Genetic insight into disease resistance gene clusters by using sequencing-based fine mapping in sunflower (Helianthus annuus L.)

Authors: MA, GUOJIA - North Dakota State University; Song, Qijian; LI, XUEHUI - North Dakota State University; Qi, Lili

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2022
Publication Date: 8/23/2022
Citation: Ma, G., Song, Q., Li, X., Qi, L. 2022. Genetic insight into disease resistance gene clusters by using sequencing-based fine mapping in sunflower (Helianthus annuus L.). International Journal of Molecular Sciences. 23(17):9516. https://doi.org/10.3390/ijms23179516.
DOI: https://doi.org/10.3390/ijms23179516

Interpretive Summary: Worldwide, sunflower production has been challenged by different biotic and abiotic stresses. Rust and downy mildew are two destructive sunflower diseases that impair sunflower production. The use of resistant hybrids is the first choice for disease management in sunflower for economic and environmental reasons. In this study, two previously mapped rust resistance genes, R13a and R16, and a downy mildew resistance gene, Pl33, were fine mapped in large segregated populations using new genomic tools. The significantly increased map resolution for the three genes not only provided precise gene locations but also facilitate the development of diagnostic markers to accelerate resistance breeding in sunflower.

Technical Abstract: Rust and downy mildew (DM) are two important sunflower diseases that lead to significant yield losses globally. The use of resistant hybrids to control rust and DM in sunflower has a long history. The rust resistance genes, R13a and R16, were previously mapped to a 3.4-Mb region at the lower end of sunflower chromosome 13, while the DM resistance gene, Pl33, was mapped to a 4.2-Mb region located at the upper end of chromosome 4. High-resolution fine mapping was conducted using whole genome sequencing of HA-R6 (R13a) and TX16R (R16 and Pl33) and large segregated populations. R13a and R16 were fine mapped to a 0.48-cM region in chromosome 13 corresponding to a 790-kb physical interval on the XRQr1.0 genome assembly. Four-disease defense-related genes with nucleotide-binding leucine-rich repeat (NLR) motifs were found in this region from XRQr1.0 gene annotation as candidate genes for R13a and R16. Pl33 was fine mapped to a 0.04-cM region in chromosome 4 corresponding to a 63-kb physical interval. One NLR gene, HanXRQChr04g0095641, was predicted as the candidate gene for Pl33. The diagnostic SNP markers developed for each gene in the current study will facilitate marker-assisted selections of resistance genes in sunflower breeding programs.