The genetic basis of apple quality

基因组学正在成为帮助建立环境可持续农业的未来的关键工具，从而带来安全可靠的粮食供应。基因组学工具的发展主要依赖于发现基因型和表型之间的关系，这是通过进行遗传作图来完成的。拟议中的研究涉及到苹果的基因图谱，苹果是世界上种植最广泛的水果作物之一，也是加拿大在数量和价值上都领先的水果。***我建议发现预测苹果质量的遗传标记，加拿大苹果育种者将使用这些遗传标记进行基因组辅助育种：他们将在苗期使用我们发现的标记筛选后代，并丢弃那些预测质量差的标记。苹果需要近十年的时间才能成熟和评估，因此使用传统的表型评估来育种苹果是非常耗时和昂贵的。因此，标记辅助选择在苹果中具有特别的前景，因为它可以显著提高效率，降低生产所需化学投入较少的理想苹果的成本。***为了实现苹果的基因组辅助育种，我建立了苹果生物多样性收集（ABC）——一个拥有1000多个苹果品种的果园，它是世界上最多样化、可以说是最强大的苹果遗传图谱群体。ABC于2013年种植，专门用于基因定位，并将在未来几年从幼年期开始。这是我提出的NSERC发现研究的基础。***我的长期目标是详尽地列出ABC中存在的所有遗传变异。在这里，我建议通过开发新的生物信息学工具，对1000多个苹果品种的DNA进行测序，并从这些数据中提取尽可能多的遗传标记。然而，果实品质性状遗传定位的挑战显然在于表型数据的收集。因此，本提案的主要活动包括开发和使用自动化、高通量表型设备和代谢组学/蛋白质组学分析，以查询尽可能多的苹果表型。此外，我还建议评估苹果在中亚的野生祖先，以确定是否值得利用其功能遗传变异来改进未来的苹果。***拟议的研究不仅将产生通过育种加速苹果品质改善的标记，而且还将产生创新的生物信息学工具，提高其他非模式生物遗传作图的能力。因此，拟议中的项目有望使整个加拿大苹果价值链上的利益相关者受益，从种植者到消费者，并有助于加速基因组学在农业、生物燃料和林业等多个领域的影响。

Genomics is emerging as a key tool to help build a future of environmentally sustainable agriculture that leads to a safe and secure food supply. The development of genomics tools relies primarily on the discovery of relationships between genotypes and phenotypes, which is accomplished by performing genetic mapping. The proposed research involves genetic mapping in apples (Malus domestica), one of the world's most widely grown fruit crops and Canada's leading fruit in both volume and value.***I propose to discover genetic markers that predict apple quality that Canadian apple breeders will then use to perform genomics-assisted breeding: they will screen offspring at the seedling stage using the markers we discover and discard those predicted to have poor quality. Apples take nearly a decade to grow to maturity and evaluate, and breeding apples using traditional phenotypic evaluations is therefore extremely time-consuming and expensive. Marker-assisted selection thus holds particular promise in apples because it can dramatically increase the efficiency and reduce the costs of generating desirable apples that require less chemical input to grow.***To enable genomics-assisted breeding in apples, I established the Apple Biodiversity Collection (ABC) – an orchard with over 1000 apple varieties that serves as the most diverse and arguably most powerful genetic mapping population of apples in the world. The ABC was planted in 2013 specifically for the purposes of genetic mapping and is emerging from juvenility over the next few years. It is the foundation of my proposed NSERC Discovery research.***It is my long-term objective to exhaustively catalogue all of the genetic variation present in the ABC. Here I propose to sequence the DNA of the 1000+ apple varieties and extract as many genetic markers from these data by developing novel bioinformatics tools. However, the challenge in genetically mapping fruit quality traits clearly lies in the collection of the phenotype data. Therefore, a primary activity in this proposal involves the development and use of automated, high-throughput phenotyping devices and metabolomic/proteomic assays to query as much of the apple's phenome as possible. In addition, I also propose to evaluate the apple's wild ancestor in Central Asia to determine if it is worth exploiting its functional genetic variation for future apple improvement.***The proposed research will not only result in markers that accelerate the improvement of apple quality through breeding, but it will also generate innovative bioinformatics tools that improve the power of genetic mapping in other non-model organisms. Thus, the proposed project promises to benefit stakeholders along the entire Canadian apple value chain, from grower to consumer, and to help accelerate the impact of genomics in several fields including agriculture, biofuels and forestry.