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

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.

Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt

“…These results suggest that NBS-LRR genes are distributed non-randomly across all chromosomes, showing a clustered distribution. The enrichment of NBS-LRRs in corresponding genomic regions suggested that the evolution of resistance genes may involve tandem duplications of linked gene families, as reported by previous studies [8,30].…”

“…Furthermore, only 33.8% of the NBS-LRRs were identified as orthologs between V. montana and V. fordii . Despite the similarity in genomic features between the two species [ 2 , 29 ], this discrepancy in NBS-LRR counts suggests that they might have undergone gene gains or losses to adapt to distinct environments [ 30 , 48 ]. This divergence might also explain the contrasting susceptibility of V. fordii to Fusarium wilt and the resistance of V. montana to this disease [ 3 , 4 , 49 ].…”

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

“…Since then, many highly variable NLR gene loci that provide resistance to a variety of pathogens have been identified and isolated [11]. The release of high-throughput sequencing data enables genome-wide identification and analysis of NLR proteins [13,14] as well species-wide inventories of these proteins [8,15]. Release of the wheat reference genome (IWGSC RefSeq v1.0) [16] and mass resequencing data [17][18][19][20] have allowed us to identify the genome-wide repertoire of NLRs in wheat, determine their diversity in wheat relatives, and recover the diverse NLR gene pool through breeding and improvement of disease resistance in wheat.…”

PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

“…NBS-LRR family genes are involved in the response of the plant’s innate immune system to pathogen infection and play an important role in defense against pathogens ( 39 ). The NBS-LRR family in seven pear varieties’ genomes was identified and classified into different subfamilies and integrated into PearMODB ( Figure 8 ).…”