Mol Plant：中科院作物所何忠虎研究组发表育种芯片评述性论文

2017年6月28日，国际著名学术杂志《Cell》子刊《Molecular Plant》杂志在线发表了中国农业科学院作物科学研究所何忠虎研究组的评述性论文“作物育种芯片与基因型鉴定平台：进展、挑战与展望”(Crop breeding chips and genotyping platforms: progress, challenges and perspectives)，论文对作物分子标记发展概况、分子育种进展、基因型与表型关系、现有高通量基因型检测平台利弊、育种芯片的高通量与灵活性等方面进行了系统评述分析，认为随着基因组学技术的发展，分子标记在作物遗传育种领域应用将更加广泛。目前在25种作物中已开发出50多种SNP芯片及15种基于测序技术的基因型检测平台，但真正符合育种家需要的并不多，为此提出了发展高通量、低成本兼具灵活性的实用分子育种平台策略，将极大提高育种效率，加速培育适应全球气候变化的作物新品种。

SNP芯片已成为作物遗传改良的重要工具。该团队在前期成功开发小麦KASP基因型检测平台的基础上，与公司合作研制出新型50K小麦育种芯片，概括起来有四大优点：(1)标记多态性高、应用范围广，适用于不同遗传背景的小麦材料检测;(2)标记分布均匀，每条染色体含2000多个SNP标记;(3)含功能基因及与性状连锁标记，包括135个品质、农艺性状和抗病性等基因标记及与重要性状紧密连锁的700个标记，这是其它芯片不具备的;(4)比同类芯片价格低20%。

原文链接：

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

原文摘要：

There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype–phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.