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ResCap: plant resistance gene prediction and probe generation pipeline for resistance gene sequence capture
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- Kushwaha, Sandeep Kumar (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding,Maulana Azad National Institute of Technology (MANIT)
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- Åhman, Inger (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding
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- Bengtsson, Therese (author)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för växtförädling,Department of Plant Breeding
- (creator_code:org_t)
- 2021-11-11
- 2021
- English.
- In: Bioinformatics Advances. - : Oxford University Press (OUP). - 2635-0041. ; 1
- Journal article (peer-reviewed)
Abstract
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- 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.
Subject headings
- LANTBRUKSVETENSKAPER -- Bioteknologi med applikationer på växter och djur -- Genetik och förädling inom lantbruksvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agricultural Biotechnology -- Genetics and Breeding in Agricultural Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
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