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

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 population

This 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.