Genetic diversity analysis reveals that geographical environment plays a more important role than rice cultivar in Villosiclava virens population selection

Abstract

Rice false smut caused by Villosiclava virens is an economically important disease of grains worldwide. The genetic diversity of 153 isolates from six fields located in Wuhan (WH), Yichang Wangjia (YCW), Yichang Yaohe (YCY), Huanggang (HG), Yangxin (YX), and Jingzhou (JZ) in Hubei province of China were phylogenetically analyzed to evaluate the influence of environments and rice cultivars on the V. virens populations. Isolates (43) from Wuhan were from two rice cultivars, Wanxian 98 and Huajing 952, while most of the other isolates from fields YCW, YCY, HG, YX, and JZ originated from different rice cultivars with different genetic backgrounds. Genetic diversity of isolates was analyzed using random amplified polymorphic DNA (RAPD) and single-nucleotide polymorphisms (SNP). The isolates from the same cultivars in Wuhan tended to group together, indicating that the cultivars had an important impact on the fungal population. The 110 isolates from individual fields tended to cluster according to geographical origin. The values of Nei's gene diversity (H) and Shannon's information index (I) showed that the genetic diversity among isolates was higher between than within geographical populations. Furthermore, mean genetic distance between groups (0.006) was higher than mean genetic distance within groups (0.0048) according to MEGA 5.2. The pairwise population fixation index (FST) values also showed significant genetic differentiation between most populations. Higher genetic similarity of isolates from individual fields but different rice cultivars suggested that the geographical factor played a more important role in the selection of V. virens isolates than rice cultivars. This information could be used to improve the management strategy for rice false smut by adjusting the cultivation measures, such as controlling fertilizer, water, and planting density, in the rice field to change the microenvironment.

FIG 1

Characteristics of four rice-growing areas in Hubei province. Yangxin and Huanggang are in the southeast hilly double-cropping rice area, Yichang and Jingzhou are in the northwest alpine single-cropping rice area, and Jianghan is in the plain single- and double-cropping rice areas. The template map, obtained from www.nipic.com (no. 272563773), was modified to show the different rice-cropping areas.

FIG 2

Dendrograms of RAPD and SNP analysis of 43 isolates collected from two rice cultivars (Wanxian 98 and Huajing 952) in one field of Huazhong Agricultural University. Isolates from the same cultivar tended to group together. (A) Dendrogram according to genetic distance by RAPD analysis. With 18 RAPD primers, 20 unambiguous bands were used to score 1 and 0 as presence and absence, respectively. (B) Dendrogram according to genetic distance by SNP analysis. The MP tree was inferred from the 1,730-bp combined DNA sequence data set. The numbers labeled at each node indicate the bootstrap percentages (n = 1000).

FIG 3

RAPD profiles of 24 Villosiclava virens isolates obtained with primer S385. M, DNA molecule size marker. The largest to smallest bands are 5.0, 3.0, 2.0, 1.0, 0.75, 0.5, 0.25, and 0.1 kb in length. Lanes 1 to 24 represent isolates JZ2, JZ9, JZ12-2011, JZ68-1, JZ71-1, YX15, YX17, YX21, YX37, YX49, YCW53, YCW81, YCW83, YCW117, YCW121, YCY201, YCY205, YCY207, YCY239, YCY247, HG67, HG68, HG93, and HG96, respectively.

FIG 4

Dendrogram constructed with the UPGMA clustering method for 110 isolates of V. virens based on 18 RAPD primers. Four groups were divided at 0.69 genetic distance level, and most isolates were grouped in group I and group II. Group I was composed of isolates from Yichang and Yangxin, and group II consisted of Huanggang, Jingzhou, and Yichang isolates.

FIG 5

Dendrograms from RAPD and SNP analysis of different geographic populations in Hubei province. (A) Dendrogram according to genetic distance by RAPD analysis. YCW and YCY populations were closely related, whereas the HG population was the most distant from other populations. (B) Dendrogram according to genetic distance by SNP analysis. YCW and YCY populations were closely related, whereas the HG and YX populations were distant from other populations.

FIG 6

Phylogeny of 110 isolates of V. virens. The MP tree was inferred from the 1,730-bp combined DNA sequences data set. The numbers labeled at each node indicate the bootstrap percentages (n = 1,000). Four genetic groups were generated; group I and group IV were the larger groups. Group I included isolates from Yangxin (YX), Huanggang (HG), and Jingzhou (JZ), while Yichang (YCY and YCW) isolates were most clustered in groups II and IV.

FIG 7

Principal component analysis (PCA) based on RAPD data for 110 individual isolates from five single fields in Hubei province. Individuals within the same population are marked using the same symbols. The first and second principal coordinates account for 22.76% and 15.66% of the variation, respectively. There was no clear separation among individuals from different populations, but isolates in the same populations tended to gather together.