high-throughput-microscale-protocol-for-analysis-processing

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize (<em>Zea mays</em> L.)

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole ...

University of Illinois at Urbana-Champaign

Genomic selection (GS) procedures have proven useful in estimating breeding value and predicting phenotype with genome-wide molecular marker information. However, issues of high dimensionality, multicollinearity, and the inability to deal effectively with epistasis can jeopardize accuracy and predictive ability. We, therefore, propose a new nonparametric method, pRKHS, which combines the features of supervised principal component analysis (SPCA) and reproducing kernel Hilbert spaces (RKHS) regression, with versions for traits with no/low epistasis, pRKHS-NE, to high epistasis, pRKHS-E. Instead of assigning a specific relationship to represent the underlying epistasis, the method maps genotype to phenotype in a nonparametric way, thus requiring fewer genetic assumptions. SPCA decreases the number of markers needed for prediction by filtering out low-signal markers with the optimal marker set determined by cross-validation. Principal components are computed from reduced marker matrix (called supervised principal components, SPC) and included in the smoothing spline ANOVA model as independent variables to fit the data. The new method was evaluated in comparison with current popular methods for practicing GS, specifically RR-BLUP, BayesA, BayesB, as well as a newer method by Crossa et al., RKHS-M, using both simulated and real data. Results demonstrate that pRKHS generally delivers greater predictive ability, particularly when epistasis impacts trait expression. Beyond prediction, the new method also facilitates inferences about the extent to which epistasis influences trait expression.

Nonparametric method for genomics-based prediction of performance of quantitative traits involving epistasis in plant breeding.

Plant breeding for crop genetic improvement involves the cycle of creating genetic diversity and exploiting that diversity to derive an improved cultivar with outstanding performance for specific traits of interest. Genetic modification through transformation essentially expands the genepool to facilitate access to genes otherwise not available through crossing. Transgenic events are defined by the DNA sequence that has been incorporated into the target genome and the specific point(s) of insertion. In the development of a new transgenic trait, typically many events are generated and evaluated with the aim of identifying one exhibiting consistent trait expression at or above specified thresholds, stable inheritance, and the absence of any negative effects. With transgenic traits for maize, once commercial candidates have been identified, these events are introgressed into elite lines, often through the use of molecular markers that can accelerate the breeding process and aid in producing a quality conversion. Converted elite lines are yield-tested to ensure performance equivalency with their unconverted counterparts. Finally, before commercial sale of seed, quality control monitoring is conducted to ensure event identity and purity and the absence of any unintended events. This monitoring complements other quality control measures to confirm seed viability and line/hybrid purity and uniformity in seed treatments, all in an effort to ensure customer satisfaction and to comply with governmental regulations. Thus, genetically modified (GM) cultivars are subject to significant testing and auditing prior to seed sale and distribution to farmers, more testing and auditing than with non-GM cultivars. 

A look at product development with genetically modified crops: examples from maize.

From a breeding standpoint, multiple trait integration (MTI) is a four-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) using backcross breeding, ultimately regaining the performance attributes of the target hybrid along with reliable expression of the value-added traits. In the light of the overarching goal of recovering equivalent performance in the finished conversion, this study focuses on the first step of MTI, single event introgression, exploring the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events, incorporating eight events into the female hybrid parent and seven into the male parent. Single event introgression is conducted in parallel streams to convert the recurrent parent (RP) for individual events, with the primary objective of minimizing residual non-recurrent parent (NRP) germplasm, especially in the chromosomal proximity to the event (i.e. linkage drag). In keeping with a defined lower limit of 96.66 % overall RP germplasm recovery (i.e. ≤120 cM NRP germplasm given a genome size of 1,788 cM), a breeding goal for each of the 15 single event conversions was developed: <8 cM of residual NRP germplasm across the genome with ~1 cM in the 20 cM region flanking the event. Using computer simulation, we aimed to identify optimal breeding strategies for single event introgression to achieve this breeding goal, measuring efficiency in terms of number of backcross generations required, marker data points needed, and total population size across generations. Various selection schemes classified as three-stage, modified two-stage, and combined selection conducted from BC1 through BC3, BC4, or BC5 were compared. The breeding goal was achieved with a selection scheme involving five generations of marker-aided backcrossing, with BC1 through BC3 selected for the event of interest and minimal linkage drag at population size of 600, and BC4 and BC5 selected for the event of interest and recovery of the RP germplasm across the genome at population size of 400, with selection intensity of 0.01 for all generations. In addition, strategies for choice of donor parent to facilitate conversion efficiency and quality were evaluated. Two essential criteria for choosing an optimal donor parent for a given RP were established: introgression history showing reduction of linkage drag to ~1 cM in the 20 cM region flanking the event and genetic similarity between the RP and potential donor parents. Computer simulation demonstrated that single event conversions with <8 cM residual NRP germplasm can be accomplished by BC5 with no genetic similarity, by BC4 with 30 % genetic similarity, and by BC3 with 86 % genetic similarity using previously converted RPs as event donors. This study indicates that MTI to produce a 'quality' 15-event-stacked hybrid conversion is achievable. Furthermore, it lays the groundwork for a comprehensive approach to MTI by outlining a pathway to produce appropriate starting materials with which to proceed with event pyramiding and trait fixation before version testing.

Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression.

Multiple trait integration (MTI) is a multi-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) through backcross breeding. From a breeding standpoint, MTI involves four steps: single event introgression, event pyramiding, trait fixation, and version testing. This study explores the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events in the light of the overall goal of MTI of recovering equivalent performance in the finished hybrid conversion along with reliable expression of the value-added traits. Using the results to optimize single event introgression (Peng et al. Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression. Mol Breed, 2013) which produced single event conversions of recurrent parents (RPs) with ≤8 cM of residual non-recurrent parent (NRP) germplasm with ~1 cM of NRP germplasm in the 20 cM regions flanking the event, this study focused on optimizing process efficiency in the second and third steps in MTI: event pyramiding and trait fixation. Using computer simulation and probability theory, we aimed to (1) fit an optimal breeding strategy for pyramiding of eight events into the female RP and seven in the male RP, and (2) identify optimal breeding strategies for trait fixation to create a 'finished' conversion of each RP homozygous for all events. In addition, next-generation seed needs were taken into account for a practical approach to process efficiency. Building on work by Ishii and Yonezawa (Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: I. Schedule of crossing between the donor lines. Crop Sci 47:537-546, 2007a), a symmetric crossing schedule for event pyramiding was devised for stacking eight (seven) events in a given RP. Options for trait fixation breeding strategies considered selfing and doubled haploid approaches to achieve homozygosity as well as seed chipping and tissue sampling approaches to facilitate genotyping. With selfing approaches, two generations of selfing rather than one for trait fixation (i.e. 'F2 enrichment' as per Bonnett et al. in Strategies for efficient implementation of molecular markers in wheat breeding. Mol Breed 15:75-85, 2005) were utilized to eliminate bottlenecking due to extremely low frequencies of desired genotypes in the population. The efficiency indicators such as total number of plants grown across generations, total number of marker data points, total number of generations, number of seeds sampled by seed chipping, number of plants requiring tissue sampling, and number of pollinations (i.e. selfing and crossing) were considered in comparisons of breeding strategies. A breeding strategy involving seed chipping and a two-generation selfing approach (SC + SELF) was determined to be the most efficient breeding strategy in terms of time to market and resource requirements. Doubled haploidy may have limited utility in trait fixation for MTI under the defined breeding scenario. This outcome paves the way for optimizing the last step in the MTI process, version testing, which involves hybridization of female and male RP conversions to create versions of the converted hybrid for performance evaluation and possible commercial release.

Optimized breeding strategies for multiple trait integration: II. Process efficiency in event pyramiding and trait fixation.

Although the system for producing yellow corn grain is well established in the US, its role among other biofeedstock alternatives to petroleum-based energy sources has to be balanced with its predominant purpose for food and feed as well as economics, land use, and environmental stewardship. We model land usage attributed to corn ethanol production in the US to evaluate the effects of anticipated technological change in corn grain production, ethanol processing, and livestock feeding through a multi-disciplinary approach. Seven scenarios are evaluated: four considering the impact of technological advances on corn grain production, two focused on improved efficiencies in ethanol processing, and one reflecting greater use of ethanol co-products (that is, distillers dried grains with solubles) in diets for dairy cattle, pigs, and poultry. For each scenario, land area attributed to corn ethanol production is estimated for three time horizons: 2011 (current), the time period at which the 15 billion gallon cap for corn ethanol as per the Renewable Fuel Standard is achieved, and 2026 (15 years out).

Land usage attributed to corn ethanol production in the United States: sensitivity to technological advances in corn grain yield, ethanol conversion, and co-product utilization.

Multiple trait integration (MTI) is the process by which a target hybrid (or variety) is converted to add value-added traits to the comprehensive performance package represented by that genotype. The goal is to recover all the attributes of the target hybrid, with the addition of the specified value-added traits. In maize, this process utilizes the backcross breeding method to incorporate transgenic events (or genes) of interest. Thus, MTI involves four main steps: single event introgression, event pyramiding, trait fixation, and version testing to ensure recovery of equivalent performance with at least one version of the converted hybrid. Based on a case study involving conversion of a target hybrid for 15 transgenic events (the female inbred parent was converted for 8 events, and the male inbred parent was converted for 7 events), we explored parameters in version testing to facilitate a high likelihood of recovering at least one version of the hybrid conversion with yield performance equivalency within 3 % of unconverted target hybrid. Using computer simulation, we explored the impact of two factors on the success rate of the MTI outcome: (1) the amount of residual NRP (non-recurrent parent) germplasm remaining in the converted hybrid and (2) the number of versions of each parental line conversion created. A range of residual NRP germplasm from 120 to 180 cM (which represents 95.0-96.6 % germplasm recovery of the target hybrid in maize) and up to 5 versions of each parental conversion were considered, with all possible hybrid combinations of each version of female and male RP (recurrent parent) conversion evaluated for yield. With 5 versions of each RP conversion and testing of 25 hybrid versions, a >95 % rate of success was realized when the amount of residual NRP germplasm in the hybrid conversion was ≤180 cM. When hybrid conversions contained ≤120-cM residual NRP germplasm, only 4 versions of one of the parental conversions were needed (rather than 5), requiring 20 versions of the hybrid conversion to be yield tested. These results have implications in the strategic design of an overall conversion program and for the upstream MTI process, especially in setting thresholds for the amount of NRP germplasm remaining in RP conversions. Furthermore, these results validate findings of (Peng et al. in Mol Breed 33:189-104, 2014a. doi:10.1007/s11032-013-9936-7, in Mole Breed 33:105-115, 2014b. doi:10.1007/s11032-013-9937-6) which outline effective breeding strategies to optimize earlier steps in MTI (preceding version testing).

Optimized breeding strategies for multiple trait integration: III. Parameters for success in version testing.

Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is crucial to assess in silico the options as well as the impact of various crossing schemes and breeding approaches on performance for traits of interest such as grain yield. For this, a means by which gene effects can be represented in the genome model is critical.

Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation.

Although previous studies have examined the concentration of various nutritional compounds in maize, little focus has been devoted to the study of commercial maize hybrids or their inbred parents. In this study, a genetically and phenotypically diverse set of maize hybrids and inbreds relevant to U.S. commercial maize germplasm was evaluated for its variability in phytochemical content. Total protein, unsaturated fatty acids, tocopherols, soluble phenolics, and insoluble-bound phenolics were evaluated in this study. Of these compounds, only soluble and insoluble-bound phenolic acids exhibited means and variances that were at least as large as the means and variances reported for other sets of germplasm. This suggests that selection for high phenolic acid content is possible in current U.S. commercial germplasm. In contrast, while the total protein, unsaturated fatty acid, or tocopherol content could possibly be improved using current U.S. commercial germplasm, the results of this study indicate that the incorporation of more diverse sources of germplasm would most likely result in quicker genetic gains.

Concentration of Beneficial Phytochemicals in Harvested Grain of U.S. Yellow Dent Maize (Zea mays L.) Germplasm.

Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.

Article	Year
Nonparametric method for genomics-based prediction of performance of quantitative traits involving epistasis in plant breeding. PloS one\| PubMed ID: 23226325	2012
A look at product development with genetically modified crops: examples from maize. Journal of agricultural and food chemistry\| PubMed ID: 23668783	2013
Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression. Molecular breeding : new strategies in plant improvement\| PubMed ID: 24482600	2014
Optimized breeding strategies for multiple trait integration: II. Process efficiency in event pyramiding and trait fixation. Molecular breeding : new strategies in plant improvement\| PubMed ID: 24482601	2014
Land usage attributed to corn ethanol production in the United States: sensitivity to technological advances in corn grain yield, ethanol conversion, and co-product utilization. Biotechnology for biofuels\| PubMed ID: 24725504	2014
Optimized breeding strategies for multiple trait integration: III. Parameters for success in version testing. Molecular breeding : new strategies in plant improvement\| PubMed ID: 26491398	2015
Method to represent the distribution of QTL additive and dominance effects associated with quantitative traits in computer simulation. BMC bioinformatics\| PubMed ID: 26852240	2016
Concentration of Beneficial Phytochemicals in Harvested Grain of U.S. Yellow Dent Maize (Zea mays L.) Germplasm. Journal of agricultural and food chemistry\| PubMed ID: 28874047	2017
Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS genetics\| PubMed ID: 28953891	2017

Rita H. Mumm

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