scholarly journals Cloning, Characterization, and Evolution of the NBS-LRR-Encoding Resistance Gene Analogue Family in Polyploid Cotton (Gossypium hirsutum L.)

2004 ◽  
Vol 17 (11) ◽  
pp. 1234-1241 ◽  
Author(s):  
Limei He ◽  
Chunguang Du ◽  
Lina Covaleda ◽  
Zhanyou Xu ◽  
A. Forest Robinson ◽  
...  
Keyword(s):  
Gene Family ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Index Analysis ◽  
Polymerase Chain ◽  
Encoding Gene ◽  
Plant Disease Resistance Genes ◽  
Encoding Genes ◽  
Selection Of

The nucleotide-binding site-leucine-rich repeat (NBS-LRR)-encoding gene family has attracted much research interest because approximately 75% of the plant disease resistance genes that have been cloned to date are from this gene family. We cloned the NBS-LRR-encoding genes from polyploid cotton by a polymerase chain reaction-based approach. A sample of 150 clones was selected from the NBS-LRR gene sequence library and was sequenced, and 61 resistance gene analogs (RGA) were identified. Sequence analysis revealed that RGA are abundant and highly diverged in the cotton genome and could be categorized into 10 distinct subfamilies based on the similarities of their nucleotide sequences. The numbers of members vary many fold among different subfamilies, and gene index analysis showed that each of the subfamilies is at a different stage of RGA family evolution. Genetic mapping of a selection of RGA indicates that the RGA reside on a limited number of the cotton chromosomes, with those from a single subfamily tending to cluster and two of the RGA loci being colocalized with the cotton bacterial blight resistance genes. The distribution of RGA between the two subgenomes A and D of cotton is uneven, with RGA being more abundant in the A subgenome than in the D subgenome. The data provide new insights into the organization and evolution of the NBS-LRR-encoding RGA family in polyploid plants.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 659-665 ◽  
Author(s):  
Evans S. Lagudah ◽  
Odile Moullet ◽  
Rudi Appels
Keyword(s):  
Disease Resistance ◽  
Gene Family ◽  
Binding Site ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Sequence ◽  
Nucleotide Binding ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Rich Region

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS – leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.Key words: cereal cyst nematode, disease resistance genes, nucleotide-binding site, leucine-rich repeat.

scholarly journals Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Manyi Sun ◽  
Mingyue Zhang ◽  
Jugpreet Singh ◽  
Bobo Song ◽  
Zikai Tang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Disease Resistance ◽  
Positive Selection ◽  
Gene Family ◽  
Selection Pressure ◽  
Black Spot ◽  
Orthologous Gene ◽  
European Pear ◽  
Encoding Gene ◽  
Encoding Genes

Abstract Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

Variability among members of the Hor-2 multigene family

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 397-403 ◽  
Author(s):  
Vladimir Kanazin ◽  
Evgeny Ananiev ◽  
Tom Blake
Keyword(s):  
Polymerase Chain Reaction ◽  
Gene Family ◽  
Storage Proteins ◽  
Gene Families ◽  
Reaction Sequence ◽  
Chain Reaction ◽  
Genes Encoding ◽  
Polymerase Chain ◽  
Encoding Gene ◽  
Barley Genotypes

The hordeins comprise the major prolamin storage proteins of barley. Two major and one minor gene families encode these alcohol-soluble proteins. The Hor-2 gene family encoding the B-hordeins has been estimated to contain 15–30 copies. Although several genes encoding B-hordeins have been cloned and sequenced, little is known about the mechanisms responsible for the generation of the enormous genetic variability at this locus. Polymerase chain reaction sequence amplification provided a simple technique that permitted the amplification of the Hor-2 gene family members from the genomes of several barley genotypes. Sequence analysis of clones permitted the identification of a region within the Hor-2 structural gene that appears to undergo recombinational and slippage-like gene conversion events. In this report we describe variability of the B-hordein genes, possible mechanisms responsible for it, and implications this may have on the evolution of prolamin-encoding gene families.Key words: barley, hordeins, polymerase chain reaction, polymorphism.

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