Scientific Reports (Nov 2023)
Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance
- Vichayanee Pumpitakkul,
- Wanna Chetruengchai,
- Chalurmpon Srichomthong,
- Chureerat Phokaew,
- Wirulda Pootakham,
- Chutima Sonthirod,
- Wanapinun Nawae,
- Sissades Tongsima,
- Pongsakorn Wangkumhang,
- Alisa Wilantho,
- Yongchai Utara,
- Ampika Thongpakdee,
- Saowaphang Sanannu,
- Umaporn Maikaew,
- Suphattharaphonnaphan Khuntawee,
- Wirongrong Changpetch,
- Phairot Phromwat,
- Kacharin Raschasin,
- Phunyaphat Sarnkhaeveerakul,
- Pannawat Supapannachart,
- Wannapol Buthasane,
- Budhan S. Pukazhenthi,
- Klaus-Peter Koepfli,
- Prapat Suriyaphol,
- Sithichoke Tangphatsornruang,
- Gunnaporn Suriyaphol,
- Vorasuk Shotelersuk
Affiliations
- Vichayanee Pumpitakkul
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University
- Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University
- Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University
- Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Wanapinun Nawae
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Yongchai Utara
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute
- Ampika Thongpakdee
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute
- Saowaphang Sanannu
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute
- Umaporn Maikaew
- Khao Kheow Open Zoo, Zoological Park Organization of Thailand
- Suphattharaphonnaphan Khuntawee
- Ubon Ratchathani Zoo, Zoological Park Organization of Thailand, Ubon Ratchathani District
- Wirongrong Changpetch
- Nakhon Ratchasima Zoo, Zoological Park Organization of Thailand
- Phairot Phromwat
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation
- Kacharin Raschasin
- Chulabhorn Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation
- Phunyaphat Sarnkhaeveerakul
- Banglamung Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation
- Pannawat Supapannachart
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University
- Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University
- Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park
- Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park
- Prapat Suriyaphol
- Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University
- Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency
- Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University
- Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University
- DOI
- https://doi.org/10.1038/s41598-023-47014-x
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 17
Abstract
Abstract Eld’s deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld’s deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld’s deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status of 35 SED and 49 BED with limited pedigree information. The results show that these subspecies diverged approximately 1.26 million years ago. All SED were found to be purebred. A low proportion of admixed SED genetic material was observed in some BED individuals. Six potential breeders from male SED with no genetic relation to any female SED and three purebred male BED with no relation to more than 10 purebred female BED were identified. This study provides valuable insights about Eld’s deer populations and appropriate breeder selection in efforts to repopulate this endangered species while avoiding inbreeding.
