Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower

Lee, Joon S.; Jahani, Mojtaba; Huang, Kaichi; Mandel, Jennifer R.; Marek, Laura F.; Burke, John M.; Langlade, Nicolas; Owens, Gregory L.

doi:10.1016/j.jare.2022.04.008

Cited by 17 publications

(25 citation statements)

References 82 publications

(112 reference statements)

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“…A previous study of the SAM population showed that the absence allele at PAVs often has deleterious impacts on yield-associated traits (Lee et al 2022), and we speculate that they may be the primary genetic cause of linkage drag. The genetic architecture of linkage drag has implications for mitigation strategies.…”

Section: Discussionmentioning

confidence: 59%

“…We show that despite the numerous benefits deriving from tapping crop wild relatives, such as the introduction of desirable traits and genetic and phenotypic variation (Warschefsky et al 2014;Dempewolf et al 2017), there can be downsides, including reductions in yield-related traits. We speculate that this is largely due to the introduction of variation in gene content; cultivars containing introgressions not only have new genes, but they also are missing genes that would otherwise be present, which can have deleterious consequences (Lee et al 2022). So, what strategies can be employed to mitigate the effects of linkage drag?…”

Section: Discussionmentioning

confidence: 99%

“…For example, Todesco et al (2020) showed that a PAV for HaFT1 was responsible for a 77-day shift in flowering time between two ecotypes of the silverleaf sunflower. More recently, Lee et al (2022) found that the complementation of PAVs in sunflower hybrids was the primary cause of heterosis.…”

Section: Discussionmentioning

confidence: 99%

“…5). We then performed GWAS of the introgression variants for 16 traits that were previously phenotyped (Mandel et al 2013;Nambeesan et al 2015;Lee et al 2022) in common gardens at three locations (Watkinsville, GA, Ames, IA, and Vancouver, BC) using a model that corrects the population structure and familial relatedness. Our results revealed that introgressions have a significant effect on the phenotypic variation in the SAM population (SI Appendix, Fig.…”

Section: Introgressions In the Cultivated Sunflower Association Mappi...mentioning

confidence: 99%

“…Introgression variants were subsequently filtered for minor allele frequency ≥ 3%. For the phenotypic analyses, we employed data for 16 traits that were generated as part of a common garden study carried out in 2011 at three locations: Watkinsville, GA and Ames, IA in the USA and Vancouver, BC, in Canada (Mandel et al 2013;Nambeeson et al 2015;Lee et al 2022). To identify associations between introgression variants and the phenotypic traits, a genome wide association (GWA) analysis was carried out using EMMAX (Kang et al 2010).…”

Section: Effects Of Introgressions On Phenotypic Variation In the Sam...mentioning

confidence: 99%

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The genomics of linkage drag in sunflower

Huang¹,

Jahani²,

Gouzy

et al. 2022

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Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions into cultivated sunflower to estimate the impacts of linkage drag. First, we generated new reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge regression model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including > 3,000 new genes. While introgressions reduced genetic load at protein-coding sequences and positively affected traits associated with abiotic stress resistance, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, pre-breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

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Section: Discussionmentioning

confidence: 59%