Genomic analyses of fall armyworm (Spodoptera frugiperda) populations from Uganda using mitochondrial cytochrome oxidase subunit 1 and nuclear triose-phosphate isomerase (Tpi) genes

Abstract The fall armyworm (FAW), Spodoptera frugiperda; J.E. Smith (Lepidoptera: Noctuidae), has become a newly established economically important pest that causes huge losses to maize productivity in sub-Saharan Africa. In 2017, a survey was conducted to collect S. frugiperda specimens across 11 agro-ecological zones in Uganda. Cytochrome oxidase subunits 1 ( CO 1A and CO 1B) and triose-phosphate isomerase ( Tpi) partial gene segments of FAW were sequenced and subjected to comparative genomic analyses, to elucidate genetic identity, diversity and determine the existence of corn sub-haplotypes, distribution, and likely origin of invading populations. Results revealed the presence of both rice and corn strains (haplotypes h4 and h1), with rice strain being more predominant. The analyses of both mitochondrial and nuclear Tpi marker sequences showed that the FAW host strain haplotypes from Uganda were identical to those found in Florida, three Asian nations (China, India, and Pakistan) and Australia. A wide distribution of both strains was observed across all agro-ecological zones in Uganda. Comparative genomic analyses showed strain identification concordant results between CO 1A and CO 1B partial gene markers. Upon comparison with Tpi marker result, discordances in discrimination of FAW strains were observed. The study findings imply that Florida, China, India and Pakistan are possible centers of origin of invasion and support a possibility of multiple introductions into Uganda and the region. There is therefore a need for in-depth characterization of FAW populations in the region and other African nations to better understand its genetics and mechanisms of invasion.