Fusarium Species and Fusarium oxysporum Species Complex Genotypes Associated With Yam Wilt in South-Central China

Abstract

Chinese yam (Dioscorea polystachya Thunb.) is an important root crop. Wilt caused by Fusarium is among the most important emerging diseases on yams. However, there is currently limited information on the molecular epidemiology of Fusarium causing yam wilt. Here, we investigated wilted yam samples from six regions in South-Central China. A total of 117 Fusarium isolates were obtained from diseased tissues of 37 wilted yam plants. These yam plants belonged to two varieties characterized by white and purple fleshy tubers, respectively. Analyses of ef1-α sequences identified that these 117 Fusarium isolates belonged to 11 putative species, with F. aff. commune being the most common (31.6%), followed by F. aff. cugenangense (29.1%), a potential undescribed species Fusarium aff. sp. (11.1%), F. aff. gossypinum (9.4%), F. aff. fujikuroi (8.5%), F. aff. nirenbergiae (6%), and one isolate each (0.85%) of F. aff. asiaticum, F. aff. curvatum, F. aff. odoratissimum, F. aff. solani, and F. aff. verticillioides. Six of these species were recently described as new species within the Fusarium oxysporum species complex (FOSC). Interestingly, 18 of the 37 yam plants were infected by two or more Fusarium species each and there was evidence for differential Fusarium species distributions based on geographic location and/or yam host variety. Multilocus microsatellite genotyping of the 67 FOSC isolates revealed that isolates of the same species from the same diseased plants often belonged to different genotypes. Interestingly, several FOSC microsatellite genotypes were shared among distinct geographic regions, consistent with long-distance dispersal. However, population genetic analyses revealed significant contributions of geographic separation to the overall genetic variation of FOSC with several pairs of geographic populations showing significant genetic differentiations, consistent with differential geographic distribution of the species within FOSC. The implications of our results to the managements of Fusarium wilt in yams were discussed.

Keywords: gene flow; geographic differentiation; host-pathogen association; multilocus microsatellite genotyping; multiple infections; yam (Dioscorea L.); yam wilt.

FIGURE 1

Phylogenetic relationships among our strains and those of the closely related Fusarium species based on ef1-α nucleotide sequences. (A) Relationships among our FOSC isolates and the representative sequences of 23 strains related to our strains. (B) Relationships among our remaining 50 Fusarium isolates with representative sequences of eight closely related Fusarium species. The names of species and type/epitype strains representing those closely related to our strains were from Lombard et al. (2019) and GenBank.

FIGURE 2

Symptoms on yam leaves inoculated with representative Fusarium isolates and negative controls 4 days after inoculation. (a) Negative control on white yam leaves; (b) F. aff. commune strain A62-W-JA; (c) F. aff. cugenangense strain A63-W-JA; (d) negative control on purple yam leaves; (e) F. aff. cugenangense strain A38-P-YC; (f) F. aff. fujikuroi strain A40-P-YC. For each leaf, the left side were inoculated two un-colonized PDA medium blocks with one on an injured site created by a cut with a sterile razor (top left) and another block on an intact site without any injury (bottom left). On the right side of each leaf, two PDA medium blocks colonized with Fusarium were inoculated, one on an injured site created by a cut with a sterile razor (top right) and another block on an intact site without any injury (bottom right). Scale bar = 2 cm.

FIGURE 3

Genetic relationships among 67 strains of FOSC isolated from yam plants with vascular wilt syndrome in six geographic regions in South-Central China. The isolate codes correspond to those in Table 3. W, yams with white tuber; P, yams with purple tuber. The last two letters correspond to their six geographic regions. The numbers in parenthesis refer to their SSR genotypes corresponding to those in Table 3. Different colors represent different species within FOSC identified based on their ef1-α nucleotide sequences as detailed in Lombard et al. (2019).

FIGURE 4

STRUCTURE results of the 67 FOSC isolates based on their genotypes at six simple sequence repeat marker loci. (A) Evidence of K = 2 as the optimal number of genetic clusters. (B) Genetic ancestry association for each of the 67 strains. The red and green represent genetic elements from these two distinct genetic clusters. The placement of individual FOSC strains into either cluster I or II is shown in Table 3.