Poster presented at Plant and Animal Genome, PAG XXII. San Diego (USA),  11-15 Jan 201

Chan, A.

Jacquemoud-Collet, J.P.

Jenny, C.

Perrier, X.

Rouard, M.

Roux, N.

Sardos, J.

Town, C.D.

English

CGSpace

Background: This project is part of a larger effort to apply genomics technologies to assess genetic diversity and to advance genetic improvement efforts in Musa (banana and plantain), a major staple food crop in the developing world.  Most cultivated varieties of bananas result from intra- or inter-specific crosses of the wild diploid species, Musa acuminata (A genome) and Musa balbisiana (B genome).  Somaclonal mutation and human selection has resulted in current day bananas with a wide morphological diversity.  The Cavendish (AAA) subgroups are believed to have derived from an individual unique initial genotype, and similarly for the subgroup plantain (AAB).  However, little or no genetic diversity can be detected within these groups using conventional molecular markers such as RFLP, SSR, DArT.  Methods: To assess genetic diversity with an improved resolution, we have selected 65 accessions with diploid and triploid combinations of the A and/or B genomes including AAB plantains and AAA Cavendish, and cultivated or wild Musa accessions from the core collection at the Global Musa Genomics Consortium (GMGC).  A high-throughput reduced representation genome sequencing approach - genotyping-by-sequencing (GBS) is used to obtain high density sequence markers [1].  Results: Using GBS reads, genotypes were determined for each diploid and triploid accession, and dissimilarity computed across all accessions.  Genetic diversity analysis was carried out using the DARwin software [2, 3].  Conclusions: GBS markers provides a high resolution approach to characterize the genetic diversity of individual Musa subgroups. ABSTRACT METHODS RESULTS (1) Factorial analysis was performed using 25,115 sites shared across all 65 Musa accessions.  The accessions were clustered according to the expected genome composition.  The A-only and B-only containing genomes were seen as the extremes of the first axis as expected. REFERENCES [1] Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S., Mitchell S.E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 4;6(5):e19379. [PMID: 21573248] [2] Perrier, X., Flori, A., Bonnot, F. (2003). Data analysis methods. In: Hamon, P., Seguin, M., Perrier, X.,Glaszmann, J. C. Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43 - 76. [3] Perrier, X., Jacquemoud-Collet, J.P. (2006). DARwin software http://darwin.cirad.fr ACKNOWLEGEMENTS We thank Ronny Swennen (KU Leuven, Belgium) for the selection of the Musa accessions, Eva Hřibová and Jaroslav Doležel (Institute of Experimental Botany, Czech Republic) for providing Musa genomic DNA, and Ed Buckler and Rob Elshire (Cornell University) for advices on the GBS method.  This work is funded by the USAID linkage funds. (1) A total of 65 Musa accessions including diploid and triploid combinations of the A or B genomes, AAB plantains, AAA Cavendish, and cultivated or wild Musa accessions were selected for GBS sequencing. 1J. Craig Venter Institute, Rockville, USA; 2CIRAD, Montpellier, France 3Bioversity International, Montpellier, France; Agnes P. Chan1, Xavier Perrier2, Christophe Jenny2, Jean-Pierre Jacquemoud-Collet2, Mathieu Rouard3, Julie Sardos3, Nicolas Roux3, and Christopher D. Town1 Using Genotyping-By-Sequencing to Understand Musa Diversity Axes 1 (40.0%)  / 2  (11.4%) -.24 -.22 -.2 -.18 -.16 -.14 -.12 -.1 -.08 -.06 -.04 -.02 .02 .04 .06 .08 .1 .1 .09 .08 .07 .06 .05 .04 .03 .02 .01 -.01 -.02 -.03 -.04 -.05 -.06 Outgroup Musa ornata AAw ABB AAB BB AB AAA AAcv (2) A neighbor-joining tree was constructed using 75,981 sites shared across 39 AAB accessions.  The node for Musa ornata was grafted afterwards for tree rooting.  The majority of the African AAB plantains (green labels) were clearly separated from other AAB accessions. Origins: •Africa •Philippines •Comoros •Papua New Guinea •Pacifics African AAB plantains Non-African AABs CONCLUSIONS (1) Genetic diversity between the A  and B versions of the Musa genome is higher than inter A-genome variations, as expected. (2) GBS markers provide a high resolution sequence-based approach to study genetic diversity for Musa subgroups such as the African plantains (AAB). (3) Further analysis will be needed to compare the resolution of the GBS method with existing genotyping methods for studying Musa diversity. (2) About 1 to 4 million Illumina reads flanking PstI sites were generated for each Musa accession.  Approximately 200,000 candidate SNP locations with reference to the doubled-haploid Pahang genome were obtained from all 65 accessions combined (labeled as “ALL_SNP_POS”).   Of which, approximately one-tenth were common locations and shared obtained across all 65 accessions (labeled as “COMMON_SNP_POS”). GBS markers obtained were distributed throughout the entire lengths of the Musa chromosomes (as expected) as shown in the chromosome position plot below. (b) Whole genome shotgun vs GBS sequencing (c) GBS sequencing workflow  (a) 65 Musa accessions ITC Name ploidy Group Subgroup1 ITC0557 Americani 3 AAA Cavendish2 ITC0002 Dwarf Cavendish 3 AAA Cavendish3 ITC1586 Grande Naine 3 AAA Cavendish4 ITC0654 Petite Naine 3 AAA Cavendish5 ITC0340 Pisang Masak Hijau 3 AAA Cavendish6 ITC0048 Valery 3 AAA Cavendish7 ITC1251 Vietnam No5 3 AAA Cavendish8 ITC0724 Cocos 3 AAA GrosMichel9 ITC0686 Pisang Umbuk 3 AAA Orotava10 ITC0671 Hom Thong Mokho 3 AAA Ambon11 ITC1305 Paji 3 AAA EA AAA12 ITC0184 One Hand Planty 3 AAB Plantain13 ITC1127 3 Vert 3 AAB Plantain14 ITC0111 Agbagba 3 AAB Plantain15 ITC0217 Akpakpak 3 AAB Plantain16 ITC0007 Asamiensa 3 AAB Plantain17 ITC1126 Batard 3 AAB Plantain18 ITC1129 Big Ebanga 3 AAB Plantain19 ITC0033 Bungaoisan 3 AAB Plantain20 ITC0034 Daluyao 3 AAB Plantain21 ITC0514 Eba Oboikpa 3 AAB Plantain22 ITC0121 Ihitisim 3 AAB Plantain23 ITC0631 Maqueno 3 AAB Plantain24 ITC0118 Mbang Okon 3 AAB Plantain25 ITC0489 Mimi Abue 3 AAB Plantain26 ITC0022 Mulolou 3 AAB Plantain27 ITC0044 Niangafelo 3 AAB Plantain28 ITC1133 Njock Kon 3 AAB Plantain29 ITC0113 Ntanga 2 3 AAB Plantain30 ITC0512 Ntanga 5 3 AAB Plantain31 ITC0192 Ntie 3 AAB Plantain32 ITC0718 Nzumoigne 3 AAB Plantain33 ITC0109 Obino I'Ewai 3 AAB Plantain34 ITC0235 Obubit Ukom 3 AAB Plantain35 ITC1325 Orishele 3 AAB Plantain36 ITC0119 Osoaboaso 3 AAB Plantain37 ITC1140 Red Yade 3 AAB Plantain38 ITC0719 Mnalouki 3 AAB plantain like Comoros39 ITC0036 Muracho 3 AAB plantain like Phillipino40 ITC0945 Bira 3 AAB Iholena41 ITC0825 Uzakan 3 AAB Iholena42 ITC0332 Laknau 3 AAB Laknau43 ITC0733 Iho U Maohi 3 AAB Maia Maoli Popoulu44 ITC1327 Poingo 3 AAB Maia Maoli Popoulu45 ITC1135 Popoulou CMR 3 AAB Maia Maoli Popoulu46 ITC1232 Bagatow 3 AAB PNG AAB47 ITC0870 Horul 3 AAB PNG AAB48 ITC0909 Kupulik 3 AAB PNG AAB49 ITC0830 Rukumamb Tambey 3 AAB Rukumamb50 ITC0875 Tigua 3 AAB Rukumamb51 ITC0312 Pisang Jari Buaya 2 AA Jari Buaya52 ITC0653 Pisang Mas 2 AA Sucrier53 ITC1187 Tomolo 2 AA AA PNG54 ITC0245 Safet Velchi 2 AB Ney Poovan55 ITC0659 Namwa Khom 3 ABB PisangAwak56 ITC0623 Banksii 2 acuminata banksii57 ITC0283 Long Tavoy 2 acuminata burmannica58 ITC0249 Calcutta 4 2 acuminata burmannicoides59 ITC1511 DH Pahang 2 acuminata malaccensis60 ITC0609 Pahang 2 acuminata malaccensis61 ITC0253 Borneo 2 acuminata microcarpa62 ITC1177 Zebrina 2 acuminata zebrina63 ITC0247 Honduras 2 balbisiana balbisiana64 ITC1063 Pisang Klutuk Wulung 2 balbisiana balbisiana65 ITC0637 Musa Ornata 2 ornata ornataP449 

Using genotyping-by-sequencing to understand Musa diversity

https://cgspace.cgiar.org/bitstream/10568/67551/1/Chan_usinggenotyping.pdf

Using genotyping-by-sequencing to understand Musa diversity

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