Agenda

Date

July 15-16, 2019

Location

Osaka, Japan

Conference Agenda

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Keynote Session:

Meetings International -  Conference Keynote Speaker Yusuf Leonard Henuk photo

Yusuf Leonard Henuk

University of Sumatera Utara, Indonesia

Title: Potential used of duckweed as an alternative protein source for human and animal nutrition

Biography:

Yusuf Leonard Henuk is a Professor in the Department of Animal Science, Faculty of Agriculture at University of Sumatera Utara (USU), Medan, North Sumatera, Indonesia. He was a prolific writer and has published many articles in international journal and mainly poultry science, e.g. World's Poultry Science Journal as well as international scientific meetings as such as 1st International Conference on Native Chicken.

Abstract:

The increasing world’s population and accompanying total food consumption raises the worldwide demand for agricultural produces. This raising demand implies a further increase of pressure on current land usage. It becomes more and more important to search for sustainable alternatives of natural resources. Duckweed has attracted attention because it (1) contains high amounts of high quality protein when grown under optimal conditions, ranging from 35 to 43% in dry matter (considering a water content of  92 to 94% in fresh duckweed); (2) contains protein with a better composition of essential amino acids, thus covering nutritional requirements to a larger extent than many other plant proteins; (3) has a high growth rate and can tolerate extreme circumstances; (4) can be cultivated in a basin on non-arable land, thereby avoiding the use of farming land. Human consumption of duckweed is common in some parts of Southeast Asia, including Laos, Thailand and Myanmar, as a vegetable named ‘Khai-Nam’. Wolffia arrhiza and Wolffia globosa are the dominating species used for human consumption. Despite the great potential of duckweed as a source of plant protein in human nutrition, it is not part of the diet in Western countries. Duckweed has been known for a long period of time as a potential source of food for humans and animals and as a source of natural products it is the only source of supplementary protein for fish, chickens ducks and pigs. Horses or ruminants could be fed on freshly harvested duckweed.  It can be concluded  that duckweed   as an alternative crop for the future as an alternative  protein source for human and animal nutrition.

Meetings International -  Conference Keynote Speaker Takayuki Momma photo

Takayuki Momma

Iwate University, Japan

Title: Study of hop stunt viroid: making of hop stunt viroid free hop plants using apical meristem culture and ultrastructure of hop stunt viroid

Biography:

Takayuki Momma got Ph.D. thesis in University of Tohoku. The title was Analysis of soybean gene structure: Glycinin. He worked as an Associate member in National Institute Agricultural Resource, Ministry of Agricultural, Forestry and Fisheries in Tsukuba-shi, Dr. Yuzoh Minobe to analyse whole rice genome for two years. He was retired from Kirin Brewery Co., Ltd. Currently, Takayuki Momma is appointed in the members of International exchange department, Iwate University.

Research Interest

Plant pathology, plant breeding, plant morphology and plant physicology

 

Abstract:

Infection of hop plants with hop stunt viroid (HSVd) result in the retardation of the growth rate except for the rate of leaf emergence and the disappearance of the fold like structure over the epidermal cell. Mature cones from HSVd-infected hop plants remained small-sized and the content of alpha acids was half to one third of that of HSVd-free hop cones. In HSVd-infected hop cones, the lupulin glands are distributed most abandantly on the bracteoles and the perianths and their numbers are reduced by at least 60% of that in the HSVd-free control. Scanning electron micrographs confirm that most of the lupulin glands on bracteoles from HSVd-infected hop cones shrivel severely, but not those from HSVd-free hop cones become withered. Shoot apical meristems of hop plant infected with HSVd were examined for cytopathic changes. No measurable changes in Ultrastructure were found in shoot tip 0.2mm long bearing apical dome and two pairs of the primordia, whereas in the 3rd leaf primordium cell walls were not observed in comparable shoot tips of the uninoculated hop  plants on HSVd-free plants obtained by meristem tip culture. We would like to discuss with what should we do after making HSVd-free hop plants and the others.

Meetings International -  Conference Keynote Speaker Najla Mezghani photo

Najla Mezghani

National Gene Bank of Tunisia, Tunisia

Title: Integrated molecular and morphological characterization of Daucus carota L. in Tunisia

Biography:

Najla Mezghani is an assistant professor in the National Gene Bank of Tunisia since 2008. She has her expertise in plant biotechnology and genetics. She is working in the field of plant genetic resources and she is particularly responsible of the Vegetable, condiment and ornamental genetic resources conservation. She has published more than 20 papers in peer reviewed journals and she is serving as a reviewer for several reputed journal.

Research Interest:

Plant biotechnology and genetics

Abstract:

Daucus carota L. is a morphologically diverse species found throughout the Mediterranean regions and in many continents worldwide. Despite the genus Daucus having been revised several times, the taxonomy of D. carota L. remains difficult and unresolved. Among Mediterranean regions, Tunisia is considered a center of diversity for Daucus and many other crops because of the diverse ecosystems and climatic conditions. A collection of 160 Daucus accessions from Tunisia including cultivated carrot (D. carota subsp. sativus) and wild relatives were morphologically characterized using international descriptors and common taxonomic criteria. Fifty-one D. carota accessions out of the whole collection were genotyped using Genotyping by sequencing (GBS) technology and compared to a worldwide collection.

Morphological characterization showed that fruit characters were efficient to identify different species in the collection whereas leaves, stems, and flowers were required to distinguish among closely related D. carota subspecies.

GBS data based on Maximum Likelihood method analysis showed a grouping of the accessions according to their geographic origin. Specifically all Tunisian wild D. carota members resolved in a same clade with the immediately adjacent western Libyan and mainland Italian accessions.

Comparison of the morphological and molecular results demonstrated concordance of grouping the taxa at species level, but great discordance of grouping within taxa suggesting that while morphology is useful to group germplasm at the species level, GBS data are required to accurately make identifications at the subspecies level.

Key words: Daucus, Diversity, morphology, GBS.

Oral Session 1:

  • Plant Genome Science | Agricultural Science | Plant Proteomics and Plant Science | Molecular Plant Breeding | Stress Signalling in Plants
Speaker

Chair

Takayuki Momma

Iwate University, Japan

Speaker

Co-Chair

Yusuf Leonard Henuk

University of Sumatera Utara, Indonesia

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Ryoung Shin photo

Ryoung Shin

RIKEN Center for Sustainable Resource Science, Japan

Title: Elucidation of Arabidopsis cyclic nucleotide-gated channels contributing to heavy metal accumulation in plants

Biography:

Ryoung Shin has completed her PhD at the age of 28 years from Korea University and Postdoctoral Studies from Donald Danforth Plant Science Center, USA. She is the Unit leader of RIKEN Center for Sustainable Resource Science. She has published more than 45 papers in reputed journals and has 7 patents and has been served the editorial board member of three journals including Scientific Reports.

Abstract:

Non-essential heavy metals and toxic concentrations of essential metals negatively affect various metabolic and cellular processes. Although only few studies have performed the regulation of heavy metals transport in plants, heavy metal ions are known to enter cells in a non-selective manner. Plant cyclic nucleotide-gated channels (CNGCs), a type of Ca2+-permeable-channel, have been suggested to be involved in transporting both essential and toxic heavy metal ions. To determine the candidates responsible for heavy metal ion transport, a series of Arabidopsis CNGC mutants were examined for their response to Pb2+ and Cd2+ ions. Results, based on the analysis of primary root length and ion content analysis verified that at least four AtCNGCs play roles in Pb2+ and/or Cd2+ accumulation in plants. These findings provide functional evidence which support the roles of these AtCNGCs in the uptake and transport of Pb2+ or Cd2+ ion in plants.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Ramanjulu Sunkar photo

Ramanjulu Sunkar

Oklahoma State university, USA

Title: Exploring plant microRNAs for engineering and understanding gene regulation

Biography:

Ramanjulu Sunkar, joined the Department of Biochemistry and Molecular Biology, Oklahoma State University as an Assistant Professor in 2006, and he was promoted to Associate Professor in 2011. In his current position at Oklahoma State University, his laboratory works on understanding the molecular basis of stress tolerance in plants with a focus on microRNA- and epigenetic-mediated regulation of gene expression. This plant molecular biology research can help unravel complex plant regulatory networks that control stress tolerance.
 

Abstract:

The genome-encoded small RNAs have emerged as critical regulators of gene expression in higher eukaryotes.  In plants, on the basis of their biogenesis, size and their roles as transcriptional or posttranscriptional gene regulators, these are divided into two major sub classes, microRNAs and small interfering RNAs. MicroRNAs fine-tune target gene expression at the posttranscriptional level either by degrading or inhibiting the protein production of the mRNA target(s) and this regulation is essential for plant growth and development as well as adaptation to stress conditions. Our research mainly focused on identifying plant microRNAs that could be important for adapting to diverse abiotic stresses such as the drought, salt and heat including nutrient deprivation. Additionally, some of our work also has been focused on identifying and engineering microRNAs that could improve biomass accumulation in biofuel and medicinally important plant species. I will discuss these results including identification of upstream signaling events that are required for regulating stress-responsive microRNAs in plants.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Thomas P. Brutnell photo

Thomas P. Brutnell

Viridis Genomics Consulting, USA

Title: Setaria viridis: a model system for gene discovery and engineering in the grasses

Biography:

Thomas P. Brutnell is the founder and CEO of Viridis Genomics Consulting formed in 2018. He is the co-founder and former CSO of Benson Hill Biosystems and former Director of the Enterprise Rent-A-Car Institute for Renewable Fuels at the Donald Danforth Plant Science Center.  He has published over 100 papers that have been cited over 10,000 times and is a Fellow of the American Association for the Advancement of Science (AAAS).

Abstract:

Setaria viridis is rapidly emerging as the premier model system for studies of C4 photosynthesis in the grasses (1).  With a rapid life cycle of just 6 to 8 weeks, a short stature that is similar to A. thaliana and relatively simple growth requirements, S. viridis is an attractive system for conducting forward and reverse genetic screens to probe the genetic networks underlying the function and regulation of C4 photosynthesis.  To exploit Setaria as a model system, we have been developing a number of genetic and genomics tools, methods and resources for the community (2).  Here I will present on methods we have developed to rapidly identify candidate genes underlying phenotypes of interest and to identify putative rate limiting steps in C4 photosynthesis through cross-species selection scans (3).  I will also discuss new methods and approaches to engineering synthetic circuits in plants and discuss how these methods could be applied to altering metabolic flux in a C4 system as well as engineering C4 traits into C3 systems.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Maria Rosa Abenavoli photo

Maria Rosa Abenavoli

Mediterranean University of Reggio Calabria, Italy

Title: Natural variation and selection for contrasting N-use efficient eggplant genotypes by key morpho-physiological traits

Biography:

Maria Rosa Abenavoli is currently working as an associate professor in the Department of Agriculture at Mediterranean University of Reggio Calabria, Italy. She has published more than 100 articles in many reputed journals.

Abstract:

Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, whose excessive use is responsible of environmental damages. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake (NUpE), utilize (NUtE) and remobilize N available in soils, could be challenging to maintain high yields. The aim of this study was to explore the natural variation among 19 eggplant accessions in response to low and high NO3- supply to identify NUE-contrasting genotypes, in hydroponic and greenhouse experiments. AM222 and AM22 accessions were identified in both growing systems as N-use efficient and inefficient, respectively. Overall, the results indicated the key role of N-utilization component (NUtE) to confer high NUE. The higher N-content in AM222 fruits suggesting the efficient N-remobilization as a strategy to enhance NUtE, suggesting GS as a key enzyme.

To deeply understanding the mechanisms underlying NUE complex trait, AM222 and AM22 were employed for both transcriptomics and metabolomics approaches. Short- and long-term N-stress were adopted in the same experimental design for both -omics approaches. Metabolomics results highlighted that alanine, aspartate and glutamate metabolism was highly affected in AM222, while RNA-seq analysis underlined differential gene transcripts involved in processes of reactive oxygen species (ROS) rate‐limiting production that could be attributed to a higher antioxidant activity ability of N-use efficient genotype.

Overall, here we demonstrated the predominant role of NUtE to confer high NUE in eggplant. More interestingly, an integrated network of differential expressed genes and metabolites belong NUtE between AM222 and AM22 were discovered.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Francesco Sunseri photo

Francesco Sunseri

Mediterranean University of Reggio Calabria, Italy

Title: Highlighting differential expressed genes and metabolites related to N-pathway in eggplants

Biography:

Francesco Sunseri is an Associate Professor of Plant Genetics and Breeding at the Dipartimento Agraria, Mediterranean University of Reggio Calabria, Italy. Genomics and Transcriptomics, QTL analysis and cloning and plant abiotic stress with particular interest to Nitrogen Use Efficiency (NUE) are his interest. Associate Editor of BMC Plant Biology. Editor-in-Chief for the open access Journal of Genetics and Plant Breeding. Occasional reviewer for several scientific journals, he is author of about 60 scientific publications indexed in ISI and Scopus databases.

Abstract:

Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, whose excessive use is responsible of environmental damages. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake (NUpE), utilize (NUtE) and remobilize N available in soils, could be challenging to maintain high yields. The aim of this study was to explore the natural variation among 19 eggplant accessions in response to low and high NO3- supply to identify NUE-contrasting genotypes, in hydroponic and greenhouse experiments. AM222 and AM22 accessions were identified in both growing systems as N-use efficient and inefficient, respectively. Overall, the results indicated the key role of N-utilization component (NUtE) to confer high NUE. The higher N-content in AM222 fruits suggesting the efficient N-remobilization as a strategy to enhance NUtE, suggesting GS as a key enzyme.

To deeply understanding the mechanisms underlying NUE complex trait, AM222 and AM22 were employed for both transcriptomics and metabolomics approaches. Short- and long-term N-stress were adopted in the same experimental design for both -omics approaches. Metabolomics results highlighted that alanine, aspartate and glutamate metabolism was highly affected in AM222, while RNA-seq analysis underlined differential gene transcripts involved in processes of reactive oxygen species (ROS) rate‐limiting production that could be attributed to a higher antioxidant activity ability of N-use efficient genotype.

Overall, here we demonstrated the predominant role of NUtE to confer high NUE in eggplant. More interestingly, an integrated network of differential expressed genes and metabolites belong NUtE between AM222 and AM22 were discovered.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Arinaitwe Ivan Kabiita photo

Arinaitwe Ivan Kabiita

University of Malaya, Malaysia

Title: Quantitative trait loci (qtl) associated with resistance to Fusarium oxysporum f. sp. cubense race 1 in bananas (musa spp.)

Biography:

Arinaitwe Ivan Kabiita is a banana breeder at the National Banana Research Programme of National Agricultural Research Organisation (NARO)-Uganda. Currently he is pursuing his  Doctorate Degree in Genetics and Molecular Biology under Gates Foundation Scholarship and University (3rd yr) at the University of Malaya pursuing of Malaya, Malaysia.

Abstract:

Fusarium oxysporum f. sp. cubense (Foc) is a disease that attacks bananas causing great economic losses to banana production worldwide. Conventional banana breeding to introgress resistance from wild relatives to susceptible cultivars is complicated and takes a long time. Markers assisted selection is a modern tool thought to over some barriers of banana breeding by increasing the breeding efficiency and shortening the breeding period. The aim of this study was to genotype two unrelated mapping populations developed Foc race 1 resistance and identify markers for analysis of Foc race 1 resistance QTL. Two F1 mapping populations were developed for Foc race 1 resistance: First population of 140 hybrids, by crossing a resistant Monyet with a susceptible Kokopo and the second of 138 hybrids by crossing a susceptible Mshale with a resistant Calcutta 4. The parents contrasting for Foc race 1 resistance were screened using IRAP, ISSR, and SSR markers. IRAP primer GyLTRev had the highest polymorphism of 76.9% between Mshale and Calcutta 4 parents and 69.2% among their F1 hybrids and  64.3 % between Monyet and Kokopo parents of and 42.9% their F1 hybrids among all the primers. One major QTL associated with Foc race 1 in an F1 population of Monyet x Kokopo was mapped at linkage groups 1 (LG1) with a  LOD score of 4.0 using 32 polymorphic markers. Results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Mustafa A. N. AL-Fayyadh photo

Mustafa A. N. AL-Fayyadh

Eskisehir Technical University, Turkey

Title: Quantitative trait loci (qtl) associated with resistance to Fusarium oxysporum f. sp. cubense race 1 in bananas (musa spp.)

Biography:

Mustafa A. N. AL-Fayyadh is a student studying Master of Science in Biotechnology at the department of Biotechnology, Eskisehir Technical University which was under name of Anatolia University.He has had a 7 months training in Biotechnology and Molecular biology at the University of Malaya in Malaysia at The Centre for Research in Biotechnology for Agriculture (CEBAR) under the supervision of Prof. Dr. Jennifer Ann  Harikrishna.

Abstract:

Fusarium oxysporum f. sp. cubense (Foc) is a disease that attacks bananas causing great economic losses to banana production worldwide. Conventional banana breeding to introgress resistance from wild relatives to susceptible cultivars is complicated and takes a long time. Markers assisted selection is a modern tool thought to over some barriers of banana breeding by increasing the breeding efficiency and shortening the breeding period. The aim of this study was to genotype two unrelated mapping populations developed Foc race 1 resistance and identify markers for analysis of Foc race 1 resistance QTL. Two F1 mapping populations were developed for Foc race 1 resistance: First population of 140 hybrids, by crossing a resistant Monyet with a susceptible Kokopo and the second of 138 hybrids by crossing a susceptible Mshale with a resistant Calcutta 4. The parents contrasting for Foc race 1 resistance were screened using IRAP, ISSR, and SSR markers. IRAP primer GyLTRev had the highest polymorphism of 76.9% between Mshale and Calcutta 4 parents and 69.2% among their F1 hybrids and  64.3 % between Monyet and Kokopo parents of and 42.9% their F1 hybrids among all the primers. One major QTL associated with Foc race 1 in an F1 population of Monyet x Kokopo was mapped at linkage groups 1 (LG1) with a  LOD score of 4.0 using 32 polymorphic markers. Results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Yalcin Kaya photo

Yalcin Kaya

Trakya University, Turkey

Title: Recent achievements in sunflower molecular breeding

Biography:

Yalcin Kaya has longer carrier and experience on plant breeding and genetics and developed many sunflower hybrids and lines. He has worked in research institute as National Sunflower Coordinator and as Project leader for over 20 years and deputy director. He had M Sc in University Of Nebraska, Lincoln, US, and Post Doc on sunflower breeding in USDA Sunflower Lab at Fargo, ND, US. Now he is Plant Breeding Research Center director and Genetic Engineering Dept. Head at university. He is also former President of Turkish Plant Breeders Union and International Sunflower Association. He published more than 200 papers.

Abstract:

Sunflower (Helianthus annuus L.) is one of the main oil crops and grows commonly non irrigated lands in the world, therefore it influences from environmental conditions especially during grain filling period. Some diseases, weeds and broomrape parasite are main limiting factors of sunflower yield in addition to abiotic stresses. Hybrids have been using largely in sunflower production since 1980s almost in all of the world. However, plant breeders have to combine many different traits to new cultivars biotic and abiotic resistance in addition to higher seed and oil yielding and higher adaptation capability. Therefore, we need seriously new molecular tools both developing new hybrids and inbred lines and accelerating breeding program in sunflower, and also gene pyramiding in such as drought tolerance, higher oleic, etc. Helianthus family has 51 species so it has huge genetic resources keeping very useful genes for plant breeders both developing new plant designs to increase leaf area then new hybrids could catch higher heterosis on seed yield etc. New developments on molecular breeding will help to breeders both screening enormous genetic materials and then determining and transferring to cultivated ones shortly utilizing from molecular markers. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies enabled these identification of new markers from huge wild species and interspecific hybrids in sunflower. On the other hand, new image analysis methods and drone technology will facilitate to work for phenotyping on huge genetic materials giving the opportunities to look different angles to breeders while analyzing to plants.  As results, the future targets will be more complex both combining classical and molecular tools together in sunflower breeding programs and also help to develop new hybrids associated multi useful genes together.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Paul Njiruh Nthakanio photo

Paul Njiruh Nthakanio

University of Embu, Kenya

Title: Induction of nodulation signals in common bean, Phaseolus valgaris by different soil growth media

Biography:

Paul Njiruh Nthakanio is Formerly lecturer of Molecular Biology at Technical University of Kenya and currently Registrar (Planning, Administration and Finance) at University of Embu (Kenya).
Research Interests:
Breeding of hybrid rice through Genetic Emasculation and Gene silencing

Abstract:

Rhizobia are known to induce nodulation signal in legumes. In this research Canadian Wonder common bean, Phaseolus valgaris was grown in different growth media up to flowering to test how soil nutrition control nodulation signal. The different growth medium were saw dust, pure sand, saw dust + sand, loam soil, saw dust + loam soil and pure tap water as the control. Plants were sacrificed to count the level of nodulation. Pure sand significantly induced higher number of nodulation than others and no nodulation was noticed in the sawdust and loam soil.  The objective was to test effectiveness of different medium-growth environment in inducing nodulation in common bean. Conclusion is that soils like pure sand that was presumed to contain minimum nutrients induced nodulation signals better than the richer soils and pure tap water control samples. Therefore, maximum advantage of using beans as a fertility restoring crop is best realized in soils with little nutrient than well-nourished soils. 

Key Words: Bean, Growth Media, Legumes, Nodulation, Signal.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Geraldine P. Muncada photo

Geraldine P. Muncada

University of Eastern Philippines, Philippines

Title: Antiviral resistance genes from abaca (Musa textilis nee) Bc2 hybrid: transcriptome responses that mediate innate Immunity against abaca bunchy top virus (abtv)

Biography:

Geraldine P. Muncada holds a MS and PhD degree in Molecular Biology and Biotechnology with a cognate in Biochemistry both from the University of the Philippines Los Banos, Philippines with a full-time scholarship privilege under the Faculty Development Program Phase II of the Commission on Higher Education (CHED-FDPII).

Abstract:

Abaca (Musa textilis Nee) is susceptible to abaca bunchy top virus (ABTV).  An abaca BC2 hybrid derived from a cross between abaca variety Abuab and the ABTV resistant donor parent Pacol (M. balbisiana), was observed to be resistant to ABTV.  The molecular mechanism underlying ABTV disease resistance in the hybrid has not been elucidated.  Currently, transcriptomic data are available to understand the molecular mechanism of resistance of the abaca BC2 hybrid to ABTV.  RNA Seq transcriptome data were obtained from the inner whorl of the pseudostems of Abuab, pacol, BC2-A2 non-inoculated, BC2-A2 two weeks post inoculated and BC2-A2 four weeks post inoculated with ABTV.  Transcriptome were assembled using CLC Bio Genomics Workbench based on reference-guided assembly with CDS of M. acuminate and M. balbisiana.  There are 349 differentially expressed (DEGs), eighty-seven of which were putatively classified as defense response genes.  These include: four pattern triggered immunity (PTI); signal receptor genes/pattern recognition receptors (PRRs); 35 effector triggered immunity (ETI)-based effector genes or R genes; four photosynthetic genes; two ER resident chaperones involved in unfolded protein response (UPR) and ER-mediated program cell death; two genes involved in molecular Ubiquitin Proteasome System (UPS); four regulatory receptors and thirty-one ABTV responsive transcription factors.  It was also observed that some genes have similar patterns of expression in the BC2 hybrid and the donor parent, Pacol.  Quantitative real-time PCR analysis validated the RNA-Seq expression results for six genes which include germin-like protein (GLP3), glutathione S-transferase F11 (GST), heat shock coat protein 70-1 (HSCP 70-1), lipid transfer protein (LTP3), senescence associated gene (SAG20) and thioredoxin superfamily protein (TXN).  This is the first report on the possible complex molecular mechanisms involved in antiviral defense response in Musa textilis Nee.

Keywords: abaca buncy top virus, abaca antiviral resistance genes, abaca transcriptome, innate immunity in abaca

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Nagesh Kancharla photo

Nagesh Kancharla

Reliance Industries Limited, India

Title: De Novo sequencing and hybrid assembly of biofuel crop Jatropha curcas L: Insights on gene annotation, comparative genomics and transcriptome analysis with identification of quantitative trait loci for geminivirus resistance

Biography:

Nagesh Kancharla has completed his PhD in Plant Genetics from Osmania University, Hyderabad. He is currently working as Senior Research Scientist at Reliance Industries Ltd, Mumbai. His major work responsibilities include molecular breeding for plant-based bio-fuel crops to develop high yielding and disease resistant hybrids through latest cutting edge technologies. He has published two articles in peer reviewed journals and presented his work in various International conferences.  

Abstract:

Jatropha curcas is an important perennial, drought tolerant plant identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of Jatropha curcas generated using Illumina and PacBio sequencing technologies and identification of quantitative loci responsible for geminivirus resistance. In this study, we generated scaffolds of 265.7 Mbp in length which is corresponding to 84.8% of the gene space using BUSCO analysis. Additionally, 96.4% of predicted protein-coding genes were captured in corresponding tissues transcriptome data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide repeat SSR markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 250, polymorphic SSR markers were employed to construct a genetic linkage map for Jatropha Mosaic Virus (JMV) resistance using interspecific F2 mapping population involving Jatropha curcas and Jatropha integerrima as parents. QTL analysis showed the identification of three minor quantitative trait locus (QTL) for JMV resistance and validated in an alternate recipient genetic background F2 mapping population. These validated QTLs were utilized in Marker Assisted Breeding (MAS) for developing Jatropha Mosaic Virus resistance hybrids in Jatropha. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2,986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha and serves as source for the development of agronomically improved virus resistant and oil producing species.

Keynote Session:

Meetings International -  Conference Keynote Speaker Wilson Boardman photo

Wilson Boardman

Micromix Plant Health Limited, UK

Title: Combating abiotic stress through changing gene expression

Biography:

Wilson Boardman in his early career was working in the pesticide industry in both technical and commercial roles for multi-national manufacturers. Micromix was acquired by the OLMIX group in June 2018 and Wilson is now the Global Ambassador for Plant Care Products for the French owned group. Micromix recently was awarded a research grant by the UK government of a little over $1m to develop its technology facilitating crop development under reduced irrigation or drought conditions.

Research Interest
Plant nutrition, Crop Protection, Plant Pathology and Agriculture

 

Abstract:

Main aim: to prove the concept of alleviating heat stress in greenhouse-grown peppers by applying micronutrients/ biostimulants

Peppers in the UK suffer from heat stress - white washes are used to cover the greenhouses

2015/16 -  Very poor summer with only low impact of heat stress  (38 degs on two occasions)

The trial also engaged the UK’s top commercial agronomist Derek Hargreaves.

Physiological Effects:

  • Under normal conditions heat stress will cause the plant to cease growth and wilt
  • Gene expression changes, some genes are suppressed, some are stimulated.
  • Plant continues to produce growth hormones, with some changes
  • Wilting is gradual and at higher temperatures
  • Flowering continues
  • Fruit set continues
  • New growth does not stop

Support for the plant is provided with both nutrients and intermediates for growth
University of Nottingham Conclusions and Future Work

  • D1 treatment shows highest yield, fruit number and sugar content;
  • D2 treatment shows the highest average weight per fruit;
  • D1: higher Se, S, K in D1
  • D2: higher Cu, Mn, Zn, Mg, Fe and P;
  • Roots: D1 has higher dry weight; D2 roots are longer;
  • D1 and D2 have significant high resistance to fruit rotting (heat stress).
  • D1 and D2 show significant differences in expression of “heat” genes.

Meetings International -  Conference Keynote Speaker Vasileios Fotopoulos photo

Vasileios Fotopoulos

Cyprus University of Technology, Cyprus

Title: Plant priming for improved growth and stress protection under climate change conditions

Biography:

Vasileios Fotopoulos is an associate professor in Structural and Functional Plant Biology at the Cyprus University of Technology. His main scientific research focuses on the study of nitro-oxidative signaling cascades involved in plant responses to stress factors, while emphasis is being given in the development of chemical treatment technologies towards the amelioration of abiotic stress factors and promotion of plant growth. To date, Dr. Fotopoulos is the author of 62 scientific articles published in peer-reviewed journals (h-index=25), while he serves as Associate Editor in BMC Plant Biology, Gene and five other journals.

Abstract:

Increased frequency of extreme environmental events resulting from global climate change greatly influences plant growth and development. Close examination of plant-to-plant communication in nature has revealed the development of unique strategies from plants for responding to abiotic stress, with one of the most interesting being through priming for improved defence responses. The process of priming involves prior exposure to a biotic or abiotic stress factor making a plant more resistant to future exposure. Priming can also be achieved by applying natural or synthetic compounds which act as signal transducers, ‘activating’ the plant’s defence system. An up-to-date overview will be presented describing the research carried out at the Cyprus University of Technology using priming agents towards induced acclimation of plants to environmental challenges. Focus will be given to NOSH-aspirin (NBS-1120), a patented nitric oxide- and hydrogen sulfide-releasing hybrid that additionally provides the pharmaceutical molecule acetylsalicylic acid. In addition, recent findings will be presented on the evaluation of chemical compounds that potentially display growth promoting properties in plants, closely related to our existing expertise and previous observations in priming against stress.

Meetings International -  Conference Keynote Speaker Anindhya Bandhyopadhyay photo

Anindhya Bandhyopadhyay

Syngenta, China

Title: Novel genome editing technology aided faster improvement of agricultural crops

Biography:

Anindya Bandyopadhyay leads Genome editing (GE) program of Syngenta and his activities span from strategizing research activities for GE program, reviewing research proposals, supervising technology integration, collaborations and coordination with expert functions such as regulatory, stewardship and IP.

Previously Dr. Bandyopadhyay was a Group Leader and Scientist at International Rice Research Institute (IRRI) , Philippines, where he led genome editing research and also worked as Deputy-coordinator for International C4 Rice Consortium funded by Bill and Melinda Gates foundation. At IRRI, Dr. Bandyopadhyay’s lab was one of the early publishers of application of CRISPR-Cpf1 in plants.

Being trained from IRRI (PhD), University of California Berkeley (Post-doctoral) and University of Kentucky (Post-doctoral)on genome engineering, followed by research activities in industry and academia as group leader /scientist / program manager,  Dr.Bandypadhyay’s research interest lies in the application of gene targeting and genome engineering using site specific recombinases and CRISPR systems for crop improvement.

Abstract:

Oral Session 1:

  • Plant Nutritional Genomics | Crop Improvement and Plant Virology | Plant Genome Science | Plant Genetics and Genomics Market | Plant Biotechnology
Speaker

Chair

Wilson Boardman

Micromix Plant Health Limited, United Kingdom

Speaker

Co-Chair

Vasileios Fotopoulos

Cyprus University of Technology, Cyprus

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Alice Brunazzi photo

Alice Brunazzi

ISI Sementi, Italy

Title: To taste or not to taste: that is the question! innovative approaches and instruments for tomato breeding

Biography:

Alice Brunazzi has completed her PhD in Agrobiosciences, genomics and crop sciences from Sant’Anna University (Pisa, Italy) after several years working as a researcher and Junior Breeder around Europe. She currently is the fresh market tomato breeder of ISI Sementi in Italy, a premier Italian seed company. She has published several papers regarding phenotypic characterization both in cereals and different horticultural species.

Abstract:

Tomato (Solanum lycopersicum L.) is an important crop worldwide and the most important vegetable in Europe. During the last decade of selection breeders successfully focused on traits as plant yield, long-shelf-life and disease resistances, nonetheless final consumers are frequently not satisfied regarding the fruit quality and taste. Furthermore, from the breeders’ point of view, the lack of phenotyping platforms and clear key traits that can efficiently identify individuals exhibiting rare, optimal genotypes from large populations is currently on of the major bottlenecks. To face this constraint, we promoted two different projects: I) APPreciation of simplification project with the aim to accelerate the development of new improved varieties thanks to the use of FieldBook App and II) Taste it ISI with the objective to create a tool for the detection of the flavor components in tomato directly into the field/greenhouse. In this study, 25 ISI Sementi commercial varieties including 5 testers, were phenotypically characterized with all the DUS test traits in order to assess the genetic stability of the hybrids. Then, organoleptic properties of each varieties were settled by a sensory analysis and MS: from mature fruits, 19 flavor traits (including L-glutammic acids that is demonstrated to be the main responsible of the peculiar umami taste in tomato) were determined and used to build specific calibrations with a micro-NIR spectrometer. These calibrations and the complete phenotypic characterization done are now successful instruments that are helping the breeders for making the right decision regarding the advancement of tasty tomato breeding lines or varieties.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Sergio Lanteri photo

Sergio Lanteri

University of Turin, Italy

Title: Population structure of tomato and eggplant germplasm based on Single Primer Enrichment genotyping

Biography:

Sergio Lanteri is currently working as Full Professor in Genetics and Plant Breeding at the DISAFA, University of Turin, Italy. He received his Masters Degree in Agricultural Science from the University of Torino, and  his PhD in Plant Biology from the University of Milan (Italy). As Post-PhD fellow, he worked at the Plant Science Laboratories, University of Reading (UK) and at the Plant Research International, Wageningen (NL).

Abstract:

G2P-SOL (www.g2p-sol.eu) is an EU-funded project, bringing together the main European and international genebanks hosting germplasm of the four major Solanaceous crops: potato, tomato, pepper and eggplant. Up to 23,900 tomato and 5,900 eggplant accessions, including wild relatives of both crops, have been inventoried. The Single Primer Enrichment Technology (SPET, US Patent 9,650,628), developed by NuGEN, was applied to assess  the genetic relationships in set of  422 and 400 entries of  eggplant and tomato primary, secondary and tertiary genepools respectively. 

As shown below, the streamlined SPET workflow consists of four main steps: fragmentation of genomic DNA, end repair to generate blunt ends, adaptor ligation, and final repair to produce the library.

Genotyping and sequencing was performed by IGA Technology Services. Reads were aligned to the eggplant and tomato reference genomes using BWA-MEM and SNP calling was performed using GATK-4.0.

An SNP/indel panel was developed by assaying the 5k best performing probes designed both on coding region and  the introns/UTRs genome space. By applying stringent criteria a whole of  22,821 and 8,546 polymorphic sites were identified in eggpland an tomato genepools respectively.

FastSTRUCTURE56 and PCA outputs, provided information on the diversity of the accessions in study and made it possible to identify duplications and mis-classifications. The obtained  results suggest that SPET genotyping is a reliable, high-throughput, low cost technology for genetic fingerprinting of crops, with a high degree of cross-transferability to their wild relatives.

Keywords: Tomato, Eggplant, Germplasm, SPET

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Xian Deng photo

Xian Deng

Chineese Academy of Sciences, China

Title: Targeting mechanism of H3K27me3 demethylase REF6 and its role in transgenerational thermomemory in Arabidopsis

Biography:

Xian Deng has completed her PhD and Postdoctoral Studies at the age of 30 years from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. She is the Associated Professor of Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. She has published more than 15 papers in reputed journals, such as PNAS, Cell Res, Curr Opin Plant Biol, Nat Sci Rev, Plant Physiol, Bio-protocol, etc.

Abstract:

RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains (1, 2). REF6 tends to bind motifs located in active chromatin states and depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, using biochemistry, structural biology, and high-throughput sequencing, we showed that REF6 binding affinity to specific regions is repelled by DNA methylation within CTCTGYTY motif. In addition, we also found that heat-induced HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2) directly activates REF6, which in turn derepresses HSFA2. REF6 and HSFA2 establish a heritable feedback loop which is involved in transgenerational thermomemory and stress adaptation.

Keywords: Arabidopsis, H3K27me3, Histone demethylase, DNA methylation, transgenerational thermomemory.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Robert Caine photo

Robert Caine

The University of Sheffield, UK

Title: Can reducing stomatal density in rice mitigate the effects of climate change?

Biography:

Robert Caine completed his undergraduate degree at Oxford Brookes University with first class honours in Biology and beginners Japanese. He subsequently competed his PhD in Plant Molecular Biology and Evolution at the University of Sheffield. He is currently a Research Associate at the University of Sheffield where he works on a Newton Fund grant focusing on protecting rice against climate change derived abiotic stresses. He has published in many high impact journals including Nature Plants, New Phytologist, Plant Physiology, Development and Current Opinion in Plant Biology.

Abstract:

As climate changes continue to unfold, climate proofing of rice will be integral in protecting future production and so therefore, future food security (Caine et al., 2019; Jagadish et al., 2015; Lang et al., 2018; Yin et al., 2017). Improvements will need to include better tolerance to increased temperature, submergence, drought and water salinity. Improving these tolerances will need to be achieved concurrently reducing rice water use; This currently equates to around 2500 litre of water per 1 kilogram of grain produced (Bouman et al., 2007). Rice (and most other plants) primarily regulate water loss via adjustments to microscopic pores on the epidermis called stomata. These adjustments can be made either via changes to stomatal aperture, or via changes to stomatal development, in this case via alterations to stomatal size and or density (Chaves et al., 2016). We have engineered rice plants with reduced stomatal density which use around 40% less water during the seedling stage. This leads to improved drought tolerance both at 30° and 40°C (Caine et al, 2019). Recently we have also begun to assay how our plants under different salt concentrations, and found that reduced stomatal density positively impacts performance under high water salinity. Taken together our results indicate that reducing stomatal density positively impacts performance under multiple abiotic stresses and thus represents an encouraging trait to select for future rice cultivation.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Sandhya Mehrotra photo

Sandhya Mehrotra

Birla Institute of Technology and Science, India

Title: Transformation and expression of a Na+-dependent high affinity bicarbonate transporter, SbtA in Nicotiana chloroplasts

Biography:

Sandhya Mehrotra completed her Ph.D in the year 2003 from National Botanical Research Institute, Lucknow, India. Thereafter she did a post doctoral fellowship at Nara Institute of Science and Technology, Nara, Japan. Currently, she is Associate Professor of Biology at Birla Institute of Technology and Science, (BITS, Pilani), Goa Campus. She has over 30 publications with an H-index of 8 and has served as reviewer of several journals.

Abstract:

Integration of cyanobacterial bicarbonate transporters into the inner envelope membrane of chloroplast of C3 plants is assumed to enhance their photosynthetic performance. SbtA transporter has been looked upon as one of the most potential candidate for achieving this objective. In the present study, we attempted installing SbtA transporter protein from Synechococcus elongatus PCC 7942 to the inner chloroplast envelope of Nicotiana chloroplasts via nuclear transformation. The sbtA gene was fused with two transit peptide sequences viz., TNaXTP (transit peptide from AT3G56160.1) and TMDTP (transit peptide from AT2G02590.1) from inner envelope targeted proteins of Arabidopsis thaliana to generate fusion constructs in a GFP vector (pCAMBIA 1302). Transient as well as stable expression of the gene was studied by transforming N. benthamiana by agroinfiltration and N. tabacum by Agrobacterium mediated co-culture method. Expression of the transgene in N. benthamiana was confirmed by PCR and RT-PCR at DNA and mRNA level respectively and by western blotting at protein level by using anti-GFP primary antibody and horseradish peroxidase (HRP) conjugated anti-rabbit secondary antibody. Stable plants of N. tabacum carrying the gene of interest were generated on MS medium with selection agents and analysed by gene specific PCR analysis. Confocal images of the protoplasts reveal chloroplastic location of the protein in both the constructs. The work highlights the importance of signal sequence (cTP) in targeting large non-chloroplastic transmembrane proteins to the chloroplasts by transformation of nuclear genome. It provides a preliminary yet valuable basis for future manipulations of chloroplast function for improving plant photosynthesis.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Abdelnaser Elashry photo

Abdelnaser Elashry

Strube Research GmbH, Germany

Title: The use of next generation sequencing to study biotic stress on sugar beet

Biography:

Abdelnaser Elashry has finished his PhD in 2004 from university of Gottingen, Germany. He has got his post-doctoral studies in BOKU University and in IAEA (UN) in Austria studying plant nematode interaction. He was an assistant professor in Bonn University making research on the nematode effectors, nematode-genome and transcriptome. His recent position is a research associate (Genomics) in Strube Research, sugar beet breeding department, Germany. His recent research is focused on the sugar beet genome studies for plant breeding.

Abstract:

Sugar beet is one of the important crops worldwide for sugar production. Several biotic and biotic-stresses can affect negatively the yield of the sugar beet. Due to the increasing demand on sugar plant breeding programs aim, on one side, to maximize the productivity and, on the other side, to minimize the loss of yield. Sugar-beet genome sequencing allows efficient and fast breeding programs.  Here we used next generation sequencing combined with genetic mapping to curate and have a better understanding of the sugar beet genome. This approach has resulted in better structural annotation of sugar beet genome (9 Chromosomes has nearly 500 MB of sequences).

We performed RNAseq on plants that were exposed to biotic stresses (i.e. Rhizomania or cyst nematodes). We compared the results of the infected- and the non-infected plants after mapping the resulted reads to the curated sugar beet genome. Our results helped us to determine the differentially regulated genes as a reaction to the infection. The determination of such subsets can help understanding sugar beet biology and help designing plant breeding programs aim to have resistant sugar beet. Also, accurate reference genome helps designing efficient molecular markers that would, in turn, help plant selection within the breeding programs.

Oral Session 2:

  • Poster Session
Meetings International - Plant Genomics 2019 Conference Keynote Speaker Al-Ghaliya H. Al-Mamari photo

Al-Ghaliya H. Al-Mamari

Ministry of Agriculture & Fisheries, Sultanate of Oman

Title: Genetic diversity of Omani date palm (Phoenix dactylifera L.) cultivars and its relationships with ‘exotic’ cultivars using SSR markers

Biography:

Al-Ghaliya Al-Mamari has completed her PhD at the age of 32 years from Nottingham University. She is the Head of Biotechnology Research Section, Ministry of Agriculture & Fisheries in the Sultanate of Oman.  She has different expertise in plant molecular and genetics, plant tissue culture and mutation breeding.

Abstract:

The present study investigated the genetic diversity of one hundred and ninety-four date palm accessions from Oman and forty-eight accessions from Italy, USDA-ARS, France, Iraq, Libya, Sudan and Iran using SSR molecular markers. Around 300 varieties of date palm are grown throughout the Sultanate and this study has provided the first molecular identification key, which enables the unambiguous discrimination of Omani date palm accessions. The genetic analysis showed that the Omani accessions were closely related to each other and there was no clear genetic differentiation between female and male cultivars. There was a quite high degree of genetic differentiation observed between germplasm from Oman, Sanremo, Bordighera, USDA-ARS, France, Iraq, Libya, Sudan and Iran as measured by Fst (19.7 %) compared with the genetic differentiation observed among the Omani accessions (2.1%) of the total variation, which probably reflects the homogeneous nature of the Omani date palm used in this study comparing to the divergent sets of other germplasm. The study also confirms that the Europe-Africa (Sanremo, Bordighera, France, Libya and Sudan) accessions are distinguished from West-Asia (Oman, Iraq and Iran) accessions, have their own autochthonous origin, a finding which was strongly validated by bootstrap consensus tree test.

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Kaixuan He photo

Kaixuan He

Chinese Academy of Sciences, China

Title: REF6, an Arabidopsis H3K27me3 demethylase, functions in high temperature response

Biography:

Kaixuan He has been studying the graduate program for PhD Degree on Genetic Biology in Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, from Sept. 2015 to now.

 

Abstract:

As the sessile organisms, plants have developed a series of mechanisms to cope with the changeable environment, such as ambient temperature. Epigenetic regulation plays fundamental roles in modulating chromatin-based processes and shaping the epigenome in multicellular eukaryotes. Arabidopsis RELATIVE OF EARLY FLOWERING 6 (REF6), a Jumonji C domain-containing histone demethylase, directly recognizes the CTCTGYTY motif by its zinc-finger domains to demethylate H3K27me3 at specific loci in Arabidopsis genome. Phenotypic analysis shows that ref6 mutant displays insensitivity to high ambient temperature, showing shorter hypocotyl length than that of Col at 28℃, indicating that REF6 may function in plant thermo-morphogenesis. Using ChIP-seq and RNA-seq analysis, we identified several REF6 targets involved in thermo-morphogenesis process. Further study will help us to uncover the essential role for H3K27me3 dynamics in diverse abiotic stresses.

Keywords: REF6, H3K27me3, thermo-morphogenesis

 

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Rym Feikh photo

Rym Feikh

Kobe University, Japan

Title: Establishing a high-throughput phenotyping method for quantifying traits of interest using NAM rice population

Biography:

Fekih Rym has completed her PhD in 2009 from the University of Tsukuba, Japan and moved to Iwate prefecture to join the research group of Rice Genetics and Genomics at the Iwate Biotechnology research Center (IBRC), Kitakami, Japan for a postdoctoral position followed by JSPS fellow for 4 years. During her research term in IBRC, one of her major achievement was done, by taking advantages of next generation sequencing technology to develop new methods for rapid isolation of novel genes in Rice (Fekih et al., 2013). Recently, she moved to Kobe University to further investigate on rice genomics and apply novel technology for efficient rice breeding.

Abstract:

Beside its economical importance, rice has long served as a model system in monocotyledon not only for research on plant development, but also a model crop for research on cereal’s genomics, pathology and physiology. It’s small genome size, complete genome sequencing and the availability of tools for functional genomics made the identification of new genes of agronomical interest easier. With the emergence of the Next Generation Sequencing (NGS) technologies, the isolation of new rice genes became more easy and rapid, revolutionizing the world of genomics. However, while genotyping protocols have advanced as a result of the technological progress achieved in Whole Genome Sequencing (WGS), establishing high-throughput phenotyping methods for quantifying traits of interest has remain challenging.

Our research group at the Food Resources Education and Research Center, Kobe University has generated two populations for genome-wide association studies (GWAS): (1) Japanese rice population composed of 112 diverse cultivars and (2) nested association mapping (NAM) population composed of 3567 lines, using the most popular Japanese cultivar Koshihikari as a common parent. For accurate and complete phenotyping of these large populations, our group is also developing efficient and economical strategies to collect phenotypic data quickly and accurately using data capture tools.

 

Meetings International - Plant Genomics 2019 Conference Keynote Speaker Behnam Derakhshani photo

Behnam Derakhshani

National Agriculture and Food Research Organization (NARO), Japan

Title: Integration of mRNA-Seq analysis and QTL mapping provides promising candidate genes for cadmium tolerance in barley

Biography:

Behnam Derakhshani is currently a guest researcher at Institute of Crop Science, National Agriculture and Food Research Organization (NARO). He has completed his PhD at the University of Zanjan, Zanjan, Iran.

Abstract:

The high toxicity and ready uptake of cadmium (Cd) by plants has become a major agricultural problem. Our QTL analysis showed that the parents of the Oregon Wolfe Barley (OWB) mapping population have distinct responses to Cd toxicity. mRNA-Seq analysis of the parental seedlings after 2 h under 5 mM Cd stress identified 583 differentially expressed genes (DEGs) out of 42,860 genes in barley as candidate genes for Cd tolerance in Rec. Cd tolerant genotype Rec showed higher gene expression levels of proteins involved in signal transduction, transcription factors, chaperones, oxidative stress protection enzymes, cell wall metabolism, transporters and ion channels relative to cd susceptible genotype Dom. Furthermore, 157,179 moderate or high ranked single nucleotide polymorphisms (SNPs) were identified between genotypes using sufficient coverage with high quality sequence reads by sequence comparisons. These may affect gene expression, mRNA conformation (stability), and the subcellular localization of mRNAs and/or proteins in the two genotypes. We found that several Cd-responsive genes have SNPs, suggesting that they may participate in tolerance. Finally, the candidate genes were narrowed down by integrating the data from mRNA-Seq and the major QTL related to Cd tolerance. We indicated that integrating mRNA-Seq and QTL analyses is a useful method for providing insight into the mechanisms of response and tolerance to Cd stress in barley.