Evolution of NLR genes in genus Arachis reveals asymmetric expansion of NLRome in wild and domesticated tetraploid species

Abstract

AbstractArachis hypogaeais an allotetraploid crop widely grown in the world. Wild relatives of genusArachisare the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genusArachisand performed their comparative genomics among four diploids (A. duranensis,A. ipaensis,A. cardenasii,A. stenosperma) and two tetraploid (wild:A. monticolaand domesticated:A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified fromA. cardenasii, A. stenospermaandA. duranensis,A. hypogaea, A. monticolaandA. ipaensisrespectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome ofA. monticolaexhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case ofA. hypogaeaprobably due to distinct natural and artificial selection pressure. In addition, diploid speciesA. cardenasiirevealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure.A. cardenasiiandA. monticolacan be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genusArachisto identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security.