Abstract:

In the process of regional test and approval of new rice varieties at all levels in China, the consistency of the varieties over testing years and the differences between testing varieties and already approved varieties are mainly judged according to the “Protocol for identification of rice varieties-SSR marker method”. Since the study of rice genome was still in its infancy, the development of these SSR markers was mainly determined based on the results of polymorphism analysis of limited rice varieties, hence there is a lack of sufficient understanding of the 48 SSR markers in terms of their validity and scientific soundness as the basis for distinguishing varieties.This study pinpointed the specific locations of these 48 SSR markers in the rice genome through primer sequence alignment analysis, aiming to explore the distribution patterns of these SSR markers on the rice genome and assess the potential biological effects of their variations. We amplified the public genome assembly data using SSR marker primers and determined the polymorphism of these markers in the indica and japonica rice subspecies groups by analyzing the amplified sequences. The results showed that these 48 markers were unevenly distributed across the 12 chromosomes of rice. Of these, 35 markers were located within genes or within 2.0 kb upstream or downstream of genes, and 3 markers were directly located in the exon regions of genes. However, it is noteworthy that the increase or decrease in SSR repeat units did not lead to frameshift mutations. Among the 193 Asian representative cultivated rice varieties analyzed, 3 markers showed no polymorphism in the japonica group (including 58 varieties), with a polymorphism information content (PIC) of 0; another 8 markers had very low polymorphism in the japonica group (PIC<0.25). Similarly, in the indica group (including 135 varieties), 5 markers also had very low polymorphism (PIC<0.25). In addition to repeat units, single nucleotide variations, as well as insertions and deletions, were observed within the amplified segments. This study not only revealed the genomic characteristics of these 48 SSR markers but also clearly pointed out that a few SSR markers still lack sufficient variety identification capability in representative populations. At the same time, we discovered nucleotide variations beyond the internal repeat sequences of SSR markers, which provides important directions and insights for optimizing existing SSR markers, developing new SSR markers for rice variety identification, and scientifically understanding the limitations of existing SSR markers in variety differentiation.

Key words: rice, SSR markers, genomic characteristics, polymorphisms, variety regional test, variety approval

摘要：

在我国各级水稻新品种区域试验和审定流程中，主要依据《水稻品种鉴定技术规程 SSR标记法》判别参试品种在试验周期内的一致性及其与已审定品种的差异性。鉴于SSR（简单重复序列）标记开发初期，水稻基因组学研究尚处于起步阶段，这些标记主要基于有限品种的SSR多态性分析结果来确定，因此对于采用该48个SSR作为品种区分依据的有效性和科学性，实际上缺乏足够的认识。本研究通过引物序列比对分析，精确定位了这48个SSR标记在水稻基因组中的具体位置，旨在探讨这些SSR标记在水稻基因组上的分布特征，并评估其变异可能引发的生物学效应。我们利用SSR标记引物对公共基因组组装数据进行扩增，并分析扩增序列标记，测定了这些标记在籼、粳亚种群体中的多态性。结果表明，这48个标记在水稻的12条染色体上呈不均匀分布。其中，35个标记位于基因内部或上下游2.0 kb内，3个标记位于基因的外显子区，但SSR重复单元的增减并未导致移码突变的发生。在分析的193份亚洲代表性栽培稻品种中，有3个标记在粳稻群体（58个品种）中未表现出多态性，多态性信息含量（PIC）为0，另有8个标记在粳稻群体中的多态性低（PIC<0.25）；同样，在籼稻群体（135个品种）中，也有5个标记多态性低（PIC<0.25）。此外，在扩增区段内，除重复单元外，还观察到了单核苷酸变异以及插入、缺失变异。本研究不仅揭示了这48个SSR标记的基因组学特征，还明确指出，在代表性群体中，少数SSR标记仍缺乏足够的品种鉴别能力，同时，我们还发现了SSR标记内部重复序列外的核苷酸变异，这为优化现有SSR标记开发新的水稻品种鉴定SSR标记，以及科学认识现有SSR标记在品种鉴别中的局限性提供了重要方向和启示。

关键词: 水稻, SSR标记, 基因组特征, 多态性, 品种区试, 品种审定