Kushwaha Sandeep K, Åhman Inger, Bengtsson Therése
Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden.
Bioinformatics, National Institute of Animal Biotechnology, Hyderabad 500 032, India.
Bioinform Adv. 2021 Nov 11;1(1):vbab033. doi: 10.1093/bioadv/vbab033. eCollection 2021.
The discovery of novel resistance genes (R-genes) is an important component in disease resistance breeding. Nevertheless, R-gene identification from wild species and close relatives of plants is not only a difficult but also a cumbersome process. In this study, ResCap, a support vector machine-based high-throughput R-gene prediction and probe generation pipeline has been developed to generate probes from genomic datasets. ResCap contains two integral modules. The first module identifies the R-genes and R-gene like sequences under four categories containing different domains such as TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), Receptor-like kinase (RLK) and Receptor-like proteins (RLPs). The second module generates probes from extracted nucleotide sequences of resistance genes to conduct sequence capture (SeqCap) experiments. For the validation of ResCap pipeline, ResCap generated probes were synthesized and a sequence capture experiment was performed to capture expressed resistance genes among six spring barley genotypes. The developed ResCap pipeline in combination with the performed sequence capture experiment has shown to increase precision of R-gene identification while simultaneously allowing rapid gene validation including non-sequenced plants.
The ResCap pipeline is available at http://rescap.ltj.slu.se/ResCap/.
sandeep.kushwaha@slu.se or sandeep@niab.org.in.
Supplementary materials are available at online.
新型抗性基因（R基因）的发现是抗病育种的重要组成部分。然而，从植物的野生物种和近缘种中鉴定R基因不仅困难，而且过程繁琐。在本研究中，开发了ResCap，这是一种基于支持向量机的高通量R基因预测和探针生成流程，用于从基因组数据集中生成探针。ResCap包含两个完整模块。第一个模块在包含不同结构域的四类中识别R基因和类R基因序列，如TIR-NBS-LRR（TNL）、CC-NBS-LRR（CNL）、受体样激酶（RLK）和受体样蛋白（RLP）。第二个模块从提取的抗性基因核苷酸序列中生成探针，以进行序列捕获（SeqCap）实验。为了验证ResCap流程，合成了ResCap生成的探针，并进行了序列捕获实验，以捕获六种春大麦基因型中表达的抗性基因。所开发的ResCap流程与所进行的序列捕获实验相结合，已显示出提高了R基因鉴定的准确性，同时允许对包括未测序植物在内的基因进行快速验证。
ResCap流程可在http://rescap.ltj.slu.se/ResCap/获取。
sandeep.kushwaha@slu.se或sandeep@niab.org.in。
补充材料可在网上获取。
