Research Project: Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

2019 Annual Report

Objectives
1. Advance and accelerate translational research for ARS and its collaborators that addresses the agricultural needs of primarily the Southeast region, through data generation, data analysis, and data management, with an emphasis on genomic approaches and on crop, animal, insect, and microbiome analyses; support germplasm analysis for breeding and for trait genetic and molecular analyses; and support gene expression analysis and gene discovery. 1.A. A cross section of GBRU operations in genomics and bioinformatics. 1.B. Specific ongoing collaborative projects. 1.C. Data Management. 2. Accelerate ARS bioinformatics community development and capacity building, primarily for the Southeast region, through training workshops, webinars, and direct project participation; develop and evaluate new tools, workflows, and systems that enable ARS and its collaborators to more efficiently manage, analyze, and share diverse streams of biological data and knowledge, including high throughput genotyping and phenotyping, thereby enhancing crop and animal genetic improvement, health, and nutrition. 2.A. Bioinformatics community development and capacity building. 2.B. Development of new tools and procedures.

Approach
The Genomics and Bioinformatics Research Unit’s (GBRU) primary function is conducting research in the areas of bioinformatics and genomics on a wide array of species and topics. Genomic technologies are powerful tools for germplasm improvement using marker assisted selection (MAS), biotechnology, or synthetic biology, and for analyzing associated biological processes (genetics, physiology, cell and molecular biology, biochemistry, and evolutionary biology). Thus, many ARS scientists, e.g., crop and animal breeders, have a direct need for genomic tools in their research. Others, e.g., soil scientists, can enhance their research dramatically using genomic tools to analyze the microbiome, if the technologies and appropriate expertise are available. However, not all ARS locations have sufficient resources to support core genomic technologies. Thus, the mission of the ARS Genomics and Bioinformatics Research Unit (GBRU), is to: (1) coordinate, facilitate, collaborate and conduct genomics and bioinformatics research emphasizing the Southeast region; (2) serve as a research and training resource for genomic technologies and bioinformatic analyses in support of ARS scientists and their collaborations; and (3) serve as a technical resource for ARS research programs that have not typically utilized these technologies, and aid in their development of genomic resources. Within the GBRU, this research project will conduct and collaborate on genome sequencing, sequence assembly and analysis, diversity analysis, marker development, haplotyping, physical and genetic map production, and transcription profiling research. Thus, essential product development includes new and improved reference genomes for plants, animals, insects, fish, and microbes that enable genomics-assisted breeding; new physical and genetic maps; improved cultivars, germplasm, or breeding lines; and new information on key agricultural problems such as disease resistance and drought tolerance.

Progress Report
During the past year the unit continued its service and research efforts in the area of genomics. In relation to genomes, the unit has contributed to several genomes like blueberry, hydrangea, several peanut related species, 10 insect pests, salmon, catfish, trout, alligator gar, fungi, and buffelgrass. The unit has helped lead the ARS Ag100Pest project which is to generate high quality genomes for 100 important insects. This has required the development of new protocols to work with small insect size but large genomes. This is a developing field and advances made to date will be used in the coming years to sequence more insects and to push the envelope of the size of insects that can be sequenced. In the first nine months of the project, the unit has generated DNA sequence for 10 insect pests. These genomes will be used by the scientific community to control and monitor pests in the field. Collaborations between informatics and breeding groups working on Cotton Leaf Curl Virus (CLCuV) have produced multiple genetic linkage maps from different populations. The results obtained offer some promising information about the location of the resistance genes that have been found in the parent lines. Additionally, the separate sets of information show that it is likely there are multiple different types of resistances found in the different parents. This will need to be confirmed but is exciting to be able to stack multiple natural resistances to provide elevated levels of resistance to the decimating CLCuV. The unit continues to expand its research into peanut genomes to understand the difference between wild and cultivated peanuts, and to advance research related to disease resistance traits. In this context, the unit has provided new genomic and scaffolding data for a diploid peanut species that is important for breeders. De novo assemblies of synthetic polyploid genomes is shedding light on the mechanism of rampant, biased gene conversion associated to creating a tetraploid species. Aspergillus flavus represents a very important pest for several crops as certain strains can produce aflatoxin. The research unit is involved in the sequencing and analysis of two isolates of Aspergillus flavus isolates that have unique interactions under stress. Genomic analysis indicates a large insert which might be related to a gene cluster and which could result in new metabolites. A gene cluster is already known from the production of aflatoxin. A novel method has been developed that will map traits faster, cheaper, and better compared to standard QTL mapping. This was done by developing new software packages including one that helped with simulations to design the rest of the pipeline. Research is going on to validate the approach using biological data. Continued analysis of population genetics and structural variation in U.S. rice cultivars (ARS) in collaboration with scientists at Mississippi State University, approximately 170 historic and modern U.S.A. rice cultivars have been sequenced. Work continues on the analysis of population genetics and structural variation in U.S. rice cultivars. In relation to cotton, one of the first quality genomes for a tetraploid species was produced and then reported by the unit in 2018. In continuation of this work and to understand cultivated cotton, four other tetraploid cotton species were also sequenced and compared. The results indicate that all tetraploid species are probably derived from one polyploidization event.

Accomplishments
1. Cultivated peanut genome sequenced with unprecedent accuracy. Cultivated peanut is a tetraploid species and earlier attempts to generate a genome required using its progenitor diploid parents. While this was helpful, it did not provide a completely accurate template to study cultivated peanut. Working with an international group, ARS researchers in Stoneville, Mississippi, contributed to the genome of a very high-quality genome of cultivated peanut. The final product was the highest quality tetraploid genome ever produced. This information has been used by the peanut research community to associate DNA markers with important agricultural traits.

2. Expanding the capacity of Quantitative Insights into Microbial Ecology (QIIME), the most popular software program for microbiome science. The software is used in agriculture, medicine and environmental sciences to identify pathogens, plant diseases, and beneficial microbes that help plants and animals grow, but the first version lacked capacity to perform certain analysis with fungi. ARS researchers in Stoneville, Mississippi, wrote part of the portion of this software that analyzes fungi, making it possible to identify and quantify the microscopic fungi in the environment. The first version of the software has been used in over 15,800 research studies and the new version with this important addition is poised to answer many more questions in science.

Review Publications
Toomer, O.T., Hulse-Kemp, A.M., Dean, L.L., Boykin, D.L., Ramon, M., Anderson, K.E. 2019. Feeding high-oleic peanuts to layer hens enhances egg yolk color and oleic fatty acid content in shell eggs. Poultry Science. 98:1732-1748. https://doi.org/10.3382/ps/pey531.
Jarret, R.L., Barboza, G., Batista, F., Chou, Y., Hulse-Kemp, A.M., Ochoa-Alejo, N., Veres, A., Berke, T., Carrizo, C., Csillery, G., Huang, Y., Kiss, E., Kovacs, Z., Kondrak, M., Arce-Rodriguez, M., Scaldaferro, M.A., Szoke, A., Tripodi, P. 2019. Capsicum - an abbreviated compendium. Journal of the American Society for Horticultural Science. 144(1):3-22. https://doi.org/10.21273/JASHS04446-18.
Gonda, I., Ashrafi, H., Lyon, S., Strickler, S., Hulse-Kemp, A.M., Thannhauser, T.W., Mueller, L., Fei, Z., Foolad, M., Giovannoni, J.J., Ma, Q., Sun, H., Stoffel, K., Powell, A., Futrell, S., Van Deynze, A. 2018. A GBS-based high-density genetic map of a tomato RIL population facilitating high resolution QTL mapping and candidate gene identification. The Plant Genome. 12:1. https://doi.org/10.3835/plantgenome2018.02.0010.
Park, S., Scheffler, J.A., Scheffler, B.E., Cantrell, C.L., Pauli, C.S. 2019. Chemical defense responses of upland cotton, Gossypium hirsutum L. to physical wounding. Plant Direct. 3:5. https://doi.org/10.1002/pld3.141.
Hussain, S., Farooq, M., Malik, H., Amin, I., Scheffler, B.E., Scheffler, J.A., Liu, S., Mansoor, S. 2019. Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species. BMC Genomics. 20:507. https://doi.org/10.1186/s12864-019-5877-9.
Shakir, S., Zaidi, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Nawaz-Ul-Rehman, M., Mansoor, S., Atiq, U. 2019. Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites. Plants. 8:127. https://doi.org/10.3390/plants8050127 .
Arias De Ares, R.S., Sobolev, V., Massa, A.N., Orner, V.A., Walk, T., Simpson, S.A., Ballard, L.L., Puppala, N., Scheffler, B.E., De Blass, F., Tallury, S.P., Guillermo, S. 2018. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-018-1355-9.
Grover, C.E., Arick, M.A., Thrash, A., Conover, J.L., Sanders, W.S., Peterson, D.G., Frelichowski, J.E., Scheffler, J.A., Scheffler, B.E., Wendel, J.F. 2018. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution. 11(1):53-71. https://doi.org/10.1093/gbe/evy256.
Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A., Pandey, M., Samoluk, S.S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Kim, K.D., Korani, W., Lanciano, S., Lui, C.G., Mirouze, M., Moretzsohn, M.C., Pham, M., Shin, J.H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N.T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E.L., Michelmore, R., Varshney, R.K., Holbrook Jr, C.C., Cannon, E.K., Scheffler, B.E., Grimwwood, J., Ozias-Akins, P., Cannon, S.B., Jackson, S.A., Schmutz, J. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 51:877-884. https://doi.org/10.1038/s41588-019-0405-z.