Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily

Abstract

The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70-80 million years ago during the Cretaceous period.

Genome-Wide Analysis of the WRKY Transcription Factor Family in Roses and Their Putative Role in Defence Signalling in the Rose–Blackspot Interaction

“…A comparative list of the sequences from both projects can be found in the Supplementary Materials (Supplement S5) . Differences in the annotation of the Rdr1 -TNL gene family in these two genomes have also been found previously [ 48 ], indicating that regional differences in the quality of the assemblies might also exist.…”

QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations

“…The first QTL, q BSD.TX2WOB-LG1.1, spanned 12.4 to 22.6 Mbp, was detected in CS 2016 and overlapped with q BSD.TX2WSE-LG1.1 (22.6–26.03 Mbp) in SV 2020. However, q BSD.TX2WOB-LG1.1 was localized closer to an Rdr1 homolog in that region [ 13 , 26 ] than q BSD.TX2WSE-LG1.1. The second LG1 QTL was discovered in CS 2016 ( q BSD.TX2WOB-LG1.2) and SV 2020 ( q BSD.TX2WSE-LG1.2), spanned 43.80–49.27 Mbp, and was also close to another region with Rdr1 homologs.…”

“…Rdr1 belongs to a large TIR-NBS-LRR (Toll/interleukin-1 receptor-nucleotide binding site-leucine rich repeat) (TNL) gene family that confers resistance to black spot. Rdr1 homologs have been found in three to four locations in LG 1 with two major clusters at the distal end of LG1 [ 26 ].…”

Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs

“…This has been recently done for MLO genes in various species, including soybean (Deshmukh et al 2014 ), Cicer arietinum and Medicago truncatula (Deshmukh et al 2017 ), Populus trichocarpa (Filiz and Vatansever 2018 ), pumpkin (Win et al 2018 ), lentil (Polanco et al 2018 ), bitter gourd (Chen et al 2021 ), for the promotor region of MLO genes in melon and other species (Andolfo et al 2019 ), and for other susceptibility genes (Pirrello et al 2021 ). In rose overviews have been generated for WRKY genes (Liu et al 2019 ), NBS-LRR genes (Lopez Arias et al 2020 ), the disease resistance gene family Rdr1 (Menz et al 2020 ), AP2/ERF transcription factors (Li et al 2021 ), and S-RNases and F-box genes involved in self-incompatibility (Vieira et al 2021 ). These inventories may be used as a basis to find or generate loss-of-function alleles of relevant MLO genes.…”