Yusheng Zhao

Leibniz Institute of Plant Genetics and Crop Plant Research · Department of Cytogenetics and Genome Analysis

Significance Selfing species wheat are bred as pure-line varieties with stagnating yield growths. In contrast, selection gain in maize is high, owing to massive investment sustained by hybrid seed sales, coupled with an efficient exploitation of hybrid vigor. We have developed a three-step strategy for establishing a heterotic pattern, which was on...

Increasing wheat yield is a key global challenge to producing sufficient food for a growing human population. Wheat grain yield can be boosted by exploiting heterosis, the superior performance of hybrids compared with midparents. Here we present a tailored quantitative genetic framework to study the genetic basis of midparent heterosis in hybrid po...

The genetics underlying heterosis, the difference in performance of crosses compared with midparents, is hypothesized to vary with relatedness between parents. We established a unique germplasm comprising three hybrid wheat sets differing in the degree of divergence between parents and devised a genetic distance measure giving weight to heterotic l...

The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were e...

The great efforts spent in the maintenance of past diversity in genebanks are rationalized by the potential role of plant genetic resources (PGR) in future crop improvement—a concept whose practical implementation has fallen short of expectations. Here, we implement a genomics-informed prebreeding strategy for wheat improvement that does not discri...

Non‑photochemical quenching (NPQ) is a protective mechanism for dissipating excess energy generated during photosynthesis in the form of heat. The accelerated relaxation of the NPQ in fluctuating light can lead to an increase in the yield and dry matter productivity of crops. Since the measurement of NPQ is time‑consuming and requires specific ligh...

Non-photochemical quenching (NPQ) is a protective mechanism for dissipating excess energy generated during photosynthesis in the form of heat. The accelerated relaxation of the NPQ in fluctuating light can lead to an increase in the yield and dry matter productivity of crops. Since the measurement of NPQ is time-consuming and requires specific ligh...

• How plants distribute biomass among organs influences resource acquisition, reproduction, and plant-plant interactions and is essential in understanding plant ecology, evolution, and yield production in agriculture. However, the genetic mechanisms regulating allocation responses to the environment are largely unknown. • We studied recombinant lin...

Vascular plants have segmented body axes with iterative nodes and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield; however, how these events are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections during domestication have extended the...

Genome-wide association studies (GWAS) are a ubiquitous tool for identifying genetic variants associated with complex traits in structured populations. During the past years, many fast GWAS algorithms based on a state-of-the-art model, namely the linear mixed model, have been published to cope with the rapidly growing data size. In this study, we p...

Genome-wide prediction is a powerful tool in breeding. Initial results suggest that genome-wide approaches are also promising for enhancing the use of the genebank material: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, underpin prebreed...

Heterosis is the improved performance of hybrids compared with their parental components and is widely exploited in agriculture. According to quantitative genetic theory, genetic distance between parents at heterotic quantitative trait loci is required for heterosis, but how heterosis varies with genetic distance has remained elusive, despite inten...

Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throu...

Vascular plants segment their body axis with iterative nodes of lateral branches and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield formation; but how they are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections under domestication ha...

Plant genetic resources (PGR) stored at genebanks are humanity’s crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 m...

This study explores the potential of Spanish germplasm for the development of hybrids adapted to southern Europe, a new region for hybrid barley (Hordeum vulgare). A set of 140 locally adapted, advanced breeding lines, developed in a Spanish public breeding program, were evaluated for their potential to widen the germplasm available for hybrid barl...

Key message Genomic prediction of genebank accessions benefits from the consideration of additive-by-additive epistasis and subpopulation-specific marker effects. Abstract Wheat (Triticum aestivum L.) and other species of the Triticum genus are well represented in genebank collections worldwide. The substantial genetic diversity harbored by more t...

Parental selection is at the beginning and contributes significantly to the success of any breeding work. The value of a cross is reflected in the potential of its progeny population. Breeders invest substantial resources in evaluating progeny to select the best performing genotypes as candidates for variety development. Several proposals have been...

To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were...

Wheat ( Triticum aestivum L.) and other species of the Triticum genus are well represented in genebank collections worldwide. The large genetic diversity harbored by more than 850,000 accessions can be explored for the exploitation in modern breeding programs. Shortcomings in the characterization of accession which limit their use so far might be o...

Key message Heterosis effects for dough quality and baking volume were close to zero. However, hybrids have a higher grain yield at a given level of bread making quality compared to their parental lines. Abstract Bread wheat cultivars have been selected according to numerous quality traits to fulfill the requirements of the bread making industry....

The great efforts spent in the maintenance of past diversity in genebanks are rationalized by the potential role of plant genetic resources in future crop improvement: a concept whose practical implementation has fallen short of expectations. Here, we implement genomics-informed parent selection to expedite pre-breeding without discriminating again...

The potential to increase barley grain yield lies in the indeterminate nature of its inflorescence meristem (IM). The IM produces spikelets, the basic reproductive unit in grasses, which are linked to reproductive success. During early reproductive growth, barley spikes pass through the maximum yield potential—a stage after which no new spikelet ri...

Reciprocal recurrent genomic selection is a breeding strategy aimed at improving the hybrid performance of two base populations. It promises to significantly advance hybrid breeding in wheat. Against this backdrop, the main objective of this study was to empirically investigate the potential and limitations of reciprocal recurrent genomic selection...

Key message Genomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers. Abstract Phenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction b...

Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis. The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions. We evaluated seed yield, seed yield related traits and seed quality t...

Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with thos...

Resistance breeding is crucial for a sustainable control of wheat leaf rust and SNP-based genome-wide association studies (GWAS) are widely used to dissect leaf rust resistance. Unfortunately, GWAS based on SNPs explained often only a small proportion of the genetic variation. We compared SNP-based GWAS with a method based on functional haplotypes...

Key message: Hybrid wheat breeding is a promising strategy to improve the level of leaf rust and stripe rust resistance in wheat. Leaf rust and stripe rust belong to the most important fungal diseases in wheat production. Due to a dynamic development of new virulent races, epidemics appear in high frequency and causes significant losses in grain y...

We assessed early vegetative growth in a population of 382 accessions of Arabidopsis thaliana using automated non-invasive high-throughput phenotyping. All accessions were imaged daily from seven to 18 days after sowing in three independent experiments and genotyped using the Affymetrix 250k SNP array. Projected leaf area (PLA) was derived from ima...

Genebank genomics promises to unlock valuable diversity for plant breeding but first, one key question is which marker system is most suitable to fingerprint entire genebank collections. Using wheat as model species, we tested for the presence of an ascertainment bias and investigated its impact on estimates of genetic diversity and prediction abil...

Resistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker‐assisted selection and map‐based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a lar...

With ongoing climate change, drought events are becoming more frequent and will affect biomass formation when occurring during pre-flowering stages. We explored growth over time under such a drought scenario, via non-invasive imaging and revealed the underlying key genetic factors in spring barley. By comparing with well-watered conditions investig...

Genebanks are valuable sources of genetic diversity, which can help to cope with future problems of global food security caused by a continuously growing population, stagnating yields and climate change. However, the scarcity of phenotypic and genotypic characterization of genebank accessions severely restricts their use in plant breeding. To warra...

Septoria tritici blotch (STB) caused by the fungus Zymoseptoria tritici is a devastating foliar disease of wheat (Triticum aestivum L.) that can lead to substantial yield losses. Quantitative genetic resistance has been proposed as a durable strategy for STB control. In this study, we dissected the genetic basis of STB infection in 371 European whe...

Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global...

The scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federal ex situ Genebank for Agricultural and Horticultural Plant Species. The dataset...

In wheat (Triticum spp.), modifying inflorescence (spike) morphology can increase grain number and size and thus improve yield. Here, we demonstrated the potential for manipulating and predicting spike morphology, based on 44 traits. In 12 wheat cultivars, we observed that detillering (removal of branches), which alters photosynthate distribution,...

Key message Historical data generated during seed regeneration are valuable to populate a bio-digital resource center for barley (Hordeum sp.). Abstract Precise estimates of trait performance of genetic resources are considered as an intellectually challenging, complex, costly and time-consuming step needed to exploit the phenotypic and genetic di...

Key message: The portfolio of available Reduced height loci (Rht-B1, Rht-D1, and Rht24) can be exploited for hybrid wheat breeding to achieve the desired heights in the female and male parents, as well as in the hybrids, without adverse effects on other traits relevant for hybrid seed production. Plant height is an important trait in wheat line br...

Genebanks are a rich source of genetic variation. Most of this variation is absent in breeding programs but may be useful for further crop plant improvement. However, the lack of phenotypic information forms a major obstacle for the educated choice of genebank accessions for research and breeding. A promising approach to fill this information gap i...

Grain yield and protein content are traits of major importance in wheat breeding, but their combination is challenging due to a tight negative correlation. Protein yield and grain protein deviation have been proposed as selection criteria to simultaneously improve both traits. Sedimentation volume is an indicator of protein quality, which plays an...

Key message: Predictabilities for wheat hybrids less related to the estimation set were improved by shifting from single- to multiple-trait genomic prediction of Fusarium head blight severity. Breeding for improved Fusarium head blight resistance (FHBr) of wheat is a very laborious and expensive task. FHBr complexity is mainly due to its highly po...

This chapter aims to outline the basic concepts underlying genomic selection (GS) in hybrid breeding. First, the concepts of dominance, heterosis, combining ability and heterotic groups are presented as a special feature of hybrid breeding, giving special attention to the breeding method of recurrent reciprocal selection. Subsequently, the cross-va...

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for...

Background Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. ResultsWith the aim to identify key genetic factors for vegetative biomass formation...

Key message: Selecting contrasting environments allows decreasing phenotyping intensity but still maintaining high accuracy to assess yield stability. Improving yield stability of wheat varieties is important to cope with enhanced abiotic stresses caused by climate change. The objective of our study was to (1) develop and implement an improved her...

Background Hybrid rice breeding facilitates to increase grain yield and yield stability. Long-term success of hybrid breeding depends on the recognition of high-yielding complementary heterotic patterns, which is lacking in crops like rice. Result The main goal of this study was to evaluate the potential and limits to use genomics for establishing...

Genomics-based prediction of hybrid performance promises to boost selection gain. The main goal of our study was to investigate the relevance of additive, dominance, and epistatic effects for determining hybrid seed yield in a biparental rapeseed population. We re-analyzed 60,000 SNP array and seed yield data points from an immortalized F2 populati...

Predicting the grain yield performance of three-way hybrids is challenging. Three-way crosses are relevant for hybrid breeding in barley ( L.) and maize ( L.) adapted to East Africa. The main goal of our study was to implement and evaluate genome-wide prediction approaches of the performance of three-way hybrids using data of single-cross hybrids f...

We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabil...

Improving seed oil yield and quality are central targets in rapeseed (Brassica napus) breeding. The primary goal of our study was to examine and compare the potential and the limits of marker-assisted selection and genome-wide prediction of six important seed quality traits of B. napus. Our study is based on a bi-parental population comprising 202...

Plants producing antisense or double-stranded RNA molecules that target specific genes of eukaryotic pests or pathogens can become protected from their attack. This beneficial effect was also reported for plant–fungus interactions and is believed to reflect uptake of the RNAs by the fungus via an as yet unknown mechanism, followed by target gene si...

Abstract Hybrid breeding in barley (Hordeum vulgare L.) offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal o...

Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of mar...

Key message: Genomic selection models can be trained using historical data and filtering genotypes based on phenotyping intensity and reliability criterion are able to increase the prediction ability. We implemented genomic selection based on a large commercial population incorporating 2325 European winter wheat lines. Our objectives were (1) to s...

Key message: Exploiting the benefits from multiple-trait genomic selection for protein content prediction relying on additional grain yield information within training sets is a realistic genomic selection approach in rye breeding. Multiple-trait genomic selection (MTGS) was specially designed to benefit from the information of genetically correla...