Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.

据信源自伊比利亚半岛和北非的同等品种在遗传上促进了巴西品种和生态型的形成。该国有许多品种和生态型的马和驴，但没有关于母体遗传多样性及其起源的广泛研究。这项研究报告了基于线粒体DNA控制区（D环）序列的巴西所有马和驴品种/生态型的首次遗传分析结果，其主要目的是表征这些动物的遗传变异。这些分析将有助于人们了解巴西目前饲养的马和驴的种群结构和品种/生态型的多样性。我们分析了310 D环代表马属和马属的41个品种/生态型的序列，包括14种本地马种/生态型，3种本地驴种/生态型和24种世界性马种。结果表明，该品种的遗传结构良好，它们包含不同的群体。分别确定了马和驴的80和14单倍型。大多数品种的马都有mtDNA单倍型，而驴的mtDNA单倍型似乎更符合群体。一些群体的繁殖距离低和/或单倍型/核苷酸多样性低，例如Lavradeiro，Criolo，Piquira和Percheron马和巴西驴。因此，必须针对每个人群设计具体的行动。不同水平的遗传多样性为适应群体的保护资源管理以及品种协会的交配方向提供了重要的信息。