Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut (Castanea spp.)

Shenghua Fan; Laura L Georgi; Frederick V Hebard; Tetyana Zhebentyayeva; Jiali Yu; Paul H Sisco; Sara F Fitzsimmons; Margaret E Staton; Albert G Abbott; C Dana Nelson

doi:10.3389/fpls.2024.1365951

Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut (Castanea spp.)

Front Plant Sci. 2024 Apr 8:15:1365951. doi: 10.3389/fpls.2024.1365951. eCollection 2024.

Authors

Shenghua Fan¹, Laura L Georgi^{2

3}, Frederick V Hebard³, Tetyana Zhebentyayeva⁴, Jiali Yu⁵, Paul H Sisco⁶, Sara F Fitzsimmons⁷, Margaret E Staton⁸, Albert G Abbott⁴, C Dana Nelson^{2

9}

Affiliations

¹ Forest Health Research and Education Center, Department of Horticulture, University of Kentucky, Lexington, KY, United States.
² Forest Health Research and Education Center, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Lexington, KY, United States.
³ Virginia Chapter, The American Chestnut Foundation, Meadowview, VA, United States.
⁴ Forest Health Research and Education Center, Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, United States.
⁵ Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States.
⁶ Carolinas Chapter, The American Chestnut Foundation, Asheville, NC, United States.
⁷ North Central Office, The American Chestnut Foundation, University Park, PA, United States.
⁸ Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States.
⁹ Southern Institute of Forest Genetics, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Saucier, MS, United States.

Abstract

Chestnut blight (caused by Cryphonectria parasitica), together with Phytophthora root rot (caused by Phytophthora cinnamomi), has nearly extirpated American chestnut (Castanea dentata) from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut (C. mollissima) genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family. We evaluated trees for resistance to blight after artificial inoculation with two fungal strains and scored nine morpho-phenological traits that are the hallmarks of species differentiation between American and Chinese chestnuts. Results support a moderately complex genetic architecture for blight resistance, as 31 QTLs were found on 12 chromosomes across all studies. Additionally, although most morpho-phenological trait QTLs overlap or are adjacent to blight resistance QTLs, they tend to aggregate in a few genomic regions. Finally, comparison between QTL intervals for blight resistance and those previously published for Phytophthora root rot resistance, revealed five common disease resistance regions on chromosomes 1, 5, and 11. Our results suggest that it will be difficult, but still possible to eliminate Chinese chestnut alleles for the morpho-phenological traits while achieving relatively high blight resistance in a backcross hybrid tree. We see potential for a breeding scheme that utilizes marker-assisted selection early for relatively large effect QTLs followed by genome selection in later generations for smaller effect genomic regions.

Keywords: Castanea; GWAS; blight resistance; chestnut; genetic architecture; morphology; multiple QTL mapping; phenology.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. Partial funding (AGA, FVH) for this project was provided by National Science Foundation’s Plant Genome Research Program (NSF-PGRP 0605135); the US Endowment for Forestry and Communities through the Forest Health Initiative (CDN, FVH); and the Forest Health Research and Education Center (Research Joint Venture Agreements 14-JV-11330126-056 and 19-JV-11330126-084 between the University of Kentucky College of Agriculture, Food, and the Environment; and the USDA Forest Service, Southern Research Station).