Projects

Discovery of genetic control of sorghum 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 length, 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

High-throughput phenotyping in Sorghum

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).

Sorghum early cold tolerance

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

Sorghum photosynthetic rate under non-stress, cold and drought stress

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 currently 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.

Testing And Release Of Forage Sorghum Cultivars Adapted To Upper Midwest States

Doubled Haploid Research Program

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.

FFAR Project Accelerated development of crops of the future

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 2^nd goal (Goal 2) is to initiate a systematic approach towards development of in vitro nurseries in any species of interest.

Genomic selection: design thinking, data mining, and optimization

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.

Phenotypic plasticity, reaction norm, and genotype by environment interaction

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 gene banks through genomic selection

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.

Soybean genomic studies

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 Phenomics

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.

Soybean Root Studies

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 stress image based phenotyping

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.