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Moderated conference on Genomics in Food and Agriculture

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Date: Wed, 20 Mar 2013 16:45:44 +0100
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This is from Sinclair Mantell, Nakhlatec International Development Advisors, Sweden.

Denis Murphy (Message 39) should be congratulated by members of the forum for presenting very effectively the perspective and reality of the practical field-level impact of -omics in the domains of tropical livestock and crop production in low to middle income countries (notice the emphasis on production as against breeding!). 

I am an agriculture/horticulture specialist with over 20 years' expertise in application of tissue culture and genetic transformation to tropical crops, many of which are mainstay root and tuber crops like cassava and Dioscorea yams, but also several tropical fruit and tree crops with notoriously lengthy breeding cycles. Having trained in the tropical branches of the land-based sciences in the Caribbean during the 1970's, I have been increasingly exposed during the late 1980's and all the way through the 1990's to the potential applications of -omics in horticulture and forestry research on tropical species. Rapidly changing developments in the field of genomics as these impact crops in low income countries is becoming challenging in view of the rapid progress being made by increasing numbers of research teams based in advanced research centres. Now away from the bench, but still supporting rural development and Higher Education, this is good and encouraging news but there remain important training and application/access implications that need attention backed up by clear strategies geared to long-term research to adoption process cycles. 

The potential for -omic tools in shortening breeding cycles and targeting specific genes to generate and identify useful genetic recombination events has already been well-articulated in this conference. The current efforts and rates of advancement for instance in countries like China to incorporate drought and salt tolerance genes in rice and other cereals by gene insertion are impressive. Some edge effects of the technologies are however already in practical use and making valuable impacts in many countries.

Molecular fingerprinting of genetically uncharacterised populations of crops, and sometimes those of their wild ancestors, is generating already a wealth of useful information and guidance by which traditional clones, cultivars and varieties can be distinguished on genome diversity grounds (not by their unreliable and environmentally dependent phenotypes alone) using a variety of genetic probes based on synthesised primers homologous to partial gene sequences of the same, sister crops or even model plants like Arabidopsis. Our own experiences with distinguishing the different cultivars of cashew (Anacardium spp) and pistachio (Pistacea spp) originating from different regions of the world has led to improved breeding strategies for these crops in long term seed orchard systems in countries like Tanzania, Mozambique, Brazil and South Africa. Applications of molecular fingerprinting are not only assisting managers of seed orchard and clonal collections of tropical fruit and nut trees but also in developing better-informed genetic conservation and management strategies in fragmented forest situations, such as those experienced in the Mata Atlantica forest of Brazil close to the large urban centres like Rio de Janeiro and Sao Paulo. Using molecular fingerprinting tools to assess relative levels of gene flow between and within refuges of fragmentary forest, conservation biologists and ecologists determine whether or not a specific tree species of importance is able to regenerate and perpetuate itself efficiently in the remaining tracts of forest. 

When it comes to application of information on the whole genome of a genus, actual uses will take more time to emerge for the reasons Denis Murphy has explained so eloquently. The work on the genome sequencing of eucalypts for instance (Novaes et al, 2008), is advancing well and can become more effective in identifying important regions of the genome which confer key traits, e.g. desirable wood fibre quality (to reduce need for environmentally deleterious postharvest processing in the paper industry), cold tolerance (to improve the geographical range of the genus for forestry and ornamental uses), sustainable resistance to key diseases and pests as well as many other significant traits like tree shape and incremental growth rate. The practical breakthroughs in such endeavours may well be on the near horizon. 

We certainly therefore need to look to more support for training and increased facilities for these technologies to be applied in centres of expertise around the world and be mindful at the same time of not making too many premature promises as far as the genetic improvement of tropical crops and livestock is concerned. 

Sinclair H. Mantell
Nakhlatec International Development Advisors,
Kvarngården, Gödelöv 141, 247 98 Genarp, 
Sweden.
Tel: +46 455 341483
Mobile: +46 707 158048
Website: www.nakhlatec.se 
e-mail: sinclair.mantell (at) nakhlatec.se

Reference:
Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M: High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. Bmc Genomics 2008, 9:312. http://www.biomedcentral.com/1471-2164/9/312 

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