DataSheet_5_Occurrence of simple sequence repeats in cDNA sequences of safflower (Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues.xlsx

Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional features of the SSR-containing genes to elucidate their role in biological and cellular processes. We identified 1,841 SSR regions in 1,667 cDNA sequences. Among all types of repeats, trinucleotide repeats were the most abundant (35.7%), followed by hexanucleotide (29.6%) and dinucleotide repeats (22.0%). Thirty five SSR primer pairs were validated by PCR reaction, detected a high rate of polymorphism (>57%) among safflower accessions, physically mapped on safflower genome and could clearly discriminate the cultivated accessions from wild relatives. The cDNA-derived SSR markers are suitable for evaluation of genetic diversity, linkage and association mapping studies and genome-based breeding programmes. Occurrence of SSR repeats in biologically-important classes of proteins such as kinases, transferases and transcription factors was inferred from functional analyses, which along with variability of their repeat copies, can endow the cell and whole organism the flexibility of facing with continuously changing environment, and indicate a structure-based evolution mechanism of the genome which acts as an up-to-dating tool for the cell and whole origanism, which is realized in GO terms such as involvement of most SSR-containing genes in biological, cellular and metabolic processes, especially in response to stimulus, response to stress, interaction to other organisms and defense responses.

红花（Carthamus tinctorius）是隶属于菊科（Asteraceae）的二倍体作物，因其籽油富含不饱和脂肪酸，作为重要油料作物之一而广为人知。近年来，其在食品、医药及工业领域的应用价值愈发受到重视，因此更新其育种方法迫在眉睫。基因内简单序列重复（simple sequence repeats, SSRs）除作为理想的分子标记外，还可调控基因功能及其对应的表型。本研究旨在从互补DNA（complementary DNA, cDNA）序列中鉴定SSRs，并进一步分析含SSRs基因的功能特征，以阐明其在生物学与细胞过程中的作用。本研究在1667条cDNA序列中共鉴定出1841个SSR位点。在各类重复序列中，三核苷酸重复占比最高（35.7%），其次为六核苷酸重复（29.6%）与二核苷酸重复（22.0%）。本研究设计的35对SSR引物经聚合酶链式反应（polymerase chain reaction, PCR）验证后，在红花种质中检测到超过57%的多态性率；这些引物可物理定位至红花基因组，并能清晰区分栽培种质与野生近缘种。基于cDNA开发的SSR标记适用于遗传多样性评估、连锁与关联定位研究以及基因组辅助育种项目。功能分析显示，激酶（kinases）、转移酶（transferases）及转录因子（transcription factors）等生物学功能关键蛋白类群中均存在SSR重复序列。这类重复及其拷贝数变异可赋予细胞乃至整个生物体应对持续变化环境的适应性，并揭示了一种基于基因组结构的进化机制——该机制可作为细胞与生物体的动态更新工具。基因本体（Gene Ontology, GO）注释结果表明，多数含SSRs的基因参与生物学过程、细胞过程与代谢过程，尤其在刺激响应、胁迫应答、生物互作及防御反应中发挥重要作用。