{"title":"巴西 Crioulo Lageano 的基因组特征：保护巴西地方牛种的启示。","authors":"Daiza Orth , Alexandre Floriani Ramos , Geraldo Magela Cortes Carvalho , Lucas Macedo Santos Basílio , Alexandre Rodrigues Caetano , Patrícia Ianella","doi":"10.1016/j.livsci.2024.105481","DOIUrl":null,"url":null,"abstract":"<div><p>Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (H<sub>E</sub> = 0.373) and observed (H<sub>O</sub> = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise F<sub>ST</sub> estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.</p></div>","PeriodicalId":18152,"journal":{"name":"Livestock Science","volume":"284 ","pages":"Article 105481"},"PeriodicalIF":1.8000,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed\",\"authors\":\"Daiza Orth , Alexandre Floriani Ramos , Geraldo Magela Cortes Carvalho , Lucas Macedo Santos Basílio , Alexandre Rodrigues Caetano , Patrícia Ianella\",\"doi\":\"10.1016/j.livsci.2024.105481\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (H<sub>E</sub> = 0.373) and observed (H<sub>O</sub> = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise F<sub>ST</sub> estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.</p></div>\",\"PeriodicalId\":18152,\"journal\":{\"name\":\"Livestock Science\",\"volume\":\"284 \",\"pages\":\"Article 105481\"},\"PeriodicalIF\":1.8000,\"publicationDate\":\"2024-05-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Livestock Science\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S187114132400088X\",\"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":"Livestock Science","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S187114132400088X","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}
引用次数: 0
摘要
Crioulo Lageano（CLAG）是巴西的一个金牛品种，传统上在位于巴西南部地区的圣卡塔琳娜州和巴拉那州的山区原生地饲养。本研究旨在分析该品种的遗传多样性和结构，为制定保护策略提供依据。研究人员对之前储存在巴西动物基因库（BAGB）中的精液和 DNA 样本，以及从巴西克鲁罗-拉加诺牛饲养者协会（ABCCL）注册的 8 个不同农场收集的样本，使用不同的 SNP 标记组（包含 50 K 至 777 K 标记）进行了基因分型。获得的平均预期（HE = 0.373）和观察（HO = 0.382）杂合性估计值表明，该品种存在较高的遗传变异性。分子方差分析（AMOVA）显示，只有 2.11% 的观察到的遗传变异可归因于分析种群之间的差异。获得的成对 FST 估计值介于 0.002 和 0.056 之间，证实了种群之间的分化程度较低。种群结构分析表明，研究种群之间存在亚结构，除其他因素外，这可能与动物是否有角有关。考虑到精液储存在 BGAB 的公牛和来自 8 个研究农场的样本集，有效种群规模（Ne）的估计值分别为 6 和 22，这表明该品种的 Ne 远远低于联合国粮农组织为保护家畜种群而建议的数值。通过对 CLAG 与该地区常规饲养的其他六个牛种和斑马牛种进行种群结构和混杂分析，发现了可能存在来自籼牛的未知引种的证据。所获得的结果为了解巴西 CLGA 品种的多样性和遗传结构提供了可靠的信息，并为制定有效的生产牛群遗传管理策略、通过收集种质丰富 BAGB 以及长期保护该品种提供了战略信息。
Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed
Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (HE = 0.373) and observed (HO = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise FST estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.
期刊介绍：
Livestock Science promotes the sound development of the livestock sector by publishing original, peer-reviewed research and review articles covering all aspects of this broad field. The journal welcomes submissions on the avant-garde areas of animal genetics, breeding, growth, reproduction, nutrition, physiology, and behaviour in addition to genetic resources, welfare, ethics, health, management and production systems. The high-quality content of this journal reflects the truly international nature of this broad area of research.
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