A receptor like kinase gene with expressional responsiveness on Xanthomonas oryzae pv. oryzae is essential for Xa21-mediated disease resistance

Profiling and Improvement of Grain Quality Traits for Consumer Preferable Basmati Rice in the United States

Basmati rice is a premium aromatic rice that consumers choose primarily because of its distinct aroma and excellent grain quality. The grain quality of Basmati rice (GQBR) reflects the perspectives of producers, processors, sellers, and consumers related to the production, processing, marketing, and consumption of Basmati rice. Consumers, an invaluable part of the production demand and value chain of the Basmati rice industry, have the freedom to choose from different types of aromatic rice. Consumers expect their preferred Basmati rice to possess all superior rice grain qualities, including the physical, biochemical, and physiological properties. Gene functional analysis explained that a 10-base pair deletion in the promoter region of the OsSPL16 gene causes the slender grains in Basmati rice, whereas an 8-base-pair deletion in exon 7 of the OsBadh2 gene (located in the fgr region on rice chromosome 8) results in the distinct aroma. Furthermore, a combination of the genetic characteristics of the gw8 and gs3 genes has led to the creation of a long-grain Basmati-type rice cultivar. It has also been demonstrated that agricultural, genetic, and environmental conditions significantly influence GQBR. Hence, research on improving GQBR requires a multidimensional approach and sophisticated elements due to the complexity of its nature and preference diversity. This review covers the basic definitions of grain quality traits, consumer preference criteria, influencing factors, and strategies for producing superior-quality Basmati rice in the United States. This knowledge will be useful in improving the grain quality of Basmati and Basmati-type rice, as well as developing appropriate breeding programs that will meet the preferences of different countries and cultures.

Genome and transcriptome exploration reveals receptor-like kinases as potential resistance gene analogs against bacterial blight in pomegranate

BACKGROUND

Pomegranate (Punica granatum L.) is a tropical fruit crop of pharma-nutritional importance. However, it faces farming challenges due to pests and diseases, particularly bacterial blight and wilt. Developing resistant cultivars is crucial for sustainable pomegranate cultivation, and understanding resistance's genetic basis is essential.

METHODS AND RESULTS

We used an extensive resistance gene analogues (RGA) prediction tool to identify 958 RGAs, classified into Nucleotide Binding Site-leucine-rich repeat (NBS-LRR) proteins, receptor-like kinases (RLKs), receptor-like proteins (RLPs), Transmembrane coiled-coil (TM-CC), and nine non-canonical RGAs. RGAs were distributed across all eight chromosomes, with chromosome 02 containing the most RGAs (161), and chromosome 08 having the highest density (4.42 RGA/Mb). NBS-LRR genes were predominantly present on chromosomes 08 and 02, whereas RLKs and RLPs were primarily located on chromosomes 04 and 07. Gene ontology analysis revealed that 475 RGAs were associated with defence against various biotic stresses. Using RNAseq, we identified 120 differentially expressed RGAs, with RLKs (74) being prominent among the differentially expressed genes.

CONCLUSION

The discovery of these RGAs is a significant step towards breeding pomegranates for pest and disease resistance. The differentially expressed RLKs hold promise for developing resistant cultivars against bacterial blight, thereby contributing to the sustainability of pomegranate cultivation.

Genetic diversity and population structure analysis of Paris polyphylla Sm. revealed by SSR marker

Paris polyphylla Sm. is a vulnerable medicinal plant distributed in the Himalayan countries. This plant has numerous pharmacological benefits, including anticancer, anti-inflammatory, analgesic, and antipyretic properties. The distribution, conservation status, and traditional usage of this species are fairly known in Nepal. However, its diversity and population structure at the molecular level are unexplored. This study analyzes, the genetic diversity and population structure of 32 P. polyphylla germplasms collected from Central, Eastern and Western regions of Nepal using 15 simple sequence repeat (SSR) markers. All the SSR primers were polymorphic and amplified 60 alleles ranging from 50 bp to 900 bp. The polymorphic information content (PIC) value ranged from 0 to 0.75. The average value of the observed heterozygosity (Ho), expected heterozygosity (He), Shannon's information index (I), and total heterozygosity (Ht) were 0.63, 0.53, 0.92 and 0.32, respectively. The analysis of molecular variance (AMOVA), showed a maximum variation of 74% within the individual in a population and only 26% variation among the population. In the population STRUCTURE analysis two clusters were formed where Eastern germplasms (EN) were separated far from the Central and Western germplasms (CWN), this clustering was in complete correspondence to the unweighted pair group method based on arithmetic average (UPGMA) and principle coordinate analysis (PCoA). Furthermore, in the UPGMA and PCoA, germplasms collected from the same or relatively similar geographic origin were closer. These findings are critical for developing conservation policies, facilitating evolutionary research, sustainable utilization and commercial cultivation of this pharmacologically important and threatened species.

Dissection of leucine-rich repeat receptor-like protein kinases: insight into resistance to Fusarium wilt in tung tree

The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana's resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.

Cytological observation and transcriptome analysis reveal dynamic changes of Rhizoctonia solani colonization on leaf sheath and different genes recruited between the resistant and susceptible genotypes in rice

Sheath blight, caused by Rhizoctonia solani, is a big threat to the global rice production. To characterize the early development of R. solani on rice leaf and leaf sheath, two genotypes, GD66 (a resistant genotype) and Lemont (a susceptible genotype), were observed using four cytological techniques: the whole-mount eosin B-staining confocal laser scanning microscopy (WE-CLSM), stereoscopy, fluorescence microscopy, and plastic semi-thin sectioning after in vitro inoculation. WE-CLSM observation showed that, at 12 h post-inoculation (hpi), the amount of hyphae increased dramatically on leaf and sheath surface, the infection cushions occurred and maintained at a huge number from about 18 to 36 hpi, and then the infection cushions disappeared gradually from about 42 to 72 hpi. Interestingly, R. solani could not only colonize on the abaxial surfaces of leaf sheath but also invade the paraxial side of the leaf sheath, which shows a different behavior from that of leaf. RNA sequencing detected 6,234 differentially expressed genes (DEGs) for Lemont and 7,784 DEGs for GD66 at 24 hpi, and 2,523 DEGs for Lemont and 2,719 DEGs for GD66 at 48 hpi, suggesting that GD66 is recruiting more genes in fighting against the pathogen. Among DEGs, resistant genes, such as OsRLCK5, Xa21, and Pid2, displayed higher expression in the resistant genotype than the susceptible genotype at both 24 and 48 hpi, which were validated by quantitative reverse transcription-PCR. Our results indicated that the resistance phenotype of GD66 was the consequence of recruiting a series of resistance genes involved in different regulatory pathways. WE-CLSM is a powerful technique for uncovering the mechanism of R. solani invading rice and for detecting rice sheath blight-resistant germplasm.

Identification and expression profile analysis of the SnRK2 gene family in cucumber

The sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific type of serine/threonine protein kinase that plays an important role in the physiological regulation of stress. The objective of this study was to identify and analyze the members of the SnRK2 gene family in cucumber and lay a foundation for further exploration of the mechanism of CsSnRK2 resistance to stress. Here, 12 SnRK2 genes were isolated from cucumber and distributed on five chromosomes, phylogenetic clustering divided these into three well-supported clades. In addition, collinearity analysis showed that the CsSnRK2 gene family underwent purifying selection pressure during evolution. CsSnRK2 genes of the same group have similar exons and conserved motifs, and intron length may be a specific imprint for the evolutionary amplification of the CsSnRK2 gene family. By predicting cis elements in the promoter, we found that the promoter region of CsSnRK2 gene members had various cis-regulatory elements in response to hormones and stress. Relative expression analysis showed that CsSnRK2.11 (group II) and CsSnRK2.12 (group III) were strongly induced by ABA, NaCl and PEG stress; whereas CsSnRK2.2 (group III) was not activated by any treatment. The response of group I CsSnRK2 to ABA, NaCl and PEG was weak. Furthermore, protein interaction prediction showed that multiple CsSnRK2 proteins interacted with four proteins including protein phosphatase 2C (PP2C), and it is speculated that the CsSnRK2 genes may also an independent role as a third messenger in the ABA signaling pathway. This study provides a reference for analyzing the potential function of CsSnRK2 genes in the future research.

Rice MPK17 Plays a Negative Role in the Xa21-Mediated Resistance Against Xanthomonas oryzae pv. oryzae

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases affecting rice production worldwide. Xa21 was the first disease resistance gene cloned in rice, which encodes a receptor kinase and confers broad resistance against Xoo stains. Dozens of components in the Xa21-mediated pathway have been identified in the past decades, however, the involvement of mitogen-activated protein kinase (MAPK) genes in the pathway has not been well described. To identify MAPK involved in Xa21-mediated resistance, the level of MAPK proteins was profiled using Western blot analysis. The abundance of OsMPK17 (MPK17) was found decreased during the rice-Xoo interaction in the background of Xa21. To investigate the function of MPK17, MPK17-RNAi and over-expression (OX) transgenic lines were generated. The RNAi lines showed an enhanced resistance, while OX lines had impaired resistance against Xoo, indicating that MPK17 plays negative role in Xa21-mediated resistance. Furthermore, the abundance of transcription factor WRKY62 and pathogenesis-related proteins PR1A were changed in the MPK17 transgenic lines when inoculated with Xoo. We also observed that the MPK17-RNAi and -OX rice plants showed altered agronomic traits, indicating that MPK17 also plays roles in the growth and development. On the basis of the current study and published results, we propose a "Xa21-MPK17-WRKY62-PR1A" signaling that functions in the Xa21-mediated disease resistance pathway. The identification of MPK17 advances our understanding of the mechanism underlying Xa21-mediated immunity, specifically in the mid- and late-stages.

The N-terminus of an Ustilaginoidea virens Ser-Thr-rich glycosylphosphatidylinositol-anchored protein elicits plant immunity as a MAMP

Many pathogens infect hosts through specific organs, such as Ustilaginoidea virens, which infects rice panicles. Here, we show that a microbe-associated molecular pattern (MAMP), Ser-Thr-rich Glycosyl-phosphatidyl-inositol-anchored protein (SGP1) from U. virens, induces immune responses in rice leaves but not panicles. SGP1 is widely distributed among fungi and acts as a proteinaceous, thermostable elicitor of BAK1-dependent defense responses in N. benthamiana. Plants specifically recognize a 22 amino acid peptide (SGP1 N terminus peptide 22, SNP22) in its N-terminus that induces cell death, oxidative burst, and defense-related gene expression. Exposure to SNP22 enhances rice immunity signaling and resistance to infection by multiple fungal and bacterial pathogens. Interestingly, while SGP1 can activate immune responses in leaves, SGP1 is required for U. virens infection of rice panicles in vivo, showing it contributes to the virulence of a panicle adapted pathogen.

Ustilaginoidea virens is a fungal pathogen that infects rice via the panicles. Here, the authors show that U. virens SGP1, a conserved Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored protein, elicits immune responses in rice leaves while contributing to virulence in panicles.

Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines

BACKGROUND

Rice (Oryza sativa L.) is an important crop and a staple food for half of the population around the world. The recent water and labor shortages are encouraging farmers to shift from traditional transplanting to direct-seeding. However, poor germination and slow elongation of the coleoptile constrains large-scale application of direct-seeding.

OBJECTIVE

This study was aimed to investigate the genetic basis of the anaerobic germination (AG) potential using a set of Oryza nivara (O. nivara) introgression lines (ILs).

METHODS

In this study, a total of 131 ILs were developed by introducing O. nivara chromosome segments into the elite indica rice variety 93-11 through advanced backcrossing and repeated selfing. A high-density genetic map has been previously constructed with 1,070 bin-markers. The seeds of ILs were germinated and used to measure coleoptile length under normal and anaerobic conditions. QTLs associated with AG potential were determined in rice.

RESULTS

Based on the high-density genetic map of the IL population, two QTLs, qAGP1 and qAGP3 associated with AG tolerance were characterized and located on chromosomes 1 and 3, respectively. Each QTL explained 15% of the phenotypic variance. Specifically, the O. nivara-derived chromosome segments of the two QTLs were positively tolerance to anaerobic condition by increasing coleoptile length. In a further analysis of public transcriptome data, a total of 26 and 36 genes within qAGP1 and qAGP3 were transcriptionally induced by anaerobic stress, respectively.

CONCLUSIONS

Utilization of O. nivara-derived alleles at qAGP1 and qAGP3 can potentially enhance tolerance to anaerobic stress at the germination stage in rice, thereby accelerating breeding of rice varieties to be more adaptative for direct-seeding.

Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice

Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation-reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.

Development of Novel Protocol to Al3+ Stress Tolerance at Germination Stage in Indica Rice through Statistical Approaches

Rice production is decreasing by abiotic stresses like heavy metals. In such circumstances, producing food for growing human population is a challenge for plant breeders. Excess of Al³⁺ in soil has become threat for high yield of rice. Improvement of crop is one of potential solution for high production. The aim of this study was to develop the new method for optimization of Al³⁺ toxicity tolerance in indica rice at germination stag using two-way ANOVA and Duncan's multiple-range test (DMRT). Seeds of two indica rice cultivars (Pokkali and Pak Basmati) were exposed in different concentrations (control, 5 mM, 15 mM, and 20 mM) of Al³⁺ toxicity at pH 4 ±0.2 for two weeks. Germination traits such as final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean time of germination (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC) and growth traits such as root length (RL), shoot length (SL), total dry biomass (TDB), and germination vigour index (GVI) were measured. To obtain the maximum number of significance (≤ 0.01%) parameters in each concentration of Al³⁺ toxicity with control, two-way ANOVA was established and comparison of mean was done using DMRT. The results showed that 5 mM, 10 mM, and 15 mM have less significant effects on the above-mentioned parameters. However, 20 mM concentration of Al³⁺ produced significant effects (≤ 0.01%). Therefore, 20 mM of Al³⁺ is considered optimized limit for indica cultivars (Pokkali and Pak Basmati).

Transcriptional insights into the pyramided resistance to rice bacterial blight

The pyramiding of resistance (R) genes provides broad-spectrum and durable resistance to plant diseases. However, the genetic basis for bacterial blight (BB) resistance remains unclear. The BB R gene pyramided line IRBB54, which expresses xa5 and Xa21, possessed a higher level of resistance than both single R gene lines. Large-scale genotyping of genetic markers in this study revealed similar genetic backgrounds among the near-isogenic lines (NILs), suggesting that resistance in the resistant NILs was mainly conferred by the individual R genes or the interaction between them. Transcriptome analysis demonstrated that more than 50% of the differentially expressed genes (DEGs), and more than 70% of the differentially expressed functions, were shared between IRBB54 and IRBB5 or IRBB21. Most of the DEGs in the resistant NILs were downregulated and are predicted to function in cellular and biological process. The DEGs common among the resistant NILs mainly showed non-additive expression patterns and enrichment in stress-related pathways. The differential expression of agronomic trait-controlled genes in the resistant NILs, especially in IRBB54, indicated the existence of potential side-effects resulting from gene pyramiding. Our findings contribute to the understanding of R gene pyramiding, as well as its effects on targeted and non-targeted trait(s).

Comparison of Structural and Functional Properties of Wheat Starch Under Different Soil Drought Conditions

Drought influences cereal crop yield and quality. However, little is known about changes in the structural and functional properties of wheat starch under soil drought conditions. In this study, two wheat cultivars were subjected to well-watered (WW), moderate soil-drought (MD), and severe soil-drought (SD) from 7 tillers in the main stem to maturity. The structural and functional properties of the resultant endosperm starch were investigated. In comparison with WW soil, the MD increased starch accumulation in grains, the proportion of large starch granules, amylose and amylopectin long branch chain contents, and average amylopectin branch chain length, which were accompanied by the increase in activities of granule bound starch synthase and soluble starch synthase. MD treated-starch had a lower gelatinization enthalpy, and swelling power, but a higher gelatinization temperature, retrogradation enthalpy, and retrogradation percentage when compared to WW conditions. The MD also increased starch resistance to acid hydrolysis, amylase hydrolysis, and in vitro digestion. The SD had the opposite effects to the MD in all cases. The results suggest that soil drought more severely affects amylose synthesis than amylopectin synthesis in wheat grains, and moderate soil-drought improves molecular structure and functional properties of the starch.

QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9

BACKGROUND

An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far.

RESULTS

In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis.

CONCLUSIONS

OsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice

BACKGROUND

Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study.

RESULTS

A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization.

CONCLUSION

QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

Disease Resistance Gene Analogs (RGAs) in Plants

Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.

Uncovering the differential molecular basis of adaptive diversity in three Echinochloa leaf transcriptomes

Echinochloa is a major weed that grows almost everywhere in farmed land. This high prevalence results from its high adaptability to various water conditions, including upland and paddy fields, and its ability to grow in a wide range of climates, ranging from tropical to temperate regions. Three Echinochloa crus-galli accessions (EC-SNU1, EC-SNU2, and EC-SNU3) collected in Korea have shown diversity in their responses to flooding, with EC-SNU1 exhibiting the greatest growth among three accessions. In the search for molecular components underlying adaptive diversity among the three Echinochloa crus-galli accessions, we performed de novo assembly of leaf transcriptomes and investigated the pattern of differentially expressed genes (DEGs). Although the overall composition of the three leaf transcriptomes was well-conserved, the gene expression patterns of particular gene ontology (GO) categories were notably different among the three accessions. Under non-submergence growing conditions, five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1. These up-regulated DEGs include major components of signal transduction pathways, such as receptor-like kinase (RLK) and calcium-dependent protein kinase (CDPK) genes, as well as previously known abiotic stress-responsive genes. Our results therefore suggest that diversified gene expression regulation of upstream signaling components conferred the molecular basis of adaptive diversity in Echinochloa crus-galli.