Sang Van Le, Panoraia Alexandri, Julius H J van der Werf, Luisa Olmo, Stephen W Walkden-Brown, Sara de Las Heras-Saldana
{"title":"老挝本地山羊气候适应和生产性状相关候选基因的选择分析。","authors":"Sang Van Le, Panoraia Alexandri, Julius H J van der Werf, Luisa Olmo, Stephen W Walkden-Brown, Sara de Las Heras-Saldana","doi":"10.1111/jbg.70006","DOIUrl":null,"url":null,"abstract":"<p><p>Detecting selection footprints offers valuable insight into evolutionary processes and the mechanisms underlying phenotypic diversity in selected traits. Domestication, natural and artificial selection, and breeding have produced indigenous goats well-adapted to their local environments, making them crucial genetic resources. Understanding the genetic foundation of these adaptations can guide the development of effective breeding strategies to preserve and improve local goat breeds. This study investigated selection signatures in Lao native goats using Illumina's Goat SNP50 BeadChip, analysing 420 Lao native goats, 87 goats from three Chinese breeds, and 51 Teddi goats from Pakistan as test populations. We applied the de-correlation composite multiple signals (DCMS) method, incorporating p values from nine statistical tests, including runs of homozygosity in the Lao goat population, and fixation index and cross-population extended haplotype homozygosity between Lao goats and test populations. Significant genomic regions were identified using a 0.05 threshold adjusted for multiple testing. Our results uncovered 24 genomic regions harbouring 68 unique-coding genes. Analysis revealed both annotated and novel candidate genes linked to a variety of characteristics, including adaptation to the tropical monsoon climate (e.g., ABHD6, GATA4 and MSRA) and economic traits like growth and status (e.g., CNTNAP5, FAM135B and GATA4), reproduction (e.g., NPHP3, ARSJ and GATA4), milk production (e.g., MRPL32, PRSS51 and EPHA7), and carcass characteristics (e.g., GNAI1, SOX7 and FAM135B). These results offered insightful information about genetic mechanisms driving economic traits and tropical climate adaptation of Lao native goats. Combining p values from various statistical tests into a single DCMS framework effectively assists in selecting and prioritising candidate genes for further analysis.</p>","PeriodicalId":54885,"journal":{"name":"Journal of Animal Breeding and Genetics","volume":" ","pages":""},"PeriodicalIF":1.9000,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Signature of Selection Analysis Reveals Candidate Genes Related to Climate Adaptation and Production Traits in Lao Native Goats.\",\"authors\":\"Sang Van Le, Panoraia Alexandri, Julius H J van der Werf, Luisa Olmo, Stephen W Walkden-Brown, Sara de Las Heras-Saldana\",\"doi\":\"10.1111/jbg.70006\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Detecting selection footprints offers valuable insight into evolutionary processes and the mechanisms underlying phenotypic diversity in selected traits. Domestication, natural and artificial selection, and breeding have produced indigenous goats well-adapted to their local environments, making them crucial genetic resources. Understanding the genetic foundation of these adaptations can guide the development of effective breeding strategies to preserve and improve local goat breeds. This study investigated selection signatures in Lao native goats using Illumina's Goat SNP50 BeadChip, analysing 420 Lao native goats, 87 goats from three Chinese breeds, and 51 Teddi goats from Pakistan as test populations. We applied the de-correlation composite multiple signals (DCMS) method, incorporating p values from nine statistical tests, including runs of homozygosity in the Lao goat population, and fixation index and cross-population extended haplotype homozygosity between Lao goats and test populations. Significant genomic regions were identified using a 0.05 threshold adjusted for multiple testing. Our results uncovered 24 genomic regions harbouring 68 unique-coding genes. Analysis revealed both annotated and novel candidate genes linked to a variety of characteristics, including adaptation to the tropical monsoon climate (e.g., ABHD6, GATA4 and MSRA) and economic traits like growth and status (e.g., CNTNAP5, FAM135B and GATA4), reproduction (e.g., NPHP3, ARSJ and GATA4), milk production (e.g., MRPL32, PRSS51 and EPHA7), and carcass characteristics (e.g., GNAI1, SOX7 and FAM135B). These results offered insightful information about genetic mechanisms driving economic traits and tropical climate adaptation of Lao native goats. Combining p values from various statistical tests into a single DCMS framework effectively assists in selecting and prioritising candidate genes for further analysis.</p>\",\"PeriodicalId\":54885,\"journal\":{\"name\":\"Journal of Animal Breeding and Genetics\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2025-08-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Animal Breeding and Genetics\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1111/jbg.70006\",\"RegionNum\":3,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"AGRICULTURE, DAIRY & ANIMAL SCIENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Animal Breeding and Genetics","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1111/jbg.70006","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"AGRICULTURE, DAIRY & ANIMAL SCIENCE","Score":null,"Total":0}
Signature of Selection Analysis Reveals Candidate Genes Related to Climate Adaptation and Production Traits in Lao Native Goats.
Detecting selection footprints offers valuable insight into evolutionary processes and the mechanisms underlying phenotypic diversity in selected traits. Domestication, natural and artificial selection, and breeding have produced indigenous goats well-adapted to their local environments, making them crucial genetic resources. Understanding the genetic foundation of these adaptations can guide the development of effective breeding strategies to preserve and improve local goat breeds. This study investigated selection signatures in Lao native goats using Illumina's Goat SNP50 BeadChip, analysing 420 Lao native goats, 87 goats from three Chinese breeds, and 51 Teddi goats from Pakistan as test populations. We applied the de-correlation composite multiple signals (DCMS) method, incorporating p values from nine statistical tests, including runs of homozygosity in the Lao goat population, and fixation index and cross-population extended haplotype homozygosity between Lao goats and test populations. Significant genomic regions were identified using a 0.05 threshold adjusted for multiple testing. Our results uncovered 24 genomic regions harbouring 68 unique-coding genes. Analysis revealed both annotated and novel candidate genes linked to a variety of characteristics, including adaptation to the tropical monsoon climate (e.g., ABHD6, GATA4 and MSRA) and economic traits like growth and status (e.g., CNTNAP5, FAM135B and GATA4), reproduction (e.g., NPHP3, ARSJ and GATA4), milk production (e.g., MRPL32, PRSS51 and EPHA7), and carcass characteristics (e.g., GNAI1, SOX7 and FAM135B). These results offered insightful information about genetic mechanisms driving economic traits and tropical climate adaptation of Lao native goats. Combining p values from various statistical tests into a single DCMS framework effectively assists in selecting and prioritising candidate genes for further analysis.
期刊介绍:
The Journal of Animal Breeding and Genetics publishes original articles by international scientists on genomic selection, and any other topic related to breeding programmes, selection, quantitative genetic, genomics, diversity and evolution of domestic animals. Researchers, teachers, and the animal breeding industry will find the reports of interest. Book reviews appear in many issues.