The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC)_n, (AT)_n and (AG)_n, were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed N_A ranged from 2 to 12, with an average of 4.2. H_E/H_O ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.

mu是一种有用且新颖的家禽，但由于它们最近的驯化，其遗传改良尚未进展。谱系信息由于其复杂的复制系统（一妻多夫制）而难以记录。为了确定the中的亲子关系，必须开发基于多态性DNA标记的亲子鉴定。在这项研究中，我们通过QDD管线从下一代测序数据中分离了超过25,000个微卫星（简单序列重复，SSR）区域，并在日本养殖的e中开发了具有多态性的49个SSR标记。二核苷酸基序（AC）_n，（AT）_n和（AG）_n，是最常被检测到的，分别在10,167（38.55％），8,114（30.76％）和4,796（18.18％）重叠群中发现。在20个个体中鉴定了49个新的SSR标记，显示N _A在2到12之间，平均为4.2。^ h _É / ^ h _Ø范围从0.389 / 0.071到0.702 / 1.000，平均值为0.601 / 0.515。PIC值介于0.059至0.886之间，平均值为0.528，49个标记中的17个显示多态性高于0.500。使用12个标记对34个个体进行基因分型，基于基因型的CERVUS模拟表明，以0.9995-1.0的概率鉴定了所有后代的父母。因此，开发了49种新颖的SSR标记和用于日本e的亲子鉴定的可靠方法。