Genetic diversity, population structure and origin of the native goats in Central Laos

Le, Sang V; de las Heras-Saldana, Sara; Alexandri, Panoraia; Olmo, Luisa; Walkden-Brown, Stephen W; Van Der Werf, Julius H J

doi:10.1111/jbg.12862

Author(s)

Le, Sang V

de las Heras-Saldana, Sara

Alexandri, Panoraia

Olmo, Luisa

Walkden-Brown, Stephen W

Van Der Werf, Julius H J

Publication Date

2024

Abstract

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011–0.043) and negligible inbreeding coefficients (FIS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85Mb, with short ROH segments (1–5Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Citation

Journal of Animal Breeding and Genetics, 141(5), p. 531-549

ISSN

1439-0388

0931-2668

Link

https://hdl.handle.net/1959.11/59358

Language

en

Publisher

Wiley-Blackwell Verlag GmbH

Rights

Attribution-NonCommercial 4.0 International

Title

Genetic diversity, population structure and origin of the native goats in Central Laos

Type of document

Journal Article

Entity Type

Publication

Author(s)	Le, Sang V de las Heras-Saldana, Sara Alexandri, Panoraia Olmo, Luisa Walkden-Brown, Stephen W Van Der Werf, Julius H J
Publication Date	2024
Abstract	<p>Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (<i>F</i><sub>ST</sub>: 0.011–0.043) and negligible inbreeding coefficients (<i>F</i><sub>IS</sub>: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85Mb, with short ROH segments (1–5Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.</p>
Citation	Journal of Animal Breeding and Genetics, 141(5), p. 531-549
ISSN	1439-0388 0931-2668
Link	https://hdl.handle.net/1959.11/59358
Language	en
Publisher	Wiley-Blackwell Verlag GmbH
Rights	Attribution-NonCommercial 4.0 International
Title	Genetic diversity, population structure and origin of the native goats in Central Laos
Type of document	Journal Article
Entity Type	Publication

Genetic diversity, population structure and origin of the native goats in Central Laos

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