Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome

Microsatellites or simple sequence repeats (SSRs) are found in most organisms and play an important role in genomic organization and function. To characterize the abundance of SSRs (1-6 base-pairs [bp]) on the cattle Y chromsome, the relative frequency and density of perfect or uninterrupted SSRs based on the published Y chromosome sequence were examined. A total of 17,273 perfect SSRs were found, with total length of 324.78 kb, indicating that approximately 0.75% of the cattle Y chromosome sequence (43.30 Mb) comprises perfect SSRs, with an average length of 18.80 bp. The relative frequency and density were 398.92 loci/Mb and 7500.62 bp/Mb, respectively. The proportions of the six classes of perfect SSRs were highly variable on the cattle Y chromosome. Mononucleotide repeats had a total number of 8073 (46.74%) and an average length of 15.45 bp, and were the most abundant SSRs class, while the percentages of di-, tetra-, tri-, penta-, and hexa-nucleotide repeats were 22.86%, 11.98%, 11.58%, 6.65%, and 0.19%, respectively. Different classes of SSRs varied in their repeat number, with the highest being 42 for dinucleotides. Results reveal that repeat categories A, AC, AT, AAC, AGC, GTTT, CTTT, ATTT, and AACTG predominate on the Y chromosome. This study provides insight into the organization of cattle Y chromosome repetitive DNA, as well as information useful for developing more polymorphic cattle Y-chromosome-specific SSRs.微卫星（simple sequence repeats，SSRs）广泛存在于多数生物体内，在基因组组织与功能调控中发挥关键作用。为明确牛Y染色体上1~6碱基对（base-pairs，bp）的SSRs丰度特征，本研究基于已发表的牛Y染色体序列，对完美型（无中断）SSRs的相对频率与密度展开分析。本次分析共检出17273个完美型SSRs，总长度达324.78 kb，结果显示牛Y染色体序列（总长43.30 Mb）中约0.75%为完美型SSRs，平均长度为18.80 bp。其相对频率与密度分别为398.92 位点/Mb与7500.62 bp/Mb。牛Y染色体上6类完美型SSRs的占比差异显著：单核苷酸重复序列数量最多，共计8073个（占比46.74%），平均长度15.45 bp，为丰度最高的SSRs类别；二核苷酸、四核苷酸、三核苷酸、五核苷酸与六核苷酸重复序列的占比依次为22.86%、11.98%、11.58%、6.65%与0.19%。不同类别的SSRs其重复单元数存在差异，其中二核苷酸重复的最高重复次数达42次。研究发现，A、AC、AT、AAC、AGC、GTTT、CTTT、ATTT及AACTG等重复类别在牛Y染色体上占据主导地位。本研究为解析牛Y染色体重复DNA的组织模式提供了重要视角，同时可为开发多态性更优的牛Y染色体特异性SSRs提供参考依据。