345. Baudouin L, Heslop-Harrison P, Pereira MG. 2018. 3.9.2 Preparing the era of marker-assisted breeding – Chapter 3. Where we need to be to secure diversity and promote use. In Bourdeix R & Prades A (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018-2028. pp 169-171. Montpellier, France. Bioversity International. ISBN 13:978-92-9043-984-4 Download from Bioversity Website.

In the volume: Bourdeix R, Prades A. and members of COGENT (compilers) 2018. A global strategy for the conservation and use of coconut genetic resources 2018-2028. COGENT 239 pp. Published by Bioversity International, Rome.

See also the Summary Brochure: Global strategy for the conservation and use of coconut genetic resources 2018 -2028 for a more concise synthesis of the full Global Strategy for
the Conservation and Use of Coconut Genetic Resources which has been developed by experts both in coconut genetics and breeding, as well as other from along the coconut value chain. COGENT considers that the Global Strategy will provide an informed and realistic foundation for prioritizing coconut research and development. The goal is to use this Strategy to invigorate the commercial coconut sector in a sustained manner, while protecting food security, by encouraging partnerships that increase the impact of research and adoption of technological innovations. COGENT encourages international, regional and national public research organizations, development agencies, NGOs, the private sector and other stakeholders to use the priorities set out herein to guide their activities
and investment decisions.

Link to book “A global strategy for the conservation and use of coconut genetic resources 2018-2028”

Grown on more than 12 million hectares, the coconut palm (Cocos nucifera L.) is a culturally and economically important livelihood crop for millions across Southeast Asia, the Asia-Pacific, Africa and Latin America. Fully developed and strategically used, coconuts could help increase food production, improve nutrition, create employment opportunities, enhance equity and help conserve the environment. The future of global coconut production and livelihoods critically depends on the availability of genetic diversity and the sustainable use of this broad genetic base to breed improved varieties. Harnessing and conserving agrobiodiversity are critical to sustainably boosting productivity and livelihoods, and addressing important challenges including those posed by climate change or pest and disease epidemics. More than 95% of coconut farmers are resource-poor smallholders lacking the voice needed to influence government policy or private sector practices.

Phenotypic differences are found between coconut plants, and particularly between four sets of populations: Indo-Atlantic Talls, Pacific Talls, Pacific Dwarfs and introgressed Talls. We plan GBS experiments where each of these genetic groups will be represented by two cultivars with 25 individuals per population, so about one and half hectares of coconut plantation will be required. This set will have to be planted by the breeders interested in developing a genomics-based approach and who are ready to plant the field plots needed for this approach. Germplasm exchanges will have to be carefully monitored, preferably going through a quarantine centre having disease indexing facilities.

Phenotypic characterization will include:
• Phenology and biomass assessment (leaves, stem, roots and reproductive apparatus) which provides the net balance of the ontogenic development and the entire integration of the metabolism efficiency at plant scale.

Nuclear DNA will be sequenced using two complementary techniques, Illumina HiSeq2500 (~150 bp) with a ≈ 80 x coverage, Roche 454/454+ (coverage ≈15x). A new BAC library will be constructed for dwarf genotype and BAC clones will be sequenced to get the coverage of 4 x. Targeted re sequencing of the coconut genome for the specific loci will be done using solexa. A saturated map will be produced by anchoring a core set of SNP markers and available SSR markers to the existing map.

Genotyping by sequencing will be followed for a minimum of 100 individuals each from a population created in Côte d’Ivoire (for saturated linkage map itself), and from a population created in the Philippines (for subsequent QTL mapping). These progenies and their parent palms will represent the global diversity of coconut. A progeny from China,
derived from the cross between the Hainan Tall and the Malayan Yellow Dwarf, will also be integrated within a few years.

Functional annotation consists of attaching biological information to genomic elements to annotate their biochemical, biological, regulatory or interactive functions.

• Measure of water use efficiency (WUE) and gas exchanges, possibly complemented
by the carbon isotopic signature (13C/12C ratio) is liable to uncover variations
between genetic groups and between individuals in the transpiration and
photosynthetic processes.
• Assessment of leaf functional traits (leaf life-span, leaf area, specific leaf area, etc)
are likely to shed light on the differences between Tall and Dwarfs.
• Finally, metabolomic analyses of biological samples (leaflets, inflorescence stalk,
sap, fruits) will reveal variations of the amount of components, such as minerals, in
relation with total non structural carbohydrates as well as metabolite profiling
across cultivars.
In complement to this approach, collecting soil samples from the sites of these
experiments for future metagenomics analysis will indicate if performance/
characteristics are related to soil microflora rather than genotype or epigenetics.
It is also essential to develop a genomic approach to identify and link molecular
marker associations with disease resistance genes. This will allow marker-assisted
selection (MAS) in segregating populations from various resistant or tolerant
germplasm sources.

 

345. Baudouin L, Heslop-Harrison P, Pereira MG. 2018. 3.9.2 Preparing the era of marker-assisted breeding – Chapter 3. Where we need to be to secure diversity and promote use. In Bourdeix R & Prades A (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018-2028. pp 169-171. Montpellier, France. Bioversity International. ISBN 13:978-92-9043-984-4 Download from Bioversity Website.

Local copy is linked here: Coconut Strategy for Conservation and Genetics Resources Bioversity Cogent Bourdeix_2018

In the volume: Bourdeix R, Prades A. and members of COGENT (compilers) 2018. A global strategy for the conservation and use of coconut genetic resources 2018-2028. COGENT 239 pp. Published by Bioversity International, Rome.

32 page Coconut Strategy Summary of the whole volume is locally linked here: Summary of Coconut Global Strategy for Conservation, Genetics and Genetic Resources Bioversity 2018