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Whole-genome sequencing enables molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.)
Tuesday, 2023/05/30 | 08:18:31

G. J. MaZ. I. TalukderQ. J. SongX. H. Li & L. L. Qi

Theoretical and Applied Genetics June 2023; vol. 136, Article number: 143

Key message

We finely mapped the rust resistance gene R12 to a 0.1248-cM region, identified a potential R12 candidate gene in the XRQ reference genome, and developed three diagnostic SNP markers for R12.


Rust is a devastating disease in sunflower that is damaging to the sunflower production globally. Identification and utilization of host-plant resistance are proven to be preferable means for disease control. The rust resistance gene R12 with broad-spectrum specificity to rust was previously localized to a 2.4 Mb region on sunflower chromosome 11. To understand the molecular mechanism of resistance, we conducted whole-genome sequencing of RHA 464 (R12 donor line) and reference genome-based fine mapping of the gene R12. Overall, the 213 markers including 186 SNPs and 27 SSRs' were identified from RHA 464 sequences and used to survey polymorphisms between the parents HA 89 and RHA 464. Saturation mapping identified 26 new markers positioned in the R12 region, and fine mapping with a large population of 2004 individuals positioned R12 at a genetic distance of 0.1248 cM 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 region; it is 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 selection in sunflower rust resistance breeding. The current study provides a new genetic resource and starting point for cloning R12 in the future.


See https://link.springer.com/article/10.1007/s00122-023-04389-9

Figure: The positions of the rust resistance gene R14 and the purple hypocotyl color gene PHC on LG 11 of the sunflower map. a A reference map of LG 11 (Tang et al. 2003), b Map position of the R14 locus and the PHC gene on LG 11, c The position of the R12 gene on a map of LG 11 (Gong et al. 2013b). Common markers are aligned and underlined among maps a–c. Common markers are in bold and italics among maps b, and Suppl. Figure 3, a and b. The distances are given in centimorgan (cM) at the left side of the maps (Ming Zhang et al. 2016)


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