Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair

Cooperation between receptors from the NLR superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.

Fine Mapping and Distribution Analysis of Hybrid Necrosis Genes Ne1 and Ne2 in Wheat in China

Hybrid necrosis of wheat is caused by two dominant complementary genes Ne1 and Ne2 present in normal phenotype parents and is regarded as a barrier to gene flow between crop species. However, the necrosis alleles still occur at high frequency in modern wheat varieties. In this study, we constructed two high-density genetic maps of Ne1 and Ne2 in winter wheat. In these cultivars, Ne1 was found to be located in a span interval of 0.50 centimorgan (cM) on chromosome 5BL delimited by markers Nwu_5B_4137 and Nwu_5B_5114, while Ne2 co-segregated with markers Lseq102 and TC67744 on 2BS. Statistical analysis confirmed that the dosage effect of Ne alleles also existed in moderate and severe hybrid necrosis systems, and the symptoms of necrosis can also be affected by the genetic background. Furthermore, we clarified the discrete distribution and proportion of the Ne1 and Ne2 in China’s major wheat regions, and concluded that introduced modern cultivars directly affect the frequencies of necrosis genes in modern Chinese cultivars (lines), especially that of Ne2. Taking investigations in spring wheat together, we proposed that hybrid necrosis alleles could positively affect breeding owing to their linked excellent genes. Additionally, based on the pedigree, we speculated that the Ne1 and Ne2 in winter wheat may directly originate from wild emmer and introduced cultivars or hexaploid triticale, respectively.

Hybrid Necrosis of Wheat: Systematic Genetic Analysis, Fine Mapping, Distribution and Evolution in China

Hybrid necrosis of wheat is caused by two incompatible natural alleles Ne1 and Ne2 residing in normal phenotype parents. It was regarded as a barrier of gene flow between crop species. However, the necrosis alleles were still frequent in modern wheat varieties. Here, we constructed two high-density genetic maps of Ne1 and Ne2 in winter wheat. Of which, Ne1 locus was located in a span interval of 0.50 centimorgan (cM) on chromosome 5BL delimited by markers Nwu_5B_4137 and Nwu_5B_5114, while Ne2 co-segregated with markers Lseq102 and TC67744 on 2BS. Genetic allelic tests confirmed that the Ne1 allele in N9134 is different from that in Spcia and TA4152-60, while Ne2 allele in Zhoumai 22 (ZH22), Manitou, WL711 and Pan555 are also varied. The statistics substantiated that the dosage effect of Ne alleles also existed in moderate and severe hybrid-necrosis system, and the necrotic symptom may also be affected by genetic background. Furthermore, we clarified the discrete distribution and proportion of the Ne1 and Ne2 in China's major wheat regions, and concluded that introduced modern cultivars directly affect the frequencies of necrosis genes in modern Chinese cultivars (lines), especially that of Ne2. Taking investigation in spring wheat together, we proposed that hybrid necrotic alleles could positively affect breeding owing to their linked excellent genes. Additionally, based on the pedigree, we speculated the Ne1 and Ne2 in winter wheat may directly originate from wild emmer and rye, respectively. Overall, this study makes an important step toward better understanding hybrid necrosis in wheat.

Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair

Cooperation between receptors from the NLR superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.

Fine Mapping of Hybrid Necrosis Gene Ne1 in Common Wheat (Triticum Aestivum L.)

Hybrid necrosis is characterized as progressive chlorosis and necrosis of plant leaves, tillers or whole plants premature death in certain wheat hybrids, which is caused by the combination of two complementary loci Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. Hybrid necrosis s is a serious barrier for combining desirable traits from various genotypes of wheat and the full utilization of heterosis in wheat. In this study, we fine mapped Ne1 on chromosome 5BL, and finally delimited Ne1 to a 4.06-Mb region with large heterogeneous inbred families (HIFs) from the RILs of ‘Zhengnong 17’ × ‘Yangbaimai’. Further characterization of the near isogenic lines derived from HIFs confirmed that Ne1 was tightly linked with a 2.89-Mb fragment that is deleted in Zhengnong 17. Additionally, a diagnostic InDel marker 5B-InDel385 for Ne1 was developed and was used to assess the existence of Ne1 in a diverse panel of 501 wheat accessions. Among them, 122 (61%) out of 200 landraces showed the presence of Ne1 gene, whereas only 79 (26%) out of 301 modern cultivars carried the Ne1 gene. The drastic decrease of Ne1 frequency in modern cultivars indicates that the Ne1 has been subjected to heavily selection pressure. This study provides a good foundation for the marker-assisted selection, gene cloning and functional studies of Ne1 in wheat.

Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances

Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.