Genetic profiles and phenotypic patterns in Taiwanese Phalaenopsis orchids: a two-step phenotype and genotype strategy using modified genetic distance algorithms

Ya-Syuan Lai; Shu-Yun Chen; Yan-Jeng Wu; Wen-Huei Chen; Hong-Hwa Chen; Yung-Yu Lin; Te-Cheng Lin; Te-Ju Lin; Chung-Feng Kao

doi:10.3389/fpls.2024.1416886

Genetic profiles and phenotypic patterns in Taiwanese Phalaenopsis orchids: a two-step phenotype and genotype strategy using modified genetic distance algorithms

Front Plant Sci. 2024 Sep 11:15:1416886. doi: 10.3389/fpls.2024.1416886. eCollection 2024.

Authors

Ya-Syuan Lai^#¹, Shu-Yun Chen^#^{1

2}, Yan-Jeng Wu^{2

3}, Wen-Huei Chen², Hong-Hwa Chen^{2

3}, Yung-Yu Lin⁴, Te-Cheng Lin⁵, Te-Ju Lin⁵, Chung-Feng Kao^{1

2}

Affiliations

¹ Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.
² Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
³ Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
⁴ Research and Development Department, Brother Orchid Nursery Co., Ltd., Taichung, Taiwan.
⁵ Research and Development Department, Wonderorchids Co., Ltd., Taichung, Taiwan.

^# Contributed equally.

Abstract

This study establishes the first core collection (CC) for Taiwanese Phalaenopsis orchids to preserve genetic diversity and key traits essential for breeding and research, thereby enhancing breeding efficiency without the need for a large maintained parent population. We examined 207 commercial orchid cultivars from ten nurseries, characterized by two phenotypes and genotypic data from eight simple sequence repeat markers. Multiple imputation was applied to estimate missing phenotypes, minimizing potential uncertainties and ensuring the reliability of population structure analysis. Weighted k-means clustering identified seven distinct clusters, highlighting substantial genetic diversity. We proposed a two-step phenotype and genotype strategy and modified genetic distance algorithms to effectively preserve both phenotypic and genetic diversity while retaining key features. Consequently, 22 core accessions were selected, distributed across seven clusters, and representing the orchid germplasm collection. Our evaluation revealed significant diversity preservation, particularly in distinct characteristics and rare features, outperforming other methodologies. Pedigree background analysis further confirmed the representativeness of the CC in maintaining diverse genetic materials. We emphasized the importance of evaluating the CC by detailing the criteria and statistical analyses used to ensure the quality, representativeness, and effectiveness of the selected accessions. This study contributes to orchid breeding, conservation efforts, and sustainable agricultural practices by providing a valuable and comprehensive resource. In conclusion, our research establishes a groundbreaking CC, offering insights into the genetic landscape of Taiwanese Phalaenopsis orchids and highlighting potential advancements in breeding commercially desirable varieties.

Keywords: 2-step P+G strategy; Phalaenopsis orchids; core collection; diversity; germplasm; modified genetic distance.

Associated data

Dryad/10.5061/dryad.fn2z34v2z

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by grant NSTC 112-2313-B-005-019, NSTC 113-2313-B-005-038, and NSTC 112-2622-B-005-001 from National Science and Technology Council. This research was supported in part by Higher Education Sprout Project, Ministry of Education to the Headquarters of University Advancement at National Cheng Kung University (NCKU).