Genetic variation is of crucial importance for selection and genetic improvement of crops. Landraces are valuable sources of diversity for germplasm improvement, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we propose a genome-based strategy for making native diversity accessible for traits with limited genetic variation in elite germplasm. We generated ~ 1,000 doubled-haploid (DH) lines from three European maize landraces, pre-selected based on molecular and phenotypic information. Using GWAS, we mapped haplotype-trait associations for early development traits at high resolution in eleven environments. Molecular haplotype inventories of landrace derived DH libraries and a broad panel of 65 breeding lines based on 501,124 SNPs revealed novel variation for target traits in the landraces. DH lines carrying these novel haplotypes outperformed breeding lines not carrying the respective haplotypes. Most haplotypes associated with target traits showed stable effects across populations and environments and only limited correlated effects with undesired traits making them ideal for introgression into elite germplasm. Our strategy was successful in linking molecular variation to meaningful phenotypes and identifying novel variation for quantitative traits in plant genetic resources.

中文翻译：

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发现地方品种复杂性状的新单倍型

遗传变异对于农作物的选择和遗传改良至关重要。地方品种是改良种质的宝贵资源，但对于数量性状而言，缺乏有效利用其靶向利用的策略。在这里，我们提出了一种基于基因组的策略，以使本地种质可用于优良种质中遗传变异有限的性状。我们从三个欧洲玉米地方品种中生成了约1,000个双单倍体（DH）品系，这些品系是根据分子和表型信息预先选择的。使用GWAS，我们在11个环境中以高分辨率绘制了早期发育性状的单倍型-性状关联。地方品种来源的DH库的分子单倍型清单和基于501,124个SNP的65个育种系的广泛面板揭示了地方品种靶性状的新变化。携带这些新单倍型的DH品系优于不携带各自单倍型的品系。与目标性状相关的大多数单倍型在种群和环境中显示出稳定的效应，并且与不良性状的相关效应有限，这使其非常适合进入优良种质。我们的策略成功地将分子变异与有意义的表型联系起来，并确定了植物遗传资源中数量性状的新变异。