Genome-wide identification and comparative analysis of resistance genes in Brassica juncea
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Genome-wide identification and comparative analysis of resistance genes in Brassica juncea Fabian Inturrisi & Philipp E. Bayer & Hua Yang & Soodeh Tirnaz & David Edwards & Jacqueline Batley
Received: 23 May 2019 / Accepted: 24 July 2020 # Springer Nature B.V. 2020
Abstract Disease resistance in Brassica juncea has been shown against several diseases including blackleg, white rust, hypocotyl rot, turnip mosaic virus, leaf blight, black rot, and Alternaria blight. The identification of disease resistance genes is important to develop elite cultivars, which can survive exposure to these diseases. The largest family of resistance genes are nucleotide-binding site leucine-rich repeat genes (NLRs) which are classified into two major subfamilies: toll/interleukin-1 receptor-NLR (TNL) and coiled-coilNLR (CNL) proteins. Here we present the first study of the genomic organization and evolutionary history of the NLR gene family in B. juncea, with comparative analysis to the diploid progenitors B. rapa and B. nigra. A total of 289 NLR genes were identified in B. juncea, with a ratio of 0.61:1 of TNL to non-TNL genes. The distribution of NLR genes was random and uneven, with chromosome A04 containing no NLR genes.
Domain structure analysis revealed that 24% of NLR genes are typical resistance genes containing all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. A total of 45% NLR genes were found to be physically clustered in the B. juncea genome. The NLR genes were analysed with OrthoFinder which showed that most physical clusters (63%) in B. juncea came from the same orthogroup. This study provides a valuable resource for the identification and characterization of candidate NLR genes for Brassica crop improvement. Keywords Nucleotide-binding site Leucine-rich repeat (NLR) . Toll/ interleukin-1 receptor (TIR) domain . Coiled-coil (CC) domain . Effector-triggered immunity (ETI) . Gene cluster . Gene duplication
Introduction Fabian Inturrisi and Philipp E. Bayer contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11032-020-01159-z) contains supplementary material, which is available to authorized users. F. Inturrisi : P. E. Bayer : H. Yang : S. Tirnaz : D. Edwards : J. Batley (*) School of Biological Sciences, University of Western Australia, Perth, WA, Australia e-mail: [email protected] H. Yang School of Agriculture and Food Science, University of Queensland, Brisbane, Queensland, Australia
Brassicas, part of the Brassicaceae, are a globally important crop species which generate high economic and export value, such as edible oils, protein meal, vegetables, condiments and biofuels (Moser et al. 2015; Wilkes et al. 2013). U (1935) explained the evolutionary relationship of the main cultivated Brassicas, known as the ‘Triangle of U’, where the three allotetraploid species, B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC), were synthesized by interspecific hybridisation from the thre
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