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Title: Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED

Author
item IEZZONI, AMY - Michigan State University
item PEACE, CAMERON - Washington State University
item Bassil, Nahla
item COE, MICHAEL - Cedar Lake Research Group
item Fazio, Gennaro
item GALLARDO, KARINA - Washington State University
item GASIC, KSENIJA - Clemson University
item LUBY, JIM - University Of Minnesota
item MCFERSON, JIM - Washington Tree Fruit Research Commission
item VAN DE WEG, ERIC - Wageningen University And Research Center
item WEEBADDE, CHO - Michigan State University

Submitted to: Acta Horticulturae
Publication Type: Proceedings
Publication Acceptance Date: 5/1/2016
Publication Date: 5/1/2016
Citation: Iezzoni, A., Peace, C., Bassil, N.V., Coe, M., Fazio, G., Gallardo, K., Gasic, K., Luby, J., Mcferson, J., Van De Weg, E.W., Weebadde, C. 2016. Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED. Acta Horticulturae. 1117:1-6. doi: 10.17660/ActaHortic.2016.1117.1.

Interpretive Summary: The complete DNA sequences of apple, peach, and wild strawberry became available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genomic and genetic information routinely used in many apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size. These new genetic tests enable breeders to determine the best parents to combine and the best seedlings to advance, reducing the need to eliminate entirely poor families or to grow out and sort through thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement resulted from an international effort led by the RosBREED project, funded by the USDA-NIFA Specialty Crop Research Initiative. DNA tests are now applied for high value trait levels where the targeted DNA sequence is responsible for a large proportion of the observed trait variation. However, challenges that limit widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge. Remaining technical challenges pose bottlenecks, such as streamlined follow-up of DNA sequences through multiple families of pedigree-linked breeding families and access to suitable commercial service providers.

Technical Abstract: The complete genomic sequences of apple (Malus × domestica Borkh), peach (Prunus persica (L.) Batsch), and diploid strawberry (Fragaria vesca L.) – one member of each of the three main fruit-producing branches of the Rosaceae family tree – were available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genomic and genetic information routinely used in many apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size. These new genetic tests enable breeders to determine the best parents to combine and the best seedlings to advance, reducing the need to eliminate entirely poor families or to grow out and sort through thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement resulted from an international effort led by the RosBREED project, funded by the USDA-NIFA Specialty Crop Research Initiative. DNA tests are now applied for high value trait levels where the targeted loci tend to explain a large proportion of the phenotypic variation. However, challenges that limit widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge, such as an understanding of genotype by environment (GxE) interactions and loci associated with variation for other valuable attributes. Remaining technical challenges pose bottlenecks, such as streamlined phasing of alleles from multiple families of pedigree-linked breeding germplasm and access to suitable commercial service providers.