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Knowledge of rice (Oryza sativa L.) genes and various DNA markers can be used in genomic breeding programs aimed at developing improved elite rice cultivars. We used an efficient genomic breeding approach to pyramid four resistance genes (Pi2, Xa23, Bph14, and Bph15) in the popular photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice line Feng39S. We performed foreground selection for the target genes, followed by recombinant selection and background selection. This process reduced the sizes of the genomic segments harboring the target genes (566.8 kb for Pi2, 1143.9 kb for Xa23, 774.7 kb for Bph14, and 1574.9 kb for Bph15) and accelerated the recovery of the recurrent parent genome to proportions ranging from 98.77% to 99.16%, thus resulting in four near-isogenic lines. To assemble the four resistance genes in Feng39S, we performed a double-way cross combined with foreground and background selection to generate two improved lines of Feng39S (Pi2 + Xa23 + Bph14 + Bph15) with a recurrent parent genome recovery of 98.98%. The two lines showed agronomic performance, grain quality, and fertility–sterility transition characteristics similar to those of the original Feng39S line. The newly developed PTGMS lines and corresponding hybrid combinations were resistant to various field blast isolates and seven representative isolates of bacterial blight. At the seedling stage, the lines also showed resistance against brown planthopper. This study provides an efficient and accurate genomic breeding approach for introducing desirable traits into PTGMS lines.

Abstract Background Rice blast caused by Magnaporthe oryzae is one of the most widespread biotic constraints that threaten rice production. Using major resistance genes for rice blast resistance improvement is considered to be an efficient and technically feasible approach to achieve optimal grain yield. Results We report here the introgression of the broad-spectrum blast resistance gene Pi2 into the genetic background of an elite PTGMS line, Feng39S, for enhancing it and its derived hybrid blast resistance through marker-assisted backcrossing (MABC) coupled with genomics-based background selection. Two PTGMS lines, designated as DB16206–34 and DB16206–38, stacking homozygous Pi2 were selected, and their genetic background had recurrent parent genome recovery of 99.67% detected by the SNP array RICE6K. DB16206–34 and DB16206–38 had high resistance frequency, with an average of 94.7%, when infected with 57 blast isolates over 2 years, and the resistance frequency of their derived hybrids ranged from 68.2% to 95.5% under inoculation of 22 blast isolates. The evaluation of results under natural blast epidemic field conditions showed that the selected PTGMS lines and their derived hybrids were resistant against leaf and neck blast. The characterizations of the critical temperature point of fertility-sterility alternation of the selected PTGMS lines, yield, main agronomic traits, and rice quality of the selected PTGMS lines and their hybrids were identical to those of the recurrent parent and its hybrids. DB16206–34/9311 or DB16206–38/9311 can be used as a blast-resistant version to replace the popular hybrid Fengliangyou 4. Likewise, DB16206–34/FXH No.1 or DB16206–38/FXH No.1 can also be used as a blast-resistant version to replace another popular hybrid Fengliangyou Xiang 1. Conclusions Our evaluation is the first successful case to apply MABC with genomics-based background selection to improve the blast resistance of PTGMS lines for two-line hybrid rice breeding.

Abstract Background Breeding two-line hybrid rice with disease resistance is an effective approach to stabilize rice yield in commercial rice production of China. Results We improved the blast and bacterial blight resistance of Guangzhan63-4S, an elite photoperiod- and thermo-sensitive male sterile (P/TGMS) line widely used in two-line hybrid rice, by introducing the R genes Pi2 and Xa7 conferring resistance to rice blast and bacterial blight, respectively. Through the backcrossing and gene pyramiding breeding coupled with molecular marker-assisted selection, a new P/TGMS line Hua1228S carrying Pi2, Xa7, and tms5 was developed. Based on 200,000 SNP markers by next-generation sequencing, Hua1228S covered 87.6% of the recurrent genome, as well as 4.5% of the donor genome from VE6219 and 7.9% from YR7029–39. When infected with seven tested Xanthomonas oryzae pv. oryzae strains, Hua1228S conferred high resistance (0 level) to six bacterial blight strains. Moreover, Hua1228S showed broad-spectrum resistance to rice blast isolates with a high resistance frequency of 90.91%. High levels of resistance to leaf blast and neck blast were observed under heavy disease pressure in natural field. Importantly, Hua1228S showed identical fertility-sterility alteration pattern to Guangzhan63-4S. Thus, two hybrid combinations Hua Liangyou 2821 and Hua Liangyou 284 derived from Hua1228S exhibited enhanced resistance and higher yield compared with the control variety Feng Liangyou 4. Conclusions These results indicate that Hua1228S has tremendous potentiality to increase and stabilize the rice yield, through the introgression of two R genes by marker-assisted selection strategy.