NSF Postdoctoral Fellowship in Biology FY 2020: Elucidating Root Knot Nematode Genetic Resistance through de novo Genome Assembly of Cultivated and Wild Chili Peppers

本行动资助NSF国家植物基因组计划2020财年生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Emily Delorean的研究和培训计划的标题是“通过栽培和野生辣椒的从头基因组组装阐明根结线虫的遗传抗性”。该奖学金的主办机构是美国农业部-农业研究服务局（USDA-ARS）和北卡罗莱纳州立大学，赞助科学家是dr。阿曼达·赫尔斯-肯普和威廉·拉特。根结线虫感染威胁着全球蔬菜作物生产。辣椒是受根结线虫（RKN）严重威胁的蔬菜作物之一，在美国每年8.886亿美元的作物中，估计损失12.2%。由于可持续田间管理控制的局限性，遗传抗性是保护作物产量的有希望的途径。然而，辣椒抗根结线虫的育种受到基因组和遗传技术的限制。该项目将利用尖端的基因组工具和资源，在辣椒基因组中已知的抗性基因“热点”中，鉴定新的抗性基因，以对抗新出现的高毒力RKN物种。抗性基因一经鉴定，将成为培育辣椒抗性品种的重要遗传资源。培训目标包括基因组组装、种质开发和植物病理学方面的技术培训，以及通过“准备教授”认证计划进行的正式教学培训。更广泛的影响包括与同侪学者计划合作，向本科生教授生物信息学，并与现有的外展计划合作，招募代表性不足群体的年轻人进入STEM领域。该项目旨在利用遗传和基因组技术鉴定并将抗RKN的新遗传多样性引入栽培辣椒中。具体来说，杂交植物将通过杂交栽培辣椒（对根结线虫品种Meloidogyne incognita、Meloidogyne javanica和Meloidogyne arenaria具有抗性）和祖先辣椒（对一种新的高毒力根结线虫品种Meloidogyne enterolobii具有抗性）来产生。由此产生的杂交后代将使用“三联体”技术进行测序，这是一种利用长读段测序和短读段测序相结合的技术，以产生所有四个亲本基因组的基因组组装。长读测序将允许高度重复的抗性基因“热点”的分辨率，改进当前的辣椒参考基因组组装，并提供该区域的泛基因组表示，已知该区域具有多个单倍型用于定位。祖先辣椒（对肠弧菌具有抗性）和栽培辣椒（对无名型、爪哇型和沙芽孢杆菌具有抗性）之间的杂交品种将被用于将所有四种辣椒的抗性基因“堆”起来，并为肠弧菌抗性基因创建一个图谱种群。最后，基于序列的基因分型标记将与精确育种方法（如标记辅助育种和基因组选择）相兼容，这些标记将利用基因组组装产生的序列数据进行开发。本研究中产生的数据和植物材料将通过同行评审出版物（表型数据）、国家生物技术信息中心数据库（全新基因组组装和测序数据）和美国国家植物种质系统（植物材料）的补充资料公开。通过本研究开发的资源、工具和产品将为辣椒育种计划提供遗传手段，以可持续地解决因根结线虫造成的产量损失。关键词：根结线虫抗性，辣椒，茄科，基因组序列和组装，三联体，基因渗透，栽培和野生祖先系，种群图谱。该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2020. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Emily Delorean is " Elucidating Root Knot Nematode Genetic Resistance Through de novo Genome Assembly of Cultivated and Wild Chili Peppers" The host institutions for the fellowship are the United States Department of Agriculture – Agricultural Research Service (USDA-ARS) and North Carolina State University and the sponsoring scientists are Drs. Amanda Hulse-Kemp and William Rutter.Root knot nematode infection threatens vegetable crop production worldwide. Chili pepper is one of the vegetable crops severely threatened by root knot nematode (RKN) with an estimated loss of 12.2% of the $898.6 million annual crop in the U.S.A. Due to the limitations in sustainable field managements controls, genetic resistance presents a promising avenue to protect crop yields. However, breeding for root knot nematode resistance in chili peppers is limited by the availability of genomic and genetic technologies. This project will address this limitation using cutting edge genomic tools and resources to identify new resistance genes to an emerging and hypervirulent RKN species in a known resistance gene "hotspot" in the chili pepper genome. Once identified, the resulting resistance genes will serve as an important new genetic resource for breeders to use in developing resistant chili pepper varieties. Training objectives include technical training in genome assembly, germplasm development and plant pathology as well as formal training in teaching through the "Preparing the Professoriate" certification program. Broader impacts include teaching bioinformatics to undergraduate students in collaboration with the Peer Scholars program and working with existing outreach programs to recruit young people of underrepresented groups to the STEM fields. This project seeks to use genetic and genomic technologies to identify and introduce new genetic diversity in RKN resistance into cultivated chili pepper. Specifically, hybrid plants will be generated by crossing cultivated chili (with resistance to root knot nematode species Meloidogyne incognita, Meloidogyne javanica, and Meloidogyne arenaria) and ancestral chili (with resistance to Meloidogyne enterolobii, a new and highly virulent root knot nematode species). The resultant hybrids will be sequenced using "trio-binning", a technique that utilizes a combination of long and short read sequencing, to generate genome assemblies for all four both parental genomes. Long read sequencing will allow resolution of the highly repetitive resistance gene "hotspot", improving the current chili pepper reference genome assembly and providing a pan-genome representation of this region that is known to have multiple haplotypes for mapping. Hybrids between ancestral chili (resistant to M. enterolobii) and cultivated chili (resistant to M. incognita, M. javanica, and M. arenaria) will be used to "stack" resistance genes to all four species and create a mapping population for the resistance genes to M. enterolobii. Finally, sequence-based genotyping markers that are compatible with precision breeding methods such as marker assisted breeding and genomic selection will be developed using sequence data generated for the genome assemblies. Data and plant material generated in this research will be made publicly available through supplements of resulting peer-reviewed publication (phenotypic data), the National Center for Biotechnology Information database (de novo genome assemblies and sequencing data), and the U.S. National Plant Germplasm System (plant material). The resources, tools and products developed through this research will provide chili pepper breeding programs with the genetic means to sustainably address the yield losses due to root knot nematode.Keywords: root knot nematode resistance, chili pepper, Solanaceae, genome sequence and assembly, trio-binning, introgression, cultivated and wild ancestral lines, mapping populationThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.