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Computer simulation to guide choice of breeding strategies for maker-aided multiple trait integration in maize

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Title: Computer simulation to guide choice of breeding strategies for maker-aided multiple trait integration in maize
Author(s): Peng, Ting
Advisor(s): Mumm, Rita H.
Department / Program: Crop Sciences
Discipline: Crop Sciences
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: M.S.
Genre: Thesis
Subject(s): Computer simulation multiple trait integration breeding strategy single event introgression linkage drag choice of donor parent event pyramiding trait fixation
Abstract: With the rapid rate of adoption by farmers worldwide of crop varieties containing multiple value-added traits, mainly genetically modified traits, as many as 15 to 20 transgenic events may be offered in new maize hybrids by 2030 (Que et al. 2010; Fraley 2012). Multiple Trait Integration (MTI) is designed to integrate the specific transgenic events conferring the value-added trait phenotypes into the elite genetic package represented by the target hybrid, regaining the performance attributes of the target hybrid along with reliable expression of the value-added traits. From a breeding standpoint, MTI involves four steps: Single Event Introgression, Event Pyramiding, Trait Fixation, and Version Testing. We considered the breeding process to introgress 15 transgenic events into a target maize hybrid, incorporating 8 into the female parent and 7 into the male parent, to design a comprehensive and efficient approach to MTI overall. Focusing on the first step, Single Event Introgression which is conducted in parallel streams to convert a given recurrent parent for individual events, the primary breeding goal is to minimize residual non-recurrent parent germplasm remaining from the trait donor, especially in the chromosomal proximity to the event (i.e. linkage drag). Setting a defined lower limit of 96.66% recurrent parent (RP) germplasm recovery (i.e. ≤ 120 cM non-recurrent parent germplasm), conversion for 15 events requires the final selections in Single Event Introgression to have < 8 cM total amount of non-recurrent parent germplasm across the genome with ~ 1 cM non-recurrent parent germplasm in the 20 cM region flanking the event. Using computer simulation, we sought to identify optimal breeding strategies for Single Event Introgression in terms of selection scheme, required population size, and selection intensity. In addition, strategies for choice of donor parent to facilitate conversion efficiency and quality were evaluated. Selection schemes classified as three-stage, modified two-stage, and combined selection conducted from BC1 through BC3, BC4, or BC5 were compared using a moderate constant population size. Criteria for evaluating efficiency included amount of total residual non-recurrent parent germplasm, amount of non-recurrent parent germplasm remaining in the chromosomal region flanking the event in the finished conversion, total number of marker data points required, total population size across generations, and total number of generations. One selection scheme successfully met the defined goals for this breeding step. It involved 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; selection intensity was set at 0.01 for all generations. Furthermore, 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 a ‘quality’ single event conversion can be accomplished earlier than BC5 given a donor parent with modest levels of genetic similarity. This study lays the groundwork for a comprehensive approach to MTI by providing appropriate starting materials with which to proceed with Event Pyramiding and Trait Fixation. Next, we focused on the second and third steps in MTI: Event Pyramiding and Trait Fixation. Using computer simulation, we aimed to 1) identify an optimal breeding strategy for pyramiding of 8 events into the female RP (and 7 in the male RP), and 2) evaluate breeding strategies for Trait Fixation to create a ‘finished’ conversion of each RP homozygous for all events in an efficient and effective manner. Building on work by Ishii and Yonezawa (2007a), a symmetric crossing/selfing schedule for Event Pyramiding was devised for stacking 8/7 events in a target RP. Trait Fixation breeding strategies considered self-pollination and doubled haploidy approaches to achieve homozygosity as well as seed chipping and tissue sampling approaches to facilitate genotyping. With self-pollination approaches, 2 generations of selfing rather than 1 for Trait Fixation (i.e. ‘F2 enrichment’ as per Bonnett et al. (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 population size across generations (NT), total number of marker data points (MDP), total number of generations (GEN), number of seeds sampled by seed chipping (NSC), and number of plants requiring tissue sampling (NTS), number of pollinations (NP) (i.e. selfing and crossing) were considered in comparisons of breeding strategies. A breeding strategy involving seed chipping and two-generation self-pollination approaches (SC+SELF) was determined to be the most efficient breeding strategy considering GEN and resource requirements such as MDP, NT, NSC, NTS, and NP. Doubled haploid 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 commercial release.
Issue Date: 2012-09-18
URI: http://hdl.handle.net/2142/34564
Rights Information: Copyright 2012 Ting Peng
Date Available in IDEALS: 2012-09-18
Date Deposited: 2012-08
 

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