背景:黑麦(SecalecerealeL.)是小麦遗传育种中使用最广泛的相关物种,通过远缘杂交将其染色体片段引入小麦基因组对于丰富小麦的遗传多样性至关重要。小麦基因组中黑麦染色质的快速准确检测对于远距离杂交具有重要意义。简单序列重复(SSR)在基因组中广泛分布,不同物种的SSR通常表现出物种特有的特征。
结果:在这项研究中,鉴定了黑麦中的全基因组SSR,并概述了它们的特点。总共选择了997,027个SSR,平均密度为115.97SSRs/Mb。各染色体上SSRs数目无显著差别。2R的SSR数量最高(15.29%),1R上的SSR数量最低(13.02%)。每条染色体上SSR的数量与染色体长度显着相关。SSR基序类型丰富,每种类型的SSR分布在黑麦的7条染色体上。单核苷酸简单序列重复(MNRs)的数量,二核苷酸简单序列重复(DNRs),三核苷酸简单序列重复(TNR)是最大的,占46.90%,18.37%,占总数的22.64%,分别。在MNR中,G/C重复数和10bp基序数最大,占MNR的26.24%和31.32%,分别。根据SSR序列,共设计了657对引物。PCR结果表明,119对引物具有黑麦特异性,可以有效检测小麦基因组中的黑麦染色质。此外,86对引物也可以检测一个或多个特定的黑麦染色体。
结论:这些结果为黑麦基因组进化研究和小麦分子育种奠定了基础。
BACKGROUND: Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.
RESULTS: In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.
CONCLUSIONS: These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.