Restriction Fragment Length Polymorphism Mapping Research Articles

Ampelopsis grossedentata Represents a New Host of the 16SrI Group of Phytoplasma Associated with Yellow Leaf Symptoms in China.

Ampelopsis grossedentata, commonly known as "Vine Tea" and well-recognized for its rich flavonoid content, is mainly distributed in the southern regions of the Yangtze River basin in China. These regions include Hunan, Hubei, Jiangxi, and Guizhou provinces. Vine Tea is mainly consumed as an herbal tea and has garnered attention for its reported health benefits, including antioxidant, anti-inflammatory, anti-tumor, anti-diabetic, and neuroprotective properties. It has been used to alleviate coughs and sore throats (Zhang et al., 2021; Wang et al., 2017; Gao et al., 2009). In the Zhangjiajie region of Hunan province alone, the Vine Tea planting area reached 7,670.5 hectares and produced commercial goods worth 1.417 billion RMB in 2022. In May 2021, leaf margins and veins fading to yellowing mottling, and crumpling of leaf blades in the shape of a boat symptoms were found in ~16% of Vine Tea plants in the Sanjiakuan Township, Yongding District, Zhangjiajie region (29°15'E, 110°30' N) (Figure 1a, b, c). (Figure 1a, b, c). Phytoplasma-like microbial cells (small oval shaped bacterial cells, around 1000 nm in size) were observed in sieve tube cells in the phloem of diseased leaves using transmission electron microscopy. No such cell was observed in the phloem of healthy leaves (Figure 2a, b). To investigate the potential association between phytoplasma and the observed symptoms of the diseased plants, total DNA was isolated from ten diseasedeaves and compared with ten healthy leaves from the same field using SteadyPure Plant Genomic DNA Extraction Kit. The isolated DNAs were analyzed first in a direct PCR using universal phytoplasma primer pair R16mF2/R16mR1 targeting the 16S rRNA gene (Gundersen and Lee 1996) and specific pair rpF1/rpR1 (Lee et al. 1998) targeting the DNA fragment encoding partial ribosomal proteins (rp) L22 (complete) and S3 and S19 (partial). The initial amplified products were used as templates and further amplified by nested PCR respectively with primer pair R16F2n/R16R2 for the 16S rRNA gene (Lee et al. 1998) and the rpF2/rpR2 primer pair for the rp gene (Martini et al. 2007). No amplification was obtained with DNA from healthy leaf samples using any of the four primer pairs. The amplified fragments from diseased leaves by nested PCR were cloned and sequenced (Qingke Biotech, China). The obtained sequences have been deposited in GenBank with accession numbers OR282806 for the 16S rRNA gene and GenBank OR353012 for the rp gene. BLASTn analysis revealed that the partial 16S rRNA gene sequence in our sample shared 99.4% nucleotide sequence identity with 'Candidatus Phytoplasma sp.' (MW364378) and 'Peony yellows phytoplasma' (KY814723) of the 16SrI group. Similarly, our rp gene sequence shared 99.6% nucleotide identity with the rpI group of phytoplasma such as the 'Balsamine virescence phytoplasma' (JN572890) and 'Paulownia witches'-broom phytoplasma' (HM146079). Phylogenetic analysis of the 16S rRNA and rp sequences using MEGA version 7.0 revealed that the phytoplasma strain associated with A. grossedentata yellow leaf syndrome in our study site belonged to the 16SrI (Candidatus Phytoplasma asteris) group of phytoplasma (Figure 3a, b). Using the interactive online phytoplasma classification tool iPhyClassifier (Zhao et al., 2009), virtual restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene sequences showed our strain having a distinct RFLP map but was closest to that of the onion yellow phytoplasma 16SrI-B subgroup (GenBank accession number: AP006628), with a similarity coefficient of 0.94 (Figure 4a, b). To confirm phytoplasma transmission, healthy plants were inoculated with three scions of infected plants of A. grossedentata. After 16 days, the new leaves of the inoculated A. grossedentata showed yellow leaf symptoms (Figure 5a, b, c), akin to the symptoms originally observed in the field, and the outer contour of the leaf margin appeared chlorotic. After 26 days, primer pairs R16mF2/R16R1 and R16F2n/R16R2 were used for nested PCR detection of phytoplasma in symptomatic A. grossedentata leaves. Phytoplasma was detected in the first and second leaves of symptomatic branches and leaves while negative control showed no amplification. Sequencing of the amplified fragments showed 100% nucleotide identity to the strain from the grafting source. Our results indicated that the pathogen and the disease can be transmitted by tissue grafting, consistent with the biological characteristics of phytoplasma, and further confirmed that the phytoplasma was the pathogen of yellow leaf syndrome of A. grossedentata. Toour knowledge, this is the first report of phytoplasma of group 16SrI affecting A. grossedentata.

Neer Award 2017: A rapid method for detecting Propionibacterium acnes in surgical biopsy specimens from the shoulder

Propionibacterium (P) acnes infection of the shoulder after arthroplasty is a common and serious complication. Current detection methods for P acnes involve anaerobic cultures that require prolonged incubation periods (typically 7-14 days). We have developed a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) approach that sensitively and specifically identifies P acnes in tissue specimens within a 24-hour period. Primers were designed to amplify a unique region of the 16S rRNA gene in P acnes that contained a unique HaeIII restriction enzyme site. PCR and RFLP analyses were optimized to detect P acnes DNA in in vitro cultures and in arthroscopic surgical biopsy specimens from patients with P acnes infections. A 564 base-pair PCR amplicon was derived from all of the known P acnes strains. HaeIII digests of the amplicon yielded a restriction fragment pattern that was unique to P acnes. P acnes-specific amplicons were detected in as few as 10 bacterial cells and in clinical biopsy specimens of infected shoulder tissues. This PCR-RFLP assay combines the sensitivity of PCR with the specificity of RFLP mapping to identify P acnes in surgical isolates. The assay is robust and rapid, and a P acnes-positive tissue specimen can be confirmed within 24 hours of sampling, facilitating treatment decision making, targeted antibiotic therapy, and monitoring to minimize implant failure and revision surgery.

Converting restriction fragment length polymorphism to single‐strand conformation polymorphism markers and its application in the fine mapping of a trichome gene in cotton

AbstractA well‐characterized and systematically organized collection of genetic markers is crucial in the study of any crop species. It is the basis of map‐based gene cloning and crop improvements through marker‐assisted selections. Single‐strand conformation polymorphism (SSCP) has been a robust way of discovering new polymorphisms in marker development without the requirement of sequencing. Here, we report the first approach of applying SSCP marker discovery methods in the genetic map construction and gene mapping of cotton species. A total of 80 restriction fragment length polymorphism (RFLP) markers were selected from a region on published cotton genetic maps around the T1 gene related to cotton trichome. Among the 80 RFLPs, 28 showed polymorphisms through SSCP, showing a polymorphic rate of approximately 35%, which is much higher than that of simple sequence repeat (SSR) markers in the same region (7.8%). By integrating these newly generated SSCP markers, a detailed genetic map was reconstructed around this region using an F2 population derived from a cross between Gossypium arboreum and G. herboceum. The reconstructed region comprises 22 SSCP markers, eight SSR markers and the T1 gene, spanning 21.6 cM. The marker order of the new map agrees well with published reference RFLP maps. The above results suggest that SSCP method can be applied very efficiently and reliably to the marker development of cotton genomes. It will prove to be even more valuable and robust after the public release of cotton whole‐genome sequences.

Quantitative trait loci controlling steamed-rice shape in a recombinant inbred population

To identify quantitative trait loci (QTLs) for steamed-rice shape in rice, we used one recombinant inbred (RI) population provided by Prof. A. Yoshimura of Kyushu University, Japan, derived from the cross between japonica cultivar Asominori and indica cultivar IR24 (IRRI). Tsunematsu et al (1996) constructed a restriction fragment length polymorphism (RFLP) map covering 1,275 cM of 12 chromosomes with 375 markers using 71 RI lines, which was used previously for mapping QTLs for important agronomic traits (Yoshimura et al 1998; Yamazaki et al 1999, 2000; Sasahara et al 1999). In this study, we used a subset of 289 RFLP markers from the original map to map QTLs affecting steamed-rice shape (with an average interval distance between marker pairs of 4.4 cM)

The Selection and Use of Sorghum (Sorghum propinquum) Bacterial Artificial Chromosomes as Cytogenetic FISH Probes for Maize (Zea maysL.)

The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

Restriction Fragment Length Polymorphism and Gene Mapping of Two Genes Associated with Milk Composition in Egyptian River Buffalo*

Restriction Fragment Length Polymorphism and Gene Mapping of Two Genes Associated with Milk Composition in Egyptian River Buffalo*

Association between manganese superoxide dismutase polymorphism and risk of lung cancer

Manganese superoxide dismutase (MnSOD) is one of the major enzymes responsible for the defense against oxidative damage due to reactive oxygen species (ROS) in the mitochondria. C→T substitution in the MnSOD gene ( SOD2) produces an Ala→Val change at amino acid 16, in the mitochondrial targeting sequence of the MnSOD precursor. This seems to reduce transport of the enzyme into mitochondria, decreasing its defense capacity against oxidative stress. The present case–control study was conducted to investigate the association of SOD2 genetic polymorphism with individual susceptibility to lung cancer. Ala16Val polymorphisms were determined using polymerase chain reaction, restriction fragment length polymorphism mapping, and agarose gel electrophoresis techniques in 100 lung cancer patients and 50 healthy control subjects. The frequency of the Val allele (OR = 1.297, 95% CI = 1.095–1.536) and the Val/Val genotype (OR = 7.00, 95% CI = 2.282–21.476) was significantly higher in lung cancer patients than in control subjects. There was a combined effect of Val/Val genotype as a genetic factor with smoking as an environment factor (OR = 2.24). The increase in risk of lung cancer was lesser with this combined effect than with the Val/Val genotype alone. Thus, the Val/Val genotype of SOD2 may be associated with lung cancer in a Turkish population.

Influence of thrombin-activatable fibrinolysis inhibitor and plasminogen activator inhibitor-1 gene polymorphisms on tissue-type plasminogen activator-induced recanalization in ischemic stroke patients.

Endogenous resistance to tissue-type plasminogen activator (t-PA) might decrease the benefit of thrombolysis-induced recanalization. Thrombin-activatable fibrinolysis inhibitor (TAFI) and plasminogen activator inhibitor-1 (PAI-1) are fibrinolysis inhibitors. TAFI removes residues from partially degraded fibrin that in turn eliminates plasminogen binding sites; PAI-1 directly inhibits the activity of t-PA. We aimed to study whether the presence of two common functional polymorphisms of the TAFI and PAI-1 genes influence rates of recanalization of the middle cerebral artery (MCA) among t-PA-treated stroke patients. TAFI and PAI-1 polymorphism determinations were performed by restriction fragment length polymorphism mapping and conventional sequencing in 139 patients with strokes involving the MCA and who received t-PA within 3 h. Recanalization was diagnosed by means of transcranial Doppler. No association was found between PAI-1 4 G/5 G polymorphism and recanalization rate. Dyslipidemia and TAFI Thr325Ile polymorphism were the main variables associated with recanalization resistance by the end of t-PA infusion: odds ratio (OR) 4.1 [95% confidence interval (95% CI) 1.6-10.8, P = 0.003] and OR 5.6 (95% CI 1.2-20, P = 0.031), respectively. The combination of the two polymorphisms doubled the risk of absence of recanalization: OR 11.1 (95% CI 1.4-89.8, P = 0.025). Polymorphic fibrinolysis inhibitor genes influence t-PA-induced recanalization resistance in ischemic stroke patients, especially when coexisting in the same patient. Efforts to individualize thrombolytic treatments are required.

Restriction Fragment Length Polymorphism and Gene Mapping of Two Genes Associated with Milk Composition in Egyptian River Buffalo

Restriction Fragment Length Polymorphism and Gene Mapping of Two Genes Associated with Milk Composition in Egyptian River Buffalo

Genes involved in biosynthesis and signalisation of ethylene in Brassica oleracea and Arabidopsis thaliana: identification and genome comparative mapping of specific gene homologues

The study reported was aimed at the identification and determination of the chromosomal organisation of genes involved in the ethylene biosynthesis and signalling pathways in Brassica oleracea, on the basis of the Arabidopsis thaliana DNA probes and in silico genome analysis. Because of its polyploidal origin, the B. oleracea genome is characterised by extensive gene redundancy. Therefore, an important aspect of gene expression in B. oleracea response to environmental stimuli is to identify the specific gene copy involved. This aspect should also be taken into consideration while studying the genetic basis of biosynthesis and signal transduction in relation to basic phytohormones. Our present work concerns the identification of homologue genes involved in ethylene biosynthesis such as SAM, ACS and ACO, as well as those involved in the ethylene signalling pathway, mainly ETR1, CTR1, MKK4, MKK5, EIN2, EIN3, EREBP, ERF5 and ERF7 on the basis of the restriction fragment length polymorphism (RFLP) and PCR mapping. In the case of ACC synthases, (ACSs) the in silico analysis of gene variants in the genome of A. thaliana was followed by the identification of homologues to ACS2, ACS6 and ACS7 in the B. oleracea database. In total, 22 loci with sequence homology to the genes under analysis were included in the existing B. oleracea RFLP chromosomal map. Based on the stress responsiveness of most of the A. thaliana genes analysed in this study, we performed initial functional analysis of some gene homologues mapped. With the use of the RT-PCR approach the conservation of differential transcriptional induction of ACS homologues in the B. oleracea and A. thaliana was demonstrated during ozone stress.

Molecular dissection of interspecific variation between Gossypium hirsutum and G. barbadense (cotton) by a backcross-self approach: II. Fiber fineness

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing two parameters reflecting lint fiber fineness and to compare the precision of these two measurements. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we were able to detect 32 and nine quantitative trait loci (QTLs) for fiber fineness and micronaire (MIC), respectively. The discovery of larger numbers of QTLs in this study than previously found in other studies based on F(2) populations grown in favorable environments reflects the ability of the backcross-self design to resolve smaller QTL effects. Although the two measurements differed dramatically in the number of QTLs detected, seven of the nine MIC QTLs were also associated with fiber fineness. This supports other data in suggesting that fiber fineness more accurately reflects the underlying physical properties of cotton fibers and, consequently, is a preferable trait for selection. "Negative transgression," with the majority of BC(3)F(2) families showing average phenotypes that were poorer than that of the inferior parent, suggests that many of the new gene combinations formed by interspecific hybridization are maladaptive and may contribute to the lack of progress in utilizing G. barbadense in conventional breeding programs to improve upland cotton.

Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content, respectively. For eight, six, and two chromosomal regions containing quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content (respectively), two-way analysis of variance showed a significant (P<0.001) among-family genotypic effect. A total of 13, two, and four loci showed genotype x family interaction, illustrating some of the complexities that are likely to be faced in introgression of exotic germplasm into the gene pool of cultivated cotton. Co-location of many QTLs for fiber length, length uniformity, and short fiber content accounted for correlations among these traits, while the discovery of many QTLs unique to each trait suggests that maximum genetic gain will require breeding efforts that target each trait (or an index including all three). The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.

Dissection of component QTL expression in yield formation in rice

Abstract Yield and its components were investigated by using a population of241 recombinant inbred lines (F 9 RILs) derived from an elite hybridrice cross of Zhenshan 97 · Minghui 63. Quantitative trait loci(QTLs) for causal analysing of yield traits were detected at differentyield component (YC) influences by conditional and unconditionalQTL mapping methods. The number of QTLs significantly affectingyield was different at component-special influence. Some QTLscontrolling yield identified in one component influence were undetect-able at the others. More QTLs for yield could be detected at differentYC influences. It is possible to reveal that causal gene expression foryield could be different at different YC influences. Mapping QTLs forcomponent effects of yield could help us in understanding the nature ofcause-effect traits for the formation of grain yield. Key words: Oryza sativa — quantitative trait loci — recom-binant inbred line — yield — yield componentGrain yield and its four components in cereal crops are alwaysone of the most important target traits in research andbreeding programmes. Faced with the same yield in differentcultivars, there mainly are three model systems of high yieldfrom the view of yield components (YC), such as heavy-panicle, multipanicle and mixture. As Donald (1968) advoca-ted the ideotype concept to describe the potential of enhancingyield by improving the individual component trait, manycomponent analyses have been studied for complex traitsbased on morphological and physiological characterization(Sparnaaij and Bos 1993, Gravois and Helms 1992, Piepho1995, Guo et al. 2002a). In addition, Sidwell et al. (1976)reported that through YC improvement to increase yield (YD)would be most effective because of lower heritability (0.12) forYD (Xiong 1992) and higher heritability for tillers per plant(TP; 0.45) and 1000-grain weight (GW; 0.50) (Li et al. 1998).However, selection for YCs in early segregating generationswas not a highly effective method because of the negativecorrelation between YCs (Li et al. 1998).To solve this contradiction, Backes et al. (1995) and Zhu(1995) suggested that focusing on component gene/quantita-tive trait locus (QTL) for YD should be a more effectiveapproach than looking for QTL for YD directly, because theformer not only allows complex traits to be divided intocomponent QTL that may be under separated and probablysimpler genetic control, but can also exclude the influence ofother components.Because the first restriction fragment length polymorphism(RFLP) map of rice was constructed, hundreds of genes andQTLs have been mapped (Xiao et al. 1995, Lin et al. 1996,Veldboom and Lee 1996, Zhuang et al. 2002). Some yieldQTLs coincided with those for component traits, explainedfrequently as pleiotropic effects or linkage. In these studies, acommon problem associated with the analyses of the datareported so far is that the analysis of QTLs for YD and itscomponents was conducted based on the phenotypic valuesseparately. Although it can provides statistical estimates forthe magnitude of the effects and the proportions of variationexplained, it is nonetheless impossible to detect the componentQTLs controlling complex yield trait based on the phenotypicvalue of yield conditional on the phenotypic value of thiscomponent (Zhu 1995).According to the theory of developmental genetics, genes areexpressed selectively at different time and position (Atchleyand Zhu 1997). Piepho (1995) proposed that the complex yieldcharacter may be regarded as the end-point of a process ofwhich the successive stages are represented by observedprimary characters TP, grains per panicle (GN), percentageseed set and GW. At different YC influences, the yield geneexpressing might behave differentially. It is necessary, there-fore, to understand the component gene expression for yield atdifferent yield factor influences as a basis for quantitative traitmanipulation (Xu 1997). So far, no report has explored thecomponent QTL expression in yield formation in rice. Thesubject of this study is by combining the newly developedstatistical procedures of analysing conditional genetic effects(Zhu 1995, Yan et al. 1998) and the composite intervalmapping method (Zeng 1993, 1994), to dissect the componentQTLs for yield at different component influences, to improveour understanding for gene expression affecting grain yield,and to provide an outline of genetic basis for the cause-resulttraits and useful information for genetic improvement of yieldpotential in rice.

Ancient duplication of cereal genomes

Ancient duplication of cereal genomes

The Ry-fsto gene from Solanum stoloniferum for extreme resistant to Potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122718 in PVY resistant potato cultivars

A novel locus for extreme resistance to Potato virus Y (PVY), Ry-fsto, was identified on potato chromosome XII. The gene Ry-fsto has been introgressed from the wild potato species Solanum stoloniferum. Inheritance of Ry-fsto in the tetraploid potato population Rysto was consistent with the model of a single, dominant gene. Bulked segregant analysis identified an ISSR (inter-simple sequence repeat) marker UBC 857980 linked to Ry-fsto. This marker mapped to linkage group XII of a reference potato RFLP (restriction fragment length polymorphism) map. Chromosome XII specific RFLP markers were converted into PCR-based STS and CAPS markers and tested for linkage with Ry-fsto in the population Rysto. CAPS marker GP122718 was tightly linked to the resistance gene and was successfully used to identify Polish and German cultivars expressing extreme resistance to PVY. This indicates that the source of Ry-fsto has been widely utilized in various potato breeding programs and can be monitored by a diagnostic marker in marker-assisted selection.

PRESIDENTIAL ADDRESS*

Fellow parasitologists, friends, and distinguished guests, Dr. Nappi's introduction reminded me of a gentleman who was driving through the countryside in New England, when he was forced to stop his car for a flock of sheep that was crossing the road. After a long wait, he made a proposition to the sheep herder. Sir, if I am able to tell you the number of sheep in your flock could I have one? After a bit of contemplation, the herder agreed, and the traveler told him he had 400 sheep. Amazed, the sheep herder told him to make his choice. Upon carrying his selected animal to his car, the herder made his own proposition. Sir, if I am able to guess your occupation, can I have my animal back? Of course this seemed only fair, so the driver agreed. Immediately, the sheep herder said You, sir, are a molecular biologist. Shocked, the traveler had to know how he could guess his occupation so easily. The herder responded, You picked up my sheep dog! Now, this good-hearted jab I just made is not new to ASP presidential addresses, and some of you might remember a story along the same lines told by Dr. Hoogstral many years ago (Hoogstral, 1985). My purpose is not to belittle a field in which I actively work, but rather to provide you with my thoughts on the critical need for a broad perspective of biology in our struggle to alleviate the devastating impact that parasites have on the majority of the world's populations who are less fortunate than us. One of the most interesting and exciting research projects I have been involved with over the years was the discovery and description (Christensen and Calentine, 1983) of a new species of caryophyllid tapeworm, Penarchigetes macrorchis. This was especially fun for me because I was able to go back and spend some time working on this with my coauthor, Robert Calentine, the individual who initiated me into the world of parasitology. Since publication in 1983, my fellow parasitologists' interest in this work was so overwhelming that I received at least 5 or 6 reprint requests. In 1995, my laboratory published an article on restriction fragment length polymorphism mapping of quantitative trait loci (QTL) for Plasmodium gallinaceum susceptibility in the mosquito Aedes aegypti, and for this article, my supply of 300 reprints was exhausted in less than a year (Severson et al., 1995). Two weeks ago, I searched both Biological Abstracts and PubMed, with the key subjects of the search being the genera Penarchigetes and Plasmodium. I recovered 5 Penarchigetes and 25,749 Plasmodium references. In the short time since my search, I seriously doubt if more has been published on Penarchigetes, but several hundred Plasmodium articles might well have entered the literature database. Does this mean my tapeworm article is not valuable? Absolutely not, it is good-quality work of which I am very proud. Does this mean work with malaria parasites is more valuable? In the real world,

OsBi1, a rice gene, encodes a novel protein with a CBS-like domain and its expression is induced in responses to herbivore feeding

Plant–herbivore interactions are complex. Plant genes respond differentially to insects of different feeding modes. In this paper, we describe the cloning and characterization of OsBi1, a rice ( Oryza sativa L.) gene significantly induced by feeding of the sucking herbivore brown planthopper ( Nilaparvata lugens Stål.). The OsBi1 gene contains an open reading frame that encodes a polypeptide of 283 amino acid residues with a predicted molecular weight of 36.2 kDa. Homology search in GenBank databases showed that the deduced OSBI1 protein was homologous to the inosine monophosphate dehydrogenase (IMPDH) protein in the CBS domain. Genomic Southern analysis indicated that the OsBi1 gene was present as a single copy sequence in the rice genome. Restriction fragment length polymorphism mapping assigned the OsBi1 gene to the long arm of chromosome 2. Increase in the level of OsBi1 expression was detected in rice plants shortly after brown planthopper feeding. OsBi1 gene expression was up-regulated in response to ethephone and water deficit. In situ hybridization indicated that transcripts of the gene accumulated specifically around the vascular bundle of stem. Evidences suggest that OsBi1 is a BPH-inducible gene that is implicated in the resistance of rice plants to brown planthopper.

Development of Co-Dominant Amplified Polymorphic Sequence Markers in Rice that Flank the Magnaporthe grisea Resistance Gene Pi7(t) in Recombinant Inbred Line 29

ABSTRACT Pi7(t), a dominant blast resistance gene derived from the rice cultivar Moroberekan, confers complete resistance against the fungal pathogen Magnaporthe grisea. Pi7(t) previously was positioned on chromosome 11 by restriction fragment length polymorphism (RFLP) mapping of a recombinant inbred line population. One derivative of this population, recombinant inbred line (RIL)29, was designated as the representative line for Pi7(t). A segregating F2 population was created from RIL29 in order to determine the location of Pi7(t). The new mapping data indicate a position for Pi7(t) 30 centimorgans distal to the original location. Pi7(t) shares a common position with the previously mapped Pi1 M. grisea resistance gene. RIL29 carries DNA not derived from either parent used to create the RIL population at the newly assigned Pi7(t) locus. RFLP analysis has identified a possible donor source.

Construction of a comparative RFLP map of Echinochloa crus-galli toward QTL analysis of flooding tolerance

To analyze quantitative trait loci (QTLs) affecting flooding tolerance and other physiological and morphological traits in Echinochloa crus-galli, a restriction fragment length polymorphism (RFLP) map was constructed using 55 plants of the F(2) population ( E. crus-galli var. praticola x E. crus-galli var. formosensis). One hundred forty-one loci formed 41 linkage groups. The total map size was 1,468 cM and the average size of linkage groups was 35.8 cM. The average distance between markers was 14.7 cM and the range was 0-37.2 cM. Early comparisons to the genetic maps of other taxa suggest appreciable synteny with buffelgrass ( Pennisetum spp.) and sorghum ( Sorghum spp.). One hundred ninty-one F(2) plants were used to analyze QTLs of flooding tolerance, plant morphology, heading date, number of leaves, and plant height. For flooding tolerance, two QTLs were detected and one was mapped on linkage group 24. Other traits, including plant morphology, heading date, number of leaves, and plant height were highly correlated. Three genomic regions accounted for most of the mapped QTLs, each explaining 2-4 of the significant marker-trait associations. The high observed correlation between the traits appears to result from QTLs with a large contribution to the phenotypic variance at the same or nearby locations.

Genetic Analysis of Seed‐Oil Concentration across Generations and Environments in Sunflower

Seed‐oil concentration is a major consideration in sunflower (Helianthus annuus L.) breeding because it is an important component of oil yield. Seed‐oil concentration is a complex trait determined by the genotype and the environmental conditions. The objectives of this study were (i) to locate quantitative trait loci (QTL) for seed‐oil concentration across generations and environments, (ii) to compare QTL detected among individual F2 plants and their F3–generation progeny, and (iii) to assess the genetic relationship between seed‐oil concentration and days to flowering in an elite sunflower population. Two hundred thirty‐five F2 plants and F3 lines of a single‐cross population of two divergent inbred lines were evaluated in four environments. Detection of QTL was facilitated with a genetic map of 205 loci defined by restriction fragment length polymorphism (RFLP) and composite interval mapping. Eight QTL on seven linkage groups accounted for 88% of the genetic variation for seed‐oil concentration across environments. Gene action was additive for four QTL and dominant or overdominant at the others. In all environments, the QTL on linkage group G20cM had the most influence on seed‐oil concentration. Four of the eight QTL were detected in two or more environments and the parental effects were the same across generations and environments. The phenotypic correlation between seed‐oil concentration and days to flower (DTF) ranged from −0.05 to –0.29. QTL on two linkage groups (B and L) affected seed‐oil concentration and DTF. The highest LOD score for these two QTL associated with seed‐oil concentration was observed at the environment with the highest rate of decline of temperature and radiation during the grain‐filling period. Additive effects for higher values of DTF and lower values of seed‐oil concentration in linkage groups B and L were derived from the same parent.