FOOD, FEED, FUEL, AND FIBER: SECURITY UNDER A CHANGING CLIMATE

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1019005
• Project No.: MIS-171810
• Multistate No.: NC-1179
• Project Start Date: Mar 15, 2019
• Project End Date: Sep 30, 2019

Project Director
Peterson, DA, G..

Recipient Organization
MISSISSIPPI STATE UNIV
(N/A)
MISSISSIPPI STATE,MS 39762

Performing Department
LSBI / IGBB

Non Technical Summary
We will contribute to the progress of the "Food, Feed, Fuel, and Fiber: Security Under a Changing Climate" multistate project by utilizingcomparative genomics and proteomics techniques to explore the molecular nature of differences between crop plants and theirwild relatives. Additionally, we will build genomic tools that will facilitate similar comparative studies in understudied aquacultural species. Traditional breeding techniques have left most crop plants (and some aquaculture species) with relatively little genetic diversity compared to their wild relatives. Inbreeding has left these key food/fiber organismssusceptible to biotic and abiotic stresses that will undoubtedly become more severe and less predictable as the affects of climate change become more readily visible. A major goal of our research willbe identifying genes/alleles in wild species that confer resistance to disease and abiotic stresses. We will work with plant and animalbreeders to introgress such advantageous genes/alleles into food/fiber species.

Animal Health Component

10%

Research Effort Categories

Basic

45%

Applied

45%

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1710	1080	50%
201	1599	1080	20%
304	3799	1080	20%
211	1710	1080	10%

Knowledge Area
211 - Insects, Mites, and Other Arthropods Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms; 304 - Animal Genome;

Subject Of Investigation
1599 - Grain crops, general/other; 3799 - Cultured aquatic animals, general/other; 1710 - Upland cotton;

Field Of Science
1080 - Genetics;

Keywords

genomics

proteomics

cotton

aquaculture

abiotic stress

biotic stress

Goals / Objectives
Enhance the understanding of the effects of climate variability and change on crop and livestock production systems Disseminate the research outcomes and educate stakeholders on the potential effects of climate variability and climate change on agricultural production resource use and adaptation options through cooperation with university extension services, state climate offices and various federal partners.

Project Methods
The PI is director of the Institute for Genomics, Biocomputing and Biotechnology at Mississippi State University. Hisresearch projects will be conducted using IGBB instrumentation. The tools most commonly used in his research include the following:(1) Illumina DNA sequencing - The IGBB owns an Illumina MiSeq sequencer and has access through contracts with BGI andNovogene to Illumina HiSeq and NovaSeq instruments. Sequencing is performed as part of externally-funded research projectsand as a service to Mississippi State faculty/staff on a fee-per-service (cost-recovery-only) basis. Illumina DNA and RNA-Seqdata is stored, manipulated, and analyzed using the supercomputers in MS State's High Performance Computing Collaboratory(HPC2) of which the IGBB is a member center. Public, commercial, and inhouse scripts are used in sequence analysis.(2) Oxford Nanopore DNA sequencing - The IGBB owns and operates a long-read, high-throughput Oxford NanoporeGridIONx5 sequencer. The long nucleotide reads produced by the nanopore sequencer are used in the assembly of eukaryoticand prokaryotic genomes.(3) Pacific Biosciences DNA sequencing - The IGBB has access to PacBio sequencing through its contract with Novogene. Theresults produced by PacBio instruments are comparable to those generated by Oxford Nanopore instruments.(4) Mass Spectrometry - The IGBB has both gel-based and liquid based mass spectrometry systems which it uses to identifyproteins, discover and characterize protein post-translational modifications, conduct quantitative proteomics, perform qualitativeand quantitative comparison of the protein complements of different tissues/stages/organisms, integrate proteomic and nucleicacids data (e.g., proteogenomic mapping), and perform functional annotation of proteins using Gene Ontology (GO) standardsand procedures. For liquid-based proteomics, the IGBB's proteomics staff uses a Waters Nano ESI Q-TOF (model Xevo G2-S)mass spectrometer and LTQ Orbitrap Velos and standard LTQ mass spectrometers fitted with upstream HPLC samplepurification systems. Gel-based proteomics is conducted using the IGBB's MALDI TOF TOF mass spectrometer. Recently, wehave also begun to perform metabolomic research using the LTQ Orbitrap Velos.(5) Computational Biology - The IGBB is one of several member centers of MS State's High Performance ComputingCollaboratory (HPC2: http://www.hpc.msstate.edu/). The HPC2 is governed by an Operations Board (Ops Board) composed of the directors of the member institutes (voting members) and the Associate Vice President for Research (non-voting member). Dr.Peterson is the IGBB's representative on the Ops Board. All IGBB faculty/staff have access to the various supercomputerslocated in the HPC Building. The HPC2 and all of its computers are managed and maintained by the HPC2's Computing Office.The HPC2 has consistently ranked in the Top500 supercomputing lists since June 1996.The HPC2 currently operates several supercomputers including a CS300-LC cluster supercomputer - specifically, a liquidcooledsystem manufactured by Cray Inc. This machine, which has been named "Shadow," serves as the primary highperformancecomputing asset for shared research. Shadow is 10 times faster than the university's previous fastest system (i.e.,Talon), but consumes far less energy. Shadow is capable of 593 TeraFLOPS and is characterized by 4,800 processor cores(Intel Xeon E5-2680 V2, 2.8 GHz), 28,800 coprocessor cores (Intel Xeon Phi 5110P), 15 terabytes of memory, and FDRInfiniBand (56 Gb/s). The second fastest computing cluster at the HPC2 is Talon. Talon (IBM iDataPlex cluster with 3,072processor cores, six-core Intel Xeon processors, more than six terabytes of RAM, and a Voltaire, Inc., high-speed quad datarate InfiniBand network). Talon has a proven peak performance of more than 34.4 TeraFLOPS. Other resources include a 10-teraflop 2048 processor AMD Opteron cluster, a 384 processor Intel Xeon cluster with InfiniBand interconnect, a 512 processorSGI ORIGIN 3900, a 128 processor SGI ORIGIN 3800, a 64 processor SGI ORIGIN 3800, and numerous additional specialpurpose machines. Data storage capabilities include a 250 terabyte high performance disk system and a 2 petabyte near-linestorage system.Genome assembly, which is notoriously RAM intensive, is performed using the shared memory machines Atlas and Skybolt.Each machine has 512 GB RAM, 16 compute cores, and 2.3 TB of local storage.High-end visualization needs are met by an immersive reconfigurable CAVE virtual reality environment driven by a 4 nodevisualization cluster. An access grid node allows for state-of-the-art video teleconferencing and remote collaboration.The network infrastructure backbone consists of both 10-Gigabit Ethernet and Gigabit Ethernet, with an extensive GigabitEthernet network for desktop connectivity. Internet connectivity is provided via Mississippi State University's 10-Gigabit Ethernetcampus backbone. Campus connectivity to the Internet at large is via a 1 Gigabit connection. Mississippi State University is acharter member of the Internet2 Consortium, and currently utilizes a 1 Gigabit connection to the Louisiana Optical NetworkInitiative (LONI) regional network for connectivity to Internet2/NewNet and the National LambdaRail (NLR) via a 10 Gigabitconnection.In addition to the HPC2 computers, the IGBB's Laboratories possesses multiple Windows, Linux, and dual boot workstations.A number of different molecular analysis programs are currently loaded on the HPC2 supercomputers.

Progress 03/15/19 to 09/30/19

Outputs
Target Audience:This project should be of interest to plant breeders, molecular biologists, geneticists, farmers, seed companies, and ecologists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Three graduate students were trained, in part, through the project. How have the results been disseminated to communities of interest?The results have been published in peer-reviewed journals and discussed at various national and international meetings. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Accomplishment under these goals include: (1) Whole de novo genome sequencing of two cotton species (Gossypium raimondii and Gossypium turneri) and two cotton relatives (Gossypioides kirkii and Kokia drynaroides). G. raimondii and G. turneri represent potential sources of disease resistance and climate adaptability traits that could ostensibly be bred into commercial cotton. Gossypioides kirkii and Kokia drynaroides serve as outgroups for studying the naturnal history of cotton. (2) Whole genome and transcriptome sequencing of the reniform nematode, a major pest of cotton. We produced and published a draft genome sequence of the reniform nematode and described changes in its transcriptome at different stages in its lifecycle. The ultimate goal of these studies is to find reniform nematode-specific gene pathways that could be preferentially interrupted as a way to control the spread and reduce the damage done by reniform nematodes. (3) Development of a kit for detection of bacterial cotton blight. A PCR-based kit was developed that allows identification of harmful strains of the cotton blight pathogen Xanthomonas citri pv. malvacearum. This kit will help scientists identify cotton blight infections at early stages thus preventing major crop loss. (4) Producing information on how bird immune systems adapt to malaria and malaria-like pathogens. (5) Illuminating the role of seasonal effects on equine follicular fluid proteomics.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: GROVER CE, ARICK 2ND MA, THRASH A, CONOVER JL, SANDERS WS, PETERSON DG, FRELICHOWSKI JE, SCHEFFLER JA, SCHEFFLER BE, WENDEL JF (2019) 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.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: SHOWMAKER KC, SANDERS WS, DEN AKKER SE-V, MARTIN BE, PLATT 2ND RN, STOKES JV, HSU C-Y, BARTLETT BD, PETERSON DG, WUBBEN MJ (2019) A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira. Journal of Nematology 51(1): https://doi.org/10.21307/jofnem-2019-013
• Type: Journal Articles Status: Published Year Published: 2019 Citation: WANG X-Q, ALLEN TW, WANG H, PETERSON DG, NICHOLS RL, LIU A-X, DENG P, JIA D, LU S (2019) Development of a qPCR protocol to detect the cotton bacterial blight pathogen, Xanthomonas citri pv. malvacearum, from cotton leaves and seeds. Plant Disease 103(3): 422-429.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: OUTLAW DC, WALSTROM VW, BODDEN HN, HSU CHUAN-YU, ARICK-2ND M, PETERSON DG (2019) Molecular evolution in immune genes across the avian tree of life. Parasitology Open 5(e3): 1-9.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: DUTRA GA, ISHAK GM, PECHANOVA O, PECHAN T, PETERSON DG, JACOB JCF, WILLARD ST, RYAN PL, GASTAL EL, FEUGANG JM (2019) Seasonal variation in equine follicular fluid proteome. Reproductive Biology and Endocrinology 17(1): 29.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: UDALL JA, LONG E, HANSON C, YUAN D, RAMARAJ T, CONOVER JL, GONG L, ARICK MA, GROVER CE, PETERSON DG, WENDEL JF (2019) De novo genome sequence assemblies of Gossypium raimondii and Gossypium turneri. G3: Genes, Genomes, Genetics 9(10): 3079-3085.
• Type: Book Chapters Status: Published Year Published: 2019 Citation: PETERSON DG, ARICK 2ND M (2019) Sequencing plant genomes. In: Progress in Botany, Vol. 80. Edited by: Matyssek R, L�ttge U, C�novas FM. - Springer Nature Switzerland, pp. 109-193.