Developing a new genic SSR primer database for Vicia faba molecular breeding

Accelerating breeding programs require the use of efficient molecular tools and enhance the diversity of local faba bean cultivars. The aim of this study is to develop a new genetic database of available SSR primers, to classify these PCR primers according to the target genes and their respective cell processes, to assess the diversity and efficacy of the microsatellite markers applied to faba bean and to study the genetic structure of some selected faba bean cultivars. Approximately 75,605 and 148,196 previously published genomic and transcriptomic sequences were used to detect possible simple sequence repetitions in faba genomic content. The number of identified SSRs was 25502 and 12319, where the distribution to different repeat type classes shows that, the trinucleotide was the highest number of repeat counts followed by dinucleotide repeats. These genic SSR sequences were used to design 1091 PCR primers, out of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers target transcriptomic sequences. The annotation of gene-targeted SSRs has shown that approximately 897 genes are targeted through our designed SSR primers. About 1890 gene ontology (GO) identification code has been obtained. The GOs keywords distributed between distinct cell molecular features, where the highest amount of redundant sentences is the technical word, domain and molecular feature phrases with 554, 196 and 160 GOs, respectively. These GOs belong to the general level of gene ontology, such as molecular function, cellular component and biological process with 544, 670 and 676 GOs, respectively. Twenty-seven SSR PCR primers were synthesized to genotype 12 Egyptian faba bean genotypes. About 11 SSR gave from 1 to 2 PCR bands, other gave only one sharp band with polymorphic band size. The number of polymorphic primers was 13 primers. The polymorphic mean polymorphism information content was 0.3 which implies moderate informativeness.

加快蚕豆育种进程需依托高效分子工具，并提升本地蚕豆栽培品种的遗传多样性。本研究旨在构建一套涵盖可用简单序列重复（Simple Sequence Repeats, SSR）引物的新型遗传数据库，依据靶标基因及其对应的细胞生物学过程对这些聚合酶链式反应（Polymerase Chain Reaction, PCR）引物进行分类，评估用于蚕豆的微卫星标记的多样性与有效性，并解析部分选定蚕豆栽培品种的遗传结构。本研究利用已发表的75605条基因组序列与148196条转录组序列，对蚕豆基因组中的潜在简单序列重复位点进行检索。共检索到25502个基因组SSR位点与12319个转录组SSR位点；不同重复类型的分布结果显示，三核苷酸重复的数量最多，其次为二核苷酸重复。基于这些基因区SSR序列，本研究共设计了1091对PCR引物，其中238对（占比21.8%）靶向基因组序列，剩余853对靶向转录组序列。对靶标基因的SSR位点注释结果显示，本研究设计的SSR引物共靶向897个功能基因。共获得1890个基因本体（Gene Ontology, GO）注释编号。这些GO关键词分布于不同的细胞分子特征类别中，其中技术术语、结构域及分子特征短语类别的GO条目数量最多，分别为554、196和160条。这些GO条目隶属于基因本体的三大核心本体：分子功能、细胞组分与生物学过程，对应的GO条目数分别为544、670和676条。本研究合成27对SSR-PCR引物，对12份埃及蚕豆基因型进行基因分型。其中11对引物可扩增出1~2条PCR条带，其余引物仅能扩增出1条条带清晰且具有多态性的条带。其中具有多态性的引物共13对，其平均多态信息含量为0.3，表明该批引物具有中等信息量。