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Isolation of a major genetic interaction associated with an extreme phenotype using assorted F2 populations in rice

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Detection of quantitative trait loci (QTLs) is dependent on the materials used in the analysis, as different combinations of parental materials may lead to different outcomes in QTLs for the same trait. On the other hand, an extreme phenotype associated with a given trait implies the potential involvement of a particular allele in various allelic interactions. A genetic factor associated with such an extreme phenotype may frequently be identified from various genetic populations consisting of different parental combinations. In this study, we attempted to uncover the genetic factor associated with extremely early heading date in rice, using various F2 populations. Heading date in rice has been characterized by at least 19 QTLs, from which 12 genes have been identified. A58, a rice strain with an extremely early heading date, is adapted to Hokkaido, the northernmost limit of rice cultivation. Six F2 populations derived from crosses of A58 with six other strains displayed a range of heading dates. Genotyping using 19 QTL markers indicated that the A58 allele of the Ghd7 locus was present in most F2 individuals exhibiting extremely early heading dates. This analysis also demonstrated that when the wild-type Ehd1 allele was present, the Ghd7 allele from A58 accelerated floral induction. The results of this study demonstrate that assorted F2 populations are valuable materials for comprehensive genotyping to explore major genetic factors for extreme phenotypes, and that this methodology is broadly applicable to other unknown traits.

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We are especially grateful to Ms. Takako Takeuchi (Research Faculty of Agriculture, Hokkaido University) for technical assistance and Drs. Kaworu Ebana and Masahiro Yano (QTL Genomic Research Center, National Institute of Agrobiological Sciences) for technical advice regarding the field data recording system. This research was supported by funding from the Scientific Technique Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry.

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Correspondence to Yuji Kishima.

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Ota, Y., Ishiguro, S., Aoyama, E. et al. Isolation of a major genetic interaction associated with an extreme phenotype using assorted F2 populations in rice. Mol Breeding 33, 997–1003 (2014). https://doi.org/10.1007/s11032-013-9998-6

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  • Assorted F2 populations
  • Extreme phenotype
  • Heading date
  • Ghd7
  • Ehd1
  • Rice