Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 6:13:1056231.
doi: 10.3389/fpls.2022.1056231. eCollection 2022.

Association mapping for broomrape resistance in sunflower

Álvaro Calderón-González  1 , Begoña Pérez-Vich  1 , Nicolas Pouilly  2 , Marie-Claude Boniface  2 , Johann Louarn  2 , Leonardo Velasco  1 , Stéphane Muños  2
Affiliations

Association mapping for broomrape resistance in sunflower

Álvaro Calderón-González et al. Front Plant Sci. .

Abstract

Introduction: Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance.

Methods: The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments.

Results and discussion: The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.

Keywords: Orobanche cumana; broomrape resistance; candidate genes; genome-wide association mapping (GWAS); parasitic plants.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Principal coordinate analysis of 104 sunflower accessions genotypes with SNP markers.
Figure 2
Figure 2
Linkage disequilibrium decay using SNP markers data set. Estimation of r2 versus distance in base pair (bp) was represented. LD decay was established around 0.25e6 bp.
Figure 3
Figure 3
Quantile-quantile (Q-Q) plots of observed versus expected P values of the GWAS results using GLM+PCA (A) and MLM+K+PCA (B). The straight line represents concordance of observed and expected values.
Figure 4
Figure 4
Manhattan-plots illustrating significant associations for resistance to three broomrape populations (SP, Bourret and GT) in a panel of 104 sunflower accessions evaluated in two environments each using GLM+PCA. The P values were adjusted using the Bonferroni threshold and false detection rate (FDR) correction (5% and 20%) to reduce false positive associations. The solid line corresponds to the 5% threshold and the dotted line to the 20% threshold. The vertical axis indicates –log10 of p-value and horizontal axis indicates chromosomes and physical positions of SNPs.
Figure 5
Figure 5
Manhattan-plots illustrating significant associations for resistance to three broomrape populations (SP, Bourret and GT) in a panel of 104 sunflower accessions evaluated in two environments each using MLM+K+PCA. The P values were adjusted using the Bonferroni threshold and false detection rate (FDR) correction (5% and 20%) to reduce false positive associations. The solid line corresponds to the 5% threshold and the dotted line to the 20% threshold. The vertical axis indicates –log10 of p-value and horizontal axis indicates chromosomes and physical positions of SNPs.
See this image and copyright information in PMC

References

    1. Adewale S. A., Badu-Apraku B., Akinwale R. O., Paterne A. A., Gedil M., Garcia-Oliveira A. L. (2020). Genome-wide association study of striga resistance in early maturing white tropical maize inbred lines. BMC Plant Biol. 20, 203. doi: 10.1186/s12870-020-02360-0 - DOI - PMC - PubMed
    1. Akhtouch B., Del Moral L., Leon A., Velasco L., Fernández-Martínez J. M., Pérez-Vich B. (2016). Genetic study of recessive broomrape resistance in sunflower. Euphytica 209, 419–428. doi: 10.1007/s10681-016-1652-z - DOI
    1. Alonso L. C., Fernández-Escobar J., López G., Rodríguez-Ojeda M. I., Sallago F. (1996). “New highly virulent sunflower broomrape (O. cernua loefl.) pathotypes in Spain,” in Proceedings of the 6th international symposium in parasitic weeds. Eds. Moreno M. T., Cubero J. I., Berner D., Musselman L. J., Parker C. (Seville, Spain: Junta de Andalucía; ), 639–644.
    1. Amri M., Abbes Z., Ben Youssef S., Bouhadida M., Ben Salah H., Kharrat M. (2012). Detection of the parasitic plant, orobanche cumana on sunflower (Helianthus annuus l.) in Tunisia. Afr. J. Biotechnol. 11, 4163–4167. doi: 10.5897/AJB11.3031 - DOI
    1. Badouin H., Gouzy J., Grassa C. J., Murat F., Staton S. E., Cottret L., et al. . (2017). The sunflower genome provides insights into oil metabolism, flowering and asterid evolution. Nature 546, 148–152. doi: 10.1038/nature22380 - DOI - PubMed

LinkOut - more resources