An effective strategy for fertility improvement of indica-japonica hybrid rice by pyramiding S5-n, f5-n, and pf12-j


Though inter-subspecific hybrids from indica and japonica rice have gained great success for yield increases over the recent decade, there are severe sterility problems in such hybrids. To overcome hybrid sterility, we previously obtained the line PL-(S5-n + f5-n) in the genetic background of an elite indica restorer line 9311, via breeding strategy for construction of wide compatibility line, which was proven to be an effective strategy in improving the seed setting rate of indica-japonica hybrid rice. Here, a novel strategy for developing japonica-compatible indica lines was employed by introducing the japonica allele pf12-j into 9311. The obtained NIL-(pf12-j) could significantly improve pollen and embryo-sac fertility by 29.7% and 28.6% in indica-japonica hybrids, thus leading to 20.9% improvement of spikelet fertility. In addition, we achieved the pyramiding line PL-(S5-n + f5-n + pf12-j) by a combinational strategy using both wide compatibility line and japonica-compatible indica line. Compared to PL-(S5-n + f5-n) with 38.9% increase of spikelet fertility, the pyramiding line PL-(S5-n + f5-n + pf12-j) showed 49.7% increase of spikelet fertility, suggesting cumulative effect of wide compatibility alleles S5-n + f5-n and japonica allele pf12-j to shape normal fertility of inter-subspecies hybrid. Interestingly, these lines also showed compatibility to indica. Hence, our results demonstrate that the two strategies could be simultaneously applied for indica-japonica hybrid breeding, and S5-n + f5-n + pf12-j are the optional allelic combination for overcoming hybrid sterility. This finding will greatly enhance our understanding for breeding indica-japonica hybrid rice by molecular-assisted selection strategy.

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We are indebted to Dr. Lin Zhang from Yangzhou University for discussion.


This research was supported by grants from the National Key Research and Development Program of China (2016YFD0100803), the China Postdoctoral Science Foundation, and the Science and Technology Major Projects of Genetically Modified Organisms Breeding of China (High Yield Transgenic Rice Breeding, Grant No. 2016ZX08001004-001-007).

Author information




J.M., Y.O., and T.M. conceived and designed the experiments; J.M. and Y.L. performed the experiments, including artificial crossing, genotyping, and selecting for breeding in the field; J.M. and G. P. analyzed the data; S. K., G. P., Y.O., and J.M. wrote the paper.

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Correspondence to Tongmin Mou.

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Fig. S1

Background selection using the array RICE6K in the generations BC2F1, BC2F3, and MF2. Numbers above the each chromosome indicate chromosome numbers. The blue and red lines indicate the heterozygous alleles of both the parents and homozygous alleles of donor parent, respectively. Gray lines indicate recipient parent alleles. The reference genome is based on MSU Rice Genome Annotation Project Release 6. (TIF 9270 kb)

Table S1

Primer sequence of InDel markers used for foreground and background selections (DOCX 22 kb)

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Mi, J., Lei, Y., Kim, SR. et al. An effective strategy for fertility improvement of indica-japonica hybrid rice by pyramiding S5-n, f5-n, and pf12-j. Mol Breeding 39, 138 (2019).

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  • Oryza sativa L.
  • indica-japonica hybrids
  • Hybrid sterility
  • japonica-compatible indica
  • Wide-compatibility line