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2025 Vol.37, Issue 4 Preview Page

Research Article

Molecular Characterization of Doubled Haploid Lines Informs Core SNP Panel Selection in Waxy Maize
Seung-Hyun Wang1*
,
Si-Hwan Ryu2
,
Min Namgung1
,
Jung-Heon Han1
,
Jae-Keun Choi1
,
Hee-Sun Noh1
,
Hye-Lim Choi1
,
Yong-Jin An2
1Research Scientist, Maize Research Institute, Gangwon Provincial Agricultural Research and Extension Services, Hongcheon 25160, Korea
2Senior Research Scientist, Maize Research Institute, Gangwon Provincial Agricultural Research and Extension Services, Hongcheon 25160, Korea
*Corresponding Author
31 December 2025. pp. 307-322
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Abstract

Doubled haploid (DH) technology accelerates the development of inbred lines but can also reduce genetic diversity and extend long-range linkage disequilibrium. We profiled 155 waxy maize lines encompassing DH groups, elite lines, and conventional inbreds using genome-wide SNPs to quantify population structure and to develop a practical core SNP panel. Linkage disequilibrium decay was summarized using in 50 kb distance bins up to 5 Mb, and population structure was assessed using Nei’s genetic distance, principal coordinate analysis (PCoA), and nearest-neighbor purity. Three core marker selection strategies were compared for core panels: Shannon-index-based selection, random sampling with genetic distance optimization, and genetic/physical map－balanced binning. Across the collection, nearest-neighbor purity reached 86.5%, far exceeding a randomized baseline of 23.5% ± 3.9%, supporting the presence of a well-defined group structure. Elite lines showed the highest diversity (He = 0.315; 1,432 group-specific alleles), whereas one DH set (18DHW) exhibited the lowest diversity across most indices. Random sampling with genetic distance optimization (RS) yielded a 21-SNP panel that achieved 99.98% pairwise discrimination among 155 lines, the SI method delivered a compact 10-SNP set maximizing diversity metrics, and binning produced 30/39/47-SNP panels providing uniform chromosomal coverage. Collectively, the results support a hybrid strategy—RS for maximal discrimination and bin-based markers for genome-wide coverage—as the most practical design for fingerprinting and core-collection development in maize breeding. The selected panel will be implemented in genotyping assays for cross-laboratory validation and transferability testing on external germplasm.

Keywords
Doubled haploid
Linkage disequilibrium
SNP panel
Waxy maize
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Information
  • Publisher :Agriculture and Life Sciences Research Institute, Kangwon National University
  • Publisher(Ko) :None
  • Journal Title :Journal of Agricultural, Life and Environmental Sciences
  • Volume : 37
  • No :4
  • Pages :307-322
  • Received Date : 2025-09-22
  • Revised Date : 2025-11-06
  • Accepted Date : 2025-11-14
  • DOI :https://doi.org/10.22698/jales.20250026
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