Browsing by Subject "Hybride"

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Comparison of omics technologies for hybrid prediction
(2019) Westhues, Matthias; Melchinger, Albrecht E.
One of the great challenges for plant breeders is dealing with the vast number of putative candidates, which cannot be tested exhaustively in multi-environment field trials. Using pedigree records helped breeders narrowing down the number of candidates substantially. With pedigree information, only a subset of candidates need to be subjected to exhaustive tests of their phenotype whereas the phenotype of the majority of untested relatives is inferred from their common pedigree. A caveat of pedigree information is its inability to capture Mendelian sampling and to accurately reflect relationships among individuals. This shortcoming was mitigated with the advent of marker assays covering regions harboring causal quantitative trait loci. Today, the prediction of untested candidates using information from genomic markers, called genomic prediction, is a routine procedure in larger plant breeding companies. Genomic prediction has revolutionized the prediction of traits with complex genetic architecture but, just as pedigree, cannot properly capture physiological epistasis, referring to complex interactions among genes and endophenotypes, such as RNA, proteins and metabolites. Given their intermediate position in the genotype-phenotype cascade, endophenotypes are expected to represent some of the information missing from the genome, thereby potentially improving predictive abilities. In a first study we explored the ability of several predictor types to forecast genetic values for complex agronomic traits recorded on maize hybrids. Pedigree and genomic information were included as the benchmark for evaluating the merit of metabolites and gene expression data in genetic value prediction. Metabolites, sampled from maize plants grown in field trials, were poor predictors for all traits. Conversely, root-metabolites, grown under controlled conditions, were moderate to competitive predictors for the traits fat as well as dry matter yield. Gene expression data outperformed other individual predictors for the prediction of genetic values for protein and the economically most relevant trait dry matter yield. A genome-wide association study suggested that gene expression data integrated SNP interactions. This might explain the superior performance of this predictor type in the prediction of protein and dry matter yield. Small RNAs were probed for their potential as predictors, given their involvement in transcriptional, post-transcriptional and post-translational regulation. Regardless of the trait, small RNAs could not outperform other predictors. Combinations of predictors did not considerably improve the predictive ability of the best single predictor for any trait but improved the stability of their performance across traits. By assigning different weights to each predictor, we evaluated each predictors optimal contribution for attaining maximum predictive ability. This approach revealed that pedigree, genomic information and gene expression data contribute equally when maximizing predictive ability for grain dry matter content. When attempting to maximize predictive ability for grain yield, pedigree information was superfluous. For genotypes having only genomic information, gene expression data were imputed by using genotypes having both, genomic as well as gene expression data. Previously, this single-step prediction framework was only used for qualitative predictors. Our study revealed that this framework can be employed for improving the cost-effectiveness of quantitative endophenotypes in hybrid prediction. We hope that these studies will further promote exploring endophenotypes as additional predictor types in breeding.
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.
Optimum strategies to implement genomic selection in hybrid breeding
(2022) Marulanda Martinez, Jose Joaquin; Melchinger, Albrecht E.
To satisfy the rising demand for more agricultural production, a boost in the annual expected selection gain (ΔGa) of traits such as grain yield and especially yield stability has to be rapidly achieved. Hybrid breeding has contributed to a notable increment in performance for numerous allogamous species and has been proposed as a way to match the increased demand for autogamous cereals such as rice, wheat, and barley. An additional tool to increase the rate of annual selection gain is genomic selection (GS), a method to assess the merit of an individual by simultaneously accounting for the effects associated with hundreds to thousands of DNA markers. Successful integration of GS and hybrid breeding should go beyond the study of GS prediction accuracy and focus on the design of breeding strategies, for which GS maximizes ΔGa and optimizes the allocation of resources. The main goal of this thesis was to examine strategies for optimum implementation of GS in hybrid breeding with emphasis on estimation set design to perform GS within biparental populations and on the optimization of hybrid breeding strategies through model calculations. One strategy, GSrapid, with moderate nursery selection, one stage of GS, and one stage of phenotypic selection, reached the greatest ΔGa for single trait selection regardless of the budget, costs, variance components, and accuracy of genomic prediction. GSrapid was also the most efficient strategy for the simultaneous improvement of two traits regardless of the correlation between traits, selection index chosen, and economic weights assigned to each trait. The success of this strategy relies principally on the reduction of breeding cycle length and marginally on the increase in selection intensity. Moving from traditional breeding strategies based on phenotypic selection to strategies using GS for single trait improvement in hybrid breeding could lead not only to increments in ΔGa but also to large savings in the budget. The implementation of nursery selection in breeding strategies boosted the importance of efficient systems for inbred generation accompanied by improvements in the methods of hybrid seed production for experimental tests. When it comes to multiple trait improvement, the choice between optimum and base selection indices had minor impact on the net merit. However, considerable differences for ΔGa of single traits were observed when applying optimum or base indices if the variance components of the traits to be improved differed. The role of the economic weights assigned to each trait was determinant and small variations in the weights led to a remarkable genetic loss in one of the traits. The optimum design of estimation sets to perform GS within biparental populations should be based on phenotypic data, rather than molecular marker data. This finding poses major challenges for GS-based strategies aiming to select the best new inbreds within second cycle breeding populations, as breeding cycle length might not be reduced. Then, the ES design to optimize GS within biparental populations would have a defined application on the exploitation of within-family variation by increasing selection intensity in biparental populations with the largest potential of producing high-performing inbreds. Based on the results of this thesis, future challenges for the optimum implementation of GS in hybrid breeding strategies include (i) reductions in breeding cycle length and increments in selection intensity by refinements of DH technology or implementation of speed breeding, (ii) improvements in the methods for hybrid seed production, facilitating the reallocation of resources to the production of more candidates tested during the breeding cycle, and (iii) precise estimation of economic weights, reflecting the importance of the traits for breeding programs and farmers, and maximizing long term ΔGa for the most relevant traits.
Phenotypic and genotypic assessment of traits with relevance for hybrid breeding in European winter wheat
(2015) Langer, Simon Martin; Würschum, Tobias
Hybrid breeding in wheat has recently received increased interest, especially in Europe, and large public and private projects investigating hybrid wheat breeding have been launched. Hybrid breeding has been a great success story for allogamous crops and is seen as a promising approach to increase the yield potential in wheat. Wheat covers more of the world’s surface than any other food crop and is the second main staple crop for human consumption. It can be produced under widely varying conditions and is grown all around the globe, yet, yield gain has declined and is lagging behind the needs of the constantly growing human population. Future challenges in wheat breeding such as the establishment of hybrid varieties and the adaptation of breeding germplasm to increasing stresses caused by climatic changes also in Europe require knowledge-based improvements of relevant traits and phenotyping approaches suited for applied high-throughput plant breeding. A major limitation for the establishment and the production of hybrid wheat is the lack of a cost-efficient hybrid seed production system. This requires the generation of parental ideotypes which maximize the cross-fertilization capability. Male parents should have an extended time of flowering, extrude anthers and widely shed large amounts of viable pollen. Females need increased receptivity for male pollen by opening the glumes and extruding stigmatic hair. Furthermore, male plants should be taller than females and a synchronized timing of flowering between the two parents is also of utmost importance. Employing a set of European elite winter wheat lines, we developed and evaluated phenotyping methods for important floral and flowering traits with relevance for improved cross-pollination (Publication I). We observed high heritabilities for important traits such as ‘pollen mass’ (h2=0.72) and ‘anther extrusion’ (h2=0.91). In addition, genotypic variances were significant which warrants further breeding success. Positive correlations were found among important flowering and floral characteristics which enables the improvement of outcrossing by indirect selection. ‘Pollen mass’ for example, was associated with ‘anther extrusion’, ‘anther length’ and ‘plant height’. Our findings suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross-fertilization. We investigated the genetic architecture of flowering time and plant height (Publication II and III). A panel of 410 European winter wheat varieties was genotyped by a genotyping-by-sequencing approach and in addition, analyzed for the effects of specific candidate genes. The major factor affecting flowering time was the photoperiod regulator Ppd-D1 (58.2% of explained genotypic variance) followed by Ppd-B1 copy number variation (3.2%). For plant height, the two candidate loci Rht-D1 (37.0%) and Rht-B1 (14.0%) had the largest effects on the trait but contrary to reports in the literature did not contribute to flowering time control. In addition, we identified several small effect QTL and epistatic QTL responsible for fine-adjustments of these two traits. Population structure and genetic relatedness in European elite wheat lines was assessed using different types of markers (Publication IV). Results for relatedness differed for the marker types but consistently showed the absence of a major population structure. Regarding the large wheat genome our results revealed that a high number of markers is necessary as there are regions with only low coverage. Concordantly, we were not able to identify the major flowering locus Ppd-D1 without targeted candidate gene analysis. Observations on the findings on population structure could be confirmed in Publication II and III and in addition, the geographical distribution of important flowering time and plant height genes displayed the historical development of wheat breeding in Europe. This information on genetic relatedness among lines can also be employed to assist the establishment of hybrid wheat.
Phenotypic, genetic, and genomic assessment of triticale lines and hybrids
(2017) Losert, Dominik; Würschum, Tobias
Triticale (×Triticosecale Wittmack) is a small grain cereal used for livestock feeding and as renewable energy source. These diverse types of usage lead to different breeding strategies, ideally resulting in continued increase of both, grain and biomass yield. Briefly, the objectives of this thesis were to explore aspects with relevance for line and hybrid breeding in triticale by phenotypic, genetic and genomic assessment of important traits. More specifically, the objectives of this study were to (i) evaluate agronomic traits, assess trait correlations, and investigate the amount of heterosis in triticale hybrids, (ii) examine the potential of line and hybrid cultivars for production of biomass, (iii) assess the phenotypic and genotypic variability in triticale germplasm, (iv) investigate long-term phenotypic trends based on cultivars registered in the past three decades, and (v) identify QTL for agronomical relevant traits. In conclusion, hybrids of triticale possess an increased biomass yield potential compared with their mid-parent values as well as compared with commercial reference cultivars. The findings on triticale germplasm and its breeding history provide important information for breeding programs. Furthermore, based on the obtained results, genomic approaches like marker-assisted or genomic selection appear promising to assist triticale breeding in the future.
Stirring up sorghum hybrid breeding targeting West African smallholder farmers low input environments
(2019) Kante, Papa Ndiaga Moctar; Haussmann, Bettina
Food supply and income in rural areas of West Africa (WA) depend strongly on the local production, and mostly on farmers’ field production of root and tuber crops, and cereals. To feed an ever-increasing population in a context of climate-change and low-input cultural conditions, breeding for resilient crops can guarantee smallholder farmers food security and cash income for a sustainable rural development. Sorghum hybrids for WA were first explored in the early 1970s and hybrid crosses of Malian landraces with introduced Caudatum-race seed parents were evaluated in the early 80s. Although those hybrids exhibited good heterosis for grain yield, their lack of grain quality made them commercially unsustainable. Efforts by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and its partners resulted in the first series of Guinea-race based hybrids. The short statured hybrids were evaluated in several on-farm farmer-managed yield trials, and showed satisfactory grain yield and quality under farmers’ cultivation conditions. Although taller- relative to shorter- height sorghum can help reduce risks of panicle loss by grazing transhumant cattle, no indication on the yield potential of the tall statured hybrids is available. The advances achieved by ICRISAT and its partners in hybrid development justified establishing a long-term hybrid breeding program to provide farmers with hybrids with sufficient grain yield and good grain quality under low input conditions. However, the lack of quantitative genetic information about the genetic value of new experimental hybrids and their parents (Guinea-Caudatum to complete Guinea background, from different WA origins), or about the efficiency of alternative selection methods for targeting yield performance in the predominantly low-input and phosphorous-deficient sorghum production conditions hinders sorghum hybrid development for this region. Sorghum hybrid breeding was commercially feasible only after the identification of a heritable and stable cytoplasmic male sterility (CMS) mechanism. Hybrid breeding in WA can benefit from molecular marker, especially for the fertility restoration/sterility maintenance of the predominant A1-type of CMS. The major outcomes of this thesis are presented as follow: Mean yields of tall hybrids were 3 to 17% (ranging from 6 to 28 g m−2) higher than that of the local check across all 37 on-farm farmer-managed environments and were highest (14–47%) averaged across the seven trials with the lowest mean yields. The yields of the new set of experimental hybrids were substantially superior to farmers’ local Guinea-race varieties, with 20 to 80% higher means over all hybrids in both low phosphorus (LP) and high phosphorus (HP) environments. Average mid-parent and better-parent heterosis estimates were respectively 78 and 48% under HP, and 75 and 42% under LP. Direct selection under LP was predicted to be 20 to 60% more effective than indirect selection under HP conditions, for hybrid performance under LP. The combining ability estimates provide initial insights into the potential benefit of germplasm from further east in West and Central Africa for developing a male parental pool that is distinct and complimentary to the Malian female pool. On chromosome SBI-05, we found a major A1 CMS fertility restorer locus (Rf5) explaining 19 and 14% of the phenotypic variation in either population. Minor quantitative trait loci (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 A1 CMS fertility restorer locus on chromosome SBI-02, Rf2, explaining 31% of the phenotypic variation in the F2 mapping population. 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 an F2:3 validation population and clearly separating B- from R-lines. The Guinea-race hybrids’ substantial yield superiorities over well adapted local Guinea-race varieties suggests that a strategy of breeding hybrids based on Guinea-germplasm can contribute to improving the livelihood of many smallholder farmers in WA. Although the usefulness of direct selection under LP for hybrid performance in the predominantly P-limited target environments was proven, companion evaluations of hybrids under HP would be desirable to identify also new hybrids that can respond to improved fertility conditions for sustainable intensification. The developed KASP marker stands as a promising tool for routine use in WA breeding programs.