Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Proc Natl Acad Sci U S A. 2023 Apr 4;120(14):e2205783119. doi: 10.1073/pnas.2205783119. Epub 2023 Mar 27.
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.
野生近缘种代表了作物改良的有价值的等位基因资源，包括对气候变化和新出现疾病的适应。然而，由于连锁累赘，野生近缘种的渗入可能对包括产量在内的理想性状产生有害影响。在这里，我们分析了栽培向日葵自交系中野生近缘种的基因组和表型影响，以估计连锁累赘的影响。首先，我们为 7 个栽培和 1 个野生向日葵基因型以及另外 2 个栽培品种生成了参考序列。接下来，我们依赖于来自野生供体物种的先前生成的序列，鉴定了在栽培参考序列中的渗入，以及它们所包含的序列和结构变异。然后，我们使用基于岭回归的最佳线性无偏预测（BLUP）模型来测试渗入对栽培向日葵关联作图群体中表型性状的影响。我们发现，渗入已经将大量的序列和结构变异引入了栽培向日葵的基因库中，包括>3000 个新基因。虽然渗入降低了蛋白质编码序列的遗传负荷，但它们主要对产量和质量性状产生负面影响。在栽培基因库中高频发现的渗入比低频渗入的影响更大，这表明前者可能是人工选择的目标。此外，与栽培向日葵野生祖先亲缘关系较远的物种的渗入比亲缘关系较近的物种更有可能是适应不良的。因此，育种工作应尽可能集中在亲缘关系密切且完全相容的野生近缘种上。
