One of the most advantageous aspects of hybridization breeding is the ability to provide individuals with favorable gene combinations through recombination between genetically polymorphic parents. However, significant distortions of the transmission ratio, which are associated with reproductive barriers, are frequently observed in crosses between diverging cultivars in rice. Such segregation distortions often prevent the occurrence of favorable gene combinations in the hybrid progeny produced in rice breeding. Thus, it is very important to identify such factors and determine the chromosomal location of the genes in order to facilitate hybridization breeding between distantly related rice cultivars.

During the development of chromosome segment substitution lines (CSSLs) between 'Koshihikari' (a japonica cultivar) and 'Nona Bokra' (an indica cultivar), we observed segregants with poor growth in the self-pollinated progeny of BC₃F₁, in which a part of chromosome 2 was heterozygous in the genetic background of 'Koshihikari'. These plants eventually died before the heading stage in the paddy field.

To determine the inheritance mode for the genes responsible for the poor growth, we monitored the growth habit of 288 plants derived from one BC₃F₃ segregating population in a growth chamber. The segregation ratio of normal seedlings to those with poor growth was 213:75 (close to the expected ratio of 3:1, χ²= 0.68^ns), suggesting that the poor growth was controlled by a single recessive gene. The phenotype of these plants was characterized by the production of shorter leaves and leaf sheaths compared with those of normal segregants and by mortality during the seedling stage (Fig. 1).

In order to determine the chromosomal location of the gene for poor growth, we selected 248 plants thought to be recessive homozygous at the target locus from a total segregant population of 1056 plants (BC₃F₃). Using these plants, we performed linkage analysis using simple sequence repeat (SSR) and insertion/deletion (Indel) markers. We mapped the causal gene at a position between K/Nindel-1 and RM12463 on the short arm of chromosome 2 (Fig. 2) and no recombinant was observed between the causal gene and RM12453. So far, several genes have been identified for poor growth in the genetic analysis of progeny between distantly related cultivars (Fukuoka et al. 1998, 2005, Kubo and Yoshimura 2002). The chromosomal location of the gene identified in this study was different from those of genes previously reported. Therefore, the gene was tentatively designated as hbd1(hybrid breakdown 1).

Based on the results of the linkage analysis, plants homozygous for the 'Nona Bokra' allele at hbd1(t) are preferentially eliminated by mortality during the early seedling stage. However, the 'Nona Bokra' parental line did not itself show such a phenotype, suggesting that other gene(s) interact with the 'Nona Bokra' hbd1 (t) allele. It will be necessary to identify such gene(s) in order to deeply understand phenomena of hybrid breakdown.

References

Fukuoka S., H. Namai and K. Okuno, 1998. RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.). Theor. Appl. Genet. 97: 446-449.

Fukuoka S., M. C. V. Newingham, M. Ishtiaq, T. Nagamine, M. Kawase and K. Okuno, 2005. Identification and mapping of two new loci for hybrid breakdown in cultivated rice. RGN 22: 29-31.

Harushima Y., M. Yano, A. Shomura, M. Sato, T. Shimano, Y. Kuboki, T. Yamamoto, S. Y. Lin, B. A. Antonio, A. Parco, H. Kajiya, N. Huang, K. Yamamoto, Y. Nagamura, N. Kurata, G. S. Khush and T. Sasaki, 1998. A high density rice genetic linkage map with 2275 markers using a single F₂ population. Genet. 148: 479-494.

Kubo T. and A. Yoshimura, 2002. Genetic basis of hybrid breakdown in a Japonica/Indica cross of rice, Oryza sativa L. Theor. Appl. Genet. 105: 906-911.