Bode

I obtained a BS degree in botany at Obafemi Awolowo University, a MS degree in genetics at University of Ibadan, and a PhD in genetics at Clemson University. Following postdoctoral positions at Clemson University and NC State University, and an appointment as a Research Assistant Professor, I joined the Department of Entomology and Plant Pathology at the University of Tennessee, Knoxville.

By integrating quantitative genetics and the more recent genomic technologies, my goal is to understand the genetic and molecular mechanisms underlying important agronomic traits, particularly complex diseases in plants. My research interest focuses on understanding how multi-way plant-pathogen-microbe interactions modulate plant diseases and defense response pathways. To achieve this at the systems level, I am developing new methods and bioinformatic tools to aid integration of multi-omic datasets.

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Research focus

My research focuses on dissecting genome structure and function to better understand:

  1. Complex plant-pathogen-microbe interactions within the context of agricultural systems. Studies aim to capture naturally occurring metagenomic communities and validate specific interactions with synthetic communities. Pathogens interact with both host plants and host-associated microbial community; hence the study of complex diseases can benefit from modeling these interactions to better model disease incidence and severity. We are currently focusing on Fusarium ear and stalk rot and identifying biocontrol and beneficial microbes that are well adapted to the host.
  2. How the host-associated metagenome impacts variation in agronomic traits and partition this variation between host and microbial genetic components. This is aimed to improve accuracy and precision for identifying host genetic factors and genomic predictions.
  3. Genetic factors underlying traits and their application for modern crop improvement strategies.

To facilitate translational genomics for crop breeding in a high-throughput and streamlined manner, I am optimizing and developing genomic tools and resources that include:

  1. An inexpensive quantitative reduced representation sequencing protocol for genomes and metagenomes. This assay allows for fast turnaround time with generating and computationally processing big data that fits time requirement of breeding programs.
  2. Integrating hierarchical shotgun sequencing and femto-scale sequencing for high-quality and haplotype-resolved genome assemblies.
  3. Completely automated and user-friendly computational tools/pipelines for empirically based next-generation sequence data quality filtering, variant calling, and metagenomic profiling.
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Teaching focus

At the core of my teaching philosophy is an enthusiasm to not only perpetuate knowledge and inspire eagerness for learning, but to also teach independent critical listening and thinking. I hope to motivate and nurture the atmosphere of ownership and involvement by providing information in formats that accommodate differences in learning styles.

Courses

EPP 633 – Statistical Genetics and Genomics
EPP 504 – Statistical Genetics and Genomics (Lab)

bode olukolu

Assistant Professor
office (865) 974-7786
mobile (864) 650-3310
EPP main office (865) 974-7135
EPP fax (865) 974-4744
bolukolu@utk.edu

352 Plant Biotechnology Building
2505 EJ Chapman Drive
Knoxville, TN 37996-4560

Education

B.S., Botany, Obafemi Awolowo
M.S., Genetics, University of Ibadan
Ph.D., Genetics, Clemson University

websites
GBSapp
ngsComposer

Professional appointment
90% Research, 10% Teaching

Graduate program concentrations
Bioinformatics, Genomics, and Molecular Interactions

Areas of expertise

Plant-Microbe interactions, quantitative genetics, integrative genomics, and bioinformatics

KEY WORDS
QTL, GWAS, defense response, quantitative disease resistance, fusarium, maize, sweet potato

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Research questions in our laboratory

  • How does the host-associated metagenome modulate pathogenesis, plant defense response and immunity?
  • Can host-associated metagenomes within the context of the holobiont improve statistical power for GWAS/QTL analysis and genomic prediction?
  • Can selection during breeding, identify individuals to efficiently recruit beneficial microbes (from environment and probiotics) in an environmental-independent manner?
  • What are the major factors driving rapid crop adaptation?
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Current lab members

  • Alison Adams (PhD Student)
  • Alhagie Cham
  • Dana Landry (Lab Manager)

Selected Publications

Samayoa LF, Olukolu BA, Yang CJ, Chen Q, Stetter MG, York AM, Sanchez-Gonzalez JDJ, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Yang J, Ross-Ibarra J, Buckler ES, Doebley JF, Holland JB (2021) Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte. PLoS Genetics. 17 (12), e1009797

Chen Q, Samayoa LF, Yang CJ, Olukolu BA, York AM, Sanchez-Gonzalez JDJ, Xue W, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Buckler ES, Holland JB, and Doebley JF (2021) A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication. Proc Natl Acad Sci U S A. 118(43). 10.1073/pnas.2112970118

Kuster R**, Yencho GC, and Olukolu BA (2021). ngsComposer: An automated pipeline for empirically based NGS data quality filtering. Briefings in Bioinformatics. Brief Bioinform. bbab092. doi: 10.1093/bib/bbab092

Oloka BM, Pereira G, Amankwaah A., Mollinari M, Pecota KV, Olukolu BA, Zeng ZB, and Yencho GC (2021) Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas). Theor Appl Genet. doi: 10.1007/s00122-021-03797-z

Sapkota S, Boggess SL, Trigiano RN, Klingeman WE, Hadziabdic D, Coyle DR, Olukolu BA, Kuster RD, Nowicki M (2021) Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear (Pyrus calleryana) in the Species Native Range and in the North American Cultivars. Life 2021, 11, 531. doi.org/10.3390/life11060531

Zhou C, Olukolu BA et al. (2020) Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nat Genet 52, 1256–1264.

Bararyenya A, Olukolu BA, Tukamuhabwa P, Grüneberg WJ, Ekaya W, Low J, Ochwo-Ssemakula M, Odong TL, Talwana H, Badji A, Kyalo M, Nasser Y, Gemenet D, Kitavi M, Mwanga ROM (2020) Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploidy sweetpotato. BMC Plant Biol. 20(1):3.

Mollinari M, Olukolu BA, Pereira GDS, Khan A, Gemenet D, Yencho GC, Zeng ZB (2020) Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3. 10(1):281-292.

Gemenet DC, Pereira G, De Boeck B, Wood JC, Mollinari M, Olukolu BA, Diaz F; Mosquera V; Ssali RT, David M, Kitavi MN, Burgos G, Felde TZ, Ghislain M, Carey E, Swanckaert J, Coin LJM, Fei Z, Hamilton JP, Yada B, Yencho GC, Zeng ZB, Mwanga ROM, Khan A, Gruneberg WJ, Buell CR (2020) Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively-associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. Theor Appl Genet. 133(1):23-36.

1Yang CJ, Samayoa LF, Bradbury PJ, Olukolu BA, Xue W, York AM, Tuholski MR, Wang W, Daskalska LL, Neumeyer MA, Sanchez-Gonzalez JDJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB, Doebley JF (2019) The evolutionary genetics of maize domestication: heritabilities, genetic correlations, constraint and selection. Proc Natl Acad Sci U S A. 116(12):5643-5652.

Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet D, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z. (2018) Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat Commun. 9(1):4580.

Xiaodong X*, Olukolu BA*, Yang Q, Balint-Kurti, PJ (2018) Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of Southern Leaf Blight. Theor Appl Genet. 131(12):2601-2612.

Wadl PA, Olukolu BA, Branham SE, Jarret RL, Yencho GC, Jackson DM (2018) Genetic diversity and population structure of the USDA sweetpotato (Ipomoea batatas) germplasm collection using GBSpoly. Front Plant Sci. 9:1166.

Patent
Olukolu BA and Yenco GC (PCT/US20/35470): Compositions and methods related to quantitative reduced representation sequencing. May 30, 2020

For complete list of publications please visit my