HANIR_PubliLinkageDrag2022_SEQUELII
The genomics of linkage drag in sunflower (IR Sequel II)
Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases.  But, introgressions from wild relatives may also have maladaptive effects on desirable traits, including yield (i.e., linkage drag).  Here we comprehensively analyzed the genomic and phenotypic impacts of wild introgressions in sunflower to estimate the impacts of linkage drag.  First, we generated new reference sequences for eight cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars.  Then, 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 also used a genomic prediction 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.  While introgressions reduced genetic load and positively affected traits associated with abiotic stress resistance, they negatively impacted yield and quality traits.  Introgressions from more distantly related species were more likely to be maladaptive than those from sunflower's wild progenitor. Also, introgressions found at high frequency in the crop gene pool had fewer negative effects than low frequency introgressions, suggesting that sunflower breeders have been successful in eliminating the most harmful introgressions.  Introgressions were less harmful in heterozygous than homozygous cultivated lines, indicating that hybrid crop production offers a means for using wild relative introgressions for improvement without sacrificing productivity.