KMITL

Permanent URI for this communityhttps://dspace.kmitl.ac.th/handle/kmitl/1

Browse

Settings

Subject: search.filters.subject.population structure

Search Results

Now showing 1 - 3 of 3
  • Loading...
    Thumbnail Image
    Some of the metrics are blocked by your 
    consent settings
    Item type:Publication,
    Whole-Genome Sequencing Reveals SNP-Based Genetic Diversity and Population Structure of the Thai Rice Blast Fungus
    (2026-01-01)
    Longya, Apinya
    ;
    Suktrakul, Worrawit
    ;
    Suksirt, Mantira
    ;
    Korinsak, Siripar
    ;
    Pootakham, Wirulda
    Rice blast, caused by Magnaporthe oryzae, is a devastating disease threatening global rice production. While Southeast Asia is a centre of origin, the pathogen's population dynamics in Thailand are not well understood. We analysed whole-genome sequences from 191 M. oryzae isolates (60 from Thailand and 131 global) to investigate their genetic diversity, structure and pathogenicity. Phylogenomic analysis revealed that Thai isolates cluster with other Asian populations but exhibit greater within-population diversity, forming two major genetic clusters. We found that Thai rice isolates from rain-fed lowland and irrigated rice in the northeast and central regions cluster in World Group 3, while isolates from upland rice in northern Thailand cluster in World Group 1. This revised interpretation provides a more accurate representation of the population structure and highlights previously uncharacterised diversity. To link molecular data with phenotypes, we performed avirulence gene profiling and pathogenicity assays on 31 rice blast resistance near-isogenic lines. A correlation analysis showed a strong relationship for key gene pairs, including AvrPik and AvrPi9, highlighting their functional importance. In contrast, the correlation was low for Pii, Pizt and Pib due to the low frequency of their corresponding avirulence genes. The Avr-Pita interaction displayed a complex, haplotype-specific correlation. Our findings provide new insights into the genomic and pathogenic variation of M. oryzae in Thailand, establishing a robust link between avirulence gene profiles and observed pathogenicity phenotypes. This work offers a refined foundation for region-specific resistance breeding and disease management strategies.
      1
  • Loading...
    Thumbnail Image
    Some of the metrics are blocked by your 
    consent settings
    Item type:Publication,
    Genetic Divergence of Thai Indigenous Pigs from Three Distinct Geographic Regions Revealed by Microsatellite Marker Analysis
    (2023-02-01)
    Chaweewan, Kamon
    ;
    Mahinchai, Prapas
    ;
    Kongsook, Sornchai
    ;
    Soponchit, Surasak
    ;
    Weerasamith, Phuree
    Thai indigenous pigs (TIPs) are important genetic resources. Crosses with exotic pig breeds and wild boars may cause genetic losses. To date, the physical characteristics of TIPs have been inconsistent. The classification of TIPs by genetic information is needed to pursue an appropriate conservation program. In this study, the genetic diversity, cluster analysis, and phylogenetic relationship of TIPs were investigated using twenty-nine pig microsatellite markers. Blood samples were collected from TIPs from three regions of Thailand: north (NT, n = 118), northeast (NE, n = 61), and south (ST, n = 75). The mean total number of distinct alleles and the effective number of alleles per locus were 11.851 and 5.497, respectively. The mean observed heterozygosity (Ho) and mean expected heterozygosity (He) were 0.562 and 0.837, respectively. The F values of the microsatellite loci were positive under Hardy–Weinberg Equilibrium at p < 0.001, with overall mean values of Fis, Fit, and Fst of 0.247, 0.281, and 0.046, respectively. A total of 5, 5, and 17 private alleles were found at frequencies greater than 0.050 in the NT, NE, and ST pigs, respectively. Three optimal clusters (K = 3) were proposed within the TIP populations. Pigs from the NT and NE regions were mixed in two clusters, while members of the ST region were clearly separated. The phylogenetic tree confirmed that the pigs from NT and NE were each divided into two subgroups, while the pigs from ST were clustered into one group. A microsatellite analysis revealed the high genetic diversity of the TIP populations and confirmed the genetic divergence of the TIPs from the European and Chinese breeds. A genetic admixture of the TIP with the local wild boars was detected.
  • Loading...
    Thumbnail Image
    Some of the metrics are blocked by your 
    consent settings
    Item type:Publication,
    Iterative PCA for population structure analysis
    (2011-08-18)
    Limpiti, T.
    ;
    Intarapanich, A.
    ;
    Assawamakin, A.
    ;
    Wangkumhang, P.
    ;
    Tongsima, S.
    An extension of principal component analysis called ipPCA has been proposed earlier for analyzing structure in genetic data. This non-parametric framework iteratively classifies individuals into subpopulations. However, it is prone to false positives when dealing with large datasets and mixed-type genetic markers. We address these shortcomings by introducing a unified encoding scheme and suggesting a new terminating criterion for ipPCA. To validate the improvements, simulated datasets as well as real bovine and large human genetic datasets are analyzed. It is observed that the estimation of the number of subpopulations and the individual assignment accuracy have been improved. Furthermore, the structure resolved by this approach can be used to identify subset of individuals for further parametric population structure analysis. © 2011 IEEE.
      1