Abstract
BackgroundThe 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.ResultsIn 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.ConclusionProximal 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.
Highlights
The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections
Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes
These results indicated that the percentage of NBS-encoding genes derived from dispersed and proximal duplication were 27.81 and 28.11% in P. bretschneideri, and 20.15 and 40.05% in P. communis, respectively (Additional file 4)
Summary
The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Due to independent domestication under distinct geographical conditions, Asian and European pears display prominent differences in genetic and phenotypic diversity [2, 3]. The wild populations of these two pear groups have likely experienced unique disease pressures due to their completely different habitats. Independent domestications of Asian and European pear [3] might have intensified the selection on a few genomic regions that have relevance for the specific diseases associated with their cultivation habitats. Characterizing disease-related gene families can provide opportunities to understand the role of divergence and domestication in shaping host resistance responses in pear
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