Comparison and evolutionary analysis of <i>Brassica</i> nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

Zhang, Yueqi; Edwards, David; Batley, Jacqueline

doi:10.1002/tpg2.20060

Cited by 9 publications

(9 citation statements)

References 77 publications

(206 reference statements)

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“…None of the NAM line alleles appear to contain the functional Ht1 allele, but the comparatively high level of PAV at this unclustered locus once again points to high variability being indicative of functional NLR loci. These findings are in keeping with work in several other species, which has repeatedly pointed to the role of NLR clusters with high PAV in conferring disease resistance (Dolatabadian et al, 2020;Walkowiak et al, 2020;Zhang et al, 2021).…”

Section: Discussionsupporting

confidence: 90%

“…Cross-species comparisons within Brassica have shown that such complex NLR loci are subject to frequent birth and death events, with all members of some large NLR clusters showing high sequence homology to a singleton NLR of a closely related species (Fu et al, 2019;Zhang et al, 2021). More recently conducted pangenomic analyses have further shed light on the high level of intraspecies NLR diversity.…”

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confidence: 99%

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The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation, integrated domain diversity, and mobility

Thatcher

Jung

Panangipalli

et al. 2023

Molecular Plant Pathology

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Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease‐resistant varieties. We analysed the nucleotide‐binding leucine‐rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence–absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified.

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Section: Discussionsupporting

confidence: 90%

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confidence: 99%

The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation, integrated domain diversity, and mobility

Thatcher

Jung

Panangipalli

et al. 2023

Molecular Plant Pathology

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“…Species-specific NLR gene duplications and clustering patterns have been reported earlier (Dolatabadian et al ., 2020; Inturrisi et al ., 2020; Zhang et al ., 2021; Zhang et al ., 2016). In our study also, we find that NLR clusters in the B-genome of diploids and tetraploids are collinear, however, there are changes in the NLR gene content within these clusters.…”

Section: Discussionmentioning

confidence: 99%

A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

Paritosh

Rajarammohan

Yadava

et al. 2022

Preprint

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Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the Northeastern regions of Africa. Although it is grown in a limited manner, B. carinata is of value as it is resistant/highly tolerant to most of the pathogens affecting cultivated Brassica species of the U's triangle that are grown worldwide as oilseed and vegetable crops. We report a chromosome-scale genome assembly of B. carinata accession HC20 using long-read Oxford Nanopore and Illumina sequencing and BioNano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the available long-read genome assemblies of the six species of the U's triangle and found a highly conserved gene number and collinearity suggesting that B. juncea (AABB), B. napus (AACC), and B. carinata are strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire of B. carinata resulting in the identification of 465 NLRs. We investigated the extent and nature of early generation genomic interactions between the subgenomes of B. carinata and B. juncea in interspecific crosses between the two species. We found that C chromosome additions are well tolerated, with homoeologous exchanges occurring between the A and C genomes. Based on the genomic interactions, we propose strategies to utilize the interspecific crosses for transferring disease resistance from B. carinata to B. juncea and other Brassica species.

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“…Several candidate CR genes have been identified to encode NLR proteins in B. rapa (Hatakeyama et al, 2017(Hatakeyama et al, , 2022Huang et al, 2017;Matsumoto et al, 2012;Wang et al, 2022;Yang et al, 2022;Zhang et al, 2021). CRa and Crr1a were successfully iso- and CRA8.1b, and those three genes could be responsible for the clubroot resistance, the TIR-NBS-LRRs BraA08g039211E…”

Section: Club Root Re S Is Tan Cementioning

confidence: 99%

“…Due to the lack of CR genes in B. napus (canola, genome AACC) germplasm, the canola progenitor B. rapa (Chinese cabbage, genome AA) is considered as a major source in CR breeding (Huang et al, 2017 ; Yang et al, 2022 ). Several candidate CR genes have been identified to encode NLR proteins in B. rapa (Hatakeyama et al, 2017 , 2022 ; Huang et al, 2017 ; Matsumoto et al, 2012 ; Ueno et al, 2012 ; Wang et al, 2022 ; Yang et al, 2022 ; Zhang et al, 2021 ). CRa and Crr1a were successfully isolated and characterized from Chinese cabbage lines of B. rapa , and both confer resistance to clubroot and encode TNLs (Hatakeyama et al, 2013 ; Ueno et al, 2012 ).…”

Section: Clubroot Resistancementioning

confidence: 99%

The clubroot pathogen Plasmodiophora brassicae: A profile update

Schwelm

Zamani-Noor

Salih

et al. 2022

Molecular Plant Pathology

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Background Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide. Disease symptoms In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club‐shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients. Host range Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile. Taxonomy Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877). Distribution Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries. Pathotyping Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts. Effectors and resistance After the identification and characterization of the clubroot pathogen SABATH‐type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide‐binding (NB) site leucine‐rich‐repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date. Important Link Canola Council of Canada is constantly updating information about clubroot and P. brassicae as part of their Canola Encyclopedia: https://www.canolacouncil.org/canola-encyclopedia/diseases/clubroot/. Phytosanitary categorization PLADBR: EPPO A2 list; Annex designation 9E.

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Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding

Cited by 9 publications

References 77 publications

The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation, integrated domain diversity, and mobility

The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence–absence variation, integrated domain diversity, and mobility

A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)

The clubroot pathogen Plasmodiophora brassicae: A profile update

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