Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale

Abstract

Secale cereale is an important crop in the Triticeae tribe of the Poaceae family, and it has unique agronomic characteristics and genome properties. It possesses resistance to many diseases and serves as an important resource for the breeding of other Triticeae crops. We performed a genome-wide study on S. cereale to identify the largest group of plant disease resistance genes (R genes), the nucleotide-binding site-leucine-rich repeat receptor (NBS-LRR) genes. In its genome, 582 NBS-LRR genes were identified, including one from the RNL subclass and 581 from the CNL subclass. The NBS-LRR gene number in the S. cereale genome is greater than that in barley and the diploid wheat genomes. S. cereale chromosome 4 contains the largest number of NBS-LRR genes among the seven chromosomes, which is different from the pattern in barley and the genomes B and D of wheat but similar to that in the genome A of wheat. Further synteny analysis suggests that more NBS-LRR genes on chromosome 4 have been inherited from a common ancestor by S. cereale and the wheat genome A than the wheat genomes B and D. Phylogenetic analysis revealed that at least 740 NBS-LRR lineages are present in the common ancestor of S. cereale, Hordeum vulgare and Triticum urartu. However, most of them have only been inherited by one or two species, with only 65 of them preserved in all three species. The S. cereale genome inherited 382 of these ancestral NBS-LRR lineages, but 120 of them have been lost in both H. vulgare and T. urartu. This study provides the full NBS-LRR profile of the S. cereale genome, which is a resource for S. cereale breeding and indicates that S. cereale can be an important material for the molecular breeding of other Triticeae crops.

Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica

“…For example, the ratios of CNL and TNL genes were nearly 1:2 in A. thaliana and potato and 1:3 in grape ( Meyers et al, 2003 ; Lozano et al, 2012 ; The Tomato Genome Consortium, 2012 ). Moreover, no TNL genes have been detected in many Gramineous, and only a minority of RNL genes have been found ( Cheng et al, 2012 ; The Tomato Genome Consortium, 2012 ; Li et al, 2021 ; Qian et al, 2021 ). However, in our study, the ratio of typical CNL and TNL was close to 1:1, with slight differences in the numbers of genes in the CNL (198) and TNL (136) subclasses.…”

“…A large amount of homology information is contained in syntenic chromosome blocks at the DNA level between related species ( Wang et al, 2012 ). Intra-species syntenic analysis could be used to confirm the homology of different chromosomes and analyze the duplication of regions or genes with multiple copies, while inter-species analysis could show genome homology ( Qian et al, 2021 ). The syntenic analysis of NLR genes in M. ruthenica revealed 23 NLR gene pairs located on syntenic chromosomal blocks associated with chromosomes 6 and 7, 3 and 8, and 4 and 7.…”

“…For example, Li et al (2021) identified NLR genes in barely, which contains one RNL and 468 CNL genes. Qian et al (2021) identified one RNL and 581 CNL genes in Secale cereale . Similarly, studies have reported no TNL subclass in monocotyledons, while both TNL and CNL subclasses have been found in dicotyledons, and RNL has been detected in angiosperms ( Andersen et al, 2018 ; Zhang et al, 2020 ).…”

“…Moreover, NLR genes existed before the differentiation of green plants and greatly amplified after plants occupied land ( Shao et al, 2019 ; Liu et al, 2021 ). The genetic diversity analysis of NLR genes based on whole-genome data has not only provided important resources for the exploration of functional disease-resistant genes but also has important value for molecular marker-assisted breeding in plants ( Qian et al, 2021 ). Many genes or resistance gene analogs (RGAs), such as Rpi-amr3i from Solanum americanum ( Witek et al, 2016 ), Sm1 from wheat ( Walkowiak et al, 2020 ), and SRC7 from soybean ( Yan et al, 2022 ), have been cloned by genome-wide NLR gene identification.…”

Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding

“…Rye chromosome 6R contained the highest number of predicted NBS-LRR genes than any other rye chromosomes ( Rabanus-Wallace et al., 2021 ). The 6RL distal region with homology to linkage group 7 region has accumulated NLR genes ( Qian et al., 2021 ). Several genes for rust and powdery mildew resistance genes were characterized in the NLR rich gene clusters in the telomeric regions of wheat group 7 chromosomes, such as Pm1 ( Hewitt et al., 2021 ).…”