Safaa Hosam M, Helal Mostafa, Yasser Seif, Raafat Zahra, Ayman Habiba, Mostafa Hasnaa, Bozhilova-Sakova Milena, Elsayed Dalia A A
Department of Biology, College of Science, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia.
Department of Animal Production, Faculty of Agriculture, Cairo University, Giza 12613, Egypt.
Animals (Basel). 2024 Dec 18;14(24):3659. doi: 10.3390/ani14243659.
This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chromosomes. There were no microsatellites detected in mitochondrial DNA. The highest relative microsatellite abundance was obtained for chromosome 19, followed by 13 and 6. The highest estimated SSR density was obtained for chromosome 14, and the lowest was for mitochondrial DNA, followed by chromosome 13. The polymorphism was 81.63% and 75.51% for Baladi and NZW rabbits, respectively. The number of detected alleles ranged between two and seven alleles/loci, and polymorphic information content was from 35% to 71%. The AMOVA analysis showed that the total variance of all levels of population structure was 15.734. The results definitely confirmed higher genetic diversity in Baladi compared with NZW rabbits.
本研究旨在利用计算机模拟方法对兔基因组中的微卫星进行特征分析，并开发和验证微卫星标记。从15只巴拉丁兔和18只新西兰白兔（NZW兔）采集血样。使用GMATA软件在提取的序列中定义简单序列重复（SSRs）。使用12对引物验证所鉴定的位点和所开发的引物。在所有染色体上检测到的微卫星位点总数为1,136,253个。双核苷酸微卫星重复占主导地位，在所有染色体中超过检测到的微卫星的88%。在线粒体DNA中未检测到微卫星。19号染色体的相对微卫星丰度最高，其次是13号和6号染色体。14号染色体的估计SSR密度最高，线粒体DNA的最低，其次是13号染色体。巴拉丁兔和NZW兔的多态性分别为81.63%和75.51%。检测到的等位基因数量在2至7个等位基因/位点之间，多态信息含量为35%至71%。方差分析（AMOVA）表明，所有种群结构水平的总方差为15.734。结果明确证实，与NZW兔相比，巴拉丁兔具有更高的遗传多样性。
