Conference abstracts

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S1.OP1. Results from the Peanut Genome Initiative and the Impacts on Cultivar Development

C.Corley Holbrook1*, Peggy Ozias-Akins2, Scott Jackson2, Ye (Juliet) Chu2, Josh Clevenger3, Albert K. Culbreath2, Tim B. Brenneman2, Thomas G. Isleib4, Carolina Chavarro2, David Bertioli2, Renjie Cui2, Baozhu Guo1, and Soraya Leal-Bertioli2.

1USDA-ARS, Tifton, GA

2Univ. of Georgia

3M&M Mars and Wrigley, Athens, GA

4North Carolina State Univ., Raleigh, NC

The Peanut Genome Initiative (PGI) was a five year international effort which began in 2012.  The objectives were to sequence the peanut genome and develop and apply new genomic technologies to peanut science.  A large part of the funding came from the U.S. peanut industry.  Their primary goal was to develop marker-assisted selection (MAS) methodologies that lead to improved cultivars.  Peanut is an allotetraploid with a very large genome.  One of the first accomplishment of the PGI was to sequence the genomes of the two progenitor diploid species of peanut.  Recently, the sequence of the cultivated species was completed.  To develop genetic markers for MAS, several structured populations were developed, genotyped, and phenotyped.  Molecular markers have been developed for several economically important traits and are being implemented in breeding programs.  This is having a great impact on the efficiency and effectiveness of peanut cultivar development.

Email: Corley.Holbrook@ars.usda.gov


S1.OP2. Modernizing the Peanut Breeding Program at ICRISAT

  1. Janila1*, T.V. Murali1, SS. Manohar1, Sunil Chauddhari1.

1Groundnut Breeding Unit, Research Program-Asia, International Crops Research Institute (ICRISAT), Patancheru, Telangana, India 502324.

Stage-gate system of product design, development, advancement and delivery are some of the key elements of modernizing peanut breeding program at ICRISAT. Peanut Network Groups of Asia and Africa represented by ICRISAT, NARS, NGO’s and private sector will be a platform to for product Design, development, testing, advancement and delivery. A multi-stakeholder engagement is expected to enable designing the products to the market needs. The strategy for product design at ICRISAT’s peanut breeding program employs genetic gain estimate as a metric to measure the health of the breeding pipeline. A study conducted showed an annual genetic gain of 0.7% for pod yield equivalent to 57Kg/ha per year and indicated need to focus on shelling outturn to further enhance the genetic gain in Spanish bunch types. Process innovations such as rapid recycling of elite parents, rapid generation advancement (RGA), cost-effective genotyping, early generation testing in target sites, multi-environment testing to address G X E have contributed to enhanced rate of genetic gain in peanut Breeding and Testing Pipelines at ICRISAT in recent years. For example, the ‘process innovations’ resulted to drastically cut down the number of years required to develop high oleic lines in Spanish and Virginia Bunch background adapted to Africa and Asia. The hybridization stated in 2011 and in 2017, 16 high oleic lines were advanced to national release testing in India and over 200 lines were shared with partners from nine different countries.

Email: p.janila@cgiar.org


S1.OP3. Wild Arachis Species, Valuable Germplasm Still to be Known

Guillermo Seijo1,2,*, A. García1, S. Samoluk1, L. Chalup1, A. Ortiz1, O., A.M. González1,3, G. Lavia 1,2 and G. Robledo1,2

1Northeast Botanical Institute (IBONE), UNNE–CONICET, Argentina

2FACENA, Argentina

3FCA, National University of Northeast, Corrientes, Argentina

Wild species related to agricultural crops can increase the adaptive capacity of agricultural systems around the world. They represent a large pool of genetic diversity from which to draw new allelic variation required in breeding programs. Arachis wild species are not the exception. New species are being discovered at a rate of almost one species a year since the Krapovickas and Gregory monograph was published in 1994. New characters were described for the genus, and the geographic distribution have been extended for most of the known species. Cytogenetic data has helped to arranged them in genome groups and genomic information was generated for a few of them including the wild relatives that originated peanut. Arachis wild relatives probed to be extremely valuable in providing resistant alleles to peanut commercial varieties for diverse diseases. Unfortunately, wild Arachis species are a threatened resource and biological knowledge on them is still very limited. Examples are the assumptions that all Arachis species are autogamous and that all of them have the same reproductive efficiency. Moreover, the delimitation of species is still very difficult in many cases and the intraspecific and intrapopulation variability, both morphological and genetic, is almost unknown. Here, we review and discuss (i) past and current efforts to generate knowledge on wild Arachis germplasm, (ii), what constraints continue to hinder increased use of wild species in breeding and (iii) what measures need to be taken to improve their protection, both in the wild and in genebanks.

Email: jgseijo@yahoo.com


S1.OP4. Could Small-seeded Wild Relatives of Cultivated Peanut be Used to Increase the Size of Peanut Seeds?

Daniel Fonceka1,2,*, Hodo-Abalo Tossim2, Joel Romaric Nguepjop2, Aissatou Sambou2, David Bertioli3, Soraya Leal-Bertioli3, Scott Jackson3, Jean-François Rami1, Peggy Ozias-Akins3

1CIRAD, UMR AGAP, Montpellier, France

2Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse. Thiès Senegal

3 University of Georgia, USA

Seed size is a major agronomic trait that has been selected in crops during the domestication process. However, many studies reported agronomically important alleles that have been left behind or lost during this process. Cultivated peanut is characterized by the paucity of DNA polymorphism. Conversely, high level of polymorphism exists with peanut wild relatives that can be harnessed together with important agronomic traits to improve the cultivated varieties. In a collaborative project with CIRAD, ISRA, UGA and EMBRAPA we developed interspecific QTL mapping populations (AB-QTL and CSSL) for identifying and tracing back the favorable wild alleles in breeding programs. We identified several genomic regions associated with seed size increase in two AB-QTL populations that shared a common recurrent parent. A CSSL population developed from the cross between Fleur11 and (A. ipaensis x A.duranensis)4x was used to validate those QTLs. The CSSL population is of particular interest as it represents the entire wild species genomes in a set of lines each carrying one or a few wild donor segments in the genetic background of the cultivated peanut. This allows mendelizing the QTLs, which ease their used in breeding programs. Several CSSLs that carry wild chromosome segments involved in seed size increase were crossed for pyramiding the QTLs. Additive effects were observed indicating that pyramiding of wild alleles has significant potential for increasing seed size in peanut. The recent release of the peanut genomes opens new avenues for understanding the genomic mechanisms that favored the loss of benefic alleles in cultivated peanut.

Email: daniel.fonceka@cirad.fr


S2.OP1: Overview of crops to end hunger initiative

Daniel Bailey1*, Vern Long1

1US Agency for International Development, Washington DC

This presentation is an introduction to the Crops to End Hunger Initiative. This new initiative is implemented by CGIAR research centers with leadership from USAID, UKAID, Austrailian Centre for International Agriculture Research, GIZ, and Bill and Melinda Gates Foundation. It aims to modernize and strengthen the crop improvement programs of the CGIAR in strong partnership with National Agricultural Research Programs. Efforts will include design of product profiles to guide development of improved varieties for specific geographies to support farmer productivity despite climate shocks, respond to consumer and market demands, and contribute to nutrition.

Email: dbailey@usaid.gov


S2.OP2. Research Objectives in the Feed the Future Innovation Lab for Peanut

  1. Hoisington1 and J. Rhoads1

Feed the Future Innovation Lab for Peanut, College of Agricultural and Environmental Sciences, University of Georgia, Athens GA

The Feed the Future Innovation Lab for Peanut (Peanut Innovation Lab) is one of 22 Innovation Labs funded by USAID under the US government’s Global Food Security Strategy. The University of Georgia host the management entity that provides overall leadership of the Peanut Innovation Lab. The program ultimate goal is to improve peanut production, quality and profitability for smallholder farmers in Feed the Future countries. To accomplish this goal, the innovation lab supports research partnerships between US and host country scientists working together to solve problems faced by farmers, input providers, buyers/sellers, processors and consumers along the peanut value chain. USAID has supported international peanut research since 1982, and the current program started in January of 2018. The research projects are currently being finalized with focus in varietal development, value-added gain, nutrition, gender and youth. Details on the innovation lab overall objectives and proposed research portfolio will be provided.

Email: davehois@uga.edu


S2.OP3. PeanutBase: A Resource for Molecular Research and Breeding

E.K.S. Cannon1, W. Huang1, S. Kalberer2, M. O’Connell, P. Otyama1, S.B. Cannon1,2, J.D. Campbell1, N. Weeks2, A. Farmer3

1Iowa State University, Ames, IA

2USDA-ARS, Ames, IA

3National Center for Genome Resources, Santa Fe, NM

PeanutBase is the peanut/groundnut community resource for molecular research and breeding. It hosts the three representative reference Arachis genome assemblies: Arachis duranensis (V14167), Arachis ipaensis (K30076), and Arachis hypogaea (Tifrunner), including gene models for each of the three. The gene models have been enriched with functional information and are included in legume-specific gene families generated by the Legume Federation. Inclusion in the gene families enables comparative research across the legumes. A number of expression studies, which provide additional gene function information, are hosted at PeanutBase, including a tissue atlas, and a number of biotic and abiotic stress response expression studies. Additionally, PeanutBase holds germplasm, germplasm traits, genetic maps, markers, and QTL data. A number of browsing, visualization, and analysis tools exist at PeanutBase, including BLAST, genome browsers, a tool for exploring geographic origins of peanut accessions, and others. To improve support for breeders, PeanutBase is leading a project to genotype the US peanut core collection, and is collaborating with the Integrated Breeding Platform (IBP) and with the developers of BrAPI, a protocol that permits breeding resources to exchange data.

Email:  ekcannon@iastate.edu


S2.OP4. Annotating the Peanut Transposons to Provide Resources for Peanut Improvement and Genomics

Dongying Gao1, Moaine El Baidouri2, Ye Chu3, Han Xia4, Chunming Xu1, Karolina Heyduk5, Brian Abernathy1, Peggy Ozias-Akins3, James H Leebens-Mack5, Jeremy Schmutz6,7, David J Bertioli1 and Scott A Jackson1.

1Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA

2CNRS, Perpignan, France

3Department of Horticulture, University of Georgia, Tifton, GA, USA

4Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China

5Department of Plant Biology, University of Georgia, Athens, GA, USA

6US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

7HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.

The advancement of new sequencing technologies makes it possible and affordable to sequence the organisms with large and complex genomes. However, bioinformatics tools still do not meet the demands of many data-intensive projects. Transposable Elements (TEs) are abundant in plant genomes, especially those with large genomes such as peanut (Arachis hypogaea, 2n=2x=40). Given their ubiquity, the discovery of transposons and other repeats is critical to accurately annotate the peanut genome and for other genome-related research. We developed a TE annotation bioinformatics pipeline by combining de novo annotation and homology-based sequence searches to identify transposons and generated a peanut transposon library which includes both DNA and RNA transposons. We found that transposons contribute more than 72% of the reference Tifrunner genome. Of note, numerous potentially active transposons were identified that may be a valuable resource for the development of transposon-based markers for peanut improvement and transposon tagging for functional genomics. Furthermore, the comprehensive analysis of peanut transposons revealed the horizontal transfer of genetic materials between flowering plants and animals.

Email: sjackson@uga.


S2.OP5. Considerations for Successful Genotyping of Arachis hypogaea in the Modern Genomics Era

Josh Clevenger1*, Walid Korani2, David Bertioli3, Brian Scheffler4, Justin Vaughn5

1Mars-Wrigley Confectionery, 111 Riverbend Rd, Athens, GA

2CAGT, University of Georgia, 111 Riverbend Rd, Athens, GA

3Crop and Soil Sciences, University of Georgia, 111 Riverbend Rd, Athens, GA

4USDA-ARS, Stoneville, Mississippi

5USDA-ARS, Athens, GA.

Peanut genomics has reached a crossroads, albeit an exciting crossroads.  That doesn’t mean that analysis of genomes and discrete genotypes will now be easy.  It will require nuance and foresight.  There are reference quality genomes available now of the diploid progenitors of cultivated peanut.  There are two reference quality assemblies of Arachis hypogaea; a runner type and a spanish type.  Which is the appropriate reference to use?  There are two large-scale SNP genotyping arrays.  Which one is the best to use?  Is it better to use sequence-based methods or to take advantage of the lower cost of the arrays.  The answers to these questions will have long lasting consequences on not only the quality of genomic research, but also the transferability of results, and the efficiency of collaboration.  As a global community, can we afford to let genotyping preferences divide us?

Email: jclev@uga.edu


S2.OP6. The Genome Sequence of Peanut – Genetic Exchange Between Ancestral Genomes Drives Genetic Diversity

David Bertioli1 and the International Peanut Genome Consortium

1Department of Crop and Soils Science/CAGT, The University of Georgia, Athens, GA, USA

We report the genome sequence of cultivated peanut (Arachis hypogaea cv. Tifrunner). As expected, it harbors essentially complete sets of chromosomes from the two ancestral species (A. duranensis and A. ipaënsis). However, we show that after its origin, the genome has evolved through mobile element activity, deletions and homeologous recombination; the flow of genetic information between corresponding chromosomes derived from the different ancestors. Uniformity of some of the patterns of recombination favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using a new polyploid hybrid made from the ancestral species, we demonstrate how this can generate phenotypic change: a spontaneous change of flower color. This flow of genetic information is strongly influenced by chromosome structure and is asymmetrical: chromosomes derived from A. duranensis are more modified over time than the other. Homeologous recombination is ongoing and is orders of magnitude more frequent than mutation. It seems likely that this mechanism, which creates genetic diversity, helped favor the domestication of A. hypogaea over other diploid Arachis species cultivated by man.

Email: bertioli@uga.edu


S3.OP1. Characterization of Chinese Peanut Germplasm and Trait Mapping

Huaiyong Luo1, Yong Lei1, Huifang Jiang1, Boshou Liao1.

1Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.

The peanut germplasm is fundamental to genetic enhancement for improved cultivars. A lot of germplasm accessions of the cultivated peanut and wild Arachis species have been assembled and conserved in many countries, and the Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS) is one of the major conserving agencies. A lot of peanut germplasm characterization and genetic diversity assessment work were conducted in OCRI-CAAS, and the Chinese peanut core collection, mini core collections and mini-mini collection were selected on these foundation. With the extensive and intensive germplasm characterization, elite peanut accessions with desirable traits have been identified for development of bi-parental mapping population. Using the traditional QTL mapping, association mapping and BSA-seq approaches, QTLs were identified for yield-related characters, resistance to leaf spot, rust, bacterial wilt and aflatoxin contamination, and quality-related characters such as oil content and fatty acid components. Molecular markers linked to major and stable QTLs were developed for using in marker-assisted breeding.

Email: huaiyongluo@caas.cn


S3.OP2. Phenotypic and Molecular Screening of Groundnut Varieties for Cercospora Leaf Spot Diseases

David Sewordor Gaikpa1 and James Yaw Asibuo*2

1State Plant Breeding Institute, University of  Hohenheim, 70593 Stuttgart, Germany.

2CSIR-Crop Research Institute, Fumesua, Ghana.

Twenty groundnut varieties were screened for leaf spots resistance using both phenotypic and molecular techniques to form the basis for resistance breeding. Phenotypically, the 20 genotypes were screened under natural field infection and artificial infection in screen house for combine resistance to early and late leaf spots. Eight SSR markers previously found to be linked to leaf spots resistance in groundnuts were also used to screen the DNAs of the 20 genotypes. Differences in disease incidence among individual plants, severity score, lesion diameter and defoliation across the 20 genotypes were highly significant (p<0.001) under phenotypic screening. Cluster analysis from phenotypic data grouped the genotypes into two main groups but molecular data grouped the genotypes into five groups at 70% similarity index. Significantly high and positive correlation (r=0.89) between artificial and natural field infection was observed. No complete resistance was found. However, 14 genotypes were moderately resistant while six were susceptible. Out of the eight SSR markers used, five (62.5%) were very promising. Two or more of these five promising markers viz pPGseq2F5280, pPGseq2B10280/290, pPGPseq17F6120/140/150, PMc588180/220 and PM384100 confirmed resistant genotypes at the molecular level. The resistant genotypes confirmed by the markers were ICG7878, Obolo, Oboshie, Jenkaar, Adepa, Nkosour, Azivivi, Otuhia, Nkatiesari’ and ‘Sumnut22’. Genotypes 55-437, Yenyawoso, and Shitaochi were susceptible. Hence, resistance to leaf spots exists among commercially grown groundnuts in Ghana. Combination of phenotypic and DNA molecular evaluation is very useful for proper identification of resistant genotypes in leaf spots resistance breeding programs.

Email: jyasibuo@gmail.com


S3.OP2. Phenotypic and Molecular Screening of Groundnut Varieties for Cercospora Leaf Spot Diseases

David Sewordor Gaikpa1 and James Yaw Asibuo*2

1State Plant Breeding Institute, University of  Hohenheim, 70593 Stuttgart, Germany.

2CSIR-Crop Research Institute, Fumesua, Ghana.

Twenty groundnut varieties were screened for leaf spots resistance using both phenotypic and molecular techniques to form the basis for resistance breeding. Phenotypically, the 20 genotypes were screened under natural field infection and artificial infection in screen house for combine resistance to early and late leaf spots. Eight SSR markers previously found to be linked to leaf spots resistance in groundnuts were also used to screen the DNAs of the 20 genotypes. Differences in disease incidence among individual plants, severity score, lesion diameter and defoliation across the 20 genotypes were highly significant (p<0.001) under phenotypic screening. Cluster analysis from phenotypic data grouped the genotypes into two main groups but molecular data grouped the genotypes into five groups at 70% similarity index. Significantly high and positive correlation (r=0.89) between artificial and natural field infection was observed. No complete resistance was found. However, 14 genotypes were moderately resistant while six were susceptible. Out of the eight SSR markers used, five (62.5%) were very promising. Two or more of these five promising markers viz pPGseq2F5280, pPGseq2B10280/290, pPGPseq17F6120/140/150, PMc588180/220 and PM384100 confirmed resistant genotypes at the molecular level. The resistant genotypes confirmed by the markers were ICG7878, Obolo, Oboshie, Jenkaar, Adepa, Nkosour, Azivivi, Otuhia, Nkatiesari’ and ‘Sumnut22’. Genotypes 55-437, Yenyawoso, and Shitaochi were susceptible. Hence, resistance to leaf spots exists among commercially grown groundnuts in Ghana. Combination of phenotypic and DNA molecular evaluation is very useful for proper identification of resistant genotypes in leaf spots resistance breeding programs.

Email: jyasibuo@gmail.com


S3.OP3. Evaluation of Advanced Breeding Lines of Groundnut (Arachis hypogaea L) for Foliar Disease Resistance, Drought and Productivity Traits in the Northern Dry Tract of Karnataka

Babu N. Motagi*,1, K.P. Sourabha1, M.B. Boranayaka1, R S. Bhat2, H.L. Nadaf3, and P.  Janila4

1AICSIP, Regional Agricultural Research Station (RARS), Vijayapur, Karnataka, India

2Department of Biotechnology, AC, Dharwad, Karnataka, India

3AICRP on Oilseeds, MARS, UAS, Dharwad, Karnataka, India

4ICRISAT, Patancheru, Hyderabad, Telangana, India

Groundnut is one of the principal oilseed crops of the world and India. The present study aimed at the evaluation of promising advanced breeding lines (ABLs) of groundnut developed at UAS Dharwad and ICRISAT through conventional and/or marker-assisted backcrossing(MABC) approaches. The ABLs comprised of Dh-243, Dh-256, Dh-257, Dh-268 and Dh-269 with drought tolerance and MABC lines DBG-1, DBG-2, DBG-A, DBG-B with foliar disease resistance (UAS Dharwad) and ICGV 03042,03043, 06420, 05155 with high oil, ICGV 16039, 16680, 16701 with high oleic; ICGV  07222, 07220, 02266, 00350, 91114 with drought tolerance  and ICGV 16220 to 16254 with early maturity and drought tolerance (ICRISAT, Patancheru). These ABLs were evaluated  in total of  four replicated trials along with check varieties (TMV 2, JL 24, TAG 24, GPBD 4, G 2-52) for  their reaction / tolerance to prevaling biotic and abiotic stresses and productivity traits  during kharif 2017 at RARS, Vijayapur representing the dry tract of Northern Karnataka (Zone 3). The elite lines viz., Dh 256, Dh 257, DBG-A, ICGV 03043, ICGV 16237, ICGV 00350 were selected based on their tolerance drought and iron chlorosis, resistance to LLS and rust diseases and high yield potential. From the evaluation of 210 ABLs developed at ICRISAT for drought tolerance 32 elite lines were also selected. These elite lines are being evaluated during Kharif 2018 to confirm their superiority and identify suitable genotypes for multilocation testing and one of the drought tolerant elite line Dh 256 is under farm trial evaluation in the farmers field in the region.

Email: motagibn@uasd.in


S3.OP4. The hunt for leaf spot disease tolerance in groundnut: progress made at CSIR-SARI

Richard Oteng-Frimpong1*, Rukiya Danful2, Baba Kassim Yussif2, Doris Kanvenaa Puozaa1, Nicholas Ninju Denwar1 and Richard Akromah1

1CSIR-Savanna Agricultural Research Institute P. O. Box TL 52 Tamale, Department of Crop and Soil Sciences, 2Kwame Nkrumah University of Science and Technology

In Ghana, the yield of groundnut (Arachis hypogaea, L.) is constrained by early and late leaf spot infections. Crop varieties possessing stay-green trait are known to show resistance or tolerance to some diseases and drought conditions. This study explored the stay green trait in groundnut and its relationship with leaf spot diseases. Twenty-five (25) groundnut genotypes were phenotyped for stay-green using Leaf Area Under Greenness (LAUG), leaf spot severity using Area Under Disease Progression Curve (AUDPC) and yield. The results revealed a significant (p ≤ 0.001) positive relationship between LAUG and AUDPC for early and late leaf spot disease severity (r = 0.82 and 0.63, respectively). LAUG had a significant negative association (p ≤ 0.001) with chlorophyll content at pod initiation, mid pod filling and physiological maturity as well as pod yield (r = -0.68). Based on the LAUG scores, the genotypes were grouped as stay-green or non-stay-green. Four RIL populations were developed with parents selected from the two groups and SSR markers used to confirm true hybrids.  The populations are currently at the F3 stage. Going forward, the RILs will be phenotyped across 5 locations in 2 years while the F4 will be genotyped taking advantage of the 58k SNP ‘axiom_arachis’ array. The QTLs controlling stay-greenness will be mapped through modelling of main effect QTLs and QTL-by-environment interaction. As a result, marker assisted selection will be deployed to introgress the stay-green QTL/s into our candidate varieties. Recovery of the preferred parental genome will be done through backcrossing.

Email: kotengfrimpong@gmail.com


S4.OP1. The Big Picture: Identifying the Links Between Drought, Development, and Aflatoxin Through Integromics in Aspergillus flavus

Jake C. Fountain1,2,3, Josh P. Clevenger4,5, Justin N. Vaughn6, Walid Korani5, Gaurav Agarwal1,2, Manish K. Pandey7, Hui Wang1,2, Rajeev K. Varshney7, Brian E. Scheffler6, Peggy Ozias-Akins3, Baozhu Guo2,*

1University of Georgia, Plant Pathology Dept., Tifton, GA

2USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA;

3University of Georgia, Horticulture Dept., Tifton, GA

4Center for Applied Genetic Technologies, Mars Wrigley Confectionery, Athens, GA

5Center for Applied Genetic Technologies, University of Georgia, Athens, GA

6USDA-ARS Genomics and Bioinformatics Research Unit, Stoneville, MS

7ICRISAT, Hyderabad, India

Previous “-omics” studies into Aspergillus flavus responses to drought-related oxidative stress revealed the association between oxidative stress and mechanisms regulating fungal development, stress responses, host interactions, and aflatoxin production with their expression varying among isolates. Understanding the genetic causes of this variation is critical to developing novel mitigation strategies. To identify these base causes of the variation and prevention strategies, the objectives of this study were: (1) to produce pseudomolecule-level genomes of two A. flavus isolates with contrasting aflatoxin production, mating type, and drought-related oxidative stress tolerance, AF13 (+++, MAT1-2) and NRRL3357 (+, MAT1-1), and (2) to conduct comparative integrative analyses of the “-omics” data to answer some biological questions. PacBio sequencing generated 7.73 and 7.97Gb of data with average read lengths of 12,822 and 10,437bp for AF13 and NRRL3357, respectively. Assembly resulted in 19 and 69 contigs with N50 of 2.579 and 1.998Mb for AF13 and NRRL3357, respectively. The assembled genome sizes are 37.599Mb for AF13 and 38.645Mb for NRRL3357. Several of these contigs were found to exceed 3.0 Mb and could cover the entire length of individual chromosomes. Illumina sequencing was also used to re-sequence 11 field isolates of A. flavus including AF13 and NRRL3357. These will be used for assembly correction/polishing, and to identify additional structural variants and polymorphisms influencing key traits. A novel integrated “omics” (integromics) approach will also be performed correlating transcriptome, proteome, and metabolome data with genomic variations to identify factors linking aflatoxin and other traits which are useful as targets for host resistance improvement with breeding and biotechnology for possible prevention of aflatoxin contamination.

Email: baozhu.guo@ars.usda.gov


S4.OP2. Identification of QTLs for Leaf Spot and Rust Resistance in a BC3F6 Interspecific Peanut Introgression Population in West Africa and Texas using SNP Markers

T.K. Tengey1, C. E Simpson2 N. Denwar3, P. Sankara4, Prof Joseph Ki-Zerbo5, A. Hillhouse6, V. Mendu7, and M. D. Burow*8

1Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA, and CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana

2Texas A&M AgriLife Research, Stephenville, TX 76401 USA;

3CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana

4Département de Biologie Végétale et Physiologie  Végétale, Université Ouaga I

5Ouagadougou, Burkina Faso

6Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843 USA;

7Fiber and Biopolymer Research Institute, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409;

8Texas A&M AgriLife Research, Lubbock, TX 79403, and Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409 USA

Cultivated peanut is reproductively isolated from its ancestral wild species parents because of differences in ploidy and genomes, and the self-pollinating nature of the peanut.  There is considerably less polymorphism among cultivated peanuts than among wild species. One way of introducing genetic diversity into cultivated peanut is through hybridization with wild species. A BC3F6 population developed from a cross with the synthetic amphidiploid TxAG-6 [A. batizocoi x (A. cardenasii x A. diogoi)]4x as donor and Florunner as recurrent parent resulted in isolation of individual lines having high oil contents, resistance to leaf spot disease, root-knot nematodes, and rust. Genome-specific SNP-based markers were designed and used to map 63 BC1 individuals for making a genetic map, and genotypes of 317 BC3F6 individuals from this population were obtained on the Fluidigm Biomark system.   Phenotypic evaluation was performed in Ghana, Burkina Faso, and Texas.  QTLs were identified for resistance to early leaf spot, late leaf spot, and rust.  Several QTLs were consistent across environments while others were environment-specific.  It is expected that resistant accessions and markers will be useful for marker-assisted breeding, to introgress resistance into suitable agronomic backgrounds.

Email: mburow@tamu.edu


S4.OP3. Identification of Novel genes for Resistance to Tomato Spotted Wilt and Leaf spots in Peanut (Arachis hypogaea L.) Through GWAS Analysis

  1. Zhang1, Y. Tang1,2, J. Li1, A. Hagan1, T. Jiang1, P. Dang3, Y. Chu4, J. Clevenger, P. Ozias-Akins4, C. Holbrook5, M.L. Wang6, and C.Y. Chen 1*

1Auburn University, Auburn, AL, USA

2Shandong Peanut Research Institute, Qingdao, China

3USDA-ARS, Dawson, GA, USA

4Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA

5USDA-ARS, Tifton, GA, USA

6USDA-ARS, Griffin, GA, USA.

Tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) are three serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the genes underlying those disease resistances in peanut were not well studied. In this study, we conducted a genome-wide association study (GWAS) for the three peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the U.S. peanut mini-core collection. A total of 158 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.2% to 24.1%, in which 112 QTLs are for resistance to TSW, 18 QTLs for ELS, and 28 QTLs for LLS. Among the 158 QTLs, there are six, four, and two major QTLs with PVE higher than 14% for resistance to TSW, ELS, and LLS, respectively. Of the total 12 major QTLs, 10 were located on B sub-genome and only 2 were on A sub-genome, which suggested that B sub-genome has more significantly resistance genomic regions than A sub-genome. In addition, two genomic regions on linkage group B9 were found significantly resistance to both ELS and LLS. Total of 21 candidate genes were identified significantly associated with diseases, which include 15 candidate genes for TSW, 3 candidate genes for ELS, and 3 candidate genes for LLS, respectively. Most candidate genes in the associated regions are known to be involved in immunity and defense response. The QTLs and candidate genes obtained from this study will be useful to breed peanut for resistances to the diseases.

Email: cyc0002@auburn.edu


S4.OP4. Genetic Investigation and Mapping of the White Mold Tolerance Trait in Peanut

Sarah Agmon, Ekaterina Manasherova, Yael Levy, Mery Dafni-Yelin, Judit Moy, Mwafaq Ibdah, Arik Harel and Ran Hovav

White mold, caused by Sclerotium rolfsii, imposes severe losses in several peanut growing regions of Israel. Developing genetic resistance is one way to manage this problem. Yet, breeding is difficult since not much is known about genetic, biological and chemical mechanisms for tolerance. The goals of this study were to evaluate the tolerance in a RIL population derived from a tolerant X susceptible cross (both Virginia-types), to locate QTLs and to discover potential mechanisms for tolerance. In 2017, 97 RILs were analyzed in random blocks field design. Lines were artificially inoculated in the field by placing hyphal plugs near the root crown of 100-day-old plants. Other important agronomic parameters were gouged as well. Resistance parameters were found significantly correlated to brunching habit, shell strength, shell weight, pod reticulation and oil content. Trait mapping was performed by applying the new peanut Affimetrix SNP-array, containing ~2900 polymorphic SNPs among the RILS. Five QTLs were found for resistance explaining 0.14-0.26 of the total variation*. Two lines with extreme phenotypes, B65 (tolerant) and B77 (susceptible), were further analyzed in controlled conditions. Significant differences were found in the level of mycelium and the number of heathy plants in detached inoculated shoots and small pots tests, respectively. Accordingly, RT-PCR of the fungal Actin gene was 13.2 and 2.6 higher in B77, respectively. Interestingly, plant developmental stage had an effect, while 20 days-old plants were significantly more resistance than 55 days-old. This study provides the first insight into resistance related mechanism in Virginia-type peanut and serves as a preview for MAS development.

Email: ranh@volcani.agri.gov.il