Mapping quantitative trait loci (QTLs) and estimating the epistasis controlling stem rot resistance in cultivated peanut (Arachis hypogaea)

Authors: LUO, ZILIANG - University Of Florida; CUI, RENJIE - University Of Georgia; CHAVARRO, CAROLINA - University Of Georgia; TSENG, YU-CHIEN - University Of Florida; ZHOU, HAI - University Of Florida; PENG, ZE - University Of Florida; CHU, YE - University Of Georgia; YANG, XIPING - University Of Florida; LOPEZ, YOLANDA - University Of Florida; TILLMAN, BARRY - University Of Florida; DUFAULT, NICHOLAS - University Of Florida; BRENNEMAN, TIMOTHY - University Of Georgia; ISLEIB, THOMAS - North Carolina State University; Holbrook, Carl - Corley; OZIAS-AKINS, PEGGY - University Of Georgia; WANG, JIANPING - University Of Florida

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2020
Publication Date: 2/26/2020
Citation: Luo, Z., Cui, R., Chavarro, C., Tseng, Y., Zhou, H., Peng, Z., Chu, Y., Yang, X., Lopez, Y., Tillman, B., Dufault, N., Brenneman, T., Isleib, T.G., Holbrook Jr, C.C., Ozias-Akins, P., Wang, J. 2020. Mapping quantitative trait loci (QTLs) and estimating the epistasis controlling stem rot resistance in cultivated peanut (Arachis hypogaea). Journal of Theoretical and Applied Genetics. 133:1201-1212.

Interpretive Summary: Marker assisted selection (MAS) can be used to improve the efficiency and effectiveness of developing new peanut varieties. Genetic marker linked to important traits are needed before MAS can be implemented. Stem rot is one of the most damaging disease of peanut with regards to both cost of control and yield loss. We genotyped and phenotyped a population that was segregating for resistance to stem rot to identify several genetic markers linked to resistance. Six of these were major genetic markers that explained over 10% of observed variation and could be consistently detected in multiple years or locations. Resistance to stem rot is a highly complex and quantitative trait. These genetic marker will allow breeders to use MAS to more effectively and efficiently develop peanut varieties with resistance to stem rot.

Technical Abstract: Stem rot in peanut (Arachis hypogaea) is caused by the Sclerotium rolfsii and can result in great economic loss during production. In this study, a recombinant inbred line population from the cross between NC 3033 (stem rot resistant) and Tifrunner (stem rot susceptible) that consists of 156 lines was genotyped by using 58K peanut single nucleotide polymorphism (SNP) array and phenotyped for stem rot resistance at multiple locations and in multiple years. A linkage map consisting of 1451 SNPs and 73 simple sequence repeat markers was constructed. A total of 33 additive quantitative trait loci (QTLs) for stem rot resistance were detected , and six of them with phenotypic variance explained of over 10% (qSR.A01-2, qSR.A01-5, qSR.A05/B05-2, qSR.A07/B07-1 and qSR.B05-1) can be consistently detected in multiple years or locations. Besides, 12 pairs of QTLs with epistatic (additive x additive) interaction were identified. An additive QTL qSR.A01-2 also with an epistatic effect interacted with a novel locus qSR.B07_1-1 to affect the percentage of asymptomatic plants in a row. A total of 193 candidate genes within 38 stem rot QTLs intervals were annotated with functions of biotic stress resistance such as chitinase, ethylene-responsive transcription factors and pathogenesis-related proteins. The identified stem rot resistance QTLs, candidate genes, along with the associated SNP markers in this study, will benefit peanut molecular breeding programs for improving stem rot resistance.