Genetic Architecture of Cereal Leaf Beetle Resistance in Wheat.

Wheat production can be severely damaged by endemic and invasive insect pests. Here, we investigated resistance to cereal leaf beetle in a panel of 876 winter wheat cultivars, and dissected the genetic architecture underlying this insect resistance by association mapping. We observed an effect of heading date on cereal leaf beetle infestation, with earlier heading cultivars being more heavily infested. Flag leaf glaucousness was also found to be correlated with resistance. In line with the strong effect of heading time, we identified Ppd-D1 as a major quantitative trait locus (QTL), explaining 35% of the genotypic variance of cereal leaf beetle resistance. The other identified putative QTL explained much less of the genotypic variance, suggesting a genetic architecture with many small-effect QTL, which was corroborated by a genomic prediction approach. Collectively, our results add to our understanding of the genetic control underlying insect resistances in small-grain cereals.

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.

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.

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.

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.

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.

A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1.

BACKGROUND: Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown. RESULTS: Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-кB activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time. CONCLUSIONS: Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

BACKGROUND: Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown. RESULTS: Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties' region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time. CONCLUSIONS: In conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.

Genetic control of plant height in European winter wheat cultivars.

KEY MESSAGE: Plant height variation in European winter wheat cultivars is mainly controlled by the Rht - D1 and Rht - B1 semi-dwarfing genes, but also by other medium- or small-effect QTL and potentially epistatic QTL enabling fine adjustments of plant height. Plant height is an important goal in wheat (Triticum aestivum L.) breeding as it affects crop performance and thus yield and quality. The aim of this study was to investigate the genetic control of plant height in European winter wheat cultivars. To this end, a panel of 410 winter wheat varieties from across Europe was evaluated for plant height in multi-location field trials and genotyped for the candidate loci Rht-B1, Rht-D1, Rht8, Ppd-B1 copy number variation and Ppd-D1 as well as by a genotyping-by-sequencing approach yielding 23,371 markers with known map position. We found that Rht-D1 and Rht-B1 had the largest effects on plant height in this cultivar collection explaining 40.9 and 15.5% of the genotypic variance, respectively, while Ppd-D1 and Rht8 accounted for 3.0 and 2.0% of the variance, respectively. A genome-wide scan for marker-trait associations yielded two additional medium-effect QTL located on chromosomes 6A and 5B explaining 11.0 and 5.7% of the genotypic variance after the effects of the candidate loci were accounted for. In addition, we identified several small-effect QTL as well as epistatic QTL contributing to the genetic architecture of plant height. Taken together, our results show that the two Rht-1 semi-dwarfing genes are the major sources of variation in European winter wheat cultivars and that other small- or medium-effect QTL and potentially epistatic QTL enable fine adjustments in plant height.

Flowering time control in European winter wheat.

Flowering time is an important trait in wheat breeding as it affects adaptation and yield potential. The aim of this study was to investigate the genetic architecture of flowering time in European winter bread wheat cultivars. To this end a population of 410 winter wheat varieties was evaluated in multi-location field trials and genotyped by a genotyping-by-sequencing approach and candidate gene markers. Our analyses revealed that the photoperiod regulator Ppd-D1 is the major factor affecting flowering time in this germplasm set, explaining 58% of the genotypic variance. Copy number variation at the Ppd-B1 locus was present but explains only 3.2% and thus a comparably small proportion of genotypic variance. By contrast, the plant height loci Rht-B1 and Rht-D1 had no effect on flowering time. The genome-wide scan identified six QTL which each explain only a small proportion of genotypic variance and in addition we identified a number of epistatic QTL, also with small effects. Taken together, our results show that flowering time in European winter bread wheat cultivars is mainly controlled by Ppd-D1 while the fine tuning to local climatic conditions is achieved through Ppd-B1 copy number variation and a larger number of QTL with small effects.

Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers.

Modern genomics approaches rely on the availability of high-throughput and high-density genotyping platforms. A major breakthrough in wheat genotyping was the development of an SNP array. In this study, we used a diverse panel of 172 elite European winter wheat lines to evaluate the utility of the SNP array for genomic analyses in wheat germplasm derived from breeding programs. We investigated population structure and genetic relatedness and found that the results obtained with SNP and SSR markers differ. This suggests that additional research is required to determine the optimum approach for the investigation of population structure and kinship. Our analysis of linkage disequilibrium (LD) showed that LD decays within approximately 5-10 cM. Moreover, we found that LD is variable along chromosomes. Our results suggest that the number of SNPs needs to be increased further to obtain a higher coverage of the chromosomes. Taken together, SNPs can be a valuable tool for genomics approaches and for a knowledge-based improvement of wheat.