High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot chromosome A01

Authors: WU, DONGLIANG - University Of Georgia; ZHAO, CHUANZHI - Shandong Academy Of Agricultural Sciences; KORANI, WALID - Hudsonalpha Institute For Biotechnology; THOMPSON, ETHAN - University Of Georgia; WANG, HUI - University Of Georgia; AGARWAL, GAURAV - University Of Georgia; FOUNTAIN, JAKE - University Of Georgia; CULBREATH, ALBERT - University Of Georgia; Holbrook Jr, C; WANG, XINGJUN - Shandong Academy Of Agricultural Sciences; CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology; Guo, Baozhu

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2025
Publication Date: 3/6/2025
Citation: Wu, D., Zhao, C., Korani, W., Thompson, E.A., Wang, H., Agarwal, G., Fountain, J.C., Culbreath, A., Holbrook Jr, C.C., Wang, X., Clevenger, J.P., Guo, B. 2025. High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot chromosome A01. BMC Genomics. 26:224. https://doi.org/10.1186/S12864-025-11366-7.
DOI: https://doi.org/10.1186/S12864-025-11366-7

Interpretive Summary: Peanut cultivars released in recent years are crucial to have some levels of resistance to Tomato spotted wilt virus (TSWV), a devastating disease to peanut growers in the Southeastern region of the United States. In this study, we report a high-resolution map of the peanut spotted wilt disease resistance locus, named PSWD-1, using both versions of peanut SNP arrays and five-year field disease ratings. Two QTLs are explaining phenotypic variation of 41.43% and 43.69%, respectively, on chromosome A01 using these two peanut SNP arrays. A 1.3 Mb recombination "cold spot" (11.325–12.646 Mb) was identified with only two recombination events—one in RIL S1 and the other in RIL S17, which displayed contrasting phenotypes. This cold spot was confirmed by sequencing which detected only five SNPs within this region. Therefore, based on the genetic and physical maps we named the mapped resistance locus as PSWD-1, a peanut spotted wilt disease resistance gene within the region. There were three candidate genes and the strongest candidate gene is the arahy.1PK53M in the reference genome. The application as molecular marker in breeding will be validated.

Technical Abstract: Peanut (Arachis hypogaea L.) spotted wilt disease resistance quantitative trait loci (QTLs) to Tomato spotted wilt virus (TSWV) had been mapped on chromosome A01 using a subset of a recombinant inbred line (RIL) mapping population derived from SunOleic 97R and NC94022 using SSR markers and whole genome resequencing, respectively. With the availability of high-density peanut SNP arrays, 58K ‘Axiom_ Arachis_v1’ and haplotype-based 48K ‘Axiom_ Arachis_v2’, we report a high-resolution map of the peanut spotted wilt disease resistance locus, named PSWD-1, using both versions of peanut SNP arrays. QTL analyses of five years’ TSWV disease ratings identified a major QTL explained the phenotypic variation of 41.43% and 43.69%, respectively, within 3.6 cM and 0.28 cM intervals on chromosome A01 using these two peanut SNP arrays. These QTLs corresponded to 295 kb and 235 kb physical intervals, totaling 488 kb. A comparison of the genetic map with the reference genome revealed a 1.3 Mb recombination "cold spot" (11.325–12.646 Mb) with only two recombination events—one in RIL S1 and the other in RIL S17, which displayed contrasting phenotypes. Sequencing confirmed the cold spot, detecting only five SNPs within this region. Therefore, based on the genetic and physical maps we named the mapped resistance locus as PSWD-1, a peanut spotted wilt disease resistance gene within the region. There were three candidate genes for PSWD-1, which were TIR-NBS-LRR, glutamate receptor, and MLO-like protein. The strongest candidate gene may be the arahy.1PK53M in the reference genome, a TIR-NBS-LRR, and the future functional characterization is needed using map-based cloning for genetic improvement in peanut resistance to TSWV.