Genome-wide SNPs reveal fine-scale population structure of Laodelphax
striatellus in China using double-digest restriction site-associated DNA
sequencing
Abstract
The small brown planthopper (SBPH), Laodelphax striatellus (Fallén)
(Hemiptera: Delphacidae) is a most destructive rice pest which has
caused serious economic losses in China. To effectively manage this
pest, we investigated genomic polymorphism, evaluated genetic divergence
and populations genetic structure of SBPH at 31 sampling sites in China
using a population genomics approach. In this study, we generated over
2,813,221,369 high-quality paired-end reads (413,689.55 Mb) across 306
individuals derived from double-digest restriction site-associated DNA
sequencing (ddRAD-seq), and 1925 reliable single nucleotides (SNPs) were
detected with an average sequencing depth of 13.99×. Overall, low levels
of genetic diversity and strong genetic differentiation among all of
populations were obtained (Global FST = 0.261). Neighbour-joining
dendrograms, Bayesian clustering methods, discriminant analysis of
principal components (DAPC) and principal component analysis (PCA)
revealed three genetically distinct groups: Southwestern group, Northern
group and Eastern group. Furthermore, we also observed a high degree of
admixture, widespread hybridization and gene flow among populations of
Northern China. A Mantel test indicated a pattern of
isolation-by-distance throughout China (r = 0.211, P = 0.031).
Neutrality test indicated SBPH has experienced a recent population
expansion. Accordingly, our results provide new insights into the
genetics of SBPH and thus contribute to develop effective management
strategies for this pest.