Functional Genomics of Rice

Genetic diversity within and among 50 populations of confectionery sunflower (Helianthus annuus L.) collected from different geographical areas of Iran was evaluated by using microsatellite and retrotransposon markers. The number of alleles (Na) in SSR loci ranged from 2 to 3 with an average of 2.1. The polymorphic bands in retrotransposon markers ranged from 7 in locus CR-UR1 to 15 in locus CR-816 with a mean value of 11.33. Herarchical clustering of individuals (50 × 5 = 250) by neighbor joining method in DARwin5 software subdivided them into three groups. Using Bayesian method in the software pakage of Structure, the studied individuals were subdivided into two sub-populations. Principal coordinate analysis revelaed that the two first components explaine 7.86 and 6.16% of the total variance, respectively. Analysis of molecular variance revealed a higher level of genetic variation within (70%) than between (30%) populations. High molecular variation among individuals within population possibly is due to high allogamy nature of the sunflower plant. Low genetic variation observed between populations could be considered as a consequence of genetic equilibrium that has occurred over the long period of cultivation of confectionery sunflower in this area as well as seed exchange among regions. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in confectionery sunflower.

Red rice genotypes are characterized by their huge nutritional values. Apart from this property, they also possess valuable sources of resistance to many biotic and abiotic stresses. In the present investigation, a total of 215 red rice accessions collected from north east and other parts of India were screened for their resistance against brown plant hopper (BPH) at National Rice Research Institute (NRRI), Cuttack by following modified screening technique. The results showed, among 215 genotypes, 4 were highly resistant, 11 were resistant and 13 were moderately resistant against BPH. The rest 187 genotypes were either susceptible or highly susceptible. The mechanism of resistance in these identified lines was studied. The nymphal survivility and development was lower in resistant genotypes (Mata Meher 43.33%) after 5day of release as compared to susceptible check TN-1 (100% survivility). Similarly the nymphal developmental period was less in resistant lines than TN-1 (100% nymphs w...

Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.

Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na + exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na + in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K + retention in both root and leaf mesophyll cells; and (4) incorporating Na + sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.

As the world's population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traitsi.e., "neodomestication". To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq)a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs.

High resource availability can reduce anti-herbivore resistance (a plant's ability to defend against herbivores and reduce damage) in rice, Oryza sativa L, but may also increase tolerance (a plant's ability to withstand damage by, for example, compensatory growth). Through a series of greenhouse, screenhouse and field experiments, this study examines fitness (survival and development × reproduction) of the brown planthopper, Nilaparvata lugens (Stål), on resistant (IR62) and susceptible (IR22) rice varieties and age-related rice tolerance to planthopper damage under varying resource (nitrogenous fertilizer) availability. Planthoppers reared on IR62 in the greenhouse had lower fitness than planthoppers on IR22. IR62 became increasingly resistant as plants aged. IR22 was generally more tolerant of planthopper damage, and tolerance increased in IR22, but declined in IR62, as the plants aged. Rice plants infested at pre-tillering stages (3-4 leaf stage) in the screenhouse had greater losses to root, shoot and grain yield per unit weight of planthopper than plants infested at tillering stages, particularly in IR22. These trends were mainly due to the impact of planthoppers during pre-tillering stages and the length of exposure to the planthoppers. High nitrogen compromised IR62 resistance, particularly in tillering plants in the greenhouse study; however, high nitrogen did not increase planthopper biomass-density on IR62 in greenhouse or field cages. Tolerance to damage in IR62 at mid-tillering stages declined under increasing levels of nitrogen, but nitrogen increased tolerance during late-tillering stages. Planthopper damage to IR22 in field cages was severe and hopperburn (plant death) occurred in 83% of IR22 plants under high nitrogen (60-150 kg N ha −1). In contrast, despite planthopper infestations, damage to IR62 was low in field-grown plants and productivity (tillers, roots, shoots and grain) increased in IR62 under increasing nitrogen. Our results indicate that, whereas nitrogenous fertilizer increases planthopper fitness on susceptible and resistant varieties, the net effects of high nitrogen on IR62 include decreased planthopper biomass-density (apparent in all experiments) and higher tolerance to damage during later growth stages (observed in the greenhouse, and during one of two seasons in field cages).

After the completion of its genomic sequencing, rice (Oryza sativa L.) has become firmly established as the premiere model plant among monocot crops. Various genetic resources have been developed for rice to accelerate the identification and characterization of rice genes with as-yet unknown functions. These resources include collections that carry natural variations and progeny derived from chemical and irradiation mutagenesis. Collections of rice strains with natural or artificial DNA insertions that create loss-of-function mutations have been of great importance for gene discovery and tagging. However, it is often difficult to observe mutant phenotypes for functionally duplicated genes and genes essential for plant growth and development. To overcome this disadvantage, gain-of-function strategies have been developed, including activation tagging and full-length cDNA overexpressing gene (FOX)-hunting systems. In this review, we summarize the current status and discuss the advantages and disadvantages of the gain-of-function approaches, and then, perspectives on accelerating discovery of rice genes.

Brown planthopper (BPH, Nilaparvata lugens Stal.) is the most damaging rice pest affecting stable rice yields worldwide. Currently, methods for controlling BPH include breeding a BPH-resistant cultivar and using synthetic pesticides. Nevertheless, the continuous cultivation of resistant cultivars allows for the emergence of various resistant races, and the use of synthetic pesticides can induce environmental pollution as well as the emergence of unpredictable new pest species. As plants cannot migrate to other locations on their own to combat various stresses, the production of secondary metabolites allows plants to protect themselves from stress and tolerate their reproduction. Pesticides using natural products are currently being developed to prevent environmental pollution and ecosystem disturbance caused by synthetic pesticides. In this study, after BPH infection in rice, chrysoeriol7 (C7), a secondary metabolite that induces resistance against BPH, was assessed. After C7 treatm...

Tagosodes orizicolus is one of the main plagues of rice in tropical America causing two types of damages, the direct one, feeding and oviposition effect, and an indirect one, by the transmission of the "Rice hoja blanca virus". During 2006-2007 we carried out research under greenhouse conditions at Fundación Danac, Venezuela, in order to determine the mechanisms of antixenosis, antibiosis and tolerance to T. orizicolus, which could be acting in commercial varieties and advanced lines of the rice genetic breeding programs of INIA and Fundación Danac. The method of free feeding was used for the antixenosis evaluation, whereas the method of forced feeding was used for antibiosis evaluation (effect on survival and oviposition). Additionally, we used the indirect method based on biomass depression to estimate the tolerance. Some of the evaluated traits included: grade of damage, number of insects settling on rice plants, percentage of sogata mortality at the mature state, number of eggs in the leaf midrib and an index of tolerance. The results showed that rice genotypes possess different combinations of resistance mechanisms, as well as different grades of reactions. The susceptible control 'Bluebonnet 50' was consistently susceptible across experiments and the resistant control 'Makalioka' had high antixenosis and high antibiosis based on survival and oviposition. The rest of the genotypes presented lower or higher degrees of antixenosis and antibiosis for survival and oviposition. The genotype 'FD0241-M-17-6-1-1-1-1' was identified with possible tolerance to the direct damage of sogata.

Resistance evaluation of modern rice varieties to brown planthopper Nilaparvata lugens STÅL. The research was performed to understand the resistance of modern rice varieties to the field population of brown planthopper (BPH). The research studied BPH settling preference, numbers of laid eggs, and functional plant loss index (FPLI) of resistant and susceptible rice varieties. The results showed BPH were less settle and laid fewer eggs on resistant varieties. BPH significantly settled longer on TN1 than other varieties after 24 hours. The numbers of eggs laid on rice resistant varieties (Inpari 13, Inpari 31, Inpari 33, RH, and PTB33) were fewer compared to TN1. FPLI value in TN1 was the highest among the tested rice varieties. Inpari 13 had better resistance to BPH compared to Inpari 31 and Inpari 33. In managing BPH in endemic areas, we recommend Inpari 13, Inpari 31, and Inpari 33 to be planted in rotation.

Background Bph3, a major brown planthopper (BPH) resistance locus derived from the rice cultivar Rathu Heenati (RH), has been used as a stable donor of traits that improve highly susceptible aromatic rice varieties in Thailand. Map-based cloning was initiated using a set of isogenic lines (ILs) harboring the major Bph3 locus on chromosome 6. IL genomes were scanned with a 57 K Affymetrix Rice GeneChip to identify the gene responsible for Bph3. Findings Single-feature polymorphism (SFP) mapping was used to localize 84 candidate genes. An expression analysis of 15 selected candidate genes in the aromatic rice cultivar KDML105 (KD) and the ILs under normal conditions revealed two differentially expressed sequences. Following hopper feeding, only one candidate gene, Os04g27430, was differentially expressed. Os04g27430 encodes a putative sesquiterpene synthase (STPS) gene that was induced by BPH feeding in ILs. An antixenosis test in three selected ILs revealed a major role for STPS in i...

Background: Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most destructive insect pests of rice. The molecular responses of plants to sucking insects resemble responses to pathogen infection. However, the molecular mechanism of BPH-resistance in rice remains unclear. Transcription factors (TF) are upstream regulators of various genes that bind to specific DNA sequences, thereby controlling the transcription from DNA to mRNA. They are key regulators for transcriptional expression in biological processes, and are probably involved in the BPH-induced pathways in resistant rice varieties. Results: We conducted a microarray experiment to analyze TF genes related to BPH resistance in a Sri Lankan rice cultivar, Rathu Heenati (RHT). We compared the expression profiles of TF genes in RHT with those of the susceptible rice cultivar Taichun Native 1 (TN1). We detected 2038 TF genes showing differential expression signals between the two rice varieties. Of these, 442 TF genes were probably related to BPH-induced resistance in RHT and TN1, and 229 may be related to constitutive resistance only in RHT. These genes showed a fold change (FC) of more than 2.0 (P<0.05). Among the 442 TF genes related to BPH-induced resistance, most of them were readily induced in TN1 than in RHT by BPH feeding, for instance, 154 TF genes were up-regulated in TN1, but only 31 TF genes were up-regulated in RHT at 24 hours after BPH infestation; 2-4 times more TF genes were induced in TN1 than in RHT by BPH. At an FC threshold of >10, there were 37 induced TF genes and 26 constitutive resistance TF genes. Of these, 13 were probably involved in BPH-induced resistance, and 8 in constitutive resistance to BPH in RHT. Conclusions: We explored the molecular mechanism of resistance to BPH in rice by comparing expressions of TF genes between RHT and TN1. We speculate that the level of gene repression, especially for early TF genes, plays an important role in the defense response. The fundamental point of the resistance strategy is that plants protect themselves by reducing their metabolic level to inhibit feeding by BPH and prevent damage from water and nutrient loss. We have selected 21 TF genes related to BPH resistance for further analyses to understand the molecular responses to BPH feeding in rice.

Three wild rice species and six cultivated rice varieties were evaluated to determine their mechanisms of resistance to Nilaparvata lugens (Stal.). Wild rice species, Oryza officinalis, O. punctata, and O. latifolia and cultivated rices Rathu Heenati (Bph 3), Babawee (bph 4), ARC 10550 (bph 5), Swarnalata (Bph 6), Ptb 33 (bph 2+Bph 3) and the susceptible Taichung Native (TN 1) (no resistance gene) were included in the study. In a free choice seedbox screening test, wild rice species maintained their high level of resistance through the 48 h exposure to N. lugens nymphs while plant damage ratings of cultivated rice varieties increased with time. Wild rices were non preferred and significantly more individuals settled on susceptible TN 1 followed by cultivated rices. The quantity of food ingested and assimilated by N. lugens on wild rices was less than on cultivated resistant varieties. N. lugens caged on resistant wild rices had slow nymphal development, reduced longevity, low fecundity, and low egg hatchability as compared to N. lugens on cultivated resistant varieties.

Brown planthopper (BPH) is a phloem sap-sucking insect pest of rice which causes severe yield loss. We cloned the BPH18 gene from the BPH-resistant introgression line derived from the wild rice species Oryza australiensis. Map-based cloning and complementation test revealed that the BPH18 encodes CC-NBS-NBS-LRR protein. BPH18 has two NBS domains, unlike the typical NBS-LRR proteins. The BPH18 promoter::GUS transgenic plants exhibited strong GUS expression in the vascular bundles of the leaf sheath, especially in phloem cells where the BPH attacks. The BPH18 proteins were widely localized to the endo-membranes in a cell, including the endoplasmic reticulum, Golgi apparatus, trans-Golgi network, and prevacuolar compartments, suggesting that BPH18 may recognize the BPH invasion at endo-membranes in phloem cells. Whole genome sequencing of the near-isogenic lines (NILs), NIL-BPH18 and NIL-BPH26, revealed that BPH18 located at the same locus of BPH26. However, these two genes have remark...

Terpenoid compounds in resistant rice varieties that acted as allelochemicals affecting feeding behavior of the brown planthoppers (BPHs) were extracted by solid phase microextraction (SPME) and analyzed by using gas chromatography-mass spectrometry (GC-MS). Comparative study of terpenoid profiles of susceptible Khao Dawk Mali 105 (KDML105), resistant Rathu Heenati (RH), and their isogenic lines (IL) IL162, IL302, and IL283, was performed. Six monoterpenoids which were (E)-citral, citronellal, (E)-geraniol, β-citronellol, citronellyl acetate and geranelyl acetate, were detected only in leaves of the resistant and their 3 isogenic line rices. Antibiosis, antixenosis and tolerance experiments suggested that the RH and its 3 isogenic line rices had higher level of antibiosis, antixenosis and tolerance against BPHs than KDML105. Moreover, spraying 6 standard monoterpenoids on susceptible Taichung Native 1 (TN1) rice could decrease feeding activity of BPHs. 

Terpenoid compounds in resistant rice varieties that acted as allelochemicals affecting feeding behavior of the brown planthoppers (BPHs) were extracted by solid phase microextraction (SPME) and analyzed by using gas chromatography-mass spectrometry (GC-MS). Comparative study of terpenoid profiles of susceptible Khao Dawk Mali 105 (KDML105), resistant Rathu Heenati (RH), and their isogenic lines (IL) IL162, IL302, and IL283, was performed. Six monoterpenoids which were (E)-citral, citronellal, (E)-geraniol, β-citronellol, citronellyl acetate and geranelyl acetate, were detected only in leaves of the resistant and their 3 isogenic line rices. Antibiosis, antixenosis and tolerance experiments suggested that the RH and its 3 isogenic line rices had higher level of antibiosis, antixenosis and tolerance against BPHs than KDML105. Moreover, spraying 6 standard monoterpenoids on susceptible Taichung Native 1 (TN1) rice could decrease feeding activity of BPHs.

Background Rice is staple food for over two billion people. Planthoppers like BPH and WBPH occur together in most of rice growing regions across Asia and cause extensive yield loss by feeding and transmission of disease-causing viruses. Chemical control of the pest is expensive and ecologically disastrous; breeding resistant varieties is an acceptable option. But most of such efforts are focused on BPH with an assumption that these varieties will also be effective against WBPH. No critical studies are available to understand rice resistance, common or otherwise, against these two planthoppers. Results Our studies aimed to understand the defense mechanisms in rice line RP2068 against BPH and WBPH through RNA sequencing analysis of a RIL line TR3RR derived from the cross TN1 (susceptible) and RP2068 (resistant) after infestation with BPH or WBPH. Results revealed higher number of differentially expressed genes (DEGs) in BPH infested plants than in WBPH infested plants when compared wi...

Rice is the most significant global food security. Several biotic factors limit rice production, breeding biotic-resistant rice has, therefore, become an increasingly important goal. Two elite rice lines, IR71033-121-15 (IR71033) and IR57514-PMI-5-B-1-2 (IR57514), provide potential genes for biotic stress resistance traits. In this study, genotyping by sequencing (GBS) for single nucleotide polymorphism (SNP)-based linkage map construction was used to detect quantitative trait loci (QTLs) for blast (BL), bacterial blight (BB), whitebacked planthopper (WBPH), and brown planthopper (BPH) resistance. IR71033 was derived from Oryza minuta and carried BL, BB, WBPH, and BPH resistance QTLs. IR57514 is a well-adapted rainfed lowland line that carries BL and BB resistance QTLs. Two sets of recombinant inbred line (RIL) populations derived from crosses of KDML105 × IR71033 and KDML105 × IR57514 were used to dissect the genetic basis of disease and insect pest resistance. The RIL populations were evaluated for BL, BB, WBPH, and BPH resistance from 2016 to 2018 at four rice research centers in Thailand. From these, we identified a large number of SNPs through GBS and constructed high-resolution linkage maps. By combining phenotypic evaluation with the GBS data, a total of 24 QTLs on four chromosomes were detected that confered pest resistance and explained 7.3%-61.

Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire germplasm bank (1.605 and 0.713, respectively), indicating a higher polymorphism of the representative cultivars in relation to the entire collection. The accessions selected for the core collection may be used in future studies of genome association as well as in genetic crosses in breeding programs aimed at developing improved cultivars with high genetic diversity which can meet current and future market needs.

The rice sesquiterpene synthase II gene (OsSTPS2, LOC_Os04g27430), which is involved in the antixenosis defense mechanism of rice against brown planthopper (BPH) infestation, was identified in the BPH-resistant rice variety Rathu Heenati (RH). In contrast, the gene was not functional in the BPH-susceptible rice variety KDML105 (KD). Single-nucleotide polymorphisms (SNPs) in the promoter region and in exon 5 of the gene and a seven amino acid deletion in the deduced protein sequence are suggested as factors that negatively regulate the function of the gene. Sequence analysis of the promoter region and expression analysis of the OsSTPS2 gene in several rice genotypes revealed the correlation of SNPs of the ATHB-1, SBE1, and P-factor with the expression of the gene. Genomic and complementary DNA (cDNA) sequence analysis at exon 5 of the gene showed that the 21 bp deletion naturally occurred in several rice genotypes. The antixenosis of the BPH feeding preference (AFP) of rice varieties...

Background: The development of rice varieties with broad-spectrum resistance to insect pests is the most promising approach for controlling a fast evolving insect pest such as the brown planthopper (BPH). To cope with rapid evolution, discovering new sources of broad-spectrum resistance genes is the ultimate goal. Results: We used a forward genetics approach to identify BPH resistance genes in rice (Oryza sativa L.) using double digest restriction site-associated DNA sequencing (ddRADseq) for quantitative trait loci (QTL)-seq of the backcross inbred lines (BILs) derived from a cross between the BPH-susceptible cultivar KDML105 and BPH-resistant cultivar Rathu Heenati (RH). Two major genomic regions, located between 5.78-7.78 Mb (QBPH4.1) and 15.22-17.22 Mb (QBPH4.2) on rice chromosome 4, showed association with BPH resistance in both pooled BILs and individual highly resistant and susceptible BILs. The two most significant candidate resistance genes located within the QBPH4.1 and QBPH4.2 windows were lectin receptor kinase 3 (OsLecRK3) and sesquiterpene synthase 2 (OsSTPS2), respectively. Functional markers identified in these two genes were used for reverse screening 9323 lines of the fast neutron (FN)-mutagenized population developed from the BPH-susceptible, purple-pigmented, indica cultivar Jao Hom Nin (JHN). Nineteen FN-mutagenized lines (0.24%) carried mutations in the OsLecRK3 and/or OsSTPS2 gene. Among these mutant lines, only one highly resistant line (JHN4) and three moderately resistant lines (JHN09962, JHN12005, and JHN19525) were identified using three active, local BPH populations. The 19 mutant lines together with three randomly selected mutant lines, which did not harbor mutations in the two target genes, were screened further for mutations in six known BPH resistance genes including BPH9, BPH14, BPH18, BPH26, BPH29, and BPH32. Multiple single nucleotide polymorphisms (SNPs) and insertion-deletion (Indel) mutations were identified, which formed gene-specific haplotype patterns (HPs) essential for broad-spectrum resistance to BPH in both BILs and JHN mutant populations.

Background: Bph3, a major brown planthopper (BPH) resistance locus derived from the rice cultivar Rathu Heenati (RH), has been used as a stable donor of traits that improve highly susceptible aromatic rice varieties in Thailand. Map-based cloning was initiated using a set of isogenic lines (ILs) harboring the major Bph3 locus on chromosome 6. IL genomes were scanned with a 57 K Affymetrix Rice GeneChip to identify the gene responsible for Bph3. Findings: Single-feature polymorphism (SFP) mapping was used to localize 84 candidate genes. An expression analysis of 15 selected candidate genes in the aromatic rice cultivar KDML105 (KD) and the ILs under normal conditions revealed two differentially expressed sequences. Following hopper feeding, only one candidate gene, Os04g27430, was differentially expressed. Os04g27430 encodes a putative sesquiterpene synthase (STPS) gene that was induced by BPH feeding in ILs. An antixenosis test in three selected ILs revealed a major role for STPS in insect preference during the first 120 hours of the rice-insect interaction. Functional SNPs in exon 5 that resulted in the deletion of seven amino acids in the susceptible rice line were identified. Moreover, three additional SNPs associated with three transcription binding sites were also identified, which might explain the differential response of Os04g27430 during the anti-feeding test. Conclusion: Os04g27430 is the second known rice STPS induced by BPH. The gene may involve an antixenosis BPH resistance mechanism. The combination of the STPS and the Bph3 locus was more effective than Bph3 alone in the tested ILs.

Background: Rice contains the lowest grain Fe content among cereals. One biological limiting factor is the tolerance of rice to Fe toxicity. Reverse and forward genetic screenings were used to identify tolerance to Fe toxicity in 4,500 M 4 lines irradiated by fast neutrons (FN). Findings: Fe-tolerant mutants were successfully isolated. In the forward screen, we selected five highly tolerant and four highly intolerant mutants based on the response of seedlings to 300 ppm Fe. Reverse screening based on the polymorphic coding sequence of seven Fe homeostatic genes detected by denaturing high performance liquid chromatography (dHPLC) revealed MuFRO1, a mutant for OsFRO1 (LOC_Os04g36720). The MuFRO1 mutant tolerated Fe toxicity in the vegetative stage and had 21-30% more grain Fe content than its wild type. All five highly Fe-tolerant mutants have the same haplotype as the MuFRO1, confirming the important role of OsFRO1 in Fe homeostasis in rice. Conclusions: FN radiation generated extreme Fe-tolerant mutants capable of tolerating different levels of Fe toxicity in the lowland rice environment. Mutants from both reverse and forward screens suggested a role for OsFRO1 in seedling tolerance to Fe toxicity. The MuFRO1 mutant could facilitate rice production in the high-Fe soil found in Southeast Asia.

ABSTRACT: The brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most serious insect pests in rice production worldwide. The BPH resistance genes in an indica cultivar &#x27;Abhaya&#x27; were studied using 400 BC4F2 and F3 backcross introgressed lines of ...

Rice is the most significant global food security. Several biotic factors limit rice production, breeding biotic-resistant rice has, therefore, become an increasingly important goal. Two elite rice lines, IR71033-121-15 (IR71033) and IR57514-PMI-5-B-1-2 (IR57514), provide potential genes for biotic stress resistance traits. In this study, genotyping by sequencing (GBS) for single nucleotide polymorphism (SNP)-based linkage map construction was used to detect quantitative trait loci (QTLs) for blast (BL), bacterial blight (BB), whitebacked planthopper (WBPH), and brown planthopper (BPH) resistance. IR71033 was derived from Oryza minuta and carried BL, BB, WBPH, and BPH resistance QTLs. IR57514 is a well-adapted rainfed lowland line that carries BL and BB resistance QTLs. Two sets of recombinant inbred line (RIL) populations derived from crosses of KDML105 × IR71033 and KDML105 × IR57514 were used to dissect the genetic basis of disease and insect pest resistance. The RIL populations were evaluated for BL, BB, WBPH, and BPH resistance from 2016 to 2018 at four rice research centers in Thailand. From these, we identified a large number of SNPs through GBS and constructed high-resolution linkage maps. By combining phenotypic evaluation with the GBS data, a total of 24 QTLs on four chromosomes were detected that confered pest resistance and explained 7.3%-61.

Abstract: The genetic diversity in 106 glutinous rice landraces of Assam, India, was analyzed using SSR markers. The apparent amylose content (AAC) in Chokuwa (12.24%) was higher than Bora (0.145%) genotypes. The SSR markers showed high level of polymorphism ranging from 80 to 100%. A total of 181 alleles were detected at the 37 simple sequence repeat (SSR) loci. The number of alleles per locus ranged from 2 to 13, with an average of 4.9. The polymorphism information content (PIC) values varied from 0.452 to 0.817, with ...

Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

Terpenoid compounds in resistant rice varieties that acted as allelochemicals affecting feeding behavior of the brown planthoppers (BPHs) were extracted by solid phase microextraction (SPME) and analyzed by using gas chromatography-mass spectrometry (GC-MS). Comparative study of terpenoid profiles of susceptible Khao Dawk Mali 105 (KDML105), resistant Rathu Heenati (RH), and their isogenic lines (IL) IL162, IL302, and IL283, was performed. Six monoterpenoids which were (E)-citral, citronellal, (E)-geraniol, β-citronellol, citronellyl acetate and geranelyl acetate, were detected only in leaves of the resistant and their 3 isogenic line rices. Antibiosis, antixenosis and tolerance experiments suggested that the RH and its 3 isogenic line rices had higher level of antibiosis, antixenosis and tolerance against BPHs than KDML105. Moreover, spraying 6 standard monoterpenoids on susceptible Taichung Native 1 (TN1) rice could decrease feeding activity of BPHs. 

 Terpenes comprise the most diverse collection of secondary metabolites and are the compounds that give wonderful aromas, tastes and pharmaceuticals.  Terpene hydrocarbon scaffolds are generated by the action of mechanistically intriguing family of mono-, sesqui-, and diterpene synthases collectively termed as 'Terpene synthases'.  Terpene synthases (TPS) promotes the Mg ++ dependent expulsion of the pyrophosphate group from the substrate leading to formation of carbocations which further go through cyclization to form various terpenes.

Abstract: The genetic diversity in 106 glutinous rice landraces of Assam, India, was analyzed using SSR markers. The apparent amylose content (AAC) in Chokuwa (12.24%) was higher than Bora (0.145%) genotypes. The SSR markers showed high level of polymorphism ranging from 80 to 100%. A total of 181 alleles were detected at the 37 simple sequence repeat (SSR) loci. The number of alleles per locus ranged from 2 to 13, with an average of 4.9. The polymorphism information content (PIC) values varied from 0.452 to 0.817, with ...

To organize data resulting from the phenotypic characterization of a library of 30 000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/ OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morphophysiological alterations observed during field evaluation and specific screens in a first set of 13 928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13 928 lines are characterized by at least one T-DNA and one

Data from five protein-coding loci related to dairy production were used to study the genetic diversity and population structure of Argentine and Bolivian Creole cattle breeds. Genomic DNA was extracted from blood samples of six Creole cattle breeds: Argentine (n = 230), Patagonian (n = 25); "Saavedreño" (n = 140), "Chaqueño Boliviano" (n = 30), "Yacumeño" (n = 27), and "Chusco" (n = 11). κ-casein, β-lactoglobulin, growth hormone and prolactin were measured by PCR-RFLP, while α S1 -casein was typed by PCR-ASO. The results are discussed, focusing on: historical origin, recent differentiation and selection events, Zebu gene introgression, and population structure. This work shows that: (i) For the studied genes, the observed gene frequency profiles of Argentine and Bolivian Creole cattle breeds were close to the data reported for Iberian breeds and for other South-American Creole cattle breeds which are historically related; (ii) although Zebu gene introgression has been reported at the studied loci, these breeds seem to be far from the Zebu gene frequency profiles; and (iii) the Argentine and Bolivian Creole cattle showed significant levels of subdivision, but each population has maintained its degree of genetic variability.

Brown planthopper (BPH; Nilaparvata lugens)
is a phloem feeding insect which is one of the most serious
threats to rice crops in many countries throughout Asia. 1H
NMR spectroscopy, combined with chemometrics, was
used to analyze the polar metabolome from leaf extracts of
Thai Jasmine rice (brown planthopper (BPH)-susceptible
KD) and its BPH resistant isogenic lines (BPH-resistant
IL7 and BPH-resistant? IL308 varieties) with and without
BPH infestation at various time points (days 1, 2, 3, 4 and
8). Physiological changes of the rice isogenic lines were
different based on the quantitative trait loci of BPH resistance.
Multivariate models were capable of distinguishing
between the susceptible and the resistant rice varieties
throughout the infestation. The concentration of 10
metabolites were significantly altered (p\0.05) between
the infested and the control groups of each examined rice variety. Metabolic pathway analysis suggested that BPH
infestation could perturb transamination during the early
stages of infestation (days 1–3) for all rice varieties. In
addition, the IL7 and IL308 varieties responded earlier (day
3) than the KD variety (day 8) by perturbing amino acid
metabolism, shikimate and gluconeogenesis pathways. By
day 8 of the infestation, the KD cultivar responded by
activating the amino acid-mediated-de novo pathway
whereas the IL308 variety activated the purine and
pyrimidine compound-mediated-salvage pathway for nucleotide
biosynthesis. This study has identified, for the first
time, several potential metabolic pathways for acclimatization
and defense mechanisms against BPH infestation.
These findings provide a valuable, first insight into BPH
resistance mechanisms in Thai Jasmine rice.

Terpenoid compounds in resistant rice varieties
that acted as allelochemicals affecting feeding behavior of
the brown planthoppers (BPHs) were extracted by solid
phase microextraction (SPME) and analyzed by using gas
chromatography-mass spectrometry (GC-MS).
Comparative study of terpenoid profiles of susceptible Khao
Dawk Mali 105 (KDML105), resistant Rathu Heenati (RH),
and their isogenic lines (IL) IL162, IL302, and IL283, was
performed. Six monoterpenoids which were (E)-citral,
citronellal, (E)-geraniol, β-citronellol, citronellyl acetate and
geranelyl acetate, were detected only in leaves of the
resistant and their 3 isogenic line rices. Antibiosis,
antixenosis and tolerance experiments suggested that the
RH and its 3 isogenic line rices had higher level of antibiosis,
antixenosis and tolerance against BPHs than KDML105.
Moreover, spraying 6 standard monoterpenoids on
susceptible Taichung Native 1 (TN1) rice could decrease
feeding activity of BPHs.

Data from five protein-coding loci related to dairy production were used to study the genetic diversity and population structure of Argentine and Bolivian Creole cattle breeds. Genomic DNA was extracted from blood samples of six Creole cattle breeds: Argentine (n = 230), Patagonian (n = 25); "Saavedreño" (n = 140), "Chaqueño Boliviano" (n = 30), "Yacumeño" (n = 27), and "Chusco" (n = 11). κ-casein, β-lactoglobulin, growth hormone and prolactin were measured by PCR-RFLP, while α S1 -casein was typed by PCR-ASO. The results are discussed, focusing on: historical origin, recent differentiation and selection events, Zebu gene introgression, and population structure. This work shows that: (i) For the studied genes, the observed gene frequency profiles of Argentine and Bolivian Creole cattle breeds were close to the data reported for Iberian breeds and for other South-American Creole cattle breeds which are historically related; (ii) although Zebu gene introgression has been reported at the studied loci, these breeds seem to be far from the Zebu gene frequency profiles; and (iii) the Argentine and Bolivian Creole cattle showed significant levels of subdivision, but each population has maintained its degree of genetic variability.

Data from five protein-coding loci related to dairy production were used to study the genetic diversity and population structure of Argentine and Bolivian Creole cattle breeds. Genomic DNA was extracted from blood samples of six Creole cattle breeds: Argentine (n = 230), Patagonian (n = 25); "Saavedreño" (n = 140), "Chaqueño Boliviano" (n = 30), "Yacumeño" (n = 27), and "Chusco" (n = 11). κ-casein, β-lactoglobulin, growth hormone and prolactin were measured by PCR-RFLP, while α S1 -casein was typed by PCR-ASO. The results are discussed, focusing on: historical origin, recent differentiation and selection events, Zebu gene introgression, and population structure. This work shows that: (i) For the studied genes, the observed gene frequency profiles of Argentine and Bolivian Creole cattle breeds were close to the data reported for Iberian breeds and for other South-American Creole cattle breeds which are historically related; (ii) although Zebu gene introgression has been reported at the studied loci, these breeds seem to be far from the Zebu gene frequency profiles; and (iii) the Argentine and Bolivian Creole cattle showed significant levels of subdivision, but each population has maintained its degree of genetic variability.

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland
and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to
possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The
genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36
genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of
the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine
types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major
allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in
Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the
rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major
clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in
all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively.
Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure.
AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58%
for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which
accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core
set developed will be a valuable resource for future genomic studies and crop improvement strategies.