Validation of yield-enhancing quantitative trait loci from a low-yielding wild ancestor of rice

Ize Imai, Jennifer A. Kimball, Benjamin Conway, Kathleen M. Yeater, Susan R. McCouch, Anna McClung

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


A set of introgression lines (ILs) containing chromosomal segments from O. rufipogon (IRGC 105491), a wild relative of O. sativa, in the genetic background of an elite US variety, cv. Jefferson, was developed to confirm the performance of six yield-enhancing quantitative trait loci (QTL). Fifty BC3F3 ILs containing homozygous O. rufipogon introgressions at each of the target QTL regions, and as few background introgressions as possible, were selected for evaluation of yield and 14 yield-related traits in field studies conducted over 2 years at four locations in the southern USA. Performance of the IL families was compared with three commercial inbreds and one hybrid variety. IL families carrying introgressions from the low-yielding wild parent at the QTL yld2.1 and yld6.1 yielded 27.7 and 26.1 % more than Jefferson, respectively. IL yld2A, which possesses yld2.1, also performed well under alternate wetting and drying conditions in two field locations. After the first year of field trials, 10 of the top-performing BC3F4 families, representing five of the QTL targets, were genotyped with an Illumina 1,536 assay to define the size and location of the wild introgressions. BC3F4 families with the fewest background introgressions were backcrossed to Jefferson and selfed. The resulting BC4F2 families were screened with targeted single nucleotide polymorphism assays to identify individuals carrying homozygous introgressions across the target QTL. Twelve ILs, representing each of the six QTL targets, have been submitted to the Genetic Stocks Oryza Collection for studies on transgressive variation and as interspecific pre-breeding lines.

Original languageEnglish (US)
Pages (from-to)101-120
Number of pages20
JournalMolecular Breeding
Issue number1
StatePublished - Jun 2013

Bibliographical note

Funding Information:
Acknowledgments We thank Paul Doran, Hema Liyanage and Bob Shiels from Sequenom, Inc., for technical assistance; Shannon Moon and RiceTec, Inc., for collection of field data in Jonesboro and Alvin; Tony Beaty, Laduska Simpson, Sarah Hendrix, Bill Luebke and Curtis Kerns for yield trials at Stuttgart; Jodie Cammack, Kip Landry, Carl Henry, Piper Roberts and Jason Bonnette for yield trials at Beaumont; WenGui Yan and Tiffany Sookaserm for sheath blight and straighthead evaluations; Gen Onishi and Sandy Harrington for help with crossing and managing populations at Cornell University; collaborators in the Uniform Regional Rice Nursery for agronomic, grain quality, genetic markers, and biotic and abiotic stress data; and Cheryl Utter for formatting the manuscript. This study is funded by NSF-TV Plant Genome Research Program Award #0606461 and #1026555 and USDA-NIFA Award #2009-65300-05698.


  • Crop yield
  • Genetic analysis
  • Genotypes
  • Introgression lines
  • Near isogenic lines
  • Quantitative trait loci


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