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Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa

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Abstract

This paper summarizes results from a decade of collaborative research using advanced backcross (AB) populations to a) identify quantitative trait loci (QTL) associated with improved performance in rice and to b) clone genes underlying key QTLs of interest. We demonstrate that AB-QTL analysis is capable of (1) successfully uncovering positive alleles in wild germplasm that were not obvious based on the phenotype of the parent (2) offering an estimation of the breeding value of exotic germplasm, (3) generating near isogenic lines that can be used as the basis for gene isolation and also as parents for further crossing in a variety development program and (4) providing gene-based markers for targeted introgression of alleles using marker-assisted-selection (MAS). Knowledge gained from studies examining the population structure and evolutionary history of rice is helping to illuminate a long-term strategy for exploiting and simultaneously preserving the well-partitioned gene pools in rice.

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Abbreviations

AB:

Advanced backcross

QTL:

Quantitative trait loci

MAS:

Marker-assisted-selection

NIL:

Near isogenic line

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Acknowledgments

This research was supported by grants from the Rockefeller Foundation; the U.S. Department of Agriculture (USDA) Plant Genome Research Program (National Research Initiative grant No. 96-35300-3645 and No. 00-35300-9216); CRIS Project 6225-21000-006; NSF Plant Genome awards DBI-0110004 and DBI-0319553, sub-award 2003-1054-01; RiceTec, Inc.; a graduate assistantship to Michael Thomson provided by the Cornell Plant Cell and Molecular Biology Program (DOE/NSF/USDA Interagency Training Grant); a graduate assistantship to Amanda Garris provided by USDA/CSRS Competitive Grant 97-35300-5101 representing Food and Agricultural Sciences National Needs Graduate Fellowship in Plant Biotechnology; Ph.D. support for Pilar Moncada from the National Federation of Coffee Growers (Cenicafe) of Colombia; support for QTL analysis in Korea from the Crop Functional Genomics Center of the of the 21st Century Frontier Research Program (Project code: CG3112) and from Bio Green 21 of the Rural Development Administration, Republic of Korea. We are grateful to the International Center for Tropical Agriculture (CIAT) in Cali, Colombia for population development and phenotypic evaluation of the Caiapo population; to the China National Hybrid Rice Research and Development Center, Changsha, China for population development and phenotypic evaluation of the Ce64 hybrid families; to ICABIOGRAD in Indonesia for population development and phenotypic evaluation of the IR64 population; and to the USDA-ARS Beaumont Rice Research Unit, Beaumont, TX for phenotypic evaluation of the Jefferson population.

We are grateful to Junjian Ni for the curation of QTLs in the Gramene database and for contributing to the development of Fig. 3; to Lois Swales for formatting the manuscript and creating figures from rough sketches; to all the many scientists and staff in the national breeding programs and in the McCouch lab without whose help and dedication we could not have developed the populations, collected the phenotypic data or done the fine-mapping that has been so critical to the success of these projects.

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Correspondence to Susan R. McCouch.

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McCouch, S.R., Sweeney, M., Li, J. et al. Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa . Euphytica 154, 317–339 (2007). https://doi.org/10.1007/s10681-006-9210-8

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