The genomics of linkage drag in sunflower (RHA438 IsoSeq 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.

作物野生近缘种（Crop wild relatives）是作物遗传改良的宝贵等位基因资源，可用于培育适应气候变化与新发病害的作物品种。但野生近缘种的基因渐渗，也会对产量等优良性状产生不利适应性影响，即连锁累赘（linkage drag）。本研究以向日葵为研究对象，全面解析了野生基因渐渗对其基因组与表型的影响，以量化连锁累赘的效应。首先，本研究为8个栽培向日葵基因型与1个野生向日葵基因型构建了全新的参考序列，并优化了另外2个栽培品种的基因组组装结果。随后，本研究依托预先获取的野生供体物种基因组序列，鉴定出栽培向日葵参考序列中的基因渐渗片段及其携带的序列变异与结构变异。此外，本研究借助基因组预测模型，在栽培向日葵关联作图群体中检测了基因渐渗片段对各类表型性状的效应。研究结果表明，基因渐渗为栽培向日葵的基因库引入了大量序列变异与结构变异。尽管基因渐渗可降低遗传负荷，并对非生物胁迫抗性相关性状产生正向效应，但同时会对产量与品质性状造成负面影响。相较于来自向日葵野生祖先种的渐渗片段，亲缘关系更远的物种的渐渗片段更易产生不利适应性影响。此外，在作物基因库中频率较高的渐渗片段，其负面效应低于频率较低的渐渗片段，这表明向日葵育种学家已成功剔除了危害性最强的基因渐渗片段。相较于纯合栽培株系，杂合株系中的基因渐渗片段危害性更低，这表明杂交作物培育可在不牺牲产量的前提下，利用野生近缘种的渐渗片段开展作物遗传改良。