Article

Breed classification of Lao People's Democratic Republic (Lao PDR) and Thai native chickens using synchrotron radiation-based Fourier transform infrared spectroscopy and genotyping by sequencing

Phannika KhoutsavangSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandRujjira BunnomSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandSaknarin PengsanthiaSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandPornchanok PhanhiranSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandSatoshi KubotaSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandDouangta DouangvilayNational Agriculture and Forestry Research Institute (NAFRI), Vientiane 01170, Lao PDRThongnoun PhonxaiyaNational Agriculture and Forestry Research Institute (NAFRI), Vientiane 01170, Lao PDRViengsavanh PhimphachanhvongsodForestry Research InstituteWittawat MoleeSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 ThailandKanjana ThumanuSynchrotron Light Research Institute, Nakhon Ratchasima 30000, ThailandAmonrat MoleeSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000 Thailand

2026en

ABI

Abstract

ABSTRACT Lao PDR harbors substantial genetic diversity in native chicken populations, representing an important resource for sustainable production and long-term food security. This study aimed to classify five Lao native chicken breeds—Ou, Black Bone, Horn Chou, Yolk, and Chae—and to discriminate them from a Thai native breed, Leung Hang Khao (LK), using integrative genotype-based approaches. Blood samples were collected from 50 LK and Lao native chickens (32 Ou, 10 Black Bone, 9 Horn Chou, 121 Yolk, and 41 Chae). Genomic DNA was extracted and analyzed using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) spectroscopy to characterize biochemical composition, while genotyping-by-sequencing (GBS) was employed to identify genome-wide single nucleotide polymorphisms (SNPs). SR-FTIR analysis revealed highly significant differences among breeds in nucleotide-associated functional groups, including thymine, adenine, guanine, cytosine, as well as DNA backbone and deoxyribose components (P < 0.001). Multivariate analyses demonstrated that principal component analysis (PCA) of SR-FTIR spectra effectively discriminated chicken breeds, while hierarchical cluster analysis (HCA) further resolved them into two major clusters with distinct sub-clusters, reflecting variation in DNA biochemical composition. In contrast, GBS analysis identified 1,484 common SNPs; however, PCA based on SNP data showed limited resolution in clearly separating breeds, despite revealing similar clustering trends. Overall, the results highlight the strong discriminatory power of SR-FTIR spectroscopy for rapid and effective classification of native chicken breeds at the molecular level, outperforming SNP-based differentiation under the current marker density. This study provides novel insights into the application of synchrotron-based spectroscopic techniques in poultry genetics and contributes valuable baseline information for the conservation and utilization of Lao native chicken genetic resources.

Identifiers

DOI: 10.1016/j.psj.2026.107456

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