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Projects

Research Projects funded by R.F. Baker Center for Plant Breeding are listed by PI. Scroll down to access projects by all Center Members.

William Beavis' Projects

  • 3D graph

    Historically, selection indices have been used to breed for multiple objectives. However, selection indeces provide optimal outcomes if and only if Karush, Kuhn-Tucker (KKT) conditions exist. Because KKT condition seldom exist in breeding programs, we use multi objective optimization approaches that use evolutionary algorithms to find the best breeding strategies to meet multiple objectives in the minimal amount of time. PI: Beavis, W.

  • graph

    In the absence of novel useful genetic variability response to selection is limited.  The attraction of genomic selection is that it enables greater selection intensities with fewer expensive field resources resulting in greater rates of genetic gain.  The unintended consequence is more rapid loss of useful genetic diversity and more limited response to selection in subsequent breeding cycles.  We are investigating the optimal trade-off between short term genetic gains and long term retention of useful genetic diversity based on definition of clear functional objectives and application of algorithms from mathematical programming. PI: Beavis, W.

  • Regional trial

    For the last 40 years plant breeding has been a “numbers game”.  Those with access to larger numbers of field plots and off-season nurseries have developed cultivars that perform better than plant breeders with fewer resources.  Is it possible to develop competitive cultivars with fewer resources?  PI: Beavis, W.

  • Introgression scheme

    Traditionally, introgression has been pursued using combinations of ‘gene stacking’ and backcrossing.  Molecular markers enabled development of marker assisted backcrossing (MAB), however is backcrossing the best breeding process? The answer depends on the objective.  To date, we have found that backcrossing provides a good outcome, but often is not the best breeding procedure to effectively and efficiently introgress desirable alleles at one to twenty loci from unrelated donors. PI: Beavis, W.

  • Soybean flower

    Are the designs of current plant breeding systems optimal? 
    Current cultivar development and genetic improvement projects are based on reproductive biology of the crop and have not changed significantly since 1990.  The emergence of molecular technologies and new ‘omics’ based knowledge have been integrated into breeding programs in an ad hoc manner. 

    “We do not know if integration of new technologies into our breeding pipelines are optimal.”– Ted Crosbie, 2009. 
    “We need to be more efficient and effective, not more expensive.” – Joe Byrum, 2010.
    PI: Beavis, W.

Maria Salas Fernandez's Projects

  • HTP image

    Advances in genotyping technology and reductions in cost have unraveled the need to invest in high-throughput phenotyping (HTP) technologies to be able to perform gene discovery tests at large scale. Since 2012, Dr. Salas Fernandez is part of a team that has state-of-the-art HTP devices for field ground-based acquisition of images, from which plant architecture and growth parameters are extracted and exploited in quantitative genetic studies. Novel descriptors have also been developed and validated to describe and predict biomass yield. Co-PI: Salas Fernandez , MG. Funding: USDA AFRI (USDA-DOE Plant Feedstocks Genomics for Bioenergy), Plant Sciences Institute (ISU).

  • seed germination under cold conditions

    Low soil temperature during early season is a major limitation for sorghum production in temperate climates. Cold tolerance is desirable to ensure a good stand and it would also facilitate early planting, which could translate into longer growing seasons and, higher yields. A limited number of sorghum lines have been classified as cold tolerant, but they have undesirable agronomic characteristics that have hindered their use in sorghum breeding programs. We have characterized a new set of accessions to determine their potential to contribute cold tolerant characteristics to our breeding program. PI: Salas Fernandez, MG. Funding: R.F. Baker Center for Plant Breeding, Sorghum Checkoff Program

  • Plant architecture traits

    We have conducted genome-wide and candidate gene association studies to characterize the genetic architecture of plant height, stem diameter, leaf angle, exsertion, panicle lenght, internode number, flowering time, seed number per panicle and tiller number using the Sorghum Association Panel. We have discovered genomic regions and candidate genes that are currently being validated. With the need to produce more food, feed and fuel in the same or smaller area, and considering climate change, manipulating genes to create desirable plant types in a shorter period of time will be essential in breeding programs. PI: Salas Fernandez, MG. Funding: R.F. Baker Center for Plant Breeding

  • Li-COR measurement of photosynthesis

    The complex genetic architecture of C assimilation is one of the reasons for the lack of improvements in this area. We are investigating genes/alleles associated with higher leaf photosynthetic capacity in sorghum under non-stress, cold and drought stress using both field and controlled condition experiments. Several genomic regions associated with gas exchange and chlorophyll fluorescence parameters were discovered and are curently being validated. These studies have demonstrated the existence of natural genetic variation in C fixation in sorghum that could be exploited to breed for superior germplasm. PI: Salas Fernandez, MG. Funding: NSF CAREER, PGRP.

Thomas Lübberstedt's Projects

  • Microfluidic device for cell sorting

    The ability to double haploid genomes spontaneously would make DH technology more efficient, while avoiding use of toxic colchicine. Spontaneous haploid genome doubling (SHGD) occurs at an extremely low frequency in maize germplasm. The first goal (Goal 1) is isolation of the gene underlying a major QTL for SHGD in maize and to evaluate it in various crop species. A quantum leap in the breeding timeline proposed here is the concept of an in vitro nursery (IVN). Selected genotypes can be maintained within minimal lab-space using cell cultures.Our 2nd goal (Goal 2) is to initiate a systematic approach towards development of in vitro nurseries in any species of interest.

  • Corn kernels haploid

    The objectives of our program are to (i) optimize DH technology in maize regarding haploid induction, haploid identification, and spontaneous haploid genome doubling, (ii) employ DH technology, e.g., to establish exotic introgression DH lines in collaboration with the USDA gene bank in Ames, and (iii) transfer knowledge to other species. PI Lubberstedt, T. Funding: K.J. Frey Chair in Agronomy, R.F. Baker Center for Plant Breeding, Plant Sciences Institute, USDA OREI, USDA SCRI, NSF P3, FFAR & breeding companies.

Asheesh K. Singh's Projects

  • soybean pod

    A significant portion of our research effort focuses on the identification of useful parental soybean strains in the breeding program, for which we leverage genome-wide association mapping and genomic prediction. PI: Singh A.K. Funding: Iowa Soybean Association, R. F. Baker Center for Plant Breeding, Monsanto Chair in Soybean Breeding, Iowa Soybean Research Center.

  • Soybean root

    Because of the difficulty of phenotyping and analysis, root traits often are not considered in plant breeding selection practices. The advent of computer vision and ML-enabled trait extraction and measurement have renewed the interest in utilizing root traits for genetic enhancement to develop robust and resilient cultivars. The goal of the project is to make phenotyping portable and achieving ML-enabled feature extraction of root traits, and implement them in genetic studies and breeding applications. PI: Singh A.K. Funding: Iowa Soybean Research Center, Plant Sciences Institute, R F Baker Center for Plant Breeding, Iowa Soybean Association, Monsanto Chair in Soybean Breeding.

  • Soybean early maturity

    Human rating of visual symptoms has remained the predominant method for plant stress identification and measurement. This is a tedious process and requires specialized training of those making the assessment. Even then, scalability remains an issue and data collection suffer from inter- and intra-rater variabilities. Our group works in a collaborative initiative to address and solve these issues using ML methods. PI: Singh A.K. Funding: Iowa Soybean Association, R. F. Baker Center for Plant Breeding, Monsanto Chair in Soybean Breeding, USDA-AFRI, Plant Sciences Institute.

  • field plots aerial view

    We develop strategies for a cost effective breeding and phenomics program, produce more yield per unit land, and enable cross-disciplinary teams and collaborations between plant breeding, engineering, analytics, and agronomy to positively impact farmers, breeders, and the seed industry. PI: Singh A.K. Funding: Iowa Soybean Association, R. F. Baker Center for Plant Breeding, Monsanto Chair in Soybean Breeding, USDA-AFRI, Plant Sciences Institute.

     

Jianming Yu's Projects

  • genomic selection partial scheme

    Identifying the superior cultivars among the immense number of inbreds or their combinations is a long-standing challenge. By viewing plant breeding as a process of genetic space exploration, data mining and design thinking would help reshape the next generation breeding programs. PI: Yu, Jianming. Funding: The National Science Foundation Grant IOS-1238142, the Iowa State University Raymond F. Baker Center for Plant Breeding, and the Iowa State University Plant Sciences Institute.

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    An integrated framework for gene discovery underlying phenotypic plasticity and performance prediction across environments. PI: Yu, Jianming. Funding: The Agriculture and Food Research Initiative Competitive Grant 2011-67009-30614 from the US Department of Agriculture National Institute of Food and Agriculture, National Science Foundation Grant IOS-1238142, the Kansas State University Center for Sorghum Improvement, the Iowa State University Raymond F. Baker Center for Plant Breeding, and the Iowa State University Plant Sciences Institute.

  • turbocharging scheme

    A comprehensive strategy based on genomic selection and other relevant technologies can be designed to mine the natural heritage stored in numerous gene banks. PI: Yu, Jianming. Funding: The Agriculture and Food Research Initiative competitive grant (2011-03587) from the USDA National Institute of Food and Agriculture, the National Science Foundation grant IOS-1238142, the Kansas State University Center for Sorghum Improvement, the Iowa State University Raymond F. Baker Center for Plant Breeding, and the Iowa State University Plant Sciences Institute.