State key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
BMC Genomics. 2024 Aug 12;25(1):780. doi: 10.1186/s12864-024-10689-1.
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.
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.
These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.
黑麦(Secale cereale L.)是小麦遗传育种中应用最广泛的近缘物种,通过远缘杂交将其染色体片段导入小麦基因组对于丰富小麦的遗传多样性至关重要。快速准确地检测小麦基因组中的黑麦染色质对于远缘杂交非常重要。简单重复序列(SSR)广泛分布于基因组中,不同物种的 SSR 往往具有物种特异性特征。
本研究在全基因组范围内鉴定了黑麦 SSR,并概述了其特征。共筛选到 SSR 997027 个,平均密度为 115.97 SSR/Mb,各染色体 SSR 数量无显著差异。2R 上 SSR 数量最高(15.29%),1R 上 SSR 数量最低(13.02%)。各染色体上 SSR 数量与染色体长度呈显著正相关。SSR 基元类型丰富,每种 SSR 均分布在黑麦的 7 条染色体上。单核苷酸简单重复序列(MNRs)、二核苷酸简单重复序列(DNRs)和三核苷酸简单重复序列(TNRs)数量最多,分别占总数的 46.90%、18.37%和 22.64%。在 MNRs 中,G/C 重复数和 10 bp 基元数最多,分别占 MNRs 的 26.24%和 31.32%。基于 SSR 序列,共设计了 657 对引物。PCR 结果表明,其中 119 对引物为黑麦特异性引物,可有效检测小麦基因组中的黑麦染色质,且 86 对引物可同时检测到一个或多个特定的黑麦染色体。
这些结果为黑麦的基因组进化研究和小麦的分子育种奠定了基础。