Development of the pyramiding lines with strong culm genes derived from crosses among the SCM near isogenic lines in rice

Severe lodging has recurrently occurred at strong typhoon's hitting in recent climate change. The identification of quantitative trait loci (QTLs) and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To identify QTLs for lodging resistance, the tropical japonica line, Chugoku 117 and the improved indica variety, Habataki were selected as the donor parent, as these had thick and strong culms compared with the temperate japonica varieties in Japan such as Koshihikari. By using chromosome segment substitution lines (CSSLs) in which chromosome segments from the japonica variety were replaced to them from Habataki, we identified the QTLs for strong culm on chrs. 1 and 6, which were designated as STRONG CULM1 (SCM1) and STRONG CULM2 (SCM2), respectively. By using recombinant inbred lines (BILs) derived from a cross between Chugoku 117 and Koshihikari and introgression lines, we also identified the other QTLs for strong culm on chrs. 3 and 2, which were designated as STRONG CULM3 (SCM3) and STRONG CULM4 (SCM4), respectively. Candidate region of SCM1 includes Gn1 related to grain number. SCM2 was identical to APO1, a gene related to the control of panicle branch number, and SCM3 was identical to FC1, a strigolactone signaling associated gene, by performing fine mapping and positional cloning of these genes. To evaluate the effects of SCM1~SCM4 on lodging resistance, the Koshihiakri near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of Habataki (NIL-SCM1, NIL-SCM2) and the another Koshihikari NIL with the introgeressed SCM3 or SCM4 locus of Chugoku 117 (NIL-SCM3, NIL-SCM4) were developed. Then, we developed the pyramiding lines with double or triple combinations derived from step-by-step crosses among NIL-SCM1 NIL-SCM4. Triple pyramiding lines (NIL-SCM1+2+3, ~ NIL-SCM1+3+4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.