Whole genome sequencing enables the molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.)

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

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2023
Publication Date: 5/29/2023
Citation: Ma, G., Talukder, M.I., Song, Q., Li, X., Qi, L. 2023. Whole genome sequencing enables the molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.). Journal of Theoretical and Applied Genetics. 136. Article 143. https://doi.org/10.1007/s00122-023-04389-9.
DOI: https://doi.org/10.1007/s00122-023-04389-9

Interpretive Summary: Sunflower production is challenged by different biological and environmental stresses globally. The rust pathogen is one of the most common and damaging biological stressors that needs to be controlled. The most efficient method for rust control is the use of disease resistance through genetic improvement. Molecular tags associated with rust resistance genes (R genes) are valuable tools for breeders who wish to select sunflower lines for rust resistance. Sunflower rust gene R12 is a broad-spectrum gene with resistance to all rust races identified in the USA thus far. Previously identified molecular tags for R12 have limitations due to their distance along the chromosome from the R12 gene itself. Here, we report the use of new genetic-genomic tools to develop more closely linked molecular tags. Three closely associated tags for R12 were developed in the current study, which clearly distinguish the R12 gene from other rust R genes. These results will help breeders make more efficient selections for sunflower lines that show resistance to this serious pathogen.

Technical Abstract: Rust is a devastating disease in sunflower that is damaging to the sunflower industry globally. The identification and utilization of broad-spectrum resistance genes have been proven to be a preferable means for disease control. Rust resistance gene R12 with broad-spectrum resistance to rust was previously mapped to a 2.4 Mb region on sunflower chromosome 11. To understand the molecular mechanism of the resistance, we conducted whole genome sequencing of RHA 464 (R12 donor line) and reference genome-based fine mapping of the gene R12. A total of 213 new markers were developed based on the sequence information and were used to survey the polymorphisms between parents HA 89 and RHA 464. Saturation mapping identified 26 new markers mapped to the R12 target region and fine mapping with a large population of 2,004 individuals positioned R12 to a region of 0.1248 cM genetic distance flanked by SNP markers C11_150451336 and S11_189205190. One gene, HanXRQChr11g0348661, with a defense-related NB-ARC-LRR domain, was identified in the XRQr1.0 genome assembly in the R12 target region and predicted to be a potential R12 candidate gene. Comparative analysis clearly distinguished R12 from the rust R14 gene located in the vicinity of the R12 gene on chromosome 11. Three diagnostic SNP markers, C11_147181749, C11_147312085, and C11_149085167, specific for R12 were developed in the current study, facilitating more accurate and efficient marker-assisted selection in sunflower rust resistance breeding. The current study provides a new genetic resource and a starting point for the cloning of R12 in the future.