In celebration of DNASTAR’s 40th Anniversary, we are featuring profiles of long-time Lasergene users.
Using Lasergene led to an im-peck-able career for poultry geneticist Ron Okimoto
Sharon Page, DNASTAR Senior Content Developer
January 12, 2025 | Lasergene
Our first profile features 34-year Lasergene user, Dr. Ron Okimoto. Ron’s decades of work on poultry genetics have made him a respected name in academia and industry.
Ron’s hen-durance in the field is legendary, and his publications have been cited nearly 7,000 times. After working around the cluck for many years, Ron recently egg-sitted from his career to begin retirement.
Have we beaked your interest? Great! Let’s meet Ron!
Unscrambling sequences with help from Lasergene
Ron’s journey in bioinformatics began in the 1980s as a graduate student. His first encounter with sequence analysis involved using the Staden Fortran program to assemble invertebrate mitochondrial genomes. This early exposure ignited a lifelong passion for understanding and analyzing genetic data.
As his academic career progressed, Ron embraced advancements in technology and software. He transitioned to Mac computers and began using DNASTAR Lasergene, recognizing its user-friendliness and powerful capabilities. During his postdoctoral research at Michigan State University, he further honed his skills using Lasergene to analyze sequences and identify genetic markers.
Complementing Ron’s increasing scientific knowledge were his years of experience raising poultry. Ron had grown up raising birds in his backyard, and kept backyard chickens as a graduate student. Ron says: “With access to a university library, I pretty much had a second degree in chicken genetics, and it turned out to help me out later.”
Taking wing at the University of Arkansas Poultry Science Department
Above: An example of the large array of feather colors in a single chicken breed. Below: Four live chicks are briefly restrained for a photo demonstrating different feather genotypes.
After joining the University of Arkansas Poultry Science department as an Assistant Professor in 1996, Ron continued to utilize Lasergene for advanced tasks such as assembling coding sequences, comparing sequences to identify polymorphisms, and other analyses involving both DNA and protein sequences. This research culminated in significant publications, including Kerje et al., 2004 (see link below). For the Kerje et al. study, Leif Andersson’s group assembled the gene sequences while Ron’s lab identified the initial exon sequence differences between alleles.
A key achievement during his time at the university was the rapid assembly and annotation of two chicken mitochondrial DNA sequences (The complete DNA sequence of a chicken mitocondrial genome associated with maternal type that exhibits high sperm mobility / low sperm mobility). Ron used Lasergene to compare sequences and create the sequencing primer set to amplify the mitochondrial genome and assemble the genomes. By leveraging the power of PCR and automated Sanger sequencing, Ron accomplished this feat within a couple of months, a stark contrast to the years it took using older techniques during his graduate studies.
During this time, Ron also became well-known for his work on feather color genetics, a topic of special interest to the 12 million Americans (among others) who keep backyard chickens. His popular columns on chicken genetics for the National Poultry News are still being cited by chicken-keepers today, years after his last column.
Using his eggs-pertise to help the poultry industry
In 2005, Ron transitioned to industry, joining a broiler breeder company. He continued to rely on Lasergene for crucial tasks such as searching for polymorphisms that could be used to differentiate alleles and create assays to genotype them.
His expertise played a pivotal role in the creation of the first high-density Illumina SNP array for chickens, with some of the polymorphisms he discovered being successfully integrated into this groundbreaking technology. This research culminated in Groenen et al., 2011 (see link below).
With the advent of next-generation sequencing and readily available genome sequences, Ron remained a steadfast user of Lasergene. He utilized the software for tasks ranging from polymorphism screening to developing in-house diagnostic genotyping methods and conducting comparative analyses of mitochondrial genomes.
Ron retired in 2024, but his dedication to scientific inquiry is evident in his decision to continue using Lasergene in retirement. He remains eager to explore and analyze the vast and ever-growing expanse of sequence data. For Ron, science is a lifelong pursuit, a journey of continuous learning and discovery. You can visit Ron’s new blog at Bird Brain Genetics.
Ron Okimoto’s selected publications
Kerje S, Sharma P, Gunnarsson U, Kim H, Bagchi S, Fredriksson R, Schütz K, Jensen P, von Heijne G, Okimoto R, Andersson L. The dominant white, dun and smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene. Genetics, Volume 168, Issue 3, 1 November 2004, Pages 1507–1518, https://doi.org/10.1534/genetics.104.027995. Sequence data from this article were deposited with the EMBL/GenBank Data Libraries under accession nos. AY636124, AY636125, AY636126, AY636127, AY636128, AY636129.
Groenen MA, Megens HJ, Zare Y. et al. The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12, 274, 2011. https://doi.org/10.1186/1471-2164-12-274.
Andersson L, Bed’hom B, Chuong C-M, Inaba M, Okimoto R, and Tixier-Boichard M. 2020. Chapter 3, The genetic basis for pigmentation phenotypes. In. Advances in poultry genetics and genomics. Edited by Aggrey, S.E., Zhou, H. Tixier-Boichard, M., and Rhoads, D.D.. Burleigh Dodds publishing.
We at DNASTAR salute Ron for his important scientific achievements and his loyalty to Lasergene software over three decades.
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