Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security¹. Here we examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection² of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium (LD) based haplotypes and association genetics analyses link Watkins genomes to the thousands of high-resolution quantitative trait loci (QTL), and significant marker–trait associations identified. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

通过开发新的育种能力来利用主要农作物的遗传多样性对于确保粮食安全至关重要¹ 。在这里，我们通过全基因组重测序（827 个沃特金斯地方品种和 208 个现代品种）和深入的田间评估，检查了面包小麦 ( Triticum aestivum )（一种全球主要谷物）的 AE 沃特金斯地方品种品种^{2 的}遗传和表型多样性跨越十年。我们发现，现代品种仅源自小麦七个祖先群体中的两个，并保持了非常长范围的单倍型完整性。其余五组代表未开发的遗传资源，为育种提供了地方品种特异性等位基因和单倍型的机会。基于连锁不平衡 (LD) 的单倍型和关联遗传学分析将沃特金斯基因组与数千个高分辨率数量性状基因座 (QTL) 联系起来，并确定了显着的标记-性状关联。利用这些结构化种质、基因分型和信息学资源，我们揭示了许多沃特金斯独特的有益单倍型，这些单倍型可以赋予现代小麦优良的性状。此外，我们评估了 44,338 个沃特金斯独特单倍型的表型效应，这些单倍型是从现代品种背景下的 143 个优先 QTL 渗入的，弥合了地方品种多样性和当前育种之间的差距。这项研究建立了一个框架，系统地利用遗传多样性进行作物改良，以实现可持续的粮食安全。