Cool Season Legume Workshop at PAG 2013
Cool Season Legumes Workshop
Date: Saturday, January 12
1:30 pm - 3:40 pm
Location: Pacific Salon 1
Moderators/Organizers: Kevin McPhee North Dakota State University, Rebecca McGee USDA ARS
1:30 PM - 1:50 PM
Presenters: Douglas R Cook University of California-Davis, Davis, CA, Estibaliz Larrainzar University of California-Davis, Davis, CA, Jeong-Hwan Mun National Academy of Agricultural Science, RDA, Brendan K. Riely University of California-Davis, Davis, CA, Hj Hwang National Academy of Agricultural Science, RDA, SC Kim Korea Research Institute of Bioscience & Biotechnology, Hee-Ju Yu The Catholic University of Korea, M Oh National Academy of Agricultural Science, RDA, Anand KS Rao University of California-Davis, Davis, CA, Alex Greenspan University of California-Davis, Davis, CA, KS Lee National Academy of Agricultural Science, RDA
W212 - Deep Sequencing Of The Medicago truncatula Transcriptome Reveals a Massive Early Response To Nod Factor and Ethylene Signals
Legumes establish nitrogen-fixing endosymbiosis with rhizobium bacteria involving complex developmental changes in roots. Ethylene has been shown to play a key role in the early stages of the interaction, being a negative regulator of symbiotic development. In the present work we have applied RNAseq next-generation sequencing techniques to analyze the transcriptional changes in Medicago truncatula roots at very early symbiotic stages (from 30 min to 48 h after inoculation with Sinorhizobium meliloti). To discriminate between Nod-factor and ethylene signaling, we analyzed four plant genotypes: wild type A17, mutants in Nod-factor perception nfp and lyk3, and a mutant in ethylene perception, skl. In total we have identified almost 11,000 differentially-expressed genes, with more than 8,000 differentially regulated between wild type and skl samples. Among those numerous genes are involved in ethylene perception, signal transduction and ethylene biosynthesis, including a number of novel transcription factors of the AP2/ethylene-responsive factor (ERF) superfamily involved in very early responses (i.e., 6 h post-inoculation). Functional characterization of a number of candidate genes is currently underway to further investigate their role in nodulation. The availability of this detailed information describing the early transcriptional changes triggered by rhizobium will serve as a useful resource for the community, leading to the discovery of new genes involved in this complex symbiotic interaction process.
1:50 PM - 2:10 PM
Presenters: R.Varma Penmetsa University of California-Davis, USA, Jongmin Baek University of California, Davis, Noelia Carrasquilla-Garcia University of California Davis, E.M. Bergmann University of California Davis, L.C. Vance University of California Davis, B.M. Castro University of California Davis, M.T. Kassa University of California Davis, Andrew Farmer National Center for Genome Resources, Clarice J. Coyne USDA ARS, E.J.B. Wettberg Florida International University, Rajeev Varshney ICRISAT, Douglas R. Cook University of California-Davis, Davis, CA
W213 - Genomics Of Chickpea Domestication
Chickpea (Cicer arietinum) is a widely cultivated food legume that was domesticated along with other founder crops in the fertile crescent 8,000-10,000 ya. To characterize the impact of domestication on molecular diversity, and to identify genes underlying domestication-related traits, we have used high-throughput genotyping of germplasm accessions of chickpea and its wild annual relatives and recombinant inbred populations. From phenotypic analysis in these genetic stocks we have identified multiple QTLs for the agronomic traits of flowering time, growth habit and seed color. We identified candidate genes in genetic intervals containing these QTLs from in silico analysis of the chickpea draft genome sequences. Results from ongoing studies to examine trait-to-gene associations in these agronomic trait QTL regions will be presented.
2:10 PM - 2:30 PM
Presenters: Anoop Sindhu University of Saskatchewan, Marwan Marwan University of Saskatchewan, Kirstin Bett University of Saskatchewan, Bunyamin Taran University of Saskatchewan, Andrew G. Sharpe National Research Council Canada, Larissa D. Ramsay National Research Council Canada, Tom Warkentin University of Saskatchewan
W214 - Development and Application of Genome Wide SNP Resources in Pea
Developments of genome-wide SNP markers are essential for application of a wide range of genetics and molecular breeding approaches. We used high throughput Illumina GoldenGate assays to develop a genome wide SNP screening tool. For genome wide SNP discovery, ESTs from 8 diverse pea cultivars were sequenced using 454 pyrosequencing technology. Out of fifty thousand SNP positions detected through in silico analysis, 1536 were selected for screening pea RIL populations and an association mapping panel consisting of 94 diverse worldwide pea varieties. A SNP map consisting of 13 linkage groups was generated and SNPs tagged to QTLs governing traits of economic importance were identified. Association mapping panel was used for diversity analysis and loci associated with agronomic traits were identified. This genome-wide SNP resource will help in development and resolution of pea haplotypes, assessment of diversity, genetic architecture, marker-trait association discovery, and molecular breeding.
2:30 PM - 2:50 PM
Presenters: Dorrie Main Washington State University, Chun-Huai Cheng Washington State University, Stephen P. Ficklin Washington State University, Sook Jung Washington State University, Ping Zheng Washington State University, Clarice J. Coyne USDA ARS, Rebecca McGee USDA ARS, Keithanne Mockaitis Indiana University
W215 - The Cool Season Food Legume Database: An Integrated Resource for Basic, Translational and Applied Research
The Cool Season Food Legume Genome Database (http://www.coolseasonfoodlegume.org) is being developed to assist in translating genomics into crop improvement. The main objective is to facilitate cool season food legume breeding and research by serving as a genomic, genetic and breeding data resource. Although databases exist for the model legumes, the Cool Season Food Legume Genome Database is specifically designed to collect and centralize data for pea, chickpea and lentil while using data from the model sequenced legumes for comparison and further curation. The database is built using Tripal which provides simplified site development by mrging the power of Drupal, a popular web Content Management System (CMS), with that of Chado, a community derived database schema for storage of genomic, genetic and other biological data. In this presentation we report on current and future functionality including functional analysis, marker development and comparative genomics using the sequenced model legumes.
2:50 PM - 3:10 PM
Presenters: Reetu Tuteja ICRISAT, Rachit Kumar Saxena ICRISAT, Trushar Shah ICRISAT, Jaime Davila Mayo Clinic, Wenbin Chen BGI, Yong-Li Xiao JCVI, Guangyi Fan BGI, Andrew Alverson Indiana University, Charles Spillane National University of Ireland Galway, Christopher D. Town JCVI, Rajeev Varshney ICRISAT, Rajeev Varshney ICRISAT
W216 - Mitochondrial Genome Sequencing Of Four Cajanus Genotypes
To understand the molecular basis of cytoplasmic male sterility (CMS) in pigeonpea (Cajanus cajan), we sequenced the mitochondrial genomes of three C. cajan lines (male-sterile line ICPA 2039, maintainer line ICPB 2039, hybrid line ICPH 2433) and of the wild relative (C. cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 Kb was assembled and annotated for ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding, 14 tRNA and 3 rRNA genes. Further the ICPA 2039 mitochondrial genome was used as a reference sequence for comparison to identify polymorphism in the other three genotypes. Detailed analysis of the mitochondrial genomes identified 18 and 13 chimeric mitochondrial open reading frames (ORFs) in ICPA 2039 when compared with ICPW 29 and ICPB 2039 line respectively. Amongst these chimeric ORFs, 13 chimeric ORFs identified in ICPA 2039 on comparison with ICPB 2039, comprising five carry parts of annotated mitochondrial genes, and another eight of them are in proximity to other mitochondrial genes. Together, these represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.
3:10 PM - 3:30 PM
Presenters: Manish Pandey ICRISAT, Manish Pandey USDA-Agricultural Research Service, Pasupuleti Janila ICRISAT, Channabyre Gowda University of Agricultural Sciences, Baozhu Guo USDA Agricultural Research Service, Xuanqiang Liang Crop Research Institute, GAAS, David Bertioli University of Brasilia, Jean-Francois Rami CIRAD, Sachiko Isobe Kazusa DNA Research Institute, Rajeev Varshney ICRISAT, Rajeev Varshney CGIAR Generation Challenge Programme, c/o CIMMYT
W217 - QTLs from Genome to Field Using Markers and Genetic Maps for Peanut Improvement
Peanut (Arachis hypogaea) is widely grown in the semi-arid tropics regions of Asia, Africa and Latin America where several stress factors together adversely affect productivity. Collaborative efforts led development of large scale genomic resources setting platform for genomics-assisted breeding (GAB). GAB promises to foster genetic enhancement leading to increased productivity, drought tolerance, disease resistance and improved oil quality in groundnut which are otherwise difficult through conventional breeding alone. In this context, after screening a total of 4,245 SSR markers on parental genotypes of five mapping populations, individual genetic maps with 83-191 marker loci were constructed. Using marker segregation data from 11 populations, a reference consensus genetic map was developed with 897 marker loci which was then further enriched upto 3,693 marker loci by adding mapping information from five new genetic maps. Detailed QTL analyses provided 153 QTLs for drought tolerance related traits, 43 QTLs for foliar diseases (late leaf spot and leaf rust) and 49 QTLs for oil quality. A major QTL contributing upto 82.96% phenotypic variation for rust resistance has been introgressed into three elite peanut varieties namely ICGV 91114, JL 24 and TAG 24 using marker-assisted backcrossing. Disease screening of 200 introgression lines in advanced generation (117 BC2F5 and 83 BC3F5) have recorded a rust score of 2 (scale 1 to 9). The promising lines with desirable yield and higher resistance to leaf rust could be released an improved varieties. Integration of such genomics approaches in breeding programme will enhance crop productivity of groundnut.