Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.)

Abstract

Plant disease resistance genes (R-genes) play a critical role in the defense response to pathogens. Barley is one of the most important cereal crops, having a genome recently made available, for which the diversity and evolution of R-genes are not well understood. The main objectives of this research were to conduct a genome-wide identification of barley Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) genes and elucidate their evolutionary history. We employed a Hidden Markov Model using 52 Arabidopsis thaliana CNL reference sequences and analyzed for phylogenetic relationships, structural variation, and gene clustering. We identified 175 barley CNL genes nested into three clades, showing (a) evidence of an expansion of the CNL-C clade, primarily due to tandem duplications; (b) very few members of clade CNL-A and CNL-B; and (c) a complete absence of clade CNL-D. Our results also showed that several of the previously identified mildew locus A (MLA) genes may be allelic variants of two barley CNL genes, MLOC_66581 and MLOC_10425, which respond to powdery mildew. Approximately 23% of the barley CNL genes formed 15 gene clusters located in the extra-pericentromeric regions on six of the seven chromosomes; more than half of the clustered genes were located on chromosomes 1H and 7H. Higher average numbers of exons and multiple splice variants in barley relative to those in Arabidopsis and rice may have contributed to a diversification of the CNL-C members. These results will help us understand the evolution of R-genes with potential implications for developing durable resistance in barley cultivars.

Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

“…We found a high frequency of leucine-rich repeat, NB-ARC, and serine/threonine-protein kinase-like genes as putative candidate genes in rust resistance QTL intervals of HEB-25. This finding is in agreement with the important role of those gene families, known as resistance gene analogs (RGAs), in various defence reactions of plants against pathogens [ 101 , 102 ]. Based on this study the definition of a single candidate gene responsible for the detected QTL effect is not feasible.…”

Genome-wide Identification of Disease Resistance Genes (R Genes) in Wheat

“…Therefore, proteins lacking CC or LRR domains may also contribute to resistance responses, especially those with additional domains that are involved in signaling (Baggs et al, 2017). The distribution of NBAC genes across wheat chromosomes concurs with previous studies in barley and foxtail millet, where R genes were also found in clusters in extrapericentromeric regions of chromosomes (Andersen et al, 2016;Andersen and Nepal, 2017). Unequal crossing over between chromosomes as a mechanism for duplication likely explains the formation of these clusters, which then allows for their diversification.…”

Pathogen‐inducible Ta‐Lr34res expression in heterologous barley confers disease resistance without negative pleiotropic effects

“…The combination of different resistance genes is generally considered to be a successful strategy to enhance resistance. In barley, a considerable number of resistance genes have been described (Andersen et al ., ; Seeholzer et al ., ). The most well‐known and cloned major barley resistance genes that act efficiently as single genes are Rpg1 and the Mla alleles (Brueggeman et al ., ; Chelkowski et al ., ).…”