The genomics of linkage drag in inbred lines of sunflower

Abstract

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 analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated 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 best linear unbiased prediction (BLUP) 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, 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, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication

“…Post-domestication gene flow between crops and their wild ancestor could consequently reduce the frequency of deleterious alleles. A similar correlation of genetic load and gene flow from a wild relative has also been shown in maize and sunflower, where gene flow regions from the wild relative showed reduced genetic load ( Wang et al 2017 ; Huang et al 2023 ). Similarly, work in humans has shown that gene flow from a relative with a small population size (Neanderthal) into a population with a larger population size (modern humans) led to increased genetic load ( Harris and Nielsen 2016 ), as we observe for gene flow from domesticated amaranths into A. hybridus .…”

RepeatOBserver: tandem repeat visualization and centromere detection

“… Arabidopsis thaliana genome (COLCEN) chromosome 4 (Naish et al ., 2021) (left) and Helianthus annuus (HA412 HOv2) chromosome 14 (Huang et al ., 2023) (right). (A) Heat map showing repeat lengths and their abundances across the chromosome.…”

Phased genome assemblies reveal haplotype‐specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae)

“…It was known from empirical and theoretical results that low recombination hinders purifying selection due to linkage interference (Huang et al., 2023). We again found this pattern of reduced recombination associated with high‐impact variants.…”