Assessing the Genetic Diversity in Crops with Molecular Markers: Theory and Experimental Results with CIMMYT Wheat and Maize Elite Germplasm and Genetic Resources

Genetic diversity is a valuable natural resource and plays a key role in future breeding progress. Germplasm collections as a source of genetic diversity must be well-characterized for an efficient management and effective exploitation. The advent of PCR-based molecular markers such as sim-ple sequence repeats (SSRs) has created an opportunity for fine-scale genetic characterization of germplasm collections. The objective of this research was to optimize the utilization of genetic re-sources conserved at the International Wheat and Maize Improvement Center (CIMMYT), with the aid of DNA markers. Choice of suitable dissimilarity measures is important to facilitate the interpretation of findings from DNA marker studies on a theoretically sound basis. The objective of a theoretical study was to examine 10 dissimilarity coefficients widely used in germplasm surveys, with special focus on applications in plant breeding and seed banks. The distance and Euclidean properties of the dissimi-larity coefficients were investigated as well as the underlying genetic models. Application areas for different coefficients were suggested on the basis of the theoretical findings. It has been claimed that plant breeding reduces genetic diversity in elite germplasm, which could seriously jeopardize the continued ability to improve crops. The objectives of the presented ex-perimental study with wheat were to examine the loss of genetic diversity during (i) domestication of the species, (ii) change from traditional landrace cultivars (LC) to modern breeding varieties, and (iii) intensive selection over 50 years of international breeding. A sample of 253 CIMMYT or CIMMYT-related modern wheat cultivars, LC, and Triticum tauschii accessions were characterized with up to 90 SSR markers covering the entire wheat genome. A loss of genetic diversity was ob-served from T. tauschii to LC and from LC to the elite breeding germplasm. Wheat genetic diver-sity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. The results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LC and T. tauschii contain nu-merous unique alleles that were absent in modern wheat cultivars. Consequently, both LC and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germ-plasm. In the 1980's, CIMMYT generated more than 100 maize populations and pools but little is known about the genetic diversity of this germplasm. The objective of the study with 23 CIMMYT maize populations was to characterize their population genetic structure with SSRs. The populations adapted to tropical, subtropical intermediate-maturity, subtropical early-maturity, and temperate mega-environments (ME) were fingerprinted with 83 SSR markers. Estimates of genetic differen-tiation between populations revealed that most of the molecular variation was found within the populations. Principal coordinate analysis based on allele frequencies of the populations revealed that populations adapted to the same ME clustered together and, thus, supported clearly the ME structure. Novel strategies were suggested to optimize the conservation of the genetic diversity within and among the populations. Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objective of the presented study with a subset of 20 out of the 23 maize populations was to investigate the rela-tionship between heterosis and genetic distance determined with SSR markers. The published data of three diallels and one factorial trial evaluated for grain yield were re-analyzed to calculate het-erosis in population hybrids. Correlations of squared modified Rogers distance and heterosis were mostly positive and significant, but adaption problems caused deviations in some cases. For popu-lations adapted to the target regions, genetic distance can be used as a further criterion in the search for promising heterotic patterns and groups. For intermediate- and early-maturity subtropical germ-plasm, two heterotic groups were suggested, consisting of a flint and dent composite. For the tropi-cal germplasm, it was possible to assign population (Pop29) to the established heterotic group A and propose new heterotic groups (Pop25, Pop43). Our experimental results corroborate that SSRs are a powerful tool to (i) detect relationships among different germplasm, (ii) assess the level of genetic diversity present in germplasm pools and its flux over time, and (iii) search for promising heterotic groups for hybrid breeding in complementa-tion to field trials.Die genetische Diversität ist für den zukünftigen Züchtungsfortschritt von zentraler Bedeutung. In Genbanken ist ein bedeutender Anteil der Diversität von Nahrungspflanzen konserviert. Eine optimale Erhaltung und bestmögliche Nutzung dieser genetischen Vielfalt bedarf einer fundierten Charakterisierung der vorhandenen Genotypen. DNA Marker stellen hierzu ein vielversprechendes Werkzeug dar. Die vorliegende Arbeit befasst sich daher mit dem Einsatz von Markertechnologie zur Nutzbarmachung genetischer Ressourcen des Internationalen Mais- und Weizenforschungszentrums (CIMMYT) für die Pflanzenzüchtung. Die Wahl eines geeigneten Ähnlichkeitskoeffizienten spielt bei der Interpretation von Ergebnissen aus DNA-Markerstudien eine entscheidende Rolle.In einer theoretischen Untersuchung wurden zehn häufig in Diversitätsanalysen benutzte Ähnlichkeitskoeffizienten im Hinblick auf ihre Eignung für Pflanzenzüchtungs- und Genbankstudien untersucht. Die den Ähnlichkeitskoeffizienten zugrundeliegenden mathematischen und genetischen Konzepte wurden detailliert diskutiert. Auf der Grundlage dieser Ergebnisse konnten für die unterschiedlichen Koeffizienten Anwendungsgebiete vorgeschlagen werden. Eine populäre Hypothese ist, dass Pflanzenzüchtung die genetische Diversität im Elitezuchtmaterial reduziert und somit den zukünftigen Zuchtfortschritt gefährdet. Ziel einer experimentellen Arbeit mitWeizen war, einen möglichen Diversitätsverlust zu untersuchen während (i) der Domestikation dieser Art, (ii) dem übergang von traditionellen Landsorten (LC) zu modernen Weizensorten (MWC) und (iii) 50 Jahren intensiver Selektion durch internationale Weizenzüchtung. Eine Stichprobe von 253 CIMMYT oder CIMMYT verwandten MWC, LC und Triticum Tauschii Akzessionen wurde mit 90 SSRs genotypisiert. Ein drastischer genetischer Diversitätverlust wurde beim Vergleich von T. tauschii mit den LR und LR mit den MWC beobachtet. Die genetische Vielfalt von MWC nahm von 1950 bis 1989 ab, stieg aber von 1990 bis 1997 wieder an. Die Befunde deuten darauf hin, dass die Weizenzüchter am CIMMYT die Gefahr einer Einengung der genetischen Basis erkannten und erfolgreich die genetische Diversität im Zuchtmaterial durch Introgression neuer Genressourcen erweiterten. Zahlreiche Allele waren in LC oder in T. tauschii vorhanden, die jedoch in MWC nicht gefunden wurden. Folglich stellen sowohl LC als auch T. tauschii eine wertvolle Ressource zur Erweiterung der genetischen Basis des Elitezuchtmaterials bei Weizen dar. In den 80'er Jahren wurden am CIMMYT über 100 Maispopulationen etabliert. Allerdings ist wenig über die genetische Diversität dieses Pflanzenmaterials bekannt. Eine Untersuchung von 23 Maispopulationen zielte auf die Charakterisierung ihrer populationsgenetischen Struktur mit SSR Marker Daten ab. Insgesamt 672 Genotypen der Maispopulationen, adaptiert an tropische, subtropische und gemäßigte Anbauzonen (ME), wurden mittels 83 SSR Markern molekularbiologisch charakterisiert. Der größte Teil der genetischen Varianz wurde innerhalb der Maispopulationen detektiert und der geringere Teil zwischen den Populationen. Eine Hauptkoordinatenanalyse, basierend auf den Populationsallelfrequenzen, ergab eine Gruppierung von Populationen, die an die gleichen Umweltbedingungen adaptiert sind und stützt somit die Einteilung in ME. Es konnten alternative Strategien vorgeschlagen werden, um den Erhalt der genetischen Diversität zwischen und innerhalb der Populationen zu verbessern. Heterotische Gruppen sind von grundlegender Bedeutung in der Hybridzüchtung. Eine Studie mit 20 der 23 Maispopulationen sollte die Beziehung zwischen Heterosis und genetischen Distanzen auf der Grundlage von SSR Markern untersuchen. Publizierte Ergebnisse für den Kornertrag von vier Experimenten mit diallelen bzw. faktoriellen Populationskreuzungen wurden reanalysiert und der Heterosiszuwachs der Populationshybriden berechnet. Die Korrelationen zwischen genetischen Distanzen und Heterosiszuwachs waren meist positiv und signifikant. Allerdings verursachten Adaptionsprobleme in einigen Fällen Abweichungen. Bei Populationen, die an die Zielumwelten angepasst sind, können genetische Distanzen zur Etablierung heterotischer Gruppen benutzt werden. Im subtropisch adaptierten Material wurden zwei heterotische Gruppen, bestehend aus einer Dent- und Flint-Mischpopulation, vorgeschlagen. Bei den tropischen Populationen konnte Population Pop29 in die bereits etablierte heterotische Gruppe A eingeordnet und zwei neue heterotische Gruppen (Pop25, Pop43) vorgeschlagen werden. Nach den Ergebnissen dieser Studie sind SSR Analysen eine geeignete Methode, um (i) Verwandtschaftsbeziehungen aufzudecken, (ii) den zeitlichen Trend und die vorhandene genetische Diversität in Populationen zu untersuchen und (iii) vielversprechende heterotische Gruppen in Kombination mit Feldversuchen zu etablieren

FAIRagro: Ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) für Forschungsdaten in der Agrosystemforschung : Herausforderungen und Lösungsansätze für den Aufbau einer FAIRen Forschungsdateninfrastruktur

FAIRagro ist ein Konsortium in der Nationalen Forschungsdateninfrastruktur (NFDI) in Deutschland um Forschungsdaten der Agrosystemforschung FAIR – d. h. auffindbar (F), zugänglich (A), interoperabel (I) und für andere Forschende domänenübergreifend nachnutzbar (R) zu machen. In der deutschen Forschungslandschaft rund um nachhaltige Agrosysteme werden heterogene Forschungsdaten erhoben und nur zum Teil in existierenden Forschungsdatenrepositorien veröffentlicht. Das Spektrum der Datenformate erstreckt sich beispielsweise von Laborergebnissen, über Satellitenbilder bis hin zu qualitativen Interviews mit Landwirt:innen. Um diese Daten zukünftig für Forschende verschiedener Disziplinen besser auffindbar und nachnutzbar zu machen, wird FAIRagro eine Forschungsdateninfrastruktur (FDI) für die Agrosystemforschung einrichten, in der disziplinäre Dateninfrastrukturen miteinander verknüpft werden. Spezifische Herausforderungen im Forschungsdatenmanagement (FDM) fachlicher Disziplinen wie Pflanzenzüchtung, integrierter Pflanzenschutz oder Agrarrobotik werden als Use Cases in FAIRagro adressiert und für diese Lösungen entwickelt. Darüber hinaus wird FAIRagro ein Netzwerk aus direkten Ansprechpersonen für Fragen zum Forschungsdatenmanagement in der Agrosystem-Community bereitstellen. In Übereinstimmung mit den Zielsetzungen der NFDI und der European Open Science Cloud ist FAIRagro aktiv an der konzeptionellen Implementierung eines interoperablen Datenraums beteiligt

Evolution of a Core Gene Network for Skeletogenesis in Chordates

The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB) and from dogfish as representative of jawed cartilaginous fish (ScRunx1–3). According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets) Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view that teeth and placoid scales evolved from a homologous developmental module

Meeting the challenges facing wheat production: The strategic research agenda of the Global Wheat Initiative

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper

Identification of QTL hot spots for malting quality in two elite breeding lines with distinct tolerance to abiotic stress

Abstract Background Barley (Hordeum vulgare) is an important crop cultivated across the world. Drought is a major abiotic factor compromising barley yield worldwide, therefore in modern spring barley cultivars superior seed and malting quality characteristics should be combined with reasonable level of drought tolerance. Previously we have identified a number of barley lines demonstrating the superior yield performance under drought conditions. The aim of this work was to perform a QTL analysis of malting quality traits in a doubled haploid (DH) mapping population of two elite barley lines that differ in their reaction pattern to drought stress. Results A population of DH lines was developed by crossing two drought-tolerant elite breeding lines, Victoriana and Sofiara, exploiting distinct mechanism of drought tolerance, sustaining assimilation vs remobilization. The mapping population was assayed under field conditions at four distinct locations that differed in precipitation rate. DH lines were genotyped with the Illumina 9 K iSelect assay, and linkage map including 1782 polymorphic markers and covering a total map length of 1140 cM was constructed. The result of quantitative trait loci (QTL) analysis showed that majority of the traits were affected by several main effect QTL and/or QTL x environment (QE) interactions. In total, 57, 41, and 5 QTL were associated with yield-related traits, malting quality traits and seed quality traits, respectively. 11 and 29 of mapped QTL explained more than 10 and 5% of phenotypic variation, respectively. In several chromosomal regions co-localization between QTL for various traits were observed. The largest clusters were detected on chromosomes 3H and 4H. Conclusions Our QTL mapping results revealed several novel consistent genomic regions controlling malting quality which could be exploited in marker assisted selection. In this context, the complex QTL region on chromosome 3H seems of particular interest, as it harbors several large effect QTL

Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping

Abstract Background Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content. Results GBS analysis allowed the identification of 6495 high-quality SNP-markers in our panel of 91 M. recutita plants from 33 origins (2–4 genotypes each) and 4 M. discoidea plants as outgroup, grown in the greenhouse in Gatersleben, Germany. M. recutita proved to be clearly distinct from the outgroup, as was demonstrated by different cluster and principal coordinate analyses using the SNP-markers. Chamomile genotypes from the same origin were mostly genetically similar. Model-based cluster analysis revealed one large group of tetraploid genotypes with low genetic differentiation including 39 plants from 14 origins. Tetraploids tended to display lower genetic diversity than diploids, probably reflecting their origin by artificial polyploidisation from only a limited set of genetic backgrounds. Analyses of flowering time demonstrated that diploids generally flowered earlier than tetraploids, and the analysis of alpha-bisabolol identified several tetraploid genotypes with a high content. GWAS identified highly significant (P < 0.01) SNPs for flowering time (9) and alpha-bisabolol (71). One sequence harbouring SNPs associated with flowering time was described to play a role in self-pollination in Arabidopsis thaliana, whereas four sequences harbouring SNPs associated with alpha-bisabolol were identified to be involved in plant biotic and abiotic stress response in various plants species. Conclusions The first genomic resource for future applications to enhance breeding in chamomile was created, andanalyses of diversity will facilitate the exploitation of these genetic resources. The GWAS data pave the way for future research towards the genetics underlying important traits in chamomile, the identification of marker-trait associations, and development of reliable markers for practical breeding

Genome-Based Identification of Heterotic Patterns in Rice

Abstract 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 heterotic patterns in rice. For this purpose, data of a commercial hybrid rice breeding program targeted to India was analyzed, including 1,960 phenotyped hybrids from three market segments and 262 genotyped parental lines. Our cross-validation study revealed that grain yield of all potential single-crosses can be accurately predicted. Based on the full matrix of hybrid performances, high-yielding heterotic patterns were identified. These heterotic patterns increased grain yield up to 9% compared to the currently employed groups. Heterotic groups of around 14 individuals reflect a good compromise between long-term and short-term selection response. Conclusions Our findings clearly underlined the benefits of a genome-based establishment of heterotic patterns in rice as a requirement for a sustainable long-term success of hybrid rice breeding

Efficiency of a Seedling Phenotyping Strategy to Support European Wheat Breeding Focusing on Leaf Rust Resistance

Leaf rust resistance is of high importance for a sustainable European wheat production. The expression of known resistance genes starts at different developmental stages of wheat. Breeding for resistance can be supported by a fast, precise, and resource-saving phenotyping. The examination of detached leaf assays of juvenile plants inoculated under controlled conditions and phenotyped by a robotic- and computer-based, high-throughput system is a promising approach in this respect. Within this study, the validation of the phenotyping workflow was conducted based on a winter wheat set derived from Central Europe and examined at different plant developmental stages. Moderate Pearson correlations of 0.38–0.45 comparing leaf rust resistance of juvenile and adult plants were calculated and may be mainly due to different environmental conditions. Specially, the infection under controlled conditions was limited by the application of a single rust race at only one time point. Our results suggest that the diversification with respect to the applied rust race spectrum is promising to increase the consistency of detached leaf assays and the transferability of its results to the field

Seed Quality Traits Can Be Predicted with High Accuracy in <i>Brassica napus</i> Using Genomic Data

<div><p>Improving seed oil yield and quality are central targets in rapeseed (<i>Brassica napus</i>) 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 <i>B</i>. <i>napus</i>. Our study is based on a bi-parental population comprising 202 doubled haploid lines and a diverse validation set including 117 <i>B</i>. <i>napus</i> inbred lines derived from interspecific crosses between <i>B</i>. <i>rapa</i> and <i>B</i>. <i>carinata</i>. We used phenotypic data for seed oil, protein, erucic acid, linolenic acid, stearic acid, and glucosinolate content. All lines were genotyped with a 60k SNP array. We performed five-fold cross-validations in combination with linkage mapping and four genome-wide prediction approaches in the bi-parental population. Quantitative trait loci (QTL) with large effects were detected for erucic acid, stearic acid, and glucosinolate content, blazing the trail for marker-assisted selection. Despite substantial differences in the complexity of the genetic architecture of the six traits, genome-wide prediction models had only minor impacts on the prediction accuracies. We evaluated the effects of training population size, marker density and phenotyping intensity on the prediction accuracy. The prediction accuracy in the independent and genetically very distinct validation set still amounted to 0.14 for protein content and 0.17 for oil content reflecting the utility of the developed calibration models even in very diverse backgrounds.</p></div

Seed Quality Traits Can Be Predicted with High Accuracy in <i>Brassica napus</i> Using Genomic Data - Fig 3

<p>Average prediction accuracy of genomic selection applying RR-BLUP based on (a) varying training population sizes and (b) number of markers.</p