faces continuous demands for improved grain yield. In this study, we evaluated a panel of 407 winter wheat cultivars for six characteristics of spike and kernel development. All traits showed a large genotypic variation and had high heritabilities. We observed geographic patterns for some traits in addition to long-term trends showing a continuous increase in the number of kernels per spike. This breeding progress is likely due to the increase in spikelet fertility, i.e. the number of kernels per spikelet. While the number of kernels per spike and spikelet fertility were significantly positively correlated, both traits showed a significant negative correlation with thousand-kernel weight. Genome-wide association mapping identified only small- and moderate-effect QTL and an effect of the phenology loci Rht-D1 and Ppd-D1 on some of the traits. The allele frequencies of some QTL matched the observed geographic patterns. The quantitative inheritance of all traits with contributions of additional small-effect QTL was substantiated by genomic prediction. Taken together, our results suggest that some of the examined traits were already the basis of grain yield progress in wheat in the past decades. A more targeted exploitation of the available variation, potentially coupled with genomic approaches, may assist wheat breeding in continuing to increase yield levels globally.

Rht24 reduces height in the winter wheat population 'Solitär × Bussard' without adverse effects on Fusarium head blight infection.

KEY MESSAGE: The dwarfing gene Rht24 on chromosome 6A acts in the wheat population 'Solitär × Bussard', considerably reducing plant height without increasing Fusarium head blight severity and delaying heading stage. The introduction of the Reduced height (Rht)-B1 and Rht-D1 semi-dwarfing genes led to remarkable increases in wheat yields during the Green Revolution. However, their utilization also brings about some unwanted characteristics, including the increased susceptibility to Fusarium head blight. Thus, Rht loci that hold the potential to reduce plant height in wheat without concomitantly increasing Fusarium head blight (FHB) susceptibility are urgently required. The biparental population 'Solitär × Bussard' fixed for the Rht-1 wild-type alleles, but segregating for the recently described gibberellic acid (GA)-sensitive Rht24 gene, was analyzed to identify quantitative trait loci (QTL) for FHB severity, plant height, and heading date and to evaluate the effect of the Rht24 locus on these traits. The most prominent QTL was Rht24 on chromosome 6A explaining 51% of genotypic variation for plant height and exerting an additive effect of - 4.80 cm. For FHB severity three QTL were detected, whereas five and six QTL were found for plant height and heading date, respectively. No FHB resistance QTL was co-localized with QTL for plant height. Unlike the Rht-1 semi-dwarfing alleles, Rht24b did not significantly affect FHB severity. This demonstrates that the choice of semi-dwarfing genes used in plant breeding programs is of utmost consideration where resistance to FHB is an important breeding target.

QTL mapping and validation of fertility restoration in West African sorghum A1 cytoplasm and identification of a potential causative mutation for Rf2.

Key message Major A 1 cytoplasm fertility restoration loci, Rf 2 and Rf 5 , were found in the West African sorghum. A potential causative mutation for Rf 2 was identified. KASP markers were validated on independent material. To accelerate the identification and development of hybrid parental lines in West African (WA) sorghum, this study aimed to understand the genetics underlying the fertility restoration (Rf) in WA A1 cytoplasmic male sterility system and to develop markers for a routine use in WA breeding programs. We genotyped by sequencing three F2 populations to map the Rf quantitative trait loci (QTL), validated the molecular KASP markers developed from those QTL in two F2:3 populations, and assessed the most promising markers on a set of 95 R- and B-lines from WA breeding programs. Seven QTL were found across the three F2 populations. On chromosome SBI-05, we found a major fertility restorer locus (Rf5) for two populations with the same male parent, explaining 19 and 14% of the phenotypic variation in either population. Minor QTL were detected in these two populations on chromosomes SBI-02, SBI-03, SBI-04 and SBI-10. In the third population, we identified one major fertility restorer locus on chromosome SBI-02, Rf2, explaining 31% of the phenotypic variation. Pentatricopeptide repeat genes in the Rf2 QTL region were sequenced, and we detected in Sobic.002G057050 a missense mutation in the first exon, explaining 81% of the phenotypic variation in a F2:3 population and clearly separating B- from R-lines. The KASP marker developed from this mutation stands as a promising tool for routine use in WA breeding programs.