Doctoral research in progress


Genotyping-by-sequencing in tree improvement and conservation genetics of Dipteryx panamensis

Jose P. Jimenez Madrigal


Background

Dipteryx panamensis is a tropical tree species, endemic to the Caribbean lowlands, ranging from Nicaragua to Colombia [1].  It is considered a keystone species, providing food and shelter to 16 different mammals [2] and many birds, including the endangered Ara ambiguus (great green macaw) [3].  In addition to its ecological value, D. panamensis possess high quality wood, ideal for timber products.  Unfortunately, illegal logging and habitat fragmentation have diminished natural populations to the point that trade of the wood is now controlled by international treaty (CITES) [4,5].  Due to its long time to harvest, new technologies are needed that can aid the adaptation, improvement, and conservation of this important species.


Research question

My goal is to incorporate new technologies into a D. panamensis breeding program.  I look to answer this question: How effective is Genotyping-by-Sequencing (GBS), a next-generation sequencing technology, for both tree improvement and conservation genetics?  GBS can identify thousands of single nucleotide polymorphism (SNP).  SNPs are ubiquitous, codominant, and can be in functional parts of the genome, thus making them the ideal marker for tree improvement and conservation genetics [6,7].

Methodology

To answer this question, I will work with a D. panamensis progeny trial. The trial is comprised of two plantings of 29 open-pollinated families from 3 provenances, established 5 years ago in Costa Rica.  One planting is in the South Pacific lowlands and the other is in the North Atlantic lowlands.  The sites receive different amounts of precipitation.  I will collect tissue samples for DNA extraction and genotyping [8,9,10].  To determine the effectiveness of GBS for tree improvement, I will estimate the additive genetic effects or breeding values (BV) for growth and quality related traits using a realized genomic relationship matrix derived from the marker data and linear mixed models (gBLUP) [11,12,13].  Similarly, to test the usefulness of GBS for conservation I will estimate BV for precipitation use efficiency and water use efficiency (WUE) derived from carbon isotope discrimination [14].  I will compare these with BVs obtain from pedigree and phenotype.  Traditionally obtain BVs are expensive since it takes decades to grow the trees.  gBLUPs could provide accurate estimations of BVs, and evaluations at earlier life stages significantly reduces production costs and time to harvest.  Additionally, I will estimate genetic diversity within and among provenances.  I will compare these with previous studies done with microsatellites [4,15].

Big Picture

This research is part of a broader effort lead by GENFORES, a university & farmer’s co-op that works in tree improvement and germplasm conservation of native timber species in Costa Rica [16].  Our breeding program can alleviate logging pressure from natural population by providing better-quality seeds for plantation forestry, and also contribute improved genotypes for reforestation and ecological restoration.  According to the latest climate predictions, extreme weather conditions are expected to become more frequent in the tropics; i.e. higher temperatures, drier summers, and wetter winters [17].  Identification and deployment of enhanced WUE genotypes will be crucial for resilience in this species and all others that depend on it.


Literature cited


[1] Flores, E.  1992.  Dipteryx panamensis. Arboles y Semillas del Neotropico 1:1–22.
[2] Bonaccorso, F.J., Glanz, W.E. and Sandford, C M.  1980.  Feeding assemblages of mammals at fruiting Dipteryx panamensis (Papilionaceae) trees in Panama: seed predation, dispersal and parasitism.  Revista Biologia Tropical 28(1):61-72.
[3] Chassot, O. and Monge-Arias, G.  2012.  Connectivity conservation of the great green macaw’s landscape in Costa Rica and Nicaragua (1994-2012).  Parks 18(1):61-70.
[4] Hanson, T.R., Brunsfeld, S.J., Finegan, B. and Waits, L.P.  2008.  Pollen dispersal and genetic structure of tropical tree Dipteryx panamensis in a fragmented Costa Rican landscape.  Molecular Ecology 17:2060-2073.
[5] CITES: Convention on International Trade in Endangered Species of Wild Fauna and Flora.  For more information please visit: https://www.cites.org/.
[6] Poland, J.A. and Rife, T.W.  2012.  Genotyping-by-sequencing for plant breeding and genetics.  The Plant Genome 5(3):92-102.
[7] Narum, S.R., Buerkle, C.A., Davey, J.W., Miller, M.R. and Hohenlohe, P.A.  2013.  Genotyping-by-sequencing in ecological and conservation genomics.  Molecular Ecology 22:2841-2847.
[8] Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S. and Mitchell, S.E.  2011.  A robust, simple genotype-by-sequencing (GBS) approach for high diversity species.  PLoS ONE 6(5):e19379.
[9] Rife, T.W., Wu, S., Bowden, R.L. and Poland, J.A.  2015.  Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling.  BMC Genomics 16:248.
[10] Clevenger, J., Chavarro, C., Pearl, S.A., Ozias-Akins, P. and Jackson, S.A.  2015.  Single nucleotide polymorphism identification in polyploids: A review, example, and recommendations.  Molecular Plant 8:831-846.
[11] Grattapaglia, D. and Resende, M.D.V.  2011.  Genomic selection in forest tree breeding.  Tree Genetics & Genomes 7:241-255.
[12] Isik, F.  2014.  Genomic selection in forest tree breeding: the concept and an outlook to the future.  New Forests 45:379-401.
[13] Endelman, J.B. and Jannink, J.L.  2012.  Shrinkage estimation of the realized relationship matrix.  G3: Genes, Genomes, Genetics 2:1405-1413.
[14] Farquhar GD, Ehleringer JR, Hubick KT (1989) Carbon isotope discrimination and photosynthesis. Annual Review of Plant Physiology and Plant Molecular Biology 40:503–537.
[15] Hanson, T.R., Brunsfeld, S.J., Finegan, B. and Waits, L.P.  2008.  Characterization of microsatellite markers for the almendro (Dipteryx panamensis), a tetraploid rainforest tree.  Molecular Ecology Resources 8:425-427.
[16] For more information please visit http://www.tec.ac.cr/sitios/Docencia/forestal/Paginas/genfores.aspx
[17] IPCC.  2014.  Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Core Writing Team, R.K. Pachauri and L.A. Meyer (eds.)]. IPCC, Geneva, Switzerland, 151 pp.