Population Genetic Analysis of from Taro in Japan Using SSR Markers

Overview

Journal J Fungi (Basel)

Date 2023 Apr 28

PMID 37108846

Authors

Jing Zhang

Ayaka Hieno

Kayoko Otsubo

Wenzhuo Feng

Koji Kageyama

Affiliations

Soon will be listed here.

Abstract

is an important pathogen that causes great economic losses in taro production in tropical and subtropical regions, especially in Japan. Understanding the genetic variations in populations and their transmission patterns in Japan is essential for effective disease control. Here, the genetic diversity of 358 isolates, including 348 from Japan, 7 from China, and 3 from Indonesia, was assessed using 11 simple sequence repeat (SSR) primer pairs with high polymorphism. The phylogenetic tree of the SSR locus showed that the isolates from Japan could be divided into 14 groups, with group A being the dominant group. Among foreign isolates, only six from mainland China were similar to those from Japan and clustered in groups B and E. Analysis of molecular variance (AMOVA), principal components analysis (PCA), and cluster analysis (K = 3) results revealed a moderate level of genetic diversity, mainly within individuals. Populations showed high heterozygosity, a lack of regional differentiation, and frequent gene flow. Analysis of mating types and ploidy levels revealed that A2 and self-fertile (SF) A2 types and tetraploids were dominant across populations. Explanations and hypotheses for the results can provide more effective strategies for disease management of taro leaf blight.

References

Huang K, Wang T, Dunn D, Zhang P, Sun H, Li B . A generalized framework for AMOVA with multiple hierarchies and ploidies. Integr Zool. 2020; 16(1):33-52. DOI: 10.1111/1749-4877.12460. View

Morita Y, Tojo M . Modifications of PARP Medium Using Fluazinam, Miconazole, and Nystatin for Detection of Pythium spp. in Soil. Plant Dis. 2019; 91(12):1591-1599. DOI: 10.1094/PDIS-91-12-1591. View

Cockerham C . Analyses of gene frequencies. Genetics. 1973; 74(4):679-700. PMC: 1212983. DOI: 10.1093/genetics/74.4.679. View

Wan A, Chen X . Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010. Plant Dis. 2019; 98(11):1534-1542. DOI: 10.1094/PDIS-01-14-0071-RE. View

Afandi A, Murayama E, Yin-Ling , Hieno A, Suga H, Kageyama K . Population structures of the water-borne plant pathogen Phytopythium helicoides reveal its possible origins and transmission modes in Japan. PLoS One. 2018; 13(12):e0209667. PMC: 6306214. DOI: 10.1371/journal.pone.0209667. View

Benson G . Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1998; 27(2):573-80. PMC: 148217. DOI: 10.1093/nar/27.2.573. View

Clark L, Jasieniuk M . POLYSAT: an R package for polyploid microsatellite analysis. Mol Ecol Resour. 2011; 11(3):562-6. DOI: 10.1111/j.1755-0998.2011.02985.x. View

Carleson N, Fieland V, Scagel C, Weiland J, Grunwald N . Population Structure of on in Oregon Nurseries. Plant Dis. 2019; 103(8):1923-1930. DOI: 10.1094/PDIS-12-18-2187-RE. View

Bukhari T, Rana R, Hassan M, Naz F, Sajjad M . Genetic diversity and marker trait association for phytophthora resistance in chilli. Mol Biol Rep. 2022; 49(6):5717-5728. DOI: 10.1007/s11033-022-07635-3. View

10.

Clark L, Schreier A . Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables. Mol Ecol Resour. 2016; 17(5):1090-1103. DOI: 10.1111/1755-0998.12639. View

11.

McDonald B, Linde C . Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol. 2002; 40:349-79. DOI: 10.1146/annurev.phyto.40.120501.101443. View

12.

Singh K, Singh L, Parmar N, Kumar S, Nanjundan J, Singh G . Molecular characterization and genetic diversity analysis in Indian mustard (Brassica juncea L. Czern & Coss.) varieties using SSR markers. PLoS One. 2022; 17(8):e0272914. PMC: 9417036. DOI: 10.1371/journal.pone.0272914. View

13.

Fan G, Zou A, Wang X, Huang G, Tian J, Ma X . Polymorphic Microsatellite Development, Genetic Diversity, Population Differentiation and Sexual State of Phytophthora capsici on Commercial Peppers in Three Provinces of Southwest China. Appl Environ Microbiol. 2022; 88(23):e0161122. PMC: 9746301. DOI: 10.1128/aem.01611-22. View

14.

Galindo C, McIver L, McCormick J, Skinner M, Xie Y, Gelhausen R . Global microsatellite content distinguishes humans, primates, animals, and plants. Mol Biol Evol. 2009; 26(12):2809-19. PMC: 2782327. DOI: 10.1093/molbev/msp192. View

15.

Nath V, Senthil M, Hegde V, Jeeva M, Misra R, Veena S . Genetic diversity of Phytophthora colocasiae isolates in India based on AFLP analysis. 3 Biotech. 2017; 3(4):297-305. PMC: 3723864. DOI: 10.1007/s13205-012-0101-5. View

16.

Van de Peer Y, Ashman T, Soltis P, Soltis D . Polyploidy: an evolutionary and ecological force in stressful times. Plant Cell. 2021; 33(1):11-26. PMC: 8136868. DOI: 10.1093/plcell/koaa015. View

17.

Kreike C, van Eck H, Lebot V . Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific. Theor Appl Genet. 2004; 109(4):761-8. DOI: 10.1007/s00122-004-1691-z. View

18.

Zhang S, Ding J, Han Z, Chen S, Liu Y, He W . Development of SSR markers and genetic diversity analysis based on RAD-seq technology among Chinese populations of Daphnia magna. Mol Biol Rep. 2022; 49(6):4389-4397. DOI: 10.1007/s11033-022-07274-8. View

19.

Meng Y, Zhang Q, Ding W, Shan W . : a model oomycete plant pathogen. Mycology. 2014; 5(2):43-51. PMC: 4066925. DOI: 10.1080/21501203.2014.917734. View

20.

Slatkin M . A measure of population subdivision based on microsatellite allele frequencies. Genetics. 1995; 139(1):457-62. PMC: 1206343. DOI: 10.1093/genetics/139.1.457. View