The Plant and Animal Genome XXVI Conference (PAG) – Sweetpotato and Yam Genomics

PAG XXVI – Conference: Sweetpotato and Yam Genomics, San Diego, California, USA, 16^th January 2018

Synopsis

Recent advancements in development of genomic resources and related tools for Sweetpotato (Ipomoea batatas) and yam (Dioscorea spp.) to accelerate genome-assisted improvement will be presented and discussed. Presentations will focus on development of genomic resources, including genome sequencing efforts, bioinformatic pipelines, software for identification of marker-trait associations and MAS/genomic selection as methods to improve resilience to abiotic and biotic constraints, together with other consumer preference traits and nutritional quality.

Workshop Theme: Next Generation Omics technologies for sweetpotato and yam improvement

Tuesday, January 16, 2018

4:00 PM – 6:30 PM

Town and Country Hotel – Pacific salon 1

Chairs

Ranjana Bhattacharjee

International Institute of Tropical Agriculture (IITA)

 Craig Yencho

North Carolina State University

Organizers

Ranjana Bhattacharjee, Dorcus Gemenet, and Craig Yencho

International Institute for Tropical Agriculture, International Potato Center and North Carolina State University

4:00 PM BMGF Investments in Sweetpotato and Yam Genomics

Jim Lorenzen – Welcome (Not listed on program)

Bill and Melinda Gates Foundation, USA

4:10 PM Genomic Tools for Sweetpotato (GT4SP) Improvement Project Update

1. Craig Yencho

North Carolina State University

4:20 PM Linkage and QTL mapping in complex polyploids: new algorithms and methods.

Guilherme da Silva Pereira^1,3, Marcelo Mollinari^1,3, Bode Olukolu¹, Dorcus C. Gemenet, G. Craig Yencho¹, Zhao-Bang Zeng^1,3.

 ¹Dept. of Horticultural Science, NC State University, Raleigh NC 27695-7609.

² International Potato Center, Lima, Peru

³Bioinformatics Research Center, Dept. of Statistics, NC State University, Raleigh NC 27695-7566.

Due to their intrinsic complexity, autopolyploid plant species have been left behind compared to the diploid ones regarding the usage of molecular markers for genetic studies and their effective application in breeding. Only with the advent of single nucleotide polymorphism chip arrays and ultimately next-generation sequencing-based protocols, has it become possible to properly overcome the limitations imposed by the use of single-dosage markers coupled with diploid-like approaches. The need to call higher dosage markers has led to advances on linkage and quantitative trait loci (QTL) mapping analyses in tetraploid species, mainly in potato. However, these methods are not readily applied to higher ploidy levels. For example, the number of possible genotypes of a bi-parental cross offspring increases from 36 to 400 to 4,900 in tetra-, hexa- and octoploid species, respectively. By using hexaploid sweetpotato mapping populations, we were able to (i) sample higher dosage markers in about half of the genome, (ii) build integrated linkage maps taking into account all markers simultaneously and obtain conditional genotype probabilities using a hidden Markov model, and (iii) map multiple QTL using a random model approach. To deal with the computational burden of analyzing a hexaploid genome, we have developed new tools called polymap and polyqtl to make the process relatively fast yet statistically accurate and genetically comprehensible.

 4:40 PM Linkage and QTL analysis in the hexaploid New Kawogo x Beauregard mapping population (SP2)

 Bonny Oloka^1,2, Bode Olukolu¹, Benard Yada², Milton O. Anyanga², Doreen Chelangat², Paul Musana², Agnes Alajo², Guilherme da Silva Pereira³, Marcelo Mollinari³, Zhao-Bang Zeng^1,3, G. Craig Yencho¹

¹Dept. of Horticultural Science, NC State University, Raleigh NC 27695-7609.

²National Crops Resources Research Institute, Namulonge, P.O. Box 7084, Kampala, Uganda.

³Bioinformatics Research Center, Dept. of Statistics, NC State University, Raleigh NC 27695-7566.

Genetic improvement of sweetpotato, Ipomoea batatas (L.) Lam., for important agronomic traits has been slow over the years in the global arena especially in sub-Saharan Africa where the crop is a staple. This is largely due to the crop’s complex hexaploid (2n = 6x = 90) genetics, its large genome size and out-crossing nature with significant self and cross incompatibilities, high heterozygosity, and a wide array of biotic and abiotic stresses. We developed a bi-parental mapping population from the sweetpotato cultivars “New Kawogo” x “Beauregard” (NKB), consisting of 287 segregating F1 progeny, and used next-generation sequencing, computing and bioinformatics technology to develop high quality SNPs, which we used for linkage mapping and QTL analysis. Using a modified genotyping by sequencing (GBS) pipeline, we were able to mine 1,409,131 SNPs from the alignment of sequence files from the NKB population to the I. trifida reference (version 3.0) at a rate of 74.4%. We were able to call 132,201 SNPs using SuperMASSA software and after filtering for segregation distortion and missing data we retained 5,624 high quality SNPs along with their respective dosage information. We used these SNPs to build a genetic linkage map and have identified all 15 linkage groups. QTL analysis for sweetpotato weevil, sweetpotato virus disease and storage root yield is in progress. These tools will facilitate more efficient introgression of important traits and subsequent faster genetic gain of key traits in this complex yet globally important crop.

5:00 PM Advances in sweetpotato phenotyping in the USA and SSA.

 Edward Carey¹, Maria Andrade⁴, Omar Benites², Doreen M, Chelangat⁶, Bryan Ellerbrock⁷, Raul Eyzaguirre², Dorcus C. Gemenet², Wolfgang Gruneberg², Mercy Kitavi⁵, Nicholas Morales⁷, Lukas A. Mueller⁷, Paul Musana⁶, Robert O.M. Mwanga³, Alex Ogbona⁷, Ivan Perez², Reuben T. Ssali³, Jolien Swanckaert¹, Titima Tantikanjana⁷, Benard Yada⁶, G. Craig Yencho⁸, Luka Wanjohi⁵

¹International Potato Center, Support Platform for West Africa, Kumasi, Ghana; ²International Potato Center, Avenida La Molina 1895, La Molina, Lima 12, Peru; ³International Potato Center, Support Platform for East and Central Africa, Kampala, Uganda;

⁴International Potato Center, Support Platform for Southern Africa, Maputo Mozambique;

⁵International Potato Center, Regional office, Sub-Sahara Africa, Nairobi, Kenya;

⁶National Crops Resources Research Institute (NaCRRI), Namulonge, P.O. Box 7084, Kampala, Uganda;

⁷Boyce Thompson Institute, Ithaca, New York, USA;

⁸Dept. of Horticultural Science, NC State University, Raleigh NC, USA.

Sweetpotato breeders have long recognized the benefits of standardized data collection for sharing and comparing results. Recent support for breeding efforts under the Sweetpotato Action for Security and Health in Africa (SASHA) and Genomic Tools for Sweetpotato Improvement (GT4SP) projects, have advanced development of methods and tools for phenotyping, including trait ontologies, and database and breeding program management. Training and capacity development through breeding communities of practice, and demand for high throughput phenotyping methods are strengthening user uptake and further development of these tools. Field data collection on mobile electronic devices is eliminating the need for cumbersome data transcription from paper to computer, and the use of bar code labelling is reducing errors and enhancing quality control at all stages of the breeding process. Sweetpotatobase (https://sweetpotatobase.org) a relational database designed to handle phenotypic and genotypic data, provides an increasingly versatile platform for data storage and tools for management and analysis. Linked to Sweetpotatobase, the fieldbook app (http://wheatgenetics.org/field-book) and the Highly Interactive Data Analysis Platform (HIDAP; https://research.cip.cgiar.org/gtdms/hidap/) provide increasingly integrated tools for data collection, quality control and analysis. Some traits of interest, such as yield are shared across all breeding programs, while others such as disease and pest resistances and quality attributes are specific to regions where they occur or to specific breeding programs and populations. Methods of phenotyping are and will continue to evolve with methods of data capture and understanding of traits as we move toward increasingly high throughput methods.

 5:20 PM The potential for crop improvement in yam phylogenomics

Viruel J¹, Soto M^1,2, Pokorny L¹, Dodsworth S¹,  Forest F¹, Leitch IJ¹, Gravendeel B³, Wilkin P¹.

¹Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom;  ²Department of Botany, University of British Columbia, Vancouver, Canada; ³Naturalis Biodiversity Center, Leiden, The Netherlands

 Up to seven species of Dioscorea are widely cultivated worldwide in an extensive variety of agronomic environments and social contexts. Considerable efforts in crop improvement are being developed based on genomic approaches. However, the enormous species diversity within Dioscorea (ca. 650 accepted species) constitutes an unexplored potential for crop breeding, as many wild species possess traits of interest or even the potential to become cultivated entities themselves. Evolutionary patterns within the pantropical Dioscorea have been explored using one nuclear region and five plastid regions for approximately 20% of the species, showing congruent phylogenetic topologies and subsequent divergences correlated with different kinds of underground storage organs. These organs constitute a pivotal trait with direct economic impact as species edibility is usually linked to annual tuber replacement in some species, or the potential to accumulate secondary compounds of interest in perennial underground organs. Next-generation sequencing methods provide new opportunities to gather huge amounts of genomic data to explore novel biological questions within a phylogenetic context. We will discuss the potential of HybSeq and transcriptomics methods to identify the crop wild relatives and to understand the origin of the cultivated species.

 5:35 PM Developing genomic resources for the water yam, Dioscorea alata L.

Ranjana Bhattacharjee¹ and Jessica B. Lyons²

¹International Institute of Tropical Agriculture, Ibadan, Nigeria

²University of California, Berkeley, Berkeley, CA USA

1. alata is an important food security and income generation crop for millions of smallholder farmers in the tropics and sub-tropics of West Africa, Asia, Latin America, and the Pacific islands. Water yam boasts desirable characteristics such as high nutritional content, yield under low soil fertility, and low post-harvest losses. However, production is constrained by biotic and abiotic stresses, and breeding for desired traits is arduous. In the context of surging population growth and climate change, modern genomic and genetic tools are urgently needed for the more efficient improvement of water yam. Here we report our progress towards a D. alata reference genome sequence, constructed from long- and short-read shotgun data combined with long-range linking information. Comparison between the D. alata draft genome and the recently published D. rotundata genome assembly reveals extensive conservation, but also highlights differences between the two yam species. Towards an initial SNP catalog for D. alata, we have shotgun sequenced seven accessions. These accessions are the parents of eight F1 mapping populations that comprise over 1500 offspring and segregate traits important to smallholder farmers. Genotyping of these populations is underway. In order to assess global genetic diversity of D. alata, we are also gathering material from around the world for genotyping.

5.50 PM Greater yam (Dioscorea alata L.) pre-breeding and breeding: use of genomic tools to decipher the genetic diversity and identify wild relatives.

 Chaïr^1,2, P. Mournet^1,2, S. Causse^1,2, K. Nguyen Van³, G. Gueye⁴, J. Kaoh⁵, J. Waki⁶, R. L. Senanayake⁷, B. Pachakkil⁸, M. T. Rajaonah⁹, R. Bhattacharjee⁴, C. Pavis¹⁰, M. Summo^1,2, F. Cormier ^11,2, G. Arnau^11,2 and V. Lebot^12,2

¹CIRAD, UMR AGAP, F34398-Montpellier, France

²AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France ³Plant Resources Center (PRC), An Khanh, Hoai Duc, Hanoi, Vietnam

⁴International Institute of Tropical Agriculture (IITA),  PMB 5320, Ibadan, Oyo State, Nigeria

⁵Vanuatu Agricultural Research and Technical Centre (VARTC), Espiritu Santo PB 231, Vanuatu

⁶National Agricultural Research Institute (NARI), P.O. Box 1639, Lae, Morobe Province, PNG

⁷Field Crops Research and Development Institute, 50270, Mahailluppallama, Anuradhapura, Sri Lanka

⁸Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-0054, Japan

⁹ Kew Madagascar Conservation Centre, Antananarivo 101, Madagascar

¹⁰INRA, UR1321, ASTRO Agrosystèmes tropicaux, F-97170, Petit-Bourg, Guadeloupe, France

¹¹CIRAD, UMR AGAP, F-97170, Petit Bourg, Guadeloupe, France, ¹²CIRAD, UMR AGAP, Port Vila, Vanuatu

The greater yam (Dioscorea alata L.) is the most widespread edible yam species and is cultivated throughout sub-tropical and tropical areas. The species is an important food in West Africa, the Caribbean and the Pacific where it has considerable social and cultural importance, and it is also grown in parts of upland Asia. Although D. alata production is expanding in West Africa because of its ease of cultivation, one of the major constraints to further development is its suitability for “fufu”, a traditional dish necessitating tubers with high dry matter and specific starch contents. Moreover, some varieties with agronomic importance are susceptible to anthracnose (Colletotrichum gloeosporioides). Added to that, D. alata genetic improvement is constrained by access to well documented germplasm. Nevertheless, collections of D. alata and related species exist in international and national genebanks. Thus, to overcome these main limitations, rationalise the ex situ collections, and facilitate breeding for tuber quality and anthracnose tolerance, using Genotyping By Sequencing (GBS), we are investigating the genetic diversity of a worldwide sample of more than 500 D. alata accessions. Using targeted genotyping approaches on chloroplast and nuclear genomes, we are also investigating the relationship between D. alata and D. nummularia considered as one of its wild relatives from the Pacific. To identify gene/QTLs related to key agronomic traits, genetic mapping is on-going as well. Finally, the genomic resources produced are assembled to build up a “Yam Genome Hub”.

 6:05 PM Towards comprehensive control of Yam mosaic virus in West Africa

 

1. Lava Kumar¹, A. Owati¹, C.K. Nkere^1,2, J. Oyekanmi¹, B. Osudahunsi¹, T. Oviasuyi¹, R. Matsumato¹, K. Olufisayo¹, R. Bhattacharjee¹, B. Aighewi¹, N. Maroya¹, B. Morufat¹, D. Mignouna¹, J. Onyeke², A. Montes-Lopez¹, P. Adegbola¹, A. Amele¹, M. Abberton¹, D. DeKoeyer¹, S.E. Seal³ and R. Asiedu¹

¹International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria

²National Root Crops Research Institute, Umudike, Nigeria

³Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK

Yam mosaic virus (YMV, genus Potyvirus) is the most important viral pathogen infecting yams (Dioscorea spp.) in West Africa. Annual incidence of YMV in the two most widely cultivated species, D. rotundata and D. cayenensis exceed 70%, resulting in about 40% production loss per annum in West Africa. Perpetual use of farmer-saved seed has been recognized as the major contributing factor for high YMV incidence in the farmer fields. Systematic efforts since past 5 years have contributed to mapping of YMV spread and characterization of over 120 YMV isolates that revealed circulation of diverse strains, consequence of which on symptom types and host resistance response are yet to be understood. This knowledge however helped in development of versatile diagnostic tools for YMV indexing, and establishment of virus-free planting materials of popular cultivars necessary to invigorate ‘clean’ seed systems. Efforts to understand the rate of virus infection offered clues to YMV epidemiology and this knowledge has been employed for on-farm management to reduce YMV incidence and severity. More recent efforts are oriented towards characterization of yam germplasm for identification of YMV resistance in farmer adopted cultivars and also to select promising parents for YMV resistance breeding. Integration of multiple approaches is expected to result in the comprehensive management of YMV which is critical not only to recover yield lost due to virus infection, but also to double productivity to meet the growing demand for one of the main staple food crops in West Africa. This presentation seeks to provide diversity and distribution of YMV in various yam cultivars and geographies and implication of this knowledge on decisions on YMV control strategies.