Title: Training Population Optimization for Genomic Selection in Miscanthus

Abstract

Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus × giganteus (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M×g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel of predominately Msi individuals and a 598-member diversity panels of Msa individuals. We then assessed the ability of these two diversity panels to train GS models that predict breeding values in an interspecific diploid 216-member M×g F2 panel. Low and negative prediction accuracies were observed when various subsets of the two diversity panels were used to train these GS models. To overcome the drawback of having only one interspecific M×g F2 panel available, we also evaluated prediction accuracies for traits simulated in 50 simulated interspecific M×g F2 panels derived from different sets of Msi and diploid Msa parents. Themore » results revealed that genetic architectures with common causal mutations across Msi and Msa yielded the highest prediction accuracies. Ultimately, these results suggest that the ideal training set should contain the same causal mutations segregating within interspecific M×g populations, and thus efforts should be undertaken to ensure that individuals in the training and validation sets are as closely related as possible.« less

Authors:

Olatoye, Marcus O.  ^[1];

• Search DOE PAGES for author "Olatoye, Marcus O."
• Search DOE PAGES for ORCID "0000-0001-7082-9752"

Clark, Lindsay V.  ^[1];

• Search DOE PAGES for author "Clark, Lindsay V."
• Search DOE PAGES for ORCID "0000-0002-3881-9252"

Labonte, Nicholas R. ^[1]; Dong, Hongxu ^[2]; Dwiyanti, Maria S. ^[3]; Anzoua, Kossonou G. ^[4]; Brummer, Joe E. ^[5]; Ghimire, Bimal K. ^[6]; Dzyubenko, Elena ^[7]; Dzyubenko, Nikolay ^[8]; Bagmet, Larisa ^[8]; Sabitov, Andrey ^[8]; Chebukin, Pavel ^[8]; Głowacka, Katarzyna ^[9]; Heo, Kweon ^[10]; Jin, Xiaoli  ^[11];

• Search DOE PAGES for author "Jin, Xiaoli"
• Search DOE PAGES for ORCID "0000-0003-4829-176X"

Nagano, Hironori ^[4]; Peng, Junhua ^[12]; Yu, Chang Y. ^[13]; Yoo, Ji H.  ^[13]

• Search DOE PAGES for author "Yoo, Ji H."
• Search DOE PAGES for ORCID "0000-0002-0594-8488"

more »; Zhao, Hua ^[14]; Long, Stephen P. ^[1]; Yamada, Toshihiko ^[4]; Sacks, Erik J. ^[1]; Lipka, Alexander E. ^[1] « less

---

+ Show Author Affiliations

1. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Crop Sciences
2. Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab.
3. Hokkaido Univ. (Japan). Research Faculty of Agriculture. Applied Plant Genome Lab.
4. Hokkaido Univ. (Japan). Field Science Center for Northern Biosphere
5. Colorado State Univ., Fort Collins, CO (United States). Dept. of Soil and Crop Sciences
6. Konkuk Univ., Seoul (Korea, Republic of). Dept. of Applied Bioscience
7. Vavilov All-Russian Inst. of Plant Genetic Resources, St. Petersburg (Russian Federation)
8. Vavilov All-Russian Inst. of Plant Genetic Resources, St. Petersburg (Russian Federation)
9. Univ. of Nebraska, Lincoln, NE (United States). Dept. of Biochemistry
10. Konkuk Univ., Seoul (Korea, Republic of). Dept. of Applied Plant Science
11. Zhejiang Univ., Hangzhou (China). Dept. of Agronomy
12. China National Seed Group Co. Ltd, Wuhan (China)
13. Kangwon National University, Chuncheon (Korea, Republic of). Dept. of Applied Plant Sciences
14. Huazhong Agricultural Univ., Wuhan (China). College of Plant Science and Technology

Publication Date:

Wed Jul 01 00:00:00 EDT 2020

Research Org.:

Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1802902

Grant/Contract Number:  

SC0016264

Resource Type:

Accepted Manuscript

Journal Name:

G3

Additional Journal Information:

Journal Volume: 10; Journal Issue: 7; Journal ID: ISSN 2160-1836

Publisher:

Genetics Society of America

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Miscanthus; Prediction Accuracy; Genomic selection; Population Structure; GenPred; Shared data resources