RESEARCH-PGR: A Genome-level Approach to Balancing the Vitamin Content of Maize Grain

这项合作研究项目旨在确定玉米基因组中约40,000个基因的子集，这些基因共同确定籽粒中五种必需和有限的膳食维生素的水平：维生素E和四种B维生素，B1(硫胺素)、B2(核黄素)、B3(烟酸)和B6(吡哆醇)。通过结合与人类基因组计划中使用的方法类似的方法，研究人员将识别等位基因，这些“维生素”基因的特殊变异，并学习如何将它们组合在一起，在玉米粒中产生大量维生素。这项研究的一个重要成果将是了解如何提高玉米粒中的这些微量营养素水平，以便以玉米为主要成分的日粮提供平衡的营养含量。这些发现的这种直接转化将最终纳入和固定玉米育种计划中已确定的等位基因，这些等位基因有利于提高维生素E和B的水平，以增强食品和饲料供应链。此外，这项研究将为其他农作物的平行努力提供指导原则，从而使全球范围内更有营养的作物的预测性育种和代谢工程成为可能。最后，在该项目中将研究与教育相结合，将允许培训具有植物遗传学、育种、基因组学、生物化学和生物信息学知识的下一代植物科学家。该项目旨在利用过去十年在玉米中开发的大量遗传和基因组工具集来促进和加速我们对基因、等位基因和遗传机制的基本了解，这些基因、等位基因和遗传机制控制着玉米籽粒中维生素的合成和积累，从而导致玉米饲料中的维生素缺乏：四种B类维生素(B1，硫胺素；B2，核黄素；B3，烟酸；B6，吡哆醇)和维生素E。该项目将一个具有不同但互补的知识和技能的科学家团队聚集在一起，使控制这些营养特性的基因、等位基因和潜在机制得以阐明，并在全球范围内推广。具体目标是：(I)与玉米Ames自交系(n~2,000)进行全基因组关联研究，以确定和解决控制这些微量营养素积累的数量性状座位(QTL)；(Ii)通过构建和分析来自Ames自交系的极端异常值的F2群体，评估稀有等位基因的作用；(Iii)利用授粉24天后从代表Ames自交系表型变异的500个自交系中获得的全部转录组测序数据，确定表达QTL和存在-缺失变异(PAV)对维生素组成的贡献；以及，(4)利用Ames小组进行基因组预测，以加快在发展中国家培育改良谷物微量营养素成分的效率。该项目对更广泛的科学界和公众的更广泛影响将通过一系列协调一致的活动来确保，这些活动让学生、博士后助理、科学家和公众参与进来。该项目产生的数据和生物资源将向社区开放。数据将通过出版物、项目网站和长期储存库传播，如NCBI的SRA和MaizeGDB。

This collaborative research project is directed at identifying a subset of the ~40,000 genes in the corn genome that work together to determine the levels of five essential and limiting dietary vitamins in kernels: vitamin E and the four B vitamins, B1 (thiamin), B2 (riboflavin), B3 (niacin) and B6 (pyridoxine). By combining approaches similar to those used in the Human Genome project, the researchers will identify alleles, special variations in these "vitamin" genes, and learn how to put them together to generate high amounts of vitamins in corn kernels. An important outcome of this research will be the knowledge by which to enhance these micronutrient levels in corn kernels such that diets in which maize is a major component provide a balanced nutritional content. Such direct translation of these findings will be the eventual incorporation and fixation of identified alleles in maize breeding programs that are favorable for the increased levels of vitamins E and B to enhance the food and feed supply chain. In addition, this research will provide guiding principles for parallel efforts in other agricultural crops and thus enable predictive breeding and metabolic engineering of more nutritious crops worldwide. Finally, integration of research with education within the project will permit training of the next generation of plant scientists with knowledge of plant genetics, breeding, genomics, biochemistry, and bioinformatics. This project seeks to leverage the tremendous genetic and genomic tool sets developed in maize the past decade to advance and accelerate our fundamental understanding of the genes, alleles and genetic mechanisms controlling synthesis and accumulation of vitamins that are limiting in maize grain and hence result in vitamin deficiencies in maize-based diets: four B vitamins (B1, thiamine; B2, riboflavin; B3, niacin; B6, pyridoxine) and vitamin E. This project brings together a team of scientists with divergent but complementary knowledge and skills that together will allow the genes, alleles and underlying mechanisms controlling these nutritional traits to be elucidated and the knowledge deployed on a global scale. Specific objectives are to (i) perform genome-wide association studies with the maize Ames inbred line panel (n~2,000) to identify and resolve quantitative trait loci (QTL) controlling accumulation of these micronutrients; (ii) assess the role of rare alleles by constructing and analyzing segregating F2 populations derived from Ames lines that are extreme outliers for traits; (iii) determine the contribution of expression QTL and presence-absence variants (PAVs) to vitamin composition using whole transcriptome sequencing data obtained from grain 24 days after pollination in 500 inbred lines that represents the phenotypic variation of the Ames panel; and, (iv) perform genomic prediction with the Ames panel to accelerate the efficiency of breeding improved grain micronutrient composition in developing countries. The broader impacts of this project to the broader scientific community and public will be ensured through a set of coordinated activities that engage students, postdoctoral associates, scientists and the public. Data and biological resources generated in this project will be made accessible to the community. Data will be disseminated through publications, project websites and long-term repositories such as the NCBI's SRA and MaizeGDB.