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A Synthesis of PAG Asia 2013: Part 2

Brian Fritz, Ph.D.
| Mar 25, 2013

ID 10032905

The steady accumulation of resources (e.g. reference genomes, BAC libraries, seed or tissue banks) and tools (e.g. low- and high-throughput sequencing technologies, bioinformatics analysis methods, high-throughput SNP genotyping)—especially the combination of these tools towards the analysis of individual genomes—has resulted in the most robust reference genome assemblies and facilitated the subsequent development of more refined applied tools for crop or animal improvement strategies. The past few decades’ application of molecular genetic approaches to plant and animal genomics is filled with examples of such multi-disciplinary and multi-faceted collaborations. The questions clearly before the attendees now are: Which methods will be employed in the future for plant and animal genomics?  What existing technologies will be sustained or improved? What new technologies or approaches still need to be developed or gain more widespread adoption by the field?

A number of participants noted the desirability of assaying haplotypes in larger numbers of samples. In some cases this might be achieved through longer effective sequencing read lengths such as Moleculo technology or the long-fragment reads outlined by Jun Wang. However, depending on the biology of the system being studied, the same result might be achieved by low-coverage genotyping-by-sequencing approaches. In conjunction with technical improvements, continuing efforts to decrease costs of GWAS approaches and the sequencing cost per base will further enable a broader sampling of molecular genetic biodiversity across a larger number of populations and individuals, typified by the efforts in soybean outlined by Henry Nguyen. The resulting increase in sampled variation will enable the development of more diverse and more flexible GWAS tools for genomic selection and improvement programs. These may be continuously re-evaluated and updated as needed based on the results of prior years’ selection, the entrance of previously underutilized populations to breeding strategies, or the addition of more informative markers from additional population-based resequencing. A compelling case was also made for further investment in more efficient and comprehensive field-based sampling and phenotying (typified by the tour de force effort described by Baltazar Antonio for rice and the need to avoid excessive use of shotguns in forestry research by Simon Southerton).

Finally, in addition to further development and distribution of molecular, bioanalytic (particularly cloud-based tools such as YABI), and field-based phenotyping and sample-collection resources, there was a compelling need for preserving, retaining access to, and sampling native diversity of wild and domesticated plant and animal genomes (such as that outlined by Robert Henry for rice). Sustaining the natural diversity of important food species will be critically important for ensuring food security in the face of a changing climate, and genomic approaches will be increasingly important in this effort.





Image courtesy of seaskylab /