Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice

Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease

Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.

QTL Analysis Revealed One Major Genetic Factor Inhibiting Lesion Elongation by Bacterial Blight (Xanthomonas oryzae pv. oryzae) from a japonica Cultivar Koshihikari in Rice

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen that has ravaged the rice industry as the causal agent of bacterial blight (BB) diseases in rice. Koshihikari (KO), an elite japonica cultivar, and ARC7013 (AR), an indica cultivar, are both susceptible to Xoo. Their phenotypic characteristics reveal that KO has shorter lesion length than that of AR. The F₂ population from KO × AR results in continuous distribution of lesion length by inoculation of an Xoo race (T7147). Consequently, quantitative trait loci (QTL) mapping of the F₂ population is conducted, covering 12 chromosomes with 107 simple sequence repeat (SSR) and insertion/deletion (InDel) genetic markers. Three QTLs are identified on chromosomes 2, 5, and 10. Of them, qXAR5 has the strongest resistance variance effect of 20.5%, whereas qXAR2 and qXAR10 have minor QTL effects on resistance variance, with 3.9% and 2.3%, respectively, for a total resistance variance of 26.7%. The QTLs we examine for this study differ from the loci of BB resistance genes from earlier studies. Our results can help to facilitate understanding of genetic and morphological fundamentals for use in rice breeding programs that are more durable against evolving Xoo pathogens and uncertain climatic temperature.

Accumulating candidate genes for broad-spectrum resistance to rice blast in a drought-tolerant rice cultivar

Biotic stresses, including diseases, severely affect rice production, compromising producers’ ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.

Intergenic spaces: a new frontier to improving plant health

To more sustainably mitigate the impact of crop diseases on plant health and productivity, there is a need for broader spectrum, long-lasting resistance traits. Defense response (DR) genes, located throughout the genome, participate in cellular and system-wide defense mechanisms to stave off infection by diverse pathogens. This multigenic resistance avoids rapid evolution of a pathogen to overcome host resistance. DR genes reside within resistance-associated quantitative trait loci (QTL), and alleles of DR genes in resistant varieties are more active during pathogen attack relative to susceptible haplotypes. Differential expression of DR genes results from polymorphisms in their regulatory regions, that includes cis-regulatory elements such as transcription factor binding sites as well as features that influence epigenetic structural changes to modulate chromatin accessibility during infection. Many of these elements are found in clusters, known as cis-regulatory modules (CRMs), which are distributed throughout the host genome. Regulatory regions involved in plant-pathogen interactions may also contain pathogen effector binding elements that regulate DR gene expression, and that, when mutated, result in a change in the plants' response. We posit that CRMs and the multiple regulatory elements that comprise them are potential targets for marker-assisted breeding for broad-spectrum, durable disease resistance.

MiR1885 Regulates Disease Tolerance Genes in Brassica rapa during Early Infection with Plasmodiophora brassicae

Clubroot caused by Plasmodiophora brassicae is a severe disease of cruciferous crops that decreases crop quality and productivity. Several clubroot resistance-related quantitative trait loci and candidate genes have been identified. However, the underlying regulatory mechanism, the interrelationships among genes, and how genes are regulated remain unexplored. MicroRNAs (miRNAs) are attracting attention as regulators of gene expression, including during biotic stress responses. The main objective of this study was to understand how miRNAs regulate clubroot resistance-related genes in P. brassicae-infected Brassica rapa. Two Brassica miRNAs, Bra-miR1885a and Bra-miR1885b, were revealed to target TIR-NBS genes. In non-infected plants, both miRNAs were expressed at low levels to maintain the balance between plant development and basal immunity. However, their expression levels increased in P. brassicae-infected plants. Both miRNAs down-regulated the expression of the TIR-NBS genes Bra019412 and Bra019410, which are located at a clubroot resistance-related quantitative trait locus. The Bra-miR1885-mediated down-regulation of both genes was detected for up to 15 days post-inoculation in the clubroot-resistant line CR Shinki and in the clubroot-susceptible line 94SK. A qRT-PCR analysis revealed Bra019412 expression was negatively regulated by miR1885. Both Bra019412 and Bra019410 were more highly expressed in CR Shinki than in 94SK; the same expression pattern was detected in multiple clubroot-resistant and clubroot-susceptible inbred lines. A 5′ rapid amplification of cDNA ends analysis confirmed the cleavage of Bra019412 by Bra-miR1885b. Thus, miR1885s potentially regulate TIR-NBS gene expression during P. brassicae infections of B. rapa.

Genome-Wide Association Mapping and Gene Expression Analysis Reveal the Negative Role of OsMYB21 in Regulating Bacterial Blight Resistance in Rice

BACKGROUND

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases in rice all over the world. Due to the diversity and rapid evolution of Xoo, identification and use of the non-race specific quantitative resistance QTLs has been considered the preferred strategy for effective control of this disease. Although numerous QTLs for BB resistance have been identified, they haven't been effectively used for improvement of BB resistance in rice due to their small effects and lack of knowledge on the function of genes underlying the QTLs.

RESULTS

In the present study, a genome-wide association study of BB resistance was performed in a rice core collection from South China. A total of 17 QTLs were identified to be associated with BB resistance. Among them, 13 QTLs were newly identified in the present study and the other 4 QTLs were co-localized with the previously reported QTLs or Xa genes that confer qualitative resistance to Xoo strains. Particularly, the qBBR11-4 on chromosome 11 explained the largest phenotypic variation in this study and was co-localized with the previously identified QTLs for BB and bacterial leaf streak (BLS) resistance against diverse strains in three studies, suggesting its broad-spectrum resistance and potential value in rice breeding. Through combined analysis of differential expression and annotations of the predicted genes within qBBR11-4 between two sets of rice accessions selected based on haplotypes and disease phenotypes, we identified the transcription factor OsMYB21 as the candidate gene for qBBR11-4. The OsMYB21 overexpressing plants exhibited decreased resistance to bacterial blight, accompanied with down-regulation of several defense-related genes compared with the wild-type plants.

CONCLUSION

The results suggest that OsMYB21 negatively regulates bacterial blight resistance in rice, and this gene can be a promising target in rice breeding by using the gene editing method. In addition, the potential candidate genes for the 13 novel QTLs for BB resistance were also analyzed in this study, providing a new source for cloning of genes associated with BB resistance and molecular breeding in rice.

The OsOXO2, OsOXO3 and OsOXO4 Positively Regulate Panicle Blast Resistance in Rice

BACKGROUND

Although panicle blast is more destructive to yield loss than leaf blast in rice, the cloned genes that function in panicle blast resistance are still very limited and the molecular mechanisms underlying panicle blast resistance remain largely unknown.

RESULTS

In the present study, we have confirmed that the three Oxalate oxidase (OXO) genes, OsOXO2, OsOXO3 and OsOXO4 from a blast-resistant cultivar BC10 function in panicle blast resistance in rice. The expression of OsOXO2, OsOXO3 and OsOXO4 were induced by panicle blast inoculation. Subcellular localization analysis revealed that the three OXO proteins are all localized in the nucleus and cytoplasm. Simultaneous silencing of OsOXO2, OsOXO3 and OsOXO4 decreased rice resistance to panicle blast, whereas the OsOXO2, OsOXO3 and OsOXO4 overexpression rice plants individually showed enhanced panicle blast resistance. More H₂O₂ and higher expression levels of PR genes were observed in the overexpressing plants than in the control plants, while the silencing plants exhibited less H₂O₂ and lower expression levels of PR genes compared to the control plants. Moreover, phytohormone treatment and the phytohormone signaling related gene expression analysis showed that panicle blast resistance mediated by the three OXO genes was associated with the activation of JA and ABA signaling pathways but suppression of SA signaling pathway.

CONCLUSION

OsOXO2, OsOXO3 and OsOXO4 positively regulate panicle blast resistance in rice. The OXO genes could modulate the accumulation of H₂O₂ and expression levels of PR gene in plants. Moreover, the OXO genes mediated panicle blast resistance could be regulated by ABA, SA and JA, and may be associated with the activation of JA and ABA signaling pathways but suppression of the SA signaling pathway.

A Rice NBS-ARC Gene Conferring Quantitative Resistance to Bacterial Blight Is Regulated by a Pathogen Effector-Inducible miRNA

The bacterium Xanthomonas oryzae pv. Oryzae (Xoo) causes blight in rice worldwide, resulting in significant crop loss. However, no gene underlying a quantitative trait locus (QTL) for resistance against Xoo has been cloned yet. Here, we report the map-based cloning of a QTL, in which the NBS8R gene confers quantitative resistance to Xoo. NBS8R encodes an NB-ARC protein, which is involved in pathogen/microbe-associated molecular pattern-triggered immunity and whose expression is regulated by non-TAL effector XopQ-inducible Osa-miR1876 through DNA methylation. Sequence analysis of NBS8R in wild rice species and rice cultivars suggests that the Osa-miR1876 binding sites in the 5' UTR of NBS8R are inserted by chance and have undergone variations with Osa-miR1876 throughout evolution. The interaction between NBS8R and XopQ-inducible Osa-miR1876 is partially in keeping with the zigzag model, revealing that quantitative genes may also follow this model to control the innate immune response or basal disease resistance, and may prove valuable in utilizing the existing landraces that harbor the NBS8R gene but with no Osa-miR1876 binding site in rice breeding for bacterial blight resistance.

Genetic analysis and fine mapping of the gall midge resistance gene Gm5 in rice (Oryza sativa L.)

The rice gall midge resistance gene, Gm5, confers remarkable antibiosis and is located in the same region on chromosome 12 in three different rice varieties. Fine mapping narrowed this region to a 49-kb segment and identified two candidate genes showing remarkable response to GM infestation. The Asian rice gall midge (GM; Orseolia oryzae; Diptera: Cecidomyiidae) invades rice shoots and forms galls, adversely affecting plant growth and yield production. Thus, the development of resistant varieties through the identification, mapping, and application of GM resistance genes is considered the most efficient strategy for managing this insect. Here, a GM resistance survey of F₂ populations derived from intercrosses between resistant rice varieties 'ARC5984,' '570011,' and 'ARC5833' indicated that the resistance gene Gm5 was located on the same chromosomal region in the three varieties. For the initial mapping, three independent F₂ mapping populations were developed for the three resistant varieties, and the Gm5 gene was consistently mapped to the same chromosomal region near marker 12M22.6. Fine mapping, which was conducted using the BC₁F₂ and BC₂F₂ populations derived from the 9311/ARC5984 cross, narrowed the Gm5 gene region to a 49-kb segment flanked by the markers Z57 and Z64. In the final mapped region, we detected 10 candidate genes, of which six were analyzed for their relative expression. Consequently, two of these genes, Os12g36830 and Os12g36880, showed significantly higher expression in GM-resistant plants than in GM-susceptible plants at 24 and 72 h after GM infestation. Finally, the PCR amplification of markers 12M22.5 and 12M22.6 yielded clear single bands, and these markers were effectively applied for the marker-assisted selection (MAS) of the Gm5 gene. With the developed MAS markers, the fine mapping of this resistance gene will facilitate its map-based cloning and incorporation into insect-resistant rice varieties through breeding.

Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice

Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.

QTL mapping for resistance to and tolerance for the rice root-knot nematode, Meloidogyne graminicola

Background

The root-knot nematode Meloidogyne graminicola is an obligate biotrophic pathogen considered to be the most damaging nematode species that causes significant yield losses to upland and rainfed lowland rice production in South and Southeast Asia. Mapping and identification of quantitative trait loci (QTL) for resistance to and tolerance for M. graminicola may offer a safe and economic management option to farmers. In this study, resistance to and tolerance for M. graminicola in Asian rice (Oryza sativa L.) were studied in a mapping population consisting of 300 recombinant inbred lines (RILs) derived from IR78877–208-B-1-2, an aerobic rice genotype with improved resistance to and tolerance for M. graminicola, and IR64, a popular, high-yielding rice mega-variety susceptible to M. graminicola. RILs were phenotyped for resistance and tolerance in the dry seasons of 2012 and 2013. QTL analysis was performed using 131 single nucleotide polymorphism (SNP) and 33 simple sequence repeat (SSR) markers.

Results

Three QTLs with main effects on chromosomes 4 (qMGR_4.1), 7 (qMGR_7.1) and 9 (qMGR_9.1) and two epistatic interactions (qMGR_3.1/ qMGR_11.1 and qMGR_4.2/ qMGR_8.1) associated with nematode reproduction that were consistent in the two seasons were detected. A QTL affecting root galling was found on chromosomes 4 (qGR_4.1) and 8 (qGR_8.1), and QTLs for nematode tolerance were found on chromosomes 5 (qYR_5.1) and 11 (qYR_11.1). These QTLs were consistent in both seasons. A QTL for grain yield was found on chromosome 10 (qGYLD_10.1), a QTL affecting filled grains per panicle was detected on chromosome 11 (qFG_11.1) and a QTL for fresh root weight was found on chromosomes 2 (qFRWt_2.1), 8 (qFRWt_8.1) and 12 (qFRWt_12.1) in both seasons. The donor of the alleles for qMGR_4.1, qMGR_7.1, qMGR_9.1, qGR_4.1, qGR_8.1, qYR_5.1 and qFRWt_2.1 was IR78877–208-B-1-2, whereas for qYR_11.1, qGYLD_10.1 and qFG_11.1, qFRWt_8.1 and qFRWt_12.1 was IR64. Lines having favorable alleles for resistance, tolerance and yield provided better yield under nematode-infested conditions and could be a starting point of marker-assisted breeding (MAB) for the improvement of M. graminicola resistance and tolerance in Asian rice.

Conclusion

This study identified a total of 12 QTLs with main effects and two epistatic interactions in the 1st season and 2nd season related to M. graminicola resistance and tolerance, and other agronomic traits such as plant yield, percentage of filled grains, and fresh and dry root weight. Rice genotypes that have the favorable alleles for resistance (qMGR_4.1, qMGR_7.1, qMGR_9.1, qGR_4.1, qGR_8.1) and tolerance (qYR_5.1, and qYR_11.1,) QTLs, and which are either resistant or partially resistant and tolerant, were also selected. These selected genotypes and the identified QTLs are vital information in designing MAB for the improvement of high-yielding rice genotypes but are susceptible to M. graminicola infection.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0656-1) contains supplementary material, which is available to authorized users.

Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes.

Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi-Environmental Analysis

Cassava, Manihot esculenta Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to two Xam strains (Xam318 and Xam681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response to Xam revealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance to Xam explaining between 15.8 and 22.1% of phenotypic variance, were detected and localized on a high resolution SNP-based genetic map of cassava. Four of them show stability among the two evaluated seasons. Genotype by environment analysis detected three QTL by environment interactions and the broad sense heritability for Xam318 and Xam681 were 20 and 53%, respectively. DNA sequence analysis of the QTL intervals revealed 29 candidate defense-related genes (CDRGs), and two of them contain domains related to plant immunity proteins, such as NB-ARC-LRR and WRKY.

Distinctive features and differential regulation of the DRTS genes of Arabidopsis thaliana

In plants and protists, dihydrofolate reductase (DHFR) and thymidylate synthase (TS) are part of a bifunctional enzyme (DRTS) that allows efficient recycling of the dihydrofolate resulting from TS activity. Arabidopsis thaliana possesses three DRTS genes, called AtDRTS1, AtDRTS2 and AtDRTS3, that are located downstream of three members of the sec14-like SFH gene family. In this study, a characterization of the AtDRTS genes identified alternatively spliced transcripts coding for AtDRTS isoforms which may account for monofunctional DHFR enzymes supporting pathways unrelated to DNA synthesis. Moreover, we discovered a complex differential regulation of the AtDRTS genes that confirms the expected involvement of the AtDRTS genes in cell proliferation and endoreduplication, but indicates also functions related to other cellular activities. AtDRTS1 is widely expressed in both meristematic and differentiated tissues, whereas AtDRTS2 expression is almost exclusively limited to the apical meristems and AtDRTS3 is preferentially expressed in the shoot apex, in stipules and in root cap cells. The differential regulation of the AtDRTS genes is associated to distinctive promoter architectures and the expression of AtDRTS1 in the apical meristems is strictly dependent on the presence of an intragenic region that includes the second intron of the gene. Upon activation of cell proliferation in germinating seeds, the activity of the AtDRTS1 and AtDRTS2 promoters in meristematic cells appears to be maximal at the G1/S phase of the cell cycle. In addition, the promoters of AtDRTS2 and AtDRTS3 are negatively regulated through E2F cis-acting elements and both genes, but not AtDRTS1, are downregulated in plants overexpressing the AtE2Fa factor. Our study provides new information concerning the function and the regulation of plant DRTS genes and opens the way to further investigations addressing the importance of folate synthesis with respect to specific cellular activities.

Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene

Magnaporthe oryzae infection causes rice blast, a destructive disease that is responsible for considerable decrease in rice yield. Development of resistant varieties via introgressing resistance genes with marker-assisted breeding can eliminate pesticide use and minimize crop losses. Here, resistant near-isogenic line (NIL) of Pusa Basmati-1(PB1) carrying broad spectrum rice blast resistance gene Pi9 was used to investigate Pi9-mediated resistance response. Infected and uninfected resistant NIL and susceptible control line were subjected to RNA-Seq. With the exception of one gene (Pi9), transcriptional signatures between the two lines were alike, reflecting basal similarities in their profiles. Resistant and susceptible lines possessed 1043 (727 up-regulated and 316 down-regulated) and 568 (341 up-regulated and 227 down-regulated) unique and significant differentially expressed loci (SDEL), respectively. Pathway analysis revealed higher transcriptional activation of kinases, WRKY, MYB, and ERF transcription factors, JA-ET hormones, chitinases, glycosyl hydrolases, lipid biosynthesis, pathogenesis and secondary metabolism related genes in resistant NIL than susceptible line. Singular enrichment analysis demonstrated that blast resistant NIL is significantly enriched with genes for primary and secondary metabolism, response to biotic stimulus and transcriptional regulation. The co-expression network showed proteins of genes in response to biotic stimulus interacted in a manner unique to resistant NIL upon M. oryzae infection. These data suggest that Pi9 modulates genome-wide transcriptional regulation in resistant NIL but not in susceptible PB1. We successfully used transcriptome profiling to understand the molecular basis of Pi9-mediated resistance mechanisms, identified potential candidate genes involved in early pathogen response and revealed the sophisticated transcriptional reprogramming during rice-M. oryzae interactions.

QTL identification for cassava bacterial blight resistance under natural infection conditions

La yuca, Manihot esculenta Crantz, representa la principal fuente de alimento para cerca de 1000 millones de personas. La producción de yuca se ve afectada por diversas enfermedades, una de las más serias es la bacteriosis vascular (CBB) causada por Xanthomonas axonopodis pv. manihotis (Xam). En este estudio se realizó un análisis de loci de rasgos cuantitativos (QTL) para la resistencia a CBB en condiciones naturales de infección, usando una población de mapeo constituida por 99 genotipos de hermanos completos segregantes y un mapa genético altamente denso basado en SNPs. La evaluación fenotípica se llevó a cabo en Puerto López (Meta), Colombia, durante la época de lluvias durante el segundo semestre de 2015. En la población de mapeo fueron detectados individuos con una segregación transgresiva tanto resistentes como susceptibles. A través de un análisis no paramétrico de intervalo simple, se detectaron dos QTL que explican el 10,9 y el 12,6 % de la varianza fenotípica de la resistencia en campo a CBB. Mediante análisis bioinformáticos se identificaron cuatro genes candidatos presentes en los intervalos de los QTL. Este trabajo representa un esfuerzo por dilucidar los mecanismos moleculares implicados en la resistencia de yuca a CBB.

Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.)

BACKGROUND

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains.

RESULTS

The reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map.

CONCLUSION

We characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.

Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice

Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.

The germin-like protein OsGLP2-1 enhances resistance to fungal blast and bacterial blight in rice

This is the first report that GLP gene (OsGLP2-1) is involved in panicle blast and bacterial blight resistance in rice. In addition to its resistance to blast and bacterial blight, OsGLP2-1 has also been reported to co-localize with a QTLs for sheath blight resistance in rice. These suggest that the disease resistance provided by OsGLP2-1 is quantitative and broad spectrum. Its good resistance to these major diseases in rice makes it to be a promising target in rice breeding. Rice (Oryza sativa) blast caused by Magnaporthe oryzae and bacterial blight caused by Xanthomonas oryzae pv. oryzae are the two most destructive rice diseases worldwide. Germin-like protein (GLP) gene family is one of the important defense gene families which have been reported to be involved in disease resistance in plants. Although GLP proteins have been demonstrated to positively regulate leaf blast resistance in rice, their involvement in resistance to panicle blast and bacterial blight, has not been reported. In this study, we reported that one of the rice GLP genes, OsGLP2-1, was significantly induced by blast fungus. Overexpression of OsGLP2-1 quantitatively enhanced resistance to leaf blast, panicle blast and bacterial blight. The temporal and spatial expression analysis revealed that OsGLP2-1is highly expressed in leaves and panicles and sub-localized in the cell wall. Compared with empty vector transformed (control) plants, the OsGLP2-1 overexpressing plants exhibited higher levels of H₂O₂ both before and after pathogen inoculation. Moreover, OsGLP2-1 was significantly induced by jasmonic acid (JA). Overexpression of OsGLP2-1 induced three well-characterized defense-related genes which are associated in JA-dependent pathway after pathogen infection. Higher endogenous level of JA was also identified in OsGLP2-1 overexpressing plants than in control plants both before and after pathogen inoculation. Together, these results suggest that OsGLP2-1 functions as a positive regulator to modulate disease resistance. Its good quantitative resistance to the two major diseases in rice makes it to be a promising target in rice breeding.

Multiple Disease Resistance in Plants

Many plants, both in nature and in agriculture, are resistant to multiple diseases. Although much of the plant innate immunity system provides highly specific resistance, there is emerging evidence to support the hypothesis that some components of plant defense are relatively nonspecific, providing multiple disease resistance (MDR). Understanding MDR is of fundamental and practical interest to plant biologists, pathologists, and breeders. This review takes stock of the available evidence related to the MDR hypothesis. Questions about MDR are considered primarily through the lens of forward genetics, starting at the organismal level and proceeding to the locus level and, finally, to the gene level. At the organismal level, MDR may be controlled by clusters of R genes that evolve under diversifying selection, by dispersed, pathogen-specific genes, and/or by individual genes providing MDR. Based on the few MDR loci that are well-understood, MDR is conditioned by diverse mechanisms at the locus and gene levels.

A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana

Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.

OsGF14b Positively Regulates Panicle Blast Resistance but Negatively Regulates Leaf Blast Resistance in Rice

Although 14-3-3 proteins have been reported to be involved in responses to biotic stresses in plants, their functions in rice blast, the most destructive disease in rice, are largely unknown. Only GF14e has been confirmed to negatively regulate leaf blast. We report that GF14b is highly expressed in seedlings and panicles during blast infection. Rice plants overexpressing GF14b show enhanced resistance to panicle blast but are susceptible to leaf blast. In contrast, GF14b-silenced plants show increased susceptibility to panicle blast but enhanced resistance to leaf blast. Yeast one-hybrid assays demonstrate that WRKY71 binds to the promoter of GF14b and modulates its expression. Overexpression of GF14b induces expression of jasmonic acid (JA) synthesis-related genes but suppresses expression of salicylic acid (SA) synthesis-related genes. In contrast, suppressed GF14b expression causes decreased expression of JA synthesis-related genes but activation of SA synthesis-related genes. These results suggest that GF14b positively regulates panicle blast resistance but negatively regulates leaf blast resistance, and that GF14b-mediated disease resistance is associated with the JA- and SA-dependent pathway. The different functions for 14-3-3 proteins in leaf and panicle blast provide new evidence that leaf and panicle blast resistance are controlled by different mechanisms.

A new finely mapped Oryza australiensis-derived QTL in rice confers resistance to brown planthopper

Brown planthopper (BPH) is the most destructive pest of rice in Asia. The BPH resistance in the introgression line IR65482-17-511-5-7 (IR65482-17) is derived from the wild rice species Oryza australiensis. An F2:3 population from a cross between Zhenshan 97 (ZS97) and IR65482-17 was used to map three quantitative trait loci (QTLs) for seedling resistance and feeding rate to BPH. The loci were distributed on chromosomes 2, 4 and 12. The QTL qBph4.2 on chromosome 4 had the largest effect, and contributed 36-44% of the phenotypic variance with a LOD score of 19-29. To validate the effect of qBph4.2, two near-isogenic lines (NILs) containing the qBph4.2 locus in the backgrounds of ZS97 and 9311 were developed by marker-assisted backcrossing (MABC). BPH bioassays showed that lines homozygous for the IR65482-17 allele (NIL+) of qBph4.2 tented to have significantly higher seedling resistance to BPH than those homozygous for the ZS97 or 9311 alleles (NIL-). Resistance was associated with a lower feeding rate by the insect. qBph4.2 was delimited to a ~300 kb (0.04 cM) region flanked by markers RM261 and S1, and co-segregating with XC4-27. This study will facilitate map-based cloning and marker-assisted selection of the gene, and permits further studies of gene function and resistance mechanisms in rice: BPH interaction.

Rice phenylalanine ammonia-lyase gene OsPAL4 is associated with broad spectrum disease resistance

Most agronomically important traits, including resistance against pathogens, are governed by quantitative trait loci (QTL). QTL-mediated resistance shows promise of being effective and long-lasting against diverse pathogens. Identification of genes controlling QTL-based disease resistance contributes to breeding for cultivars that exhibit high and stable resistance. Several defense response genes have been successfully used as good predictors and contributors to QTL-based resistance against several devastating rice diseases. In this study, we identified and characterized a rice (Oryza sativa) mutant line containing a 750 bp deletion in the second exon of OsPAL4, a member of the phenylalanine ammonia-lyase gene family. OsPAL4 clusters with three additional OsPAL genes that co-localize with QTL for bacterial blight and sheath blight disease resistance on rice chromosome 2. Self-pollination of heterozygous ospal4 mutant lines produced no homozygous progeny, suggesting that homozygosity for the mutation is lethal. The heterozygous ospal4 mutant line exhibited increased susceptibility to three distinct rice diseases, bacterial blight, sheath blight, and rice blast. Mutation of OsPAL4 increased expression of the OsPAL2 gene and decreased the expression of the unlinked OsPAL6 gene. OsPAL2 function is not redundant because the changes in expression did not compensate for loss of disease resistance. OsPAL6 co-localizes with a QTL for rice blast resistance, and is down-regulated in the ospal4 mutant line; this may explain enhanced susceptibility to Magnoporthe oryzae. Overall, these results suggest that OsPAL4 and possibly OsPAL6 are key contributors to resistance governed by QTL and are potential breeding targets for improved broad-spectrum disease resistance in rice.

Transcriptome Analysis of Early Responsive Genes in Rice during Magnaporthe oryzae Infection

Rice blast disease caused by Magnaporthe oryzae is one of the most serious diseases of cultivated rice (Oryza sativa L.) in most rice-growing regions of the world. In order to investigate early response genes in rice, we utilized the transcriptome analysis approach using a 300 K tilling microarray to rice leaves infected with compatible and incompatible M. oryzae strains. Prior to the microarray experiment, total RNA was validated by measuring the differential expression of rice defense-related marker genes (chitinase 2, barwin, PBZ1, and PR-10) by RT-PCR, and phytoalexins (sakuranetin and momilactone A) with HPLC. Microarray analysis revealed that 231 genes were up-regulated (>2 fold change, p < 0.05) in the incompatible interaction compared to the compatible one. Highly expressed genes were functionally characterized into metabolic processes and oxidation-reduction categories. The oxidative stress response was induced in both early and later infection stages. Biotic stress overview from MapMan analysis revealed that the phytohormone ethylene as well as signaling molecules jasmonic acid and salicylic acid is important for defense gene regulation. WRKY and Myb transcription factors were also involved in signal transduction processes. Additionally, receptor-like kinases were more likely associated with the defense response, and their expression patterns were validated by RT-PCR. Our results suggest that candidate genes, including receptor-like protein kinases, may play a key role in disease resistance against M. oryzae attack.

Genetic analysis and QTL detection for resistance to white tip disease in rice

The inheritance of resistance to white tip disease (WTDR) in rice (Oryza sativa L.) was analyzed with an artificial inoculation test in a segregating population derived from the cross between Tetep, a highly resistant variety that was identified in a previous study, and a susceptible cultivar. Three resistance-associated traits, including the number of Aphelenchoides besseyi (A. besseyi) individuals in 100 grains (NA), the loss rate of panicle weight (LRPW) and the loss rate of the total grains per panicle (LRGPP) were analyzed for the detection of the quantitative trait locus (QTL) in the population after construction of a genetic map. Six QTLs distributed on chromosomes 3, 5 and 9 were mapped. qNA3 and qNA9, conferring reproduction number of A. besseyi in the panicle, accounted for 16.91% and 12.54% of the total phenotypic variance, respectively. qDRPW5a and qDRPW5b, associated with yield loss, were located at two adjacent marker intervals on chromosome 5 and explained 14.15% and 14.59% of the total phenotypic variation and possessed LOD values of 3.40 and 3.39, respectively. qDRPW9 was considered as a minor QTL and only explained 1.02% of the phenotypic variation. qLRGPP5 contributed to the loss in the number of grains and explained 10.91% of the phenotypic variation. This study provides useful information for the breeding of resistant cultivars against white tip disease in rice.

Unraveling genomic complexity at a quantitative disease resistance locus in maize

Multiple disease resistance has important implications for plant fitness, given the selection pressure that many pathogens exert directly on natural plant populations and indirectly via crop improvement programs. Evidence of a locus conditioning resistance to multiple pathogens was found in bin 1.06 of the maize genome with the allele from inbred line "Tx303" conditioning quantitative resistance to northern leaf blight (NLB) and qualitative resistance to Stewart's wilt. To dissect the genetic basis of resistance in this region and to refine candidate gene hypotheses, we mapped resistance to the two diseases. Both resistance phenotypes were localized to overlapping regions, with the Stewart's wilt interval refined to a 95.9-kb segment containing three genes and the NLB interval to a 3.60-Mb segment containing 117 genes. Regions of the introgression showed little to no recombination, suggesting structural differences between the inbred lines Tx303 and "B73," the parents of the fine-mapping population. We examined copy number variation across the region using next-generation sequencing data, and found large variation in read depth in Tx303 across the region relative to the reference genome of B73. In the fine-mapping region, association mapping for NLB implicated candidate genes, including a putative zinc finger and pan1. We tested mutant alleles and found that pan1 is a susceptibility gene for NLB and Stewart's wilt. Our data strongly suggest that structural variation plays an important role in resistance conditioned by this region, and pan1, a gene conditioning susceptibility for NLB, may underlie the QTL.

Relationship between disease resistance and rice oxalate oxidases in transgenic rice

Differential expression of rice oxalate oxidase genes (OsOxO1-4) in rice leaves (Oryza sativa L.) in response to biotic stress was assayed using RT-PCR. OsOxO4 was induced transiently at 12 h in plants inoculated with the pathogens of bacterial blight and that of the wounding control. Inoculation with the rice blast pathogen induced OsOxO2 expression compared to the mock spray control. Overexpressing OsOxO1 or OsOxO4 in rice resulted in elevated transcript levels of the respective transgene as well as OsOxO3 in leaves compared to that in untransformed wild type (WT). In a line of RNA-i transgenic rice plants (i-12), expression of all four OsOxO genes except that of OsOxO2 was severely inhibited. Oxalate oxidase (OxO, EC 1.2.3.4) activity in plants overexpressing OsOxO1 or OsOxO4 was substantially higher than that in WT and the RNA-i lines. It was found that transgenic rice plants with substantially higher OxO activity were not more resistant to rice blast and bacterial blight than WT. In contrast, some RNA-i lines with less OxO activity seemed to be more resistant to rice blast while some overexpressing lines were more susceptible to rice blast than WT. Therefore, OxO might not be a disease resistance factor in rice.

Genetic variability of oxalate oxidase activity and elongation in water-stressed primary roots of diverse maize and rice lines

A previous study of maize primary roots under water stress showed pronounced increases in oxalate oxidase activity and apoplastic hydrogen peroxide in the apical region of the growth zone where cell elongation is maintained. We examined whether increased oxalate oxidase activity in water-stressed roots is conserved across diverse lines of maize and rice. The maize lines exhibited varied patterns of activity, with some lines lacking activity in the apical region. Moreover, none of the rice lines showed activity in the apical region. Also, although the genotypic response of root elongation to water stress was variable in both maize and rice, this was not correlated with the pattern of oxalate oxidase activity. Implications of these findings for root growth regulation under water stress are discussed.

[Genetic analysis and molecular mapping of a high-tillering mutant (ht1) in rice.]

A rice (Oryza sativa L.) mutant with a high-tillering capacity, designated as ht1, was found from a japonica rice variety Xindao18. This high-tillering mutant phenotype was stably expressed through successive five self-crossed generations, and the number of tillers in mutants was three times more than that in wild-type rice. Genetic analysis showed that the phenotype of ht1was controlled by a single dominant nuclear gene, temporarily designated as HT1. By means of molecular marker technique, the HT1 gene was mapped to an interval between two SSR markers RM25435 and RM25552 on chro-mosome 10. Through high-resolution linkage analysis, the HT1 gene was further restricted to a 0.1 cM region flanked by two SSR markers RM25523 and RM25532. The physical distance between these two markers is about 130kb.

Approaches towards nitrogen- and phosphorus-efficient rice

BACKGROUND AND AIMS

Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.

SCOPE

Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.

MAIN POINTS

For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.

The arbuscular mycorrhizal symbiosis promotes the systemic induction of regulatory defence-related genes in rice leaves and confers resistance to pathogen infection

Arbuscular mycorrhizal (AM) symbioses are mutualistic associations between soil fungi and most vascular plants. Their association benefits the host plant by improving nutrition, mainly phosphorus nutrition, and by providing increased capability to cope with adverse conditions. In this study, we investigated the transcriptional changes triggered in rice leaves as a result of AM symbiosis, focusing on the relevance of the plant defence response. We showed that root colonization by the AM fungus Glomus intraradices is accompanied by the systemic induction of genes that play a regulatory role in the host defence response, such as OsNPR1, OsAP2, OsEREBP and OsJAmyb. Genes involved in signal transduction processes (OsDUF26 and OsMPK6) and genes that function in calcium-mediated signalling processes (OsCBP, OsCaM and OsCML4) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection. In addition, the mycorrhizal rice plants exhibit a stronger induction of defence marker genes [i.e. pathogenesis-related (PR) genes] in their leaves in response to infection by the blast fungus Magnaporthe oryzae. Evidence indicates that mycorrhizal rice plants show enhanced resistance to the rice blast fungus. Overall, these results suggest that the protective effect of the AM symbiosis in rice plants relies on both the systemic activation of defence regulatory genes in the absence of pathogen challenge and the priming for stronger expression of defence effector genes during pathogen infection. The possible mechanisms involved in the mycorrhiza-induced resistance to M. oryzae infection are discussed.

Association of a novel Pinus monticola chitinase gene (PmCh4B) with quantitative resistance to Cronartium ribicola

Multiple families of pathogenesis-related (PR) proteins are believed to contribute to plant quantitative resistance to various pathogens. Along with other host PR proteins, PR3 chitinase is one protein component participating in genetic resistance of western white pine (Pinus monticola) to the white pine blister rust (WPBR) pathogen (Cronartium ribicola). In the present study, we characterized a novel P. monticola class IV chitinase gene (PmCh4B) and further analyzed its nucleotide variations in the open-pollinated seed families of diverse geographical distribution and variable levels of quantitative resistance to C. ribicola infection. PmCh4B showed high haplotype diversity (Hd=0.94) and nucleotide diversity (π=0.00965), similar to those of other conifer genes related to environmental stresses. A low level of intragenic linkage disequilibrium (LD) (but most of the levels with statistical significance) was found within a distance of ≈800 bp. Based on PmCh4B haplotype frequency, moderate to high levels of population structure were observed among P. monticola seed families currently used in breeding programs for WPBR resistance (average FST=0.163, P<0.001). Association analysis revealed that allelic variants and multiple single-nucleotide polymorphisms of PmCh4B were significantly associated with quantitative levels of P. monticola resistance against C. ribicola. This work represents the first association study for quantitative resistance in western white pine pathosystem and provides a potential for marker-assisted selection in white pine breeding.

Targeted discovery of quantitative trait loci for resistance to northern leaf blight and other diseases of maize

To capture diverse alleles at a set of loci associated with disease resistance in maize, heterogeneous inbred family (HIF) analysis was applied for targeted QTL mapping and near-isogenic line (NIL) development. Tropical maize lines CML52 and DK888 were chosen as donors of alleles based on their known resistance to multiple diseases. Chromosomal regions ("bins"; n = 39) associated with multiple disease resistance (MDR) were targeted based on a consensus map of disease QTLs in maize. We generated HIFs segregating for the targeted loci but isogenic at ~97% of the genome. To test the hypothesis that CML52 and DK888 alleles at MDR hotspots condition broad-spectrum resistance, HIFs and derived NILs were tested for resistance to northern leaf blight (NLB), southern leaf blight (SLB), gray leaf spot (GLS), anthracnose leaf blight (ALB), anthracnose stalk rot (ASR), common rust, common smut, and Stewart's wilt. Four NLB QTLs, two ASR QTLs, and one Stewart's wilt QTL were identified. In parallel, a population of 196 recombinant inbred lines (RILs) derived from B73 × CML52 was evaluated for resistance to NLB, GLS, SLB, and ASR. The QTLs mapped (four for NLB, five for SLB, two for GLS, and two for ASR) mostly corresponded to those found using the NILs. Combining HIF- and RIL-based analyses, we discovered two disease QTLs at which CML52 alleles were favorable for more than one disease. A QTL in bin 1.06-1.07 conferred resistance to NLB and Stewart's wilt, and a QTL in 6.05 conferred resistance to NLB and ASR.

Transcriptional responses of Italian ryegrass during interaction with Xanthomonas translucens pv. graminis reveal novel candidate genes for bacterial wilt resistance

Xanthomonas translucens pv. graminis (Xtg) causes bacterial wilt, a severe disease of forage grasses such as Italian ryegrass (Lolium multiflorum Lam.). In order to gain a more detailed understanding of the genetic control of resistance mechanisms and to provide prerequisites for marker assisted selection, the partial transcriptomes of two Italian ryegrass genotypes, one resistant and one susceptible to bacterial wilt were compared at four time points after Xtg infection. A cDNA microarray developed from a perennial ryegrass (Lolium perenne) expressed sequence tag set consisting of 9,990 unique genes was used for transcriptome analysis in Italian ryegrass. An average of 4,487 (45%) of the perennial ryegrass sequences spotted on the cDNA microarray were detected by cross-hybridisation to Italian ryegrass. Transcriptome analyses of the resistant versus the susceptible genotype revealed substantial gene expression differences (>1,200) indicating that great gene expression differences between different Italian ryegrass genotypes exist which potentially contribute to the observed phenotypic divergence in Xtg resistance between the two genotypes. In the resistant genotype, several genes differentially expressed after Xtg inoculation were identified which revealed similarities to transcriptional changes triggered by pathogen-associated molecular patterns in other plant-pathogen interactions. These genes represent candidate genes of particular interest for the development of tools for marker assisted resistance breeding.

High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds

Brown planthopper (Nilaparvata lugens Stål, BPH) is one of the most destructive insect pests of rice. Exploring resistance genes from diverse germplasms and incorporating them into cultivated varieties are critical for controlling this insect. The rice variety Swarnalata was reported to carry a resistance gene (designated Bph6), which has not yet been assigned to a chromosome location and the resistance mechanism is still unknown. In this study, we identified and mapped this gene using the F(2) and backcrossing populations and characterized its resistance in indica 9311 and japonica Nipponbare using near isogenic lines (NILs). In analysis of 9311/Swarnalata F(2) population, the Bph6 gene was located on the long arm of chromosome 4 between the SSR markers RM6997 and RM5742. The gene was further mapped precisely to a 25-kb region delimited between the STS markers Y19 and Y9; and the distance between these markers is 25-kb in Nipponbare genome. The Bph6 explained 77.5% of the phenotypic variance of BPH resistance in F(2) population and 84.9% in BC(2)F(2) population. Allele from Swarnalata significantly increased resistance to the BPH, resulted in a reduced damage score. In characterization of Bph6-mediated resistance, the BPH insects showed significant preference between NIL-9311 and 9311 in 3 h and between NIL-NIP and Nipponbare in 120 h after release. BPH growth and development were inhibited, and the insect's survival rates were lower on Bph6-NIL plants, compared with the parents 9311 and Nipponbare. The results indicate that the Bph6 exerted prolonged antixenotic and antibiotic effects in Bph6-NIL plants, and NIL-9311 plants showed a quicker and stronger effect toward BPH than NIL-NIP plants.

Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence

The recent release of the genome sequences of a number of crop and model plant species has made it possible to define the genome organisation and functional characteristics of specific genes and gene families of agronomic importance. For instance, Sorghum bicolor, maize (Zea mays) and Brachypodium distachyon genome sequences along with the model grass species rice (Oryza sativa) enable the comparative analysis of genes involved in plant defence. Germin-like proteins (GLPs) are a small, functionally and taxonomically diverse class of cupin-domain containing proteins that have recently been shown to cluster in an area of rice chromosome 8. The genomic location of this gene cluster overlaps with a disease resistance QTL that provides defence against two rice fungal pathogens (Magnaporthe oryzae and Rhizoctonia solani). Studies showing the involvement of GLPs in basal host resistance against powdery mildew (Blumeria graminis ssp.) have also been reported in barley and wheat. In this mini-review, we compare the close proximity of GLPs in publicly available cereal crop genomes and discuss the contribution that these proteins, and their genome sequence organisation, play in plant defence.

Peroxidase profiling reveals genetic linkage between peroxidase gene clusters and basal host and non-host resistance to rusts and mildew in barley

BACKGROUND

Higher plants possess a large multigene family encoding secreted class III peroxidase (Prx) proteins. Peroxidases appear to be associated with plant disease resistance based on observations of induction during disease challenge and the presence or absence of isozymes in resistant vs susceptible varieties. Despite these associations, there is no evidence that allelic variation of peroxidases directly determines levels of disease resistance.

METHODOLOGY/PRINCIPAL FINDINGS

The current study introduces a new strategy called Prx-Profiling. We showed that with this strategy a large number of peroxidase genes can be mapped on the barley genome. In order to obtain an estimate of the total number of Prx clusters we followed a re-sampling procedure, which indicated that the barley genome contains about 40 peroxidase gene clusters. We examined the association between the Prxs mapped and the QTLs for resistance of barley to homologous and heterologous rusts, and to the barley powdery mildew fungus. We report that 61% of the QTLs for partial resistance to P. hordei, 61% of the QTLs for resistance to B. graminis and 47% of the QTLs for non-host resistance to other Puccinia species co-localize with Prx based markers.

CONCLUSIONS/SIGNIFICANCE

We conclude that Prx-Profiling was effective in finding the genetic location of Prx genes on the barley genome. The finding that QTLs for basal resistance to rusts and powdery mildew fungi tend to co-locate with Prx clusters provides a base for exploring the functional role of Prx-related genes in determining natural differences in levels of basal resistance.

A complex genetic network involving a broad-spectrum locus and strain-specific loci controls resistance to different pathotypes of Aphanomyces euteiches in Medicago truncatula

A higher understanding of genetic and genomic bases of partial resistance in plants and their diversity regarding pathogen variability is required for a more durable management of resistance genetic factors in sustainable cropping systems. In this study, we investigated the diversity of genetic factors involved in partial resistance to Aphanomyces euteiches, a very damaging pathogen on pea and alfalfa, in Medicago truncatula. A mapping population of 178 recombinant inbred lines, from the cross F83005.5 (susceptible) and DZA045.5 (resistant), was used to identify quantitative trait loci for resistance to four A. euteiches reference strains belonging to the four main pathotypes currently known on pea and alfalfa. A major broad-spectrum genomic region, previously named AER1, was localized to a reduced 440 kb interval on chromosome 3 and was involved in complete or partial resistance, depending on the A. euteiches strain. We also identified 21 additive and/or epistatic genomic regions specific to one or two strains, several of them being anchored to the M. truncatula physical map. These results show that, in M. truncatula, a complex network of genetic loci controls partial resistance to different pea and alfalfa pathotypes of A. euteiches, suggesting a diversity of molecular mechanisms underlying partial resistance.

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive genotypic and phenotypic diversity of domesticated rice. Here, we report the distribution of 160,000 nonredundant SNPs. Introgression patterns of shared SNPs revealed the breeding history and relationships among the 20 varieties; some introgressed regions are associated with agronomic traits that mark major milestones in rice improvement. These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement.

Mapping of STS markers obtained from oat resistance gene analog sequences

Two previously isolated resistance gene analogs (RGAs) of oat have been located as RFLPs in the reference map of Avena byzantina ‘Kanota’ × Avena sativa ‘Ogle’ in regions either homologous or homoeologous to loci for resistance to Puccinia coronata , the causal agent of crown rust. In this study, the RGAs were mapped in two recombinant inbred line (RIL) populations that segregate for crown rust resistance: the diploid Avena strigosa × Avena wiestii RIL population (Asw), which has been used for mapping the complex locus PcA, and the hexaploid MN841801-1 × Noble-2 RIL population (MN), in which QTLs have been located. To obtain single-locus markers, RGAs were converted to sequence tagged site (STS) markers using a procedure involving extension of the original RGA sequence lengths by PCR genome walking, amplification and cloning of the parental fragments, and identification of single nucleotide polymorphisms. The procedure successfully obtained STSs from different members of the L7M2 family of sequences, the initial NBS of which have nucleotide similarities of >83%. However, for RGA III2.18, the parental lines were not polymorphic for the STSs assayed. A sequence characterized amplified region (SCAR) marker with features of an RGA had been previously identified for gene Pc94. This marker was also mapped in the above RIL populations. Markers based on RGA L7M2 co-localized with markers defining the QTL Prq1a in linkage group MN3, and were located 15.2 cM from PcA in linkage group AswAC. The SCAR marker for Pc94 was also located in the QTL Prq1a but at 39.5 cM from PcA in AswAC, indicating that the NBS-LRR sequence represented by this marker is not related to PcA. L7M2 was also excluded as a member of the PcA cluster, although it could be an appropriate marker for the Prq1a cluster if chromosome rearrangements are postulated.

Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure

The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.

Nonhost and basal resistance: how to explain specificity?

Nonhost resistance to plant pathogens can be constitutive or induced by microbes. Successful pathogens suppress microbe-induced plant defences by delivering appropriate effectors, which are apparently not sufficiently effective on nonhost plant species, as can be concluded from the strong host specificity of many biotroph plant pathogens. Such effectors act on particular plant targets, such as promoters or motifs in expressed sequences. Despite much progress in the elucidation of the molecular aspects of nonhost resistance to plant pathogens, very little is known about the genes that determine whether effectors can or cannot suppress the basal defence. In hosts they can, in nonhosts they cannot. The targets determining the host status of plants can be identified in inheritance studies. Recent reports have indicated that nonhost resistance is inherited polygenically, and exhibits strong similarity and association with the basal resistance of plants to adapted pathogens.

Gramene QTL database: development, content and applications

Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene–phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research.

The genomic architecture of disease resistance in lettuce

Genbank and The Compositae Genome Project database, containing over 42,000 lettuce unigenes from Lactuca sativa cv. Salinas and L. serriola accession UC96US23 were mined to identify 702 candidate genes involved in pathogen recognition (RGCs), resistance signal transduction, defense responses, and disease susceptibility. In addition, to identify sequences representing additional sub-families of nucleotide binding site (NBS)-leucine-rich repeat encoding genes; the major classes of resistance genes (R-genes), NBS-encoding sequences were amplified by PCR using degenerate oligonucleotides designed to NBS sub-families specific to the subclass Asteridae, which includes the Compositae family. These products were cloned and sequenced resulting in 18 novel NBS sequences from cv. Salinas and 15 novel NBS sequences from UC96US23. Using a variety of marker technologies, 294 of the 735 candidate disease resistance genes were mapped in our primary mapping population, which consisted of 119 F7 recombinant inbred lines derived from an interspecific cross between cv. Salinas and UC96US23. Using markers shared across multiple genetic maps, 36 resistance phenotypic loci, including two new loci for resistance to downy mildew and two quantitative trait loci for resistance to anthracnose were positioned onto the reference map to provide a global view of the genomic architecture of disease resistance in lettuce and to identify candidate genes for resistance phenotypes. The majority but not all of the resistance phenotypes were genetically associated with RGCs.