Browsing by Person "Reif, Jochen Christoph"

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Assessing the Genetic Diversity in Crops with Molecular Markers: Theory and Experimental Results with CIMMYT Wheat and Maize Elite Germplasm and Genetic Resources
(2004) Reif, Jochen Christoph; Melchinger, Albrecht E.
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.
Capturing wheat phenotypes at the genome level
(2022) Hussain, Babar; Akpınar, Bala A.; Alaux, Michael; Algharib, Ahmed M.; Sehgal, Deepmala; Ali, Zulfiqar; Aradottir, Gudbjorg I.; Batley, Jacqueline; Bellec, Arnaud; Bentley, Alison R.; Cagirici, Halise B.; Cattivelli, Luigi; Choulet, Fred; Cockram, James; Desiderio, Francesca; Devaux, Pierre; Dogramaci, Munevver; Dorado, Gabriel; Dreisigacker, Susanne; Edwards, David; El-Hassouni, Khaoula; Eversole, Kellye; Fahima, Tzion; Figueroa, Melania; Gálvez, Sergio; Gill, Kulvinder S.; Govta, Liubov; Gul, Alvina; Hensel, Goetz; Hernandez, Pilar; Crespo-Herrera, Leonardo Abdiel; Ibrahim, Amir; Kilian, Benjamin; Korzun, Viktor; Krugman, Tamar; Li, Yinghui; Liu, Shuyu; Mahmoud, Amer F.; Morgounov, Alexey; Muslu, Tugdem; Naseer, Faiza; Ordon, Frank; Paux, Etienne; Perovic, Dragan; Reddy, Gadi V. P.; Reif, Jochen Christoph; Reynolds, Matthew; Roychowdhury, Rajib; Rudd, Jackie; Sen, Taner Z.; Sukumaran, Sivakumar; Ozdemir, Bahar Sogutmaz; Tiwari, Vijay Kumar; Ullah, Naimat; Unver, Turgay; Yazar, Selami; Appels, Rudi; Budak, Hikmet
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
Differences in yield performance and yield stability between hybrids and inbred lines of wheat, barley, and triticale
(2015) Mühleisen, Jonathan; Reif, Jochen Christoph
Hybrids of wheat, barley, and triticale are expected to possess higher yield performance and yield stability compared to inbred lines. Assessment of yield performance as well as yield stability requires the evaluation of genotypes in plot-based yield trials across multiple environments. Evaluation of genotypes under stress conditions can be associated with increased field heterogeneity, which may result in imprecise estimates of genotypic values. The assessment of yield stability requires intensive testing in many environments, and it would be interesting to know how many test environments are required to reliably estimate yield stability. The key objectives of the present thesis were to (1) investigate optimal strategies to analyze field trials with high error variance due to spatially varying drought stress, (2) identify the required number of test environments to precisely estimate yield stability of individual barley genotypes, and (3) examine yield performance and yield stability of wheat, barley, and triticale hybrids and lines. Drought stress at two locations of a winter triticale trial caused increased field heterogeneity, resulting in lower heritabilities compared to the four non-stress locations. It was found that heritability could be increased by modeling incomplete block and row effects, by using visual scorings of drought stress intensity as covariates in an analysis of covariance, and by modeling a spatial covariance between adjacent plots. The most suitable model can be identified using the Akaike Information Criterion. In addition, it has to be ensured that the covariate is independent from genotypic effects and that it is linearly related with the response variable. Dynamic yield stability of genotypes was frequently found to depend strongly on the specific set of test environments. When the genotypes were evaluated in different environments, e.g. in the following year, the ranking in yield stability could be different. This would result in a low heritability. Theoretical assumptions and empirical studies showed that heritability can be increased when the number of test environments is increased. Five series of barley registration trials with a reduced number of 16 to 27 genotypes evaluated in 39 to 45 environments were used to investigate the relationship between magnitude of heritability of yield stability and number of test environments. Based on a cross-validation approach, it was found, that at least 40 test environments should be used to obtain a heritability of 0.5. Magnitude of heritability, however, varied strongly within and between series. Therefore, depending on the respective set of environments and genotypes, more or less test environments can be needed. Yield performance of wheat hybrids produced using chemical hybridizing agents (CHA) or cytoplasmic male sterility (CMS) was well investigated in other studies reporting around 10% midparent heterosis for grain yield. In the present thesis, CMS-based barley hybrids were compared with parental inbred lines and unrelated commercial inbred lines in breeding and registration trials. Midparent heterosis was around 10%. The comparison with commercial inbred lines in the registration trials revealed that hybrids could compete with and partially surpass outstanding inbred lines. Triticale hybrids, produced using CMS, were evaluated for grain yield at up to 20 environments with their parents and commercial inbred lines. Midparent heterosis amounted to 3% and no hybrid outyielded the best inbred line. The low yield performance of triticale hybrids is probably associated with CMS-system, since CHA-based triticale hybrids showed a midparent heterosis around 10% in early studies, which is comparable to the midparent heterosis found in wheat and barley. Yield stability of CHA-based wheat as well as CMS-based hybrids of barley and triticale was compared with yield stability of parental and commercial inbred lines on group level. The wheat and barley hybrids showed on average significantly higher dynamic yield stability compared to inbred lines, but the triticale hybrids did not. In the barley registration trials, hybrids had the highest dynamic yield stability on average. The CMS-based triticale hybrids, however, showed on average significantly lower dynamic yield stability as their female parents and the commercial inbred lines across 20 environments. In conclusion, hybrids of wheat and barley possessed an increased yield potential as well as an enhanced dynamic yield stability. In contrast, the CMS-based triticale hybrids showed only marginal yield advantages coupled with low dynamic yield stability. Further research is required to increase economical competitiveness of hybrids in all three crops, to identify and eliminate the reasons for poor performance of CMS-based triticale hybrids and to investigate the suitability of dynamic yield stability measures to identify vigorous and stress tolerant genotypes.
Quantitative trait loci (QTL) mapping in multi-line crosses of European maize
(2012) Steinhoff, Jana; Reif, Jochen Christoph
Multiple-line crosses (MC) have been proposed as promising mapping resource for quantitative trait loci (QTL) detection for agronomic important traits. In contrast to mapping populations derived from a single biparental population, MC can increase the statistical power of QTL detection, the accuracy of QTL location and of QTL effect estimates. Additionally, MC-QTL mapping has the advantage of using data routinely collected in plant breeding programs. The objectives of this study were to (i) assess the reliability of the maize genetic consensus map by comparing it to its six single population linkage maps, (ii) exploit the benefits of a combined analysis by applying two MC-QTL mapping models and to compare the results to single-population analyses, and (iii) investigate the genetic architecture of grain yield, grain moisture, adaptation, and flowering time in elite maize. The experiment comprised six populations with 109 to 150 individuals, resulting from crosses of elite maize breeding material. The germplasm was provided by Syngenta Seeds, Bad Salzuflen, Germany. The 788 genotypes were genotyped with 857 SNP markers. After constructing genetic linkage maps of the six single populations, the genotypic information of the single populations was integrated in a consensus map and its reliability was tested for QTL studies. The average distance between adjacent markers was 1.84 cM suggesting that the marker density is not a limiting factor for QTL analyses. Moreover, we observed medium to high heritabilities for all traits. Consequently, the quality of both genotypic and phenotypic data should allow QTL detection with substantial power. We applied two different MC-QTL mapping models on the data assuming fixed allele effects. The disconnected model estimates QTL effects nested within populations, whereas the connected model takes into account the relationship between the populations. Both models outperformed the single population analyses with regard to QTL detection rate, variance explained by the detected QTL, and the size of the confidence intervals. In all analyses, the disconnected model outperformed the connected model in terms of number of QTL and size of confidence intervals. This superiority seems to be caused by the high background dependencies of QTL effects in connected crosses, which was revealed by a modified diallel analysis of the QTL effects. We investigated the genetic architecture of grain yield, grain moisture, adaptation to maturity zones, and flowering time. Our findings suggest that all traits exhibit a complex genetic architecture with an absence of large QTL effects. Some of the studied traits appear to be influenced by epistasis, interactions between loci. In particular, for flowering time, the two-dimensional scan for epistatic interactions suggested the presence of digenic epistasis. The absence of QTL with large effects suggests that marker-assisted selection is not an appropriate tool to breed for adapted maize hybrids with improved grain yield. Consequently, more suitable approaches for complex traits such as genomic selection should be applied. The joint analyses across populations resulted in higher QTL detection power and resolution compared to single population analyses. Thus, for traits with a less complex genetic architecture, MC-QTL mapping is a powerful tool for the identification of robust diagnostic markers.