EXPLORATION OF GENOMIC SELECTION AND GENOME-WIDE ASSOCIATION STUDIES FOR ILLINOIS CROP BREEDING PROGRAMS

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1022244
• Project Start Date: Feb 26, 2020
• Project End Date: Sep 30, 2024
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801

Performing Department
Crop Sciences

Non Technical Summary
The research conducted in the Lipka Lab has great potential to have direct tangible benefits on crop breeding in Illinois. That is, the investigation and implementation of state-of-the-art GS and GWAS approaches investigated by the Lipka Lab has potential to substantially increase genetic gain and identify major-effect genes, the latter of which could be incorporated into marker-assisted plant breeding programs. Concurrently with this research program, the location and facilities at the University of Illinois are ideal for undertaking this type of research and disseminating the results to plant breeders in Illinois. That is, the excellent field facilitates and computational resources are particularly crucial for phenotypic evaluation of material in an environment in Illinois, and the world-leading computational facilities that are available can be used to ensure that the approaches developed by the Lipka Lab are implemented into computationally efficient software. Finally, many of the faculty at the University of Illinois are already engaged in interdisciplinary collaborations that seek to understand the genomic underpinnings of important crops.

Animal Health Component

35%

Research Effort Categories

Basic

25%

Applied

35%

Developmental

40%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	2410	1080	100%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
2410 - Cross-commodity research--multiple crops;

Field Of Science
1080 - Genetics;

Keywords

crop breeding

plant genetics

genomic selection

genome wide association study

Goals / Objectives
1.To maintain collaborations with breeders and experts of the most important crops in Illinois. These collaborators will be both within the Department of Crop Sciences and throughout the state of Illinois. This will help ensure that the statistical approaches developed in the Lipka Lab are directly relevant to the breeding objectives of collaborators, and thus maximize the potential for them to have a meaningful impact on plant breeding.2. To attend scientific meetings to ensure that the most up-to-date GS and GWAS statistical models are being used for genomic selection. This will help ensure that research conducted in the Lipka Lab is not repeating cutting edge research conducted at peer institutions, and instead is synergistic in the sense that it benefits the entire crop breeding research community as a whole.3. To maintain and improve computational facilities to assess the performance of GS models. This will help ensure that research conducted by the Lipka Lab is conducted in an efficient manner.

Project Methods
1. Demonstrations of the advantages of genomic selection will be made within campus and throughout Illinois, and it is anticipated that breeders within and outside of the Department of Crop Sciences will become aware of the advantages of implementing genomic selection into their programs.2. The team of scientists involved in this project will plan to attend at least one scientific meeting per year including the Allied Genetics Conference (https://genetics-gsa.org/tagc-2020/), the International Plant and Animal Genome Conference (http://www.intlpag.org), and the ASA, CSSA, and SSSA International Meetings (https://www.acsmeetings.org).3. Funds will be used for upgrading and maintaining computational facilities and for the salaries of undergraduates and other personnel directly involved in this objective.

Progress 02/26/20 to 09/30/20

Outputs
Target Audience:Since the beginning of this project's funding, we have published three papers, givenone invited talk (remotely becasue of COVID-19), and released a suite of functions in the R software that has had over 5,000 downloads to date. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One of my Ph.D. students, Brian Rice, passed his Ph.D. prelimination exam on Friday, October 30, 2020. Thus, Mr. Rice is well on his way towards obtaining a Ph.D. How have the results been disseminated to communities of interest?During this period, I was senior author on three publications, my lab released the simplePHENOTYPES R package, and I gave a virtual invited talk at a conference in South Korea. What do you plan to do during the next reporting period to accomplish the goals?I will plan to continue on the trajectory outlined in this report. In particular, we have at least three mansucripts that we are currenlty writing and bringing through the peer-reveiw progress, we have co-developed more software that can assist breeding efforts by finding candidate markers for marker-assisted selection, and I am giving a virtualinvited talk at Colorado State on March 10, 2021.

Impacts
What was accomplished under these goals? These collaborations are continuing, and to date have resulted in a total of ninepublications during the year of 2020. Due to COVID-19, it was impossible to attend scientific meetings in person. However, PD Lipka gave a virtual invited talk at theInternational Conference of the Genetics Society of Korea Asia Pacific Chromosome Colloquium 7 on November 26, 2020. The most prominent progress made for such computational facilities invovles the aforementioned simplePHENOTYPES R package.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: Fernandes, S.B. and Lipka, A.E. 2020. simplePHENOTYPES: Simulation of pleiotropic, linked and epistatic phenotypes. BMC Bioinformatics: 21(1), 491.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Olatoye, M.O., Clark, L.V., Labonte, N.R., Dong, H., Dwiyanti, M.S., Anzoua, K.G., Brummer, J.E., Ghimire, B.K., Dzyubenko, E., Dzyubenko, N., LBagmet, L., Sabitov, A., Chebukin, P., Gowacka, K., Heo, K., Jin, X., Nagano, H., Peng, J., Yu, C.Y., Yoo, J.H., Zhao, H., Long, S.P., Yamada, T., Sacks, E.J. and Lipka, A.E. 2020. Training population optimization for genomic selection in miscanthus. G3: Genes, Genomes, Genetics: 10(7), 2465-2476.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Rice, B.R., Fernandes, S.B. and Lipka, A.E. 2020. Multi-trait genome-wide association studies reveal loci associated with maize inflorescence and leaf architecture. Plant and Cell Physiology. doi.org/10.1093/pcp/pcaa039.