Diversity and evolution of Rp1 rust resistance genes in four maize lines

Abstract

This manuscript provides genome-level analysis of disease resistance genes in four maize lines, including studies of haplotype and resistance gene number as well as selection and recombination. The Rp1 locus of maize is a complex resistance gene (R-gene) cluster that confers race-specific resistance to Puccinia sorghi, the causal agent of common leaf rust. Rp1 NB-LRR disease resistance genes were isolated from two Rp1 haplotypes (HRp1-B and HRp1-M) and two maize inbred lines (B73 and H95). Sixty-one Rp1 genes were isolated from Rp1-B, Rp1-M, B73 and H95 with a PCR-based approach. The four maize lines carried from 12 to 19 Rp1 genes. From 4 to 9 of the identified Rp1 genes were transcribed in the four maize lines. The Rp1 gene nucleotide diversity was higher in HRp1-B and HRp1-M than in B73 and H95. Phylogenic analysis of 69 Rp1 genes revealed that the Rp1 genes maintained in HRp1-B, HRp1-M and H95 are evolving independently of each other, while Rp1 genes in B73 and HRp1-D appear more like each other than they do genes in the other lines. The results also revealed that the analysed Rp1 R-genes were under positive selection in HRp1-M and B73. Intragenic recombination was detected in Rp1 genes maintained in the four maize lines. This demonstrates that a genetic process that has the potential to generate new resistance genes with new specificities is active at the Rp1 locus in the four analysed maize lines and that the new resistance genes may act against newly arising pathogen races that become prevalent in the pathogen population.

Genome-wide scans of selection highlight the impact sof biotic and abiotic constraints in natural populations of the model grassBrachypodium distachyon

“…For two of these QTL regions on chromosomes 3 and 4, we found signs of positive selection and reduced haplotype diversity in the eastern cluster in the vicinity of the QTL peaks, but no sign of balancing selection. These results strongly indicate that positive selection is shaping rust resistance in B. distachyon natural populations, as suggested in other species (Dodds & Thrall, 2009; Chavan et al , 2015). On chromosome 3, our analysis identified a 16kb region spanned by an unknown protein and a serine/threonine phosphatase, a class of genes known for their role in defense response and stress signaling (País et al 2009; Durian et al 2016), to be putatively involved in resistance to rust.…”

Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

“…For two of these QTL regions on chromosomes 3 and 4, we found signs of positive selection and reduced haplotype diversity in the eastern cluster in the vicinity of the QTL peaks, but no sign of balancing selection. These results strongly indicate that positive selection is shaping rust resistance in B. distachyon natural populations, as suggested in other species (Dodds and Thrall, ; Chavan et al ., ). On chromosome 3, our analysis identified a 16‐kb region spanned by an unknown protein and a serine/threonine phosphatase, a class of genes known for their role in defense response and stress signaling (País et al ., ; Durian et al ., ), to be putatively involved in resistance to rust.…”

Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire

“…A plant genome may contain several hundred NLRs [16]. Many NLRs are under extreme diversifying selection, to the extent that two accessions from the same species can display significant NLR copy number and sequence variation, the result of the selection of new variants based on duplication, deletion, unequal crossing over and mutation [19–22]. In wheat, 15 R genes for resistance to wheat rusts and powdery mildew have been cloned that encode NLRs [23–34].…”