Applying High-Throughput SNP Genotyping and Sequencing to Accelerate Progress in Rice Breeding

Michael J. Thomson,Christine Jade Dilla-Ermita,Maria Ymber Reveche,Maria Dwiyanti,Geraldine Malitic,Geisha Sanchez,Nadia Vieira,Venice Juanillas,Ramil Mauleon,Bertrand Collard,Joong Hyoun Chin,Eero Ni 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

We are currently developing a high-throughput single nucleotide polymorphism (SNP) genotyping service at IRRI to accelerate progress in rice breeding by providing rapid and cost-effective marker services. SNP marker development and validation is being performed based on cloned genes and QTLs, GWAS hits, and whole genome sequence data to identify predictive SNP markers at important genes for key traits for the breeding programs. Trait-based and targeted SNPs are being deployed in sets of 24 and 96 SNPs on a Fluidigm EP1 system. At the same time, 384 SNP sets and a 6K SNP chip developed by Susan McCouch at Cornell University are being used for higher density genome scans on an Illumina system. Genotyping by sequencing (GBS) approaches with 96 and 384 barcoded samples per sequence lane are also being evaluated in comparison to SNP array technology based on the number of loci, call rates, turnaround times, and cost per sample. An efficient sample processing workflow with an integrated LIMS is also being optimized to enable high throughput genotyping with sample tracking to minimize errors. Moreover, web-based SNP data analysis tools have been deployed through the IRRI Galaxy workbench to speed up SNP data analysis. Future efforts will focus on large-scale deployment of GBS across breeding materials to enable QC genotyping, tracking of donor introgressions, and integration of genome-wide prediction into the variety development pipelines. The large-scale application of high-density markers will help transform IRRI’s rice breeding programs and increase the rate of genetic gain towards developing high-yielding, stress-tolerant varieties for target environments and market segments

High-Throughput SNP Genotyping to Accelerate Crop Improvement

( Michael J Thomson ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.3

Recent advances in next-generation sequencing (NGS) and single nucleotide polymorphism (SNP) genotyping promise to greatly accelerate crop improvement if properly deployed. High-throughput SNP genotyping offers a number of advantages over previous marker systems, including an abundance of markers, rapid processing of large populations, a variety of genotyping systems to meet different needs, and straightforward allele calling and database storage due to the bi-allelic nature of SNP markers. NGS technologies have enabled rapid whole genome sequencing, providing extensive SNP discovery pools to select informative markers for different sets of germplasm. Highly multiplexed fixed array platforms have enabled powerful approaches such as genome wide association studies. On the other hand, routine deployment of trait-specific SNP markers requires flexible, low-cost systems for genotyping smaller numbers of SNPs across large breeding populations, using platforms such as Fluidigm`s Dynamic Arrays™, Douglas Scientific`s Array Tape™, and LGC`s automated systems for running KASP™ markers. At the same time, genotyping by sequencing (GBS) is rapidly becoming popular for low-cost high-density genome-wide scans through multiplexed sequencing. This review will discuss the range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities, and will provide an example of SNP deployment for rice research and breeding as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.

Towards high-throughput marker-assisted backcrossing system

Chenie Zamora,Katreena Titong,Michael J. Thomson,Joong Hyoun Chin 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

The main objectives of IRRI’s variety development should meet the needs of customers/farmers from diverse rice sectors in each target region. The dynamic market change asks rapid variety development with highly valued QTLs/genes. Molecular breeding implemented through the efficient crossing, high throughput genotyping and rapid generation advancement will provide packages to breeders to develop new varieties quickly and more economically. The more efficient and cost-effective marker-assisted backcrossing service will provide the more opportunity for the success in molecular breeding platform. To make MABC system more successful, the development of molecular marker system for the high-throughput SNP genotyping is must. Currently Genotyping Service Lab (GSL) of IRRI provides high-throughput SNP genotyping service using BeadXpress and Fluidigm system. Meanwhile, the linked SNP markers for the specific traits are being developed. For abiotic stress tolerances, the markers for submergence, drought, heat, anaerobic germination, salinity, and phosphorus deficiency for Fluidigm system are being developed and tested in variety diversity panel and segregating populations. In MABC, due to the high number of crossings, the labor- and space-saving crossing system is being developed. As a result of an integrated MABC platform will speed up the development of pre-breeding line which are containing single or multiple QTLs/genes.

Tobacco Use in Bipolar Disorder

Daniel Thomson,MIchael Berk,Seetal Dodd,Marta Rapado-Castro,Shae E. Quirk,Pernille K. Ellegaard,Lesley Berk,Olivia M. Dean 대한정신약물학회 2015 CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE Vol.13 No.1

Tobacco use in mental health in general and bipolar disorder in particular remains disproportionally common, despite declining smoking rates in the community. Furthermore, interactions between tobacco use and mental health have been shown, indicating the outcomes for those with mental health disorders are impacted by tobacco use. Factors need to be explored and addressed to improve outcomes for those with these disorders and target specific interventions for people with psychiatric illness to cease tobacco smoking. In the context of bipolar disorder, this review explores; the effects of tobacco smoking on symptoms, quality of life, suicidal behaviour, the biological interactions between tobacco use and bipolar disorder, the interactions between tobacco smoking and psychiatric medications, rates and factors surrounding tobacco smoking cessation in bipolar disorder and suggests potential directions for research and clinical translation. The importance of this review is to bring together the current understanding of tobacco use in bipolar disorder to highlight the need for specific intervention.

Application of <i>indica-japonica</i> single-nucleotide polymorphism markers for diversity analysis of <i>Oryza</i> AA genome species

Lee, Yoo-Jin,Thomson, Michael J.,Chin, Joong Hyoun Cambridge University Press 2014 Plant genetic resources Vol.12 No.1

<P>High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 <I>indica-japonica</I> SNP markers, which can differentiate <I>indica</I> and <I>japonica</I> subspecies of rice, were used to characterize 227 <I>Oryza</I> accessions including 93 AA genome accessions from seven wild <I>Oryza</I> species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in <I>Oryza sativa</I> and evolutionarily close species, <I>Oryza nivara</I> and <I>Oryza rufipogon</I>. These markers can be used for distinguishing cultivated rice from the other species and <I>vice versa</I>. Eight clusters were generated through phylogenetic analysis, and <I>Oryza meridionalis</I> and <I>Oryza longistaminata</I> appeared to be the most distantly related species to cultivated rice. In this study, <I>Oryza barthii</I> and <I>Oryza glaberrima</I> accessions were found to exhibit high genetic similarity. Across the wild species, more <I>indica</I>-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across <I>O. sativa</I> accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.</P>

Development of Salt Tolerant IR64 Near Isogenic Lines Through Marker-Assisted Breeding

Viet The Ho,Michael J. Thomson,Abdelbagi M. Ismail 한국작물학회 2016 Journal of crop science and biotechnology Vol.19 No.5

Salt stress causes considerable damage to rice with a consequent reduction in grain yield, however, conventional breeding for this stress is time-consuming and costly. Recently, marker-assisted breeding has shown enormous potential to accelerate breeding of stress tolerant varieties because of its precision, time saving, and cost effectiveness. The present study was carried out to transfer Saltol, a major QTL on chromosome 1 associated with salinity tolerance, from FL478, a tolerant genotype, into IR64, a popular lowland variety through marker-assisted backcrossing (MABC). This technique considerably enhanced the recovery rate of the recurrent parent genome within three backcross generations, which could have saved several backcrosses compared with conventional schemes to achieve the same results. By using this technique, up to 99.7% of the recurrent parent genome was recovered at BC3F2 generation, saving at least three backcrosses compared with conventional breeding schemes. Salinity tolerance of IR64-Saltol lines was evaluated using saline culture solution adjusted to electrical conductivity of 12 dS m -1 using NaCl. Based on selected physiological and growth parameters, the new Saltol introgression lines showed a significantly higher tolerance of salinity than their recurrent parent IR64. The results of this study confirm the benefits of using molecular markers in plant breeding to enhance tolerance of abiotic stresses.

Evidence for several waves of global transmission in the seventh cholera pandemic

Mutreja, Ankur,Kim, Dong Wook,Thomson, Nicholas R.,Connor, Thomas R.,Lee, Je Hee,Kariuki, Samuel,Croucher, Nicholas J.,Choi, Seon Young,Harris, Simon R.,Lebens, Michael,Niyogi, Swapan Kumar,Kim, Eun J Nature Publishing Group, a division of Macmillan P 2011 Nature Vol.477 No.7365

Vibrio cholerae is a globally important pathogen that is endemic in many areas of the world and causes 3??5??million reported cases of cholera every year. Historically, there have been seven acknowledged cholera pandemics; recent outbreaks in Zimbabwe and Haiti are included in the seventh and ongoing pandemic. Only isolates in serogroup O1 (consisting of two biotypes known as ??classical?? and ??El Tor??) and the derivative O139 (refs 2, 3) can cause epidemic cholera. It is believed that the first six cholera pandemics were caused by the classical biotype, but El Tor has subsequently spread globally and replaced the classical biotype in the current pandemic. Detailed molecular epidemiological mapping of cholera has been compromised by a reliance on sub-genomic regions such as mobile elements to infer relationships, making El Tor isolates associated with the seventh pandemic seem superficially diverse. To understand the underlying phylogeny of the lineage responsible for the current pandemic, we identified high-resolution markers (single nucleotide polymorphisms; SNPs) in 154 whole-genome sequences of globally and temporally representative V.??cholerae isolates. Using this phylogeny, we show here that the seventh pandemic has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s, and identify several transcontinental transmission events. Additionally, we show how the acquisition of the SXT family of antibiotic resistance elements has shaped pandemic spread, and show that this family was first acquired at least ten years before its discovery in V.??cholerae.

The Effects of Water Deprivation on Cerebrospinal Fluid Constituents During Feeding in Sheep

Sunagawa, Katsunori,Weisinger, Richard S.,McKinley, Michael J.,Purcell, Brett S.,Thomson, Craig,Burns, Peta L. Asian Australasian Association of Animal Productio 2001 Animal Bioscience Vol.14 No.4

The internal humoral factors in the central regulation of dry feed intake during water deprivation in sheep were investigated by measurement of cerebrospinal fluid (CSF) constituents. Five animals were fed dried alfalfa chaff for 2 hours once a day. Sheep in the water deprivation treatment were deprived of water for 28 hours, while the sheep in the control treatment were given free access to water. During the first hour of the 2 hour feeding period, a rapid reduction in blood volume occured in both treatments (water deprivation and free access to water). The CSF concentrations of Na, Cl and osmolality during the second hour of the 2 hour feeding period in both treatments were greater (p<0.01) than those during the first hour. The drinking behaviors in sheep were concentrated during the second hour of the 2 hour feeding period in periods of free access to water. Water intake during feeding in periods of free access to water was 1110 ml/2 h. The levels of increase in CSF osmolality with feeding during water deprivation were greater (p<0.01) than during periods of free access to water. The changes in CSF osmolality with feeding during water deprivation produced more vigorous thirst sensations in the brain compared to during periods of free access to water. The eating rates for the first hour of the allotted 2 hour feeding period were the same under both treatments. However, the eating rates for the second hour during water deprivation periods decreased significantly (p<0.05) compared to those during periods of free access to water. The decreased eating rates for the second hour during water deprivation may be due to the vigorous thirst sensations produced in the brain. The results suggest that the increase in CSF osmolality with feeding during water deprivation acts as a thirst and satiety factor in brain mechanisms controlling feeding to decrease dry feed intake in water-deprived sheep.

The Role of Brain Somatostatin in the Central Regulation of Feed, Water and Salt Intake in Sheep

Sunagawa, Katsunori,Weisinger, Richard S.,McKinley, Michael J.,Purcell, Brett S.,Thomson, Craig,Burns, Peta L. Asian Australasian Association of Animal Productio 2001 Animal Bioscience Vol.14 No.7

The physiological role of brain somatostatin in the central regulation of feed intake in sheep was investigated through a continuous intracerebroventricular (ICV) infusion of somatostastin 1-28 (SRIF) at a small dose of $5{\mu}g/0.2ml/hr$ for 98.5 hours from day 1 to day 5. Sheep (n=5) were fed for 2 hours once a day, and water and 0.5 M NaCI solution were given ad libitum. Feed, water and salt intake were measured during ICV infusion of artificial cerebrospinal fluid (CSF) and SRIF. The feed intake during SRIF infusion on days 2 to 5 increased significantly compared to that during CSF infusion. Water intake, when compared to that during CSF infusion, only increased significantly on day 4. NaCI intake during SRIF infusion was not different from that during CSF infusion. Mean arterial blood pressure (MAP) and heart rate during SRIF infusion were not different from those during CSF infusion. The plasma concentrations of Na, K, Cl, osmolality and total protein during SRIF infusion were also not different from those values during CSF infusion.There are two possible mechanisms, that is, the suppression of brain SRIF on feed suppressing hormones and the direct actions on brain mechanisms controlling feed intake, explaining how SRIF works in the brain to bring about increases in feed intake in sheep fed on hay. The results indicate that brain SRIF increases feed intake in sheep fed on hay.

QTLs for high grain with long panicle under low phosphorus input rainfed condition in rice (O.sativa)

Ian Paul Navea,Maria Stefanie Dwiyanti,Chenie Zamora,Katreena Titong,Michael J Thomson,Sunghan Kim,Hee-Jong Koh,Joong Hyoun Chin 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

New QTLs were identified for high grain yield with long panicle in rice. A total of 137 F15 recombinant inbred lines (RILs) derived from a cross between Dasanbyeo (Tongil) and TR22183 (japonica), together with the parents were evaluated for 16 agronomic traits at IRRI in dry and wet seasons under different phosphorus (P) and irrigation conditions. A linkage map was constructed using 236 polymorphic markers in 384-plex Bead Xpress indica-japonica single nucleotide polymorphism (SNP) platform. P and water effects were significant in both wet and dry seasons. Both parents and RILs showed varying degree of sensitivities to scarcities in water and phosphorus in terms of panicle length. Collocating with 20 yield-related QTLs, the panicle QTLs on chromosomes 1 (pl01) ,2 (pl02), 9 (pl09), and 11 (pl11) under low P and rainfed conditions were identified. RILs with TR22183 allele at pl11 showed longer panicle length under low P input rainfed condition in dry and wet seasons. The whole-genome sequences of the two varieties are being compared to design the molecular markers for fine-mapping and candidate gene identification. Based on Nipponbare MSU 7.0 annotation, a total of 1464 genes with predicted function were identified within the four QTL regions. Candidate genes identified in other studies for QTLs under low P and water conditions, such as calmodulin and dehydrin genes, were targeted for designing molecular markers for fine-mapping and expression analysis. Pyramiding the panicle length QTLs correlating with yield QTLs will provide an opportunity of improving yield traits.