Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.)

Sequence conservation among resistance genes (R genes) was exploited to identify 47 R gene analogues (RGAs) from sugar beet (Beta vulgaris L.). Using degenerate primers, 11 RGAs were amplified from genomic DNA and 7 from leaf or beet cDNA. Twenty-nine were selected from an EST sequencing program. Twenty-one RGAs contained structures similar to the nucleotide binding site (NBS) leucine rich repeat (LRR) domain, a motif commonly found in several R genes. Among the remaining RGAs, 19 revealed similarity to the serine (threonine) protein kinase domain of R genes, 4 showed features related to the LRR region of the rice disease resistance gene Xa21, 1 RGA resembled the sugar beet nematode resistance gene Hs1pro-1, and 2 had homologies to other gene products associated with disease resistance. For 20 EST-derived RGAs, transcript levels were compared in leaf and root tissue revealing organ-specific transcription in 7 cases. Thirty-three RGAs were spread over all nine sugar beet chromosomes, except for a cluster of nine closely linked RGAs on chromosome 7. The analysis of linkage between RGAs and loci for rhizomania and Cercospora resistance identified alleles associated with resistance in both cases.Key words: RGA, Beta vulgaris, NBSLRR, genetic linkage map, molecular marker.

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Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽

10.1093/genetics/162.4.1961 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1961-1977

Author(s):

Michelle A Graham ◽

Laura Fredrick Marek ◽

Randy C Shoemaker

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Developmental Stages ◽

Gene Evolution ◽

Pcr Amplification ◽

Disease Resistance Genes ◽

Disease Resistance Gene ◽

R Genes ◽

Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

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Identification of a putative cation transporter gene from sugar beet (Beta vulgaris L.) by DDRT-PCR closely linked to the beet cyst nematode resistance gene Hs1pro-1

Plant Science ◽

10.1016/s0168-9452(03)00270-x ◽

2003 ◽

Vol 165 (4) ◽

pp. 777-784 ◽

Cited By ~ 3

Author(s):

Olaf Oberschmidt ◽

Florian M.W. Grundler ◽

Michael Kleine

Keyword(s):

Sugar Beet ◽

Resistance Gene ◽

Beta Vulgaris ◽

Nematode Resistance ◽

Cyst Nematode ◽

Transporter Gene ◽

Beet Cyst Nematode ◽

Nematode Resistance Gene

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Isolation, Sequence Analysis, and Linkage Mapping of Nucleotide Binding Site–Leucine-rich Repeat Disease Resistance Gene Analogs in Watermelon

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.134.6.649 ◽

2009 ◽

Vol 134 (6) ◽

pp. 649-657 ◽

Cited By ~ 8

Author(s):

Karen R. Harris ◽

W. Patrick Wechter ◽

Amnon Levi

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Linkage Mapping ◽

Citrullus Lanatus ◽

Nucleotide Binding ◽

Disease Resistance Gene ◽

Resistance Gene Analogs ◽

Leucine Rich Repeat ◽

Degenerate Primers ◽

Sequence Tagged Sites

Sixty-six watermelon (Citrullus lanatus var. lanatus) disease resistance gene analogs were cloned from ‘Calhoun Gray’, PI 296341, and PI 595203 using degenerate primers to select for the nucleotide binding sites (NBS) from the NBS–leucine-rich repeat (LRR) resistance gene family. After contig assembly, watermelon resistance gene analogs (WRGA) were identified and amino acid sequence alignment revealed that these groups contained motifs characteristic of NBS-LRR resistance genes. Using cluster analysis, eight groups of WRGA were identified and further characterized as having homology to Drosophila Toll and mammalian interleukin-1 receptor (TIR) and non-TIR domains. Three of these WRGA as well as three disease-related watermelon expressed sequence tag homologs were placed on a test-cross map. Linkage mapping placed the WRGA on linkage group XIII, an area on the watermelon map where resistance gene analogs cluster. In addition, these WRGA sequence-tagged sites (STS) were amplified from various genera of the Cucurbitaceae indicating that conservation of resistance gene analogs exists among cucurbits. These WRGA-STS markers may be useful in marker-assisted selection for the improvement for disease resistance in watermelon.

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Discovery of powdery mildew resistance gene candidates from Aegilops biuncialis chromosome 2Mb based on transcriptome sequencing

10.1101/698324 ◽

2019 ◽

Author(s):

Huanhuan Li ◽

Zhenjie Dong ◽

Chao Ma ◽

Xiubin Tian ◽

Zhiguo Xiang ◽

...

Keyword(s):

Molecular Markers ◽

Disease Resistance ◽

Powdery Mildew ◽

Resistance Gene ◽

Powdery Mildew Resistance ◽

Disease Resistance Gene ◽

R Genes ◽

Powdery Mildew Resistance Gene ◽

Mildew Resistance ◽

Resistance Gene Candidates

AbstractPowdery mildew is one of the most widespread diseases of wheat. Breeding resistant varieties by utilization of resistance genes is considered as the most economic and effective method of controlling this disease. Previous study showed that the gene(s) at 2Mb in Chinese Spring (CS)-Aegilops biuncialis 2Mb disomic addition line TA7733 conferred high resistance to powdery mildew. In this study, 15 Bgt isolates prevalent in different regions of China were used to further test the resistance spectrum of TA7733. As a result, TA7733 was high resistance to all tested isolates, indicating that the gene(s) on chromosome 2Mb was broad-spectrum powdery mildew resistance. In order to mine resistance gene candidates and develop 2Mb-specific molecular markers to assist the transfer resistance gene(s) at chromosome 2Mb, RNA-seq of TA7733 and CS was conducted before and after Bgt-infection, generating a total of 158,953 unigenes. Of which, 7,278 unigenes were TA7733-specific which were not expressed in CS, and 295 out of these 7,278 unigenes were annotated as R genes. Based on Blastn against with CS Ref Seq v1.0, 61 R genes were further mapped to homoeologous group 2. Analysis of R gene-specific molecular markers designed from R gene sequences verified 40 out of 61 R genes to be 2Mb specific. Annotation of these 40 R genes showed most genes encoded nucleotide binding leucine rich repeat (NLR) protein, being most likely resistance gene candidates. The broad-spectrum powdery mildew resistance gene(s), disease resistance gene candidates, and functional molecular markers of 2Mb-specific in present study will not only lay foundations for transferring disease resistance gene(s) from 2Mb to common wheat by inducing CS-Ae. biuncialis homoeologous recombination, but also provide useful candidates for isolating and cloning resistance gene(s) and dissecting molecular and genetic mechanisms of disease resistance from 2Mb.

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Isolation, Characterization and Phylogenetic Analysis of Nucleotide Binding Site-encoding Disease-resistance Gene Analogues from European Aspen (Populus tremula)

Silvae Genetica ◽

10.1515/sg-2010-0009 ◽

2010 ◽

Vol 59 (1-6) ◽

pp. 68-77 ◽

Cited By ~ 1

Author(s):

Yong Zhang ◽

Shougong Zhang ◽

Liwang Qi ◽

Tao Zhang ◽

Chunguo Wang ◽

...

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Gene ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Populus Tremula ◽

R Gene ◽

R Genes ◽

Degenerate Primers ◽

European Aspen

Abstract The majority of verified plant disease resistance genes (R genes) isolated to date was of the nucleotide binding site-leucine rich repeat (NBS-LRR) class. The conservation between different NBS-LRR R genes opens the avenue for the use of PCR based strategies in isolating and cloning other R gene family members or analogs (resistance gene analogue, RGA) using degenerate primers for these conserved regions. In this study, to better understand the R gene in European aspen (Populus tremula), a perennial tree, we used degenerate primers to amplify RGA sequences from European aspen. Cloning and sequence characterization identified 37 European aspen RGAs, which could be phylogenetically classified into seven subfamilies. Deduced amino acid sequences of European aspen RGAs showed strong identity, ranging from 30.41 to 46.63%, to toll interleukin receptor (TIR) R gene subfamily. BLAST searches with reference to the genomic sequence of P. trichocarpa found 209 highly homologous regions distributed in 28 genomic loci, suggesting the abundance and divergence of NBS-encoding R genes in European aspen genome. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, non-synonymous to synonymous nucleotide substitution (dN/dS) ratio were <1 for NBS domains of European aspen RGA, showing the evidence of purifying selection in this perennial tree. In further analysis, many intergenic exchanges were also detected among these RGAs, indicating a probable role in homogenising NBS domains. The present study permits insights into the origin, diversification, evolution and function of NBS-LRR R genes in perennial species like European aspen and will be useful for further R gene isolation and exploitation.

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Identification and characterization of NBS–LRR class resistance gene analogs in faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.)

Genome ◽

10.1139/g06-071 ◽

2006 ◽

Vol 49 (10) ◽

pp. 1227-1237 ◽

Cited By ~ 25

Author(s):

C. Palomino ◽

Z. Satovic ◽

J.I. Cubero ◽

A.M. Torres

Keyword(s):

Disease Resistance ◽

Amino Acid ◽

Resistance Gene ◽

Vicia Faba ◽

Cicer Arietinum ◽

Faba Bean ◽

Amino Acid Sequences ◽

Resistance Gene Analogs ◽

R Genes ◽

Degenerate Primers

A PCR approach with degenerate primers designed from conserved NBS–LRR (nucleotide binding site – leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from 5 faba bean (Vicia faba) lines and 2 chickpea (Cicer arietinum) accessions. Sixty-nine sequenced clones showed homologies to various R genes deposited in the GenBank database. The presence of internal kinase-2 and kinase-3a motifs in all the sequences isolated confirm that these clones correspond to NBS-containing genes. Using an amino-acid sequence identitiy of 70% as a threshold value, the clones were grouped into 10 classes of resistance-gene analogs (RGA01 to RGA10). The number of clones per class varied from 1 to 30. RGA classes 1, 6, 8, and 9 were comprised solely of clones isolated from faba bean, whereas classes 2, 3, 4, 5, and 7 included only chickpea clones. RGA10, showing a within-class identity of 99%, was the only class consisting of both faba bean and chickpea clones. A phylogenetic tree, based on the deduced amino-acid sequences of 12 representative clones from the 10 RGA classes and the NBS domains of 6 known R genes (I2 and Prf from tomato, RPP13 from Arabidopsis, Gro1–4 from potato, N from tobacco, L6 from flax), clearly indicated the separation between TIR (Toll/interleukin-1 receptor homology: Gro1–4, L6, N, RGA05 to RGA10)- and non-TIR (I2, Prf, RPP13, RGA01 to RGA04)-type NBS–LRR sequences. The development of suitable polymorphic markers based on cloned RGA sequences to be used in genetic mapping will facilitate the assessment of their potential linkage relationships with disease-resistance genes in faba bean and chickpea. This work is the first to report on faba bean RGAs.

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