Determination of Genetic Diversity in Chilo partellus, Busseola fusca, and Spodoptera frugiperda Infesting Sugarcane in Southern Malawi Using DNA Barcodes

Abstract

Sugarcane is one of the most valuable crops in the world. Native and exotic Lepidopteran stemborers significantly limit sugarcane production. However, the identity and genetic diversity of stemborers infesting sugarcane in Malawi is unknown. The main objectives for this study were to identify and determine genetic diversity in stemborers infesting sugarcane in Malawi. We conducted field surveys between June 2016 and March 2017 in the Lower Shire Valley district of Chikwawa and Nsanje, southern Malawi. Molecular identification was based amplification the partial cytochrome oxidase subunit I (COI) gene region. Phylogenetic trees for sequences were generated and published GenBank accessions for each species were constructed. We found that Malawi Busseola fusca (Lepidoptera: Noctuidae) specimens belonged to clade II, Spodoptera frugiperda sp. 1 (Lepidoptera: Noctuidae) and Chilo partellus (Lepidoptera: Crambidae) were infesting sugarcane. Interspecific divergence ranged from 8.7% to 15.3%. Intraspecific divergence was highest for B. fusca, 3.6%. There were eight haplotypes for B. fusca, three for S. frugiperda and three for C. partellus. The importance of accurate species identification and genetic diversity on stemborer management is presented.

Keywords: COI gene; Crambidae; Lepidoptera; Noctuidae; Sugarcane; population genetics.

Figure 1

Map of localities where Busseola fusca, Chilo partellus, and Spodoptera frugiperda were sampled in Chikwawa and Nsanje districts, southern Malawi.

Figure 2

Percent distribution of Busseola fusca, Chilo partellus, and Spodoptera frugiperda (based on morphological) collected from sugarcane fields in Chikwawa and Nsanje districts, southern Malawi (n = 217).

Figure 3

Phylogenetic tree inferred using the Maximum Likelihood (ML)) method of mtDNA CO1 region of Busseola fusca, Chilo partellus, and Spodoptera frugiperda sequences obtained from sugarcane fields in southern Malawi together with reference sequences from other African countries. (A) The tree is based on the Kimura 2-parameter method. (B) The tree is based on Tamura 3-parameter model with evolutionarily invariable (T92 + I). Both trees were resampled with 1000 bootstrap replicates. Bootstrap support values on the branches are given.

Figure 4

Phylogenetic tree inferred using the Neighbor-Joining (NJ) method of 11 mtDNA CO1 region of Busseola fusca sequences obtained from sugarcane fields in southern Malawi together with reference sequences from other African countries. The tree is based on the Kimura 2-parameter method. The tree was resampled with 1000 bootstrap replicates. Bootstrap support values on the branches are given.

Figure 5

Phylogenetic tree inferred using the Neighbor-Joining (NJ) method of 11 mtDNA CO1 region of Spodoptera frugiperda sequences obtained from sugarcane fields in southern Malawi together with reference sequences from other African countries. The tree is based on the Kimura 2-parameter method and 1000 bootstrap duplications.