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Key message: This study compares five models of GWAS, to show the added value of non-additive modeling of allelic effects to identify genomic regions controlling flowering time of sunflower hybrids. Abstract: Genome-wide association studies are a powerful and widely used tool to decipher the genetic control of complex traits. One of the main challenges for hybrid crops, such as maize or sunflower, is to model the hybrid vigor in the linear mixed models, considering the relatedness between individuals. Here, we compared two additive and three non-additive association models for their ability to identify genomic regions associated with flowering time in sunflower hybrids. A panel of 452 sunflower hybrids, corresponding to incomplete crossing between 36 male lines and 36 female lines, was phenotyped in five environments and genotyped for 2,204,423 SNPs. Intra-locus effects were estimated in multi-locus models to detect genomic regions associated with flowering time using the different models. Thirteen quantitative trait loci were identified in total, two with both model categories and one with only non-additive models. A quantitative trait loci on LG09, detected by both the additive and non-additive models, is located near a GAI homolog and is presented in detail. Overall, this study shows the added value of non-additive modeling of allelic effects for identifying genomic regions that control traits of interest and that could participate in the heterosis observed in hybrids. [ABSTRACT FROM AUTHOR]

Heterosis is a main force leading the development of the hybrid seed industry in sunflower. The purpose of this study is to evaluate if heterosis effects for morphological traits among sunflower hybrids can be related to differences in the repetitive component of the genome of parental lines. The assumption is that, at least for certain traits, heterosis results from mutations in the cis-regulatory elements of genes, largely related to retrotransposon insertions and/or removals. Our experimental approach consists of a correlation study between hybrid performance and retrotransposon-related genetic distances between inbreds. Six sunflower inbred lines of different origin were crossed in a half diallel fashion; comparing parental lines and hybrids, mid parent heterosis of F hybrids was evaluated for six traits. We estimated the parental genetic distances between the six inbreds on data gathered by the inter-retrotransposon-amplified-polymorphism (IRAP) protocol. Different retrotransposons previously isolated in sunflower were targeted by 11 primer pairs designed on conserved LTR domains. As a control, genetic distances were also calculated using 86 genic SNPs. We analysed the correlation between the mid-parent heterosis for each of the six traits analysed and the genetic distance (calculated on data obtained by SNP or IRAP analyses) between the parental lines. Differences between parents showed to be largely related to variations in the retrotransposon component of the genome. Retrotransposon-related genetic distance between parents resulted to be larger than that related to genic SNPs, and significantly correlated to seed yield and, at a lesser extent, to plant height and stem diameter in hybrids. The hypothesis that variations in the repetitive component of the genome, especially LTR-retrotransposons, affect the displaying of heterosis is discussed. [ABSTRACT FROM AUTHOR]

Sunflower rust, caused by the fungus Puccinia helianthi Schwein., was not a serious problem for many decades because of successful deployment of effective resistance genes in commercial sunflower ( Helianthus annuus L.) hybrids in North America. In the 1980s and early 1990s, however, a shift in virulence of the rust race population in North America rendered most of the commercial hybrids susceptible to new virulent races. A germplasm line, HA-R2, carrying the rust resistance gene R was released as a multi-race rust-resistant line in 1985 but has not been widely used in commercial hybrid production. R remains effective against the prevalent rust races of sunflower in North America. This gene was previously reported to be associated with two simple sequence repeat (SSR) markers, ORS316 and ORS630, which were mapped to linkage group (LG) 13 of sunflower. However, out of the 63 markers of LG13 screened in the present study, only 18, including ORS316 and ORS630, were polymorphic. These markers, which covered all of LG 13, were assayed in 94 individual F2 progenies derived from the cross of HA 89 with HA-R2. All failed to detect any locus in LG13 associated with the gene R . Subsequently, a bulked segregant analysis was employed with an additional 510 SSR markers selected from the remaining 16 LGs of the sunflower genome. This analysis demonstrated that the LG2 markers showed association with rust resistance . Genotyping of the 94 F2 individuals with 23 polymorphic SSR markers from LG2 confirmed the R location on LG2, flanked by two SSR markers, ORS1197-2 and ORS653a, at 3.3 and 1.8 cM of genetic distance, respectively. The markers for R developed in this study will provide a useful tool for speeding up deployment of the R gene in commercial sunflower hybrid production. [ABSTRACT FROM AUTHOR]