Functional Interactions Between Major Rice Blast Resistance Genes, Pi-ta and Pi-b, and Minor Blast Resistance Quantitative Trait Loci

Lesion mimic mutant 8 balances disease resistance and growth in rice

Lesion-mimic mutants (LMM) spontaneously produce necrotic spots, a process not affected by environmental stress or pathogen infection. In this study, we identified a LMM, lesion mimic mutant 8 (lmm8) in rice (Oryza sativa). The lmm8 mutant produces brown and off-white lesions on its leaves during the second- and third-leaf stages. The lesion mimic phenotype of the lmm8 mutant was enhanced by light. At the mature stage, lmm8 mutant are shorter and exhibit inferior agronomic traits than the wild type. Contents of photosynthetic pigments and chloroplast fluorescence were significantly reduced in lmm8 leaves, along with increased production of reactive oxygen species and programmed cell death compared to the wild type. The mutated gene was identified as LMM8 (LOC_Os01g18320) by map-based cloning. A point mutation occurred in LMM8, causing a Leu to Arg mutation of the 146th amino acid of LMM8. It is an allele of SPRL1, encoding a protoporphyrinogen IX oxidase (PPOX) located in chloroplasts and involved in the biosynthesis of tetrapyrrole in chloroplasts. The lmm8 mutant showed enhanced resistance and broad-spectrum resistance. Together, our results demonstrate the importance of rice LMM8 protein in defense responses and plant growth in rice, and provides theoretical support for resistance breeding to improve rice yield.

Mapping Blast Resistance Genes in Rice Varieties 'Minghui 63' and 'M-202'

Rice blast caused by the fungus Magnaporthe oryzae (syn. Magnaporthe grisea) is one of the most lethal diseases for sustainable rice production worldwide. Blast resistance mediated by major resistance genes is often broken down after a short period of deployment, while minor blast resistance genes, each providing a small effect on disease reactions, are more durable. In the present study, we first evaluated disease reactions of two rice breeding parents 'Minghui 63' and 'M-202' with 11 blast races, IA45, IB1, IB45, IB49, IB54, IC1, IC17, ID1, IE1, IG1, and IH1, commonly present in the United States, under greenhouse conditions using a category disease rating resembling infection types under field conditions. 'Minghui 63' exhibited differential resistance responses in comparison with those of 'M-202' to the tested blast races. A recombinant inbred line (RIL) population of 275 lines from a cross between 'Minghui 63' and 'M-202' was also evaluated with the above-mentioned blast races. The population was genotyped with 156 simple sequence repeat (SSR) and insertion and deletion (Indel) markers. A linkage map with a genetic distance of 1,022.84 cM was constructed using inclusive composite interval mapping (ICIM) software. A total of 10 resistance QTLs, eight from 'Minghui 63' and two from 'M-202', were identified. One major QTL, qBLAST2 on chromosome 2, was identified by seven races/isolates. The remaining nine minor resistance QTLs were mapped on chromosomes 1, 3, 6, 9, 10, 11, and 12. These findings provide useful genetic markers and resources to tag minor blast resistance genes for marker-assisted selection in rice breeding program and for further studies of underlying genes.

Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq

Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.

Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

BACKGROUND

As rice (Oryza sativa) is the staple food of more than half the world's population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles.

RESULTS

We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast.

CONCLUSIONS

The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.

Dissecting the genetic basis of wheat blast resistance in the Brazilian wheat cultivar BR 18-Terena

BACKGROUND

Wheat blast, caused by Magnaporthe oryzae Triticum (MoT) pathotype, is a global threat to wheat (Triticum aestivum L.) production. Few blast resistance (R) genes have been identified to date, therefore assessing potential sources of resistance in wheat is important. The Brazilian wheat cultivar BR 18-Terena is considered one of the best sources of resistance to blast and has been widely used in Brazilian breeding programmes, however the underlying genetics of this resistance are unknown.

RESULTS

BR 18-Terena was used as the common parent in the development of two recombinant inbred line (RIL) F₆ populations with the Brazilian cultivars Anahuac 75 and BRS 179. Populations were phenotyped for resistance at the seedling and heading stage using the sequenced MoT isolate BR32, with transgressive segregation being observed. Genetic maps containing 1779 and 1318 markers, were produced for the Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179 populations, respectively. Five quantitative trait loci (QTL) associated with seedling resistance, on chromosomes 2B, 4B (2 QTL), 5A and 6A, were identified, as were four QTL associated with heading stage resistance (1A, 2B, 4A and 5A). Seedling and heading stage QTL did not co-locate, despite a significant positive correlation between these traits, indicating that resistance at these developmental stages is likely to be controlled by different genes. BR 18-Terena provided the resistant allele for six QTL, at both developmental stages, with the largest phenotypic effect conferred by a QTL being 24.8% suggesting that BR 18-Terena possesses quantitative resistance. Haplotype analysis of 100 Brazilian wheat cultivars indicates that 11.0% of cultivars already possess a BR 18-Terena-like haplotype for more than one of the identified heading stage QTL.

CONCLUSIONS

This study suggests that BR 18-Terena possesses quantitative resistance to wheat blast, with nine QTL associated with resistance at either the seedling or heading stage being detected. Wheat blast resistance is also largely tissue-specific. Identification of durable quantitative resistances which can be combined with race-specific R gene-mediated resistance is critical to effectively control wheat blast. Collectively, this work facilitates marker-assisted selection to develop new varieties for cultivation in regions at risk from this emerging disease.

Comprehensive evaluation of resistance effects of pyramiding lines with different broad-spectrum resistance genes against Magnaporthe oryzae in rice (Oryza sativa L.)

BACKGROUND

Broad-spectrum resistance gene pyramiding helps the development of varieties with broad-spectrum and durable resistance to M. oryzae. However, detailed information about how these different sources of broad-spectrum resistance genes act together or what are the best combinations to achieve broad-spectrum and durable resistance is limited.

RESULTS

Here a set of fifteen different polygene pyramiding lines (PPLs) were constructed using marker-assisted selection (MAS). Using artificial inoculation assays at seedling and heading stage, combined with natural induction identification under multiple field environments, we evaluated systematically the resistance effects of different alleles of Piz locus (Pigm, Pi40, Pi9, Pi2 and Piz) combined with Pi1, Pi33 and Pi54, respectively, and the interaction effects between different R genes. The results showed that the seedling blast and panicle blast resistance levels of PPLs were significantly higher than that of monogenic lines. The main reason was that most of the gene combinations produced transgressive heterosis, and the transgressive heterosis for panicle blast resistance produced by most of PPLs was higher than that of seedling blast resistance. Different gene pyramiding with broad-spectrum R gene produced different interaction effects, among them, the overlapping effect (OE) between R genes could significantly improve the seedling blast resistance level of PPLs, while the panicle blast resistance of PPLs were remarkably correlated with OE and complementary effect (CE). In addition, we found that gene combinations, Pigm/Pi1, Pigm/Pi54 and Pigm/Pi33 displayed broad-spectrum resistance in artificial inoculation at seedling and heading stage, and displayed stable broad-spectrum resistance under different disease nursery. Besides, agronomic traits evaluation also showed PPLs with these three gene combinations were at par to the recurrent parent. Therefore, it would provide elite gene combination model and germplasms for rice blast resistance breeding program.

CONCLUSIONS

The development of PPLs and interaction effect analysis in this study provides valuable theoretical foundation and innovative resources for breeding broad-spectrum and durable resistant varieties.