Rice tillering is an important agronomic trait for grain production. The HIGH-TILLERING DWARF1 (HTD1) gene encodes an ortholog of Arabidopsis MAX3. Complementation analyses for HTD1 confirm that the ...defect in HTD1 is responsible for both high-tillering and dwarf phenotypes in the htd1 mutant. The rescue of the Arabidopsis max3 mutant phenotype by the introduction of Pro₃₅S:HTD1 indicates HTD1 is a carotenoid cleavage dioxygenase that has the same function as MAX3 in synthesis of a carotenoid-derived signal molecule. The HTD1 gene is expressed in both shoot and root tissues. By evaluating ProHTD₁:GUS expression, we found that the HTD1 gene is mainly expressed in vascular bundle tissues throughout the plant. Auxin induction of HTD1 expression suggests that auxin may regulate rice tillering partly through upregulation of HTD1 gene transcription. Restoration of dwarf phenotype after the removal of axillary buds indicates that the dwarfism of the htd1 mutant may be a consequence of excessive tiller production. In addition, the expression of HTD1, D3 and OsCCD8a in the htd1 and d3 mutants suggests a feedback mechanism may exist for the synthesis and perception of the carotenoid-derived signal in rice. Characterization of MAX genes in Arabidopsis, and identification of their orthologs in pea, petunia and rice indicates the existence of a conserved mechanism for shoot-branching regulation in both monocots and dicots.
Rice is one of the staple foods for the majority of the global population that depends directly or indirectly on it. The yield of this important crop is constantly challenged by various biotic ...stresses. Rice blast, caused by
(
), is a devastating rice disease causing severe yield losses annually and threatening rice production globally. The development of a resistant variety is one of the most effective and economical approaches to control rice blast. Researchers in the past few decades have witnessed the characterization of several qualitative resistance (
) and quantitative resistance (
) genes to blast disease as well as several avirulence (
) genes from the pathogen. These provide great help for either breeders to develop a resistant variety or pathologists to monitor the dynamics of pathogenic isolates, and ultimately to control the disease. Here, we summarize the current status of the isolation of
,
and
genes in the rice-
interaction system, and review the progresses and problems of these genes utilized in practice for reducing rice blast disease. Research perspectives towards better managing blast disease by developing a broad-spectrum and durable blast resistance variety and new fungicides are also discussed.
Rice blast, caused by the
fungus, is one of the most devastating rice diseases worldwide. Developing resistant varieties by pyramiding different blast resistance (
) genes is an effective approach to ...control the disease. However, due to complex interactions among
genes and crop genetic backgrounds, different
-gene combinations may have varying effects on resistance. Here, we report the identification of two core
-gene combinations that will benefit the improvement of
(
) rice blast resistance. We first evaluated 68
rice cultivars at seedling stage by challenging with 58
isolates. To evaluate panicle blast resistance, we inoculated 190
rice cultivars at boosting stage with five groups of mixed conidial suspensions (MCSs), with each containing 5-6 isolates. More than 60% cultivars displayed moderate or lower levels of susceptibility to panicle blast against the five MCSs. Most cultivars contained two to six
genes detected by the functional markers corresponding to 18 known
genes. Through multinomial logistics regression analysis, we found that
,
,
, and
loci contributed significantly to seedling blast resistance, and
,
,
, and
contributed significantly to panicle blast resistance. For gene combinations,
+
and
+
yielded more stable pyramiding effects on panicle blast resistance against all five MCSs and were designated as core
-gene combinations. Up to 51.6%
cultivars in the Jiangsu area contained
, but less than 30% harbored either
or
, leading to less cultivars containing
+
(15.8%) or
+
(5.8%). Only a few varieties simultaneously contained
and
, implying the opportunity to use hybrid breeding procedures to efficiently generate varieties with either
+
or
+
. This study provides valuable information for breeders to develop
rice cultivars with high resistance to blast, especially panicle blast.
Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to ...control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.
Rice blast, caused by
Magnaporthe oryzae
(
M. oryzae
), is one of the most destructive diseases threatening rice production worldwide. Development of resistant cultivars using broad-spectrum ...resistance (
R
) genes with high breeding value is the most effective and economical approach to control this disease. In this study, the breeding potential of
Pigm
gene in
geng
/
japonica
rice breeding practice in Jiangsu province was comprehensively evaluated. Through backcross and marker-assisted selection (MAS),
Pigm
was introduced into two
geng
rice cultivars (Wuyungeng 32/WYG32 and Huageng 8/HG8). In each genetic background, five advanced backcross lines with
Pigm
(ABLs) and the same genotypes as the respective recurrent parent in the other 13 known
R
gene loci were developed. Compared with the corresponding recurrent parent, all these ABLs exhibited stronger resistance in seedling inoculation assay using 184 isolates collected from rice growing regions of the lower region of the Yangtze River. With respect to panicle blast resistance, all ABLs reached a high resistance level to blast disease in tests conducted in three consecutive years with the inoculation of seven mixed conidial suspensions collected from different regions of Jiangsu province. In natural field nursery assays, the ABLs showed significantly higher resistance than the recurrent parents. No common change on importantly morphological traits and yield-associated components was found among the ABLs, demonstrating the introduction of
Pigm
had no tightly linked undesirable effect on rice economically important traits and its associated grain weight reduction effect could be probably offset by others grain weight genes or at least in the background of the aforementioned two varieties. Notably, one rice line with
Pigm
, designated as Yangnonggeng 3091, had been authorized as a new variety in Jiangsu province in 2021, showing excellent performance on both grain yield and quality, as well as the blast resistance. Together, these results suggest that the
Pigm
gene has a high breeding value in developing rice varieties with durable and broad-spectrum resistance to blast disease.
Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most ...economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).
Background
The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and ...effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date.
Results
In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The
aus
,
indica
and
tropical japonica
sub-populations displayed higher RBSDV resistance than the
aromatic
and
temperate japonica
sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them,
qRBSDV-4.2
and
qRBSDV-6.3
were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that
qRBSDV-6.3
significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of
qRBSDV-6.3
into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of
qRBSDV-6.3
in enhancing RBSDV resistance.
Conclusions
The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.
MicroRNAs (miRNAs) is a class of non-coding RNAs involved in post- transcriptional control of gene expression, via degradation and/or translational inhibition. Six-hundred sixty-one rice miRNAs are ...known that are important in plant development. However, flowering-related miRNAs have not been characterized in Oryza rufipogon Griff. It was approved by supervision department of Guangdong wild rice protection. We analyzed flowering-related miRNAs in O. rufipogon using high-throughput sequencing (deep sequencing) to understand the changes that occurred during rice domestication, and to elucidate their functions in flowering.
Three O. rufipogon sRNA libraries, two vegetative stage (CWR-V1 and CWR-V2) and one flowering stage (CWR-F2) were sequenced using Illumina deep sequencing. A total of 20,156,098, 21,531,511 and 20,995,942 high quality sRNA reads were obtained from CWR-V1, CWR-V2 and CWR-F2, respectively, of which 3,448,185, 4,265,048 and 2,833,527 reads matched known miRNAs. We identified 512 known rice miRNAs in 214 miRNA families and predicted 290 new miRNAs. Targeted functional annotation, GO and KEGG pathway analyses predicted that 187 miRNAs regulate expression of flowering-related genes. Differential expression analysis of flowering-related miRNAs showed that: expression of 95 miRNAs varied significantly between the libraries, 66 are flowering-related miRNAs, such as oru-miR97, oru-miR117, oru-miR135, oru-miR137, et al. 17 are early-flowering -related miRNAs, including osa-miR160f, osa-miR164d, osa-miR167d, osa-miR169a, osa-miR172b, oru-miR4, et al., induced during the floral transition. Real-time PCR revealed the same expression patterns as deep sequencing. miRNAs targets were confirmed for cleavage by 5'-RACE in vivo, and were negatively regulated by miRNAs.
This is the first investigation of flowering miRNAs in wild rice. The result indicates that variation in miRNAs occurred during rice domestication and lays a foundation for further study of phase change and flowering in O. rufipogon. Complicated regulatory networks mediated by multiple miRNAs regulate the expression of flowering genes that control the induction of flowering.
Sheath blight (ShB) disease, caused by
Kühn, is one of the most serious rice diseases. Rice breeding against ShB has been severely hindered because no major resistance genes or germplasms are ...available in rice. Here, we report that introduction of
antifungal protein (GAFP) genes from
B1 into rice significantly enhances resistance to rice ShB. Four GAFP genes were cloned from
B1, and all displayed a strong ability to inhibit
growth in plate assays. Two versions, with or without a signal peptide, for each of the four GAFP genes were introduced into XD3 and R6547 rice cultivars, and all transgenic lines displayed stronger ShB resistance than the corresponding wild-type control in both greenhouse and field conditions. Importantly,
showed the highest ShB resistance; GAFPs with and without its signal peptide showed no significant differences in enhancing ShB resistance. We also evaluated the agronomic traits of these transgenic rice and found that ectopic expression of
in rice at appropriate levels did not affect agronomic traits other than enhancing ShB resistance. Together, these results indicate that
genes, especially
, have great potential in rice breeding against ShB disease.
Lesion-mimic mutants are useful materials to dissect mechanisms controlling programmed cell death (PCD) and defense response in plants. Although dozens of lesion-mimic mutant genes have been ...identified in plants, the molecular mechanisms underlying PCD and defense response remain to be extensively elucidated. Here, we identified a rice lesion mimic mutant, named
lesion mimic 42
(
lm42
), from an ethylmethylsulfone (EMS)-induced mutant population. The
lm42
mutant displayed flame-red spots on the leaves and sheaths at the 3-leaf developmental stage and exhibited impaired photosynthetic capacity with decreased chlorophyll content and decomposed chloroplast thylakoids. The lesion development of
lm42
was light- and temperature-dependent. We identified a single base mutation (T38A), changing a Leu to Gln, in the first exon of
LOC_Os12g16720
(
LM42
), which encodes a tryptamine 5-hydroxylase, by map-based cloning. We carried out transgenic complementation to confirm that this mutation caused the
lm42
phenotype. We further knocked out the
LM42
gene by CRISPR/Cas9 to recreate the
lm42
phenotype.
LM42
is highly expressed in leaves, leaf sheaths and roots. Loss-of-function of
LM42
activated expression of ROS-generating genes and inhibited expression of ROS-scavenging genes, leading to ROS accumulation and eventually cell death. Furthermore, its disruption induced expression of defense-response genes and enhanced host resistance to both fungal pathogen
Magnaporthe oryzae
and bacterial pathogen
Xanthomonas oryzae pv. oryzae
. Our transcriptomic data suggested that the way
lm42
led to lesion-mimic was probably by affecting ribosome development. Overall, our results demonstrate that tryptamine 5-hydroxylase-coding gene
LM42
is required for suppression of cell death and uncontrolled activation of defense responses in rice.
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