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. 2020 Apr 15;20(1):22.
doi: 10.1186/s12898-020-00293-8.

Genetic diversity and differentiation of populations of Chlorops oryzae (Diptera, Chloropidae)

Ailin Zhou  1 , Ping Tian  1 , Zhongcai Li  2 , Xinwen Li  3 , Xiaoping Tan  3 , Zhengbing Zhang  3 , Lin Qiu  1 , Hualiang He  1 , Wenbing Ding  1   4 , Youzhi Li  5   6
Affiliations

Genetic diversity and differentiation of populations of Chlorops oryzae (Diptera, Chloropidae)

Ailin Zhou et al. BMC Ecol. .

Abstract

Background: Chlorops oryzae is an important pest of rice crops. There have been frequent outbreaks of this pest in recent years and it has become the main rice pest in some regions. To elucidate the molecular mechanism of frequent C. oryzae outbreaks, we estimated the genetic diversity and genetic differentiation of 20 geographical populations based on a dataset of ISSR markers and COI sequences.

Results: ISSR data revealed a high level of genetic diversity among the 20 populations as measured by Shannon's information index (I), Nei's gene diversity (H), and the percentage of polymorphic bands (PPB). The mean coefficient of gene differentiation (Gst) was 0.0997, which indicates that only 9.97% genetic variation is between populations. The estimated gene flow (Nm) value was 4.5165, indicating a high level of gene flow and low, or medium, genetic differentiation among some populations. The results of a Mantel test revealed no significant correlation between genetic and geographic distance among populations, which means there is no evidence of significant genetic isolation by distance. An UPGMA (unweighted pair-group method with arithmetic averages) dendrogram based on genetic identity, did not indicate any major geographic structure for the 20 populations examined. mtDNA COI data indicates low nucleotide (0.0007) and haplotype diversity (0.36) in all populations. Fst values suggest that the 20 populations have low, or medium, levels of genetic differentiation. And the topology of a Neighbor-Joining tree suggests that there are no independent groups among the populations examined.

Conclusions: Our results suggest that C. oryzae populations have high genetic diversity at the species level. There is evidence of frequent gene flow and low, or medium, levels of genetic differentiation among some populations. There is no significant correlation between genetic and geographic distance among C. oryzae populations, and therefore no significant isolation by distance. All results are consistent with frequent gene exchange between populations, which could increase the genetic diversity, and hence, adaptability of C. oryzae, thereby promoting frequent outbreaks of this pest. Such knowledge may provide a scientific basis for predicting future outbreaks.

Keywords: Chlorops oryzae; Genetic differentiation; Genetic diversity; ISSR; Mitochondrial DNA.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Median-joining network based on the single gene of COI haplotypes. Each circle represents a haplotype, and the area of a circle is proportional to the number of individuals with that haplotype. Colors within nodes refer to C. oryzae sampling regions
Fig. 2
Fig. 2
Neighbor-joining tree (model Kimura-2 parameter) of the phylogenetic relationships among 20 C. oryzae populations based on COI gene variation (1000 bootstrap replicates)
Fig. 3
Fig. 3
Relationship between genetic distance and geographic distance of 20 C. oryzae populations
Fig. 4
Fig. 4
UPGMA dendrogram of 20 C. oryzae populations
Fig. 5
Fig. 5
Collection sites of populations. ZJ and GZ are populations from Zhejiang and Guizhou province, about 900 km and 810 km from Hunan province, respectively. They are not shown on the figure. The figure was created by Ailin Zhou
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