Development and evaluation of improved lines with broad-spectrum resistance to rice blast using nine resistance genes

Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method

Genetic resistance is the most effective and eco-friendly approach to combat rice blast. The application of resistance genes may be facilitated by the availability of molecular markers that allow marker-assisted selection during the breeding process. The Pi1 gene, considered to be a broad-spectrum resistance gene, might contribute to enhancing resistance to rice blast, but it lacks a suitable marker that can be used. In this study, we investigated nucleotide polymorphism in the Pik locus and combined the SNAP protocol with the touch-up gradient amplification method to develop a SNAP marker. The Pi1 SNAP marker could distinguish Pi1 from Pik alleles, and when used for screening a germplasm bank and an F2 population, it consistently identified germplasms carrying the Pi1 gene. The P1 SNAP marker offers as advantages to involve only the presence/absence analysis of PCR amplicons resolved on an agarose gel.

Improvement of Rice Blast Resistance in TGMS Line HD9802S through Optimized Anther Culture and Molecular Marker-Assisted Selection

Rice blast caused by Magnaporthe oryzae is one of the most serious rice diseases worldwide. The early indica rice thermosensitive genic male sterile (TGMS) line HD9802S has the characteristics of stable fertility, reproducibility, a high outcrossing rate, excellent rice quality, and strong combining ability. However, this line exhibits poor blast resistance and is highly susceptible to leaf and neck blasts. In this study, backcross introduction, molecular marker-assisted selection, gene chipping, anther culture, and resistance identification in the field were used to introduce the broad-spectrum blast-resistance gene R6 into HD9802S to improve its rice blast resistance. Six induction media were prepared by varying the content of each component in the culture medium. Murashige and Skoog's medium with 3 mg/L 2,4-dichlorophenoxyacetic acid, 2 mg/L 1-naphthaleneacetic acid, and 1 mg/L kinetin and N6 medium with 800 mg/L casein hydrolysate, 600 mg/L proline, and 500 mg/L glutamine could improve the callus induction rate and have a higher green seedling rate and a lower white seedling rate. Compared to HD9802S, two doubled haploid lines containing R6 with stable fertility showed significantly enhanced resistance to rice blast and no significant difference in spikelet number per panicle, 1000-grain weight, or grain shape. Our findings highlight a rapid and effective method for improving rice blast resistance in TGMS lines.

Available cloned genes and markers for genetic improvement of biotic stress resistance in rice

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

Haplotype analysis and marker development of five salt-tolerant-related genes in rice (Oryza sativa L.)

Salinity stress is a great threat to the growth and productivity of crops, and development of salt-tolerant crops is of great necessity to ensure food security. Although a few genes with natural variations that confer salt tolerance at germination and seedling stage in rice have been cloned, effective intragenic markers for these genes are awaited to be developed, which hinder the use of these genes in genetic improvement of salt tolerance in rice. In this study, we first performed haplotype analysis of five rice salt-tolerant-related genes using 38 rice accessions with reference genome and 4,726 rice germplasm accessions with imputed genotypes and classified main haplotype groups and haplotypes. Subsequently, we identified unique variations for elite haplotypes reported in previous studies and developed 11 effective intragenic makers. Finally, we conducted genotyping of 533 of the 4,726 rice accessions from worldwide and 70 approved temperate geng/japonica cultivars in China using the developed markers. These results could provide effective donors and markers of salt-tolerant-related genes and thus could be of great use in genetic improvement of salt tolerance in rice.

Pyramiding of Multiple Genes to Improve Rice Blast Resistance of Photo-Thermo Sensitive Male Sterile Line, without Yield Penalty in Hybrid Rice Production

Rice blast caused by pathogenic fungus Magnaporthe oryzae is one of the most serious diseases in rice. The pyramiding of effective resistance genes into rice varieties is a potential approach to reduce the damage of blast disease. In this study, combinations of three resistance genes, Pigm, Pi48 and Pi49, were introduced into a thermo-sensitive genic male sterile (PTGMS) line Chuang5S through marker-assisted selection. The results showed that the blast resistance of improved lines increased significantly compared with Chuang5S, and the three gene pyramiding lines (Pigm + Pi48 + Pi49) had higher rice blast resistance level than monogenic line and digenic lines (Pigm +Pi48, Pigm + Pi49). The genetic backgrounds of the improved lines were highly similar (>90%) to the recurrent parent Chuang5S by using the RICE10K SNP chip. In addition, agronomic traits evaluation also showed pyramiding lines with two or three genes similar to Chuang5S. The yields of the hybrids developed from improved PTGMS lines and Chuang5S are not significantly different. The newly developed PTGMS lines can be practically used for the breeding of parental lines and hybrid varieties with broad spectrum blast resistance.

Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection

Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group.

Culturable Screening of Plant Growth-Promoting and Biocontrol Bacteria in the Rhizosphere and Phyllosphere of Wild Rice

Wild rice is an important improved resource for cultivated rice and its unique ability to resist biotic and abiotic stress has attracted the attention of many scholars. The microbial community structure in the rhizosphere and leaf area of different rice varieties is also different, which may be one of the reasons for the difference in stress resistance between wild rice and cultivated rice. Forty-six bacteria were screened from the rhizosphere and phyllospheric of four different wild rice varieties. The results of functions of the screened strains showed that 18 strains had a good inhibitory effect on rice blast, and 33 strains had the ability to dissolve phosphorus, potassium, or fix nitrogen. Through potted experiment, the three bacterial strains, 499G2 (Peribacillus simplex), 499G3 (Bacillus velezensis), and 499G4 (B. megaterium) have a positive effect on the growth of cultivated rice in addition to the resistance to rice blast. The contents of total nitrogen, total phosphorus, total potassium, indole acetic acid (IAA), and chlorophyll in plant leaves were increased. In addition, in the verification test of rice blast infection, the application of inoculants can significantly reduce the content of malondialdehyde (MDA), increase the content of soluble sugar, and increase the activity of plant antioxidant enzymes, which may thereby improve rice in resisting to rice blast.

Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions

Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.

Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Oryza sativa L.)

Asian cultivated rice consists of two main subspecies, xian/indica (XI) and geng/japonica (GJ), and GJ accessions have significantly lower nitrogen-use efficiency (NUE) than XI accessions. In order to facilitate genetic improvement of NUE in GJ accessions, we conducted haplotype analysis of 14 cloned NUE genes using 36 rice germplasm accessions with high-quality reference genome and developed 18 intragenic markers for elite haplotypes, which were then used to evaluate NUE genes in another 41 genetically diverse germplasm accessions from 12 countries and 71 approved GJ cultivars from northern provinces of China. Our results show that elite haplotypes of 12 NUE genes are mainly existed in XI accessions, but few is distributed in GJ accessions. The number of elite haplotypes carried by an XI accession can reach 10, while that carried by a GJ accession is less than 3. Surprisingly, the elite haplotype of gene DEP1 is nearly fixed in approved GJ cultivars, and elite haplotypes of gene MYB61 and NGR5 have been introduced into some approved GJ cultivars. The developed intragenic markers for NUE genes and evaluated 77 genetically diverse rice accessions could be of great use in the improvement of NUE in GJ cultivars.

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge. Here, we review the concept and practices of Green Super Rice (GSR) that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture. The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources, functional gene discoveries, and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving, environmentally friendly crop production systems. We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agriculture and better nourish the world population.

Recent Progress in Rice Broad-Spectrum Disease Resistance

Rice is one of the most important food crops in the world. However, stable rice production is constrained by various diseases, in particular rice blast, sheath blight, bacterial blight, and virus diseases. Breeding and cultivation of resistant rice varieties is the most effective method to control the infection of pathogens. Exploitation and utilization of the genetic determinants of broad-spectrum resistance represent a desired way to improve the resistance of susceptible rice varieties. Recently, researchers have focused on the identification of rice broad-spectrum disease resistance genes, which include R genes, defense-regulator genes, and quantitative trait loci (QTL) against two or more pathogen species or many isolates of the same pathogen species. The cloning of broad-spectrum disease resistance genes and understanding their underlying mechanisms not only provide new genetic resources for breeding broad-spectrum rice varieties, but also promote the development of new disease resistance breeding strategies, such as editing susceptibility and executor R genes. In this review, the most recent advances in the identification of broad-spectrum disease resistance genes in rice and their application in crop improvement through biotechnology approaches during the past 10 years are summarized.

Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54

BACKGROUND

Emergence of new pathogen strains of Magnaporthe oryzae is a major reason for recurrent failure of the resistance mediated by a single resistance gene (Pi) in rice. Stacking various Pi genes in the genome through marker-assisted selection is thus an effective strategy in rice breeding for achieving durable resistance against the pathogen. However, the effect of pyramiding of multiple Pi genes using transgenesis still remains largely unknown.

RESULTS

Three Pi genes Pib, Pi25 and Pi54 were transferred together into two rice varieties, the indica variety Kasalath and the japonica variety Zhenghan 10. Transgenic plants of both Kasalath and Zhenghan 10 expressing the Pi transgenes showed imparted pathogen resistance. All the transgenic lines of both cultivars also exhibited shorter growth periods with flowering 2-4 days early, and shorter plant heights with smaller panicle. Thus, pyramiding of the Pi genes resulted in reduced grain yields in both rice cultivars. However, tiller numbers and grain weight were generally similar between the pyramided lines and corresponding parents. A global analysis of gene expression by RNA-Seq suggested that both enhancement and, to a lesser extent, inhibition of gene transcription occurred in the pyramided plants. A total of 264 and 544 differentially expressed genes (DEGs) were identified in Kasalath and Zhenghan 10, respectively. Analysis of the DEGs suggested that presence of the Pi transgenes did not alter gene expression only related to disease resistance, but also impacted many gene transcriptions in the pathways for plant growth and development, in which several were common for both Kasalath and Zhenghan 10.

CONCLUSION

Pyramiding of the Pi genes Pib, Pi25 and Pi54 via transgenesis is a potentially promising approach for improving rice resistance to the pathogen Magnaporthe oryzae. However, pleiotropic effects of the Pi genes could potentially result in yield loss. These findings support the idea that immunity is often associated with yield penalties. Rational combination of the Pi genes based on the genetic background may be important to balance yield and disease resistance.

Engineering broad-spectrum disease-resistant rice by editing multiple susceptibility genes

Rice blast and bacterial blight are important diseases of rice (Oryza sativa) caused by the fungus Magnaporthe oryzae and the bacterium Xanthomonas oryzae pv. oryzae (Xoo), respectively. Breeding rice varieties for broad-spectrum resistance is considered the most effective and sustainable approach to controlling both diseases. Although dominant resistance genes have been extensively used in rice breeding and production, generating disease-resistant varieties by altering susceptibility (S) genes that facilitate pathogen compatibility remains unexplored. Here, using CRISPR/Cas9 technology, we generated loss-of-function mutants of the S genes Pi21 and Bsr-d1 and showed that they had increased resistance to M. oryzae. We also generated a knockout mutant of the S gene Xa5 that showed increased resistance to Xoo. Remarkably, a triple mutant of all three S genes had significantly enhanced resistance to both M. oryzae and Xoo. Moreover, the triple mutant was comparable to the wild type in regard to key agronomic traits, including plant height, effective panicle number per plant, grain number per panicle, seed setting rate, and thousand-grain weight. These results demonstrate that the simultaneous editing of multiple S genes is a powerful strategy for generating new rice varieties with broad-spectrum resistance.

Designing Future Crops: Genomics-Assisted Breeding Comes of Age

Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.

Clubroot in Brassica: recent advances in genomics, breeding, and disease management

Clubroot disease, caused by Plasmodiophora brassicae, affects Brassica oilseed and vegetable production worldwide. This review is focused on various aspects of clubroot disease and its management, including understanding the pathogen and resistance in the host plants. Advances in genetics, molecular biology techniques, and omics research have helped to identify several major loci, QTL, and genes from the Brassica genomes involved in the control of clubroot resistance. Transcriptomic studies have helped to extend our understanding of the mechanism of infection by the pathogen and the molecular basis of resistance/susceptibility in the host plants. A comprehensive understanding of the clubroot disease and host resistance would allow developing a better strategy by integrating the genetic resistance with cultural practices to manage this disease from a long-term perspective.

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

BACKGROUND

Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers.

RESULT

In this study, 14 genes related to grain size (GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7 and GW8) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for GW2, GS2 and GL3.1 were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the indica and japonica subspecies. Significant trait contributions were found for most of the FNPs, especially GS3, GW5 and GL7. Of note, GW5 could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F2 population, and GW5 was further identified as the major locus with the largest contribution to grain width and length to width ratio.

CONCLUSIONS

The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

Development of a Sinitic Clubroot Differential Set for the Pathotype Classification of Plasmodiophora brassicae

Plasmodiophora brassicae, which is known for its broad genetic diversity for virulence, is the causal agent of clubroot disease of Brassica crops worldwide. Studies on pathotype characterization with four differential hosts according to Williams' classification system showed the predominance of pathotype 4 in China. However, the genetic variability within pathotype 4 complicates the breeding of durable clubroot-resistant (CR) cultivars. Herein, a Sinitic clubroot differential (SCD) set was developed using a set of eight differential inbred lines of Chinese cabbage with known or novel CR genes. The presence of immense diversity within pathotype 4 of Williams' system was verified, and 11 pathotypes were characterized using the developed SCD system. The scalability and practicability of the system was further confirmed with a subset of 95 field isolates from different Brassica crops and different regions of China and Korea. Sixteen pathotypes were detected from 132 field isolates, named Pb1 to Pb16, respectively. Among them, Pb1 and Pb4 were prevalent in diverse Brassica crops in the southern and northern regions of China. Pb12, Pb13, Pb14, and Pb16 showed area-specific distribution. The SCD set developed herein will provide important genetic resources for pathogenicity studies of P. brassicae and for CR breeding in Chinese cabbage and other Brassica crops.