Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages

doi:10.1016/j.rsci.2023.06.004

Abstract

Abstract:

Germplasm resource innovation is a crucial factor for cultivar development, particularly within the context of hybrid rice breeding based on the three-line system. Quan 9311A, a cytoplasmic male sterile (CMS) line, has been successfully cultivated using rice restoration materials and extensively employed as a female parent in hybrid breeding program in China. This line was developed by crossing the CMS line Zhong 9A with a two-line restorer line 93-11, with the intention of eliminating the restoring ability of 93-11 while retaining the sterility gene WA352c from Zhong 9A. Quan 9311A effectively amalgamates the most favorable agronomic traits from both parental lines. In this study, the relationship between phenotypic characteristics and the known functional genes of Quan 9311A were analyzed using the rice genome navigation technology based on whole-genome sequencing. The findings revealed that Quan 9311A harbors multiple superior alleles from both 93-11 and Zhong 9A, providing exceptional agronomic traits that are unavailable in earlier CMS lines. Despite the removal of the fertility restorer gene Rf3 from 93-11, numerous chromosomal segments from 93-11 persist in the Quan 9311A genome. Furthermore, the hybrid rice Quanyousimiao (QYSM) and the restorer line Wushansimiao (WSSM) were used as examples to illustrate the important role of Quan 9311A as the female parent in heterosis. It was found that QYSM carries a great number of superior alleles, which accounts for its high grain yield and wide adaptability. These insights not only advanced the utilization of hybrid rice pairing groups but also provided guidance for future breeding endeavors. The study introduced innovative concepts to further integrate genomics with traditional breeding techniques. Ultimately, Quan 9311A signified a significant milestone in rice breeding technology, opening up novel avenues for hybrid rice development.

Key words: breeding, hybrid rice, phenotype, quantitative trait nucleotide locus, rice genome navigation system, whole-genome sequencing

Li Qianlong, Feng Qi, Wang Heqin, Kang Yunhai, Zhang Conghe, Du Ming, Zhang Yunhu, Wang Hui, Chen Jinjie, Han Bin, Fang Yu, Wang Ahong. Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages[J]. Rice Science, 2023, 30(6): 552-565.

Figures/Tables 7

References 44

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Trait	Chromosome	Gene	Alteration allele caused function ^a	93-11	Zhong 9A	Quan 9311A	WSSM	QYSM
HD	1	OsMADS51	Delaying HD	√	○	√	√	√
YC	2	Rf2	Fertility restoration	√	○	√	√	√
TQ	6	SSG6/OsACS6	Controls starch grain size	√	○	√	√	√
TQ	6	Waxy/GBSSI	Changing amylose content	√	○	√	√	√
HD	6	Hd1	Promoting HD under long days	√	○	√	○	√○
YC	6	DLT/GS6	Dwarf and low-tillering	√	○	√	○	√○
YC	7	BG2/GE	Increasing grain size	√	○	√	○	√○
OT	7	Sdr4	Controlling seed dormancy	√	○	√	○	√○
YC	8	GW8/OsSPL16	Increasing grain width	√	○	√	√	√
ABS	9	Sub1A	Submergence tolerance	√	○	√	√	√
BS	11	STV11	Increasing resistance to rice stripe virus	√	○	√	√	√
PA	1	D2/SMG11	Decreasing plant height	○	√	√	○	√○
YC	1	Rf3/OsMADS3	Fertility restoration	○	√	√	√	√
OT	3	BOC1	Callus browning	○	√	√	○	√○
BS	4	Xa1	Increasing blight resistance	○	√	√	○	√○
HD	7	Ghd7/Hd4	Promoting HD under long days	○	√	√	○	√○
BS	11	Xa3/Xa26	Increasing blight resistance	○	√	√	○	√○
YC	1	NOG1	Increasing grain number	√	√	○	√	√○
YC	1	LAX1	Increasing grain number	√	√	√	○	√○
BS	4	Pi21	Increasing blast resistance	○	√	○	√	√○
BS	4	Bph3	Increasing brown planthopper resistance	√	○	○	√	√○
YC	5	PTB1	Increasing seed-setting rate	√	○	○	√	√○
YC	5	GW5/GSE5	Increasing grain width	○	○	√	○	√○
BS	6	Bph29	Increasing brown planthopper resistance	√	○	○	√	√○
BS	6	Pi9	Increasing blast resistance	○	○	○	√○	√○
HD	7	Ghd7.1	Promoting HD under long days	√	√	√	○	√○
YC	8	Ghd8	Promoting HD under long days	○	○	○	√	√○
PA	8	TIG1	Smaller tiller angle	√	√	√	○	√○
BS	9	Pi5	Increasing blast resistance	○	○	○	√	√○
BS	9	Pi56	Increasing blast resistance	○	○	○	√	√○
YC	10	Rf4	Fertility restoration	○	○	○	√	√○
YC	10	Rf1b	Fertility restoration	○	○	○	√	√○
BS	11	Pi-ta	Increasing blast resistance	○	○	○	√	√○

Trait	Chromosome	Gene	Alteration allele caused function ^a	93-11	Zhong 9A	Quan 9311A	WSSM	QYSM
HD	1	OsMADS51	Delaying HD	√	○	√	√	√
YC	2	Rf2	Fertility restoration	√	○	√	√	√
TQ	6	SSG6/OsACS6	Controls starch grain size	√	○	√	√	√
TQ	6	Waxy/GBSSI	Changing amylose content	√	○	√	√	√
HD	6	Hd1	Promoting HD under long days	√	○	√	○	√○
YC	6	DLT/GS6	Dwarf and low-tillering	√	○	√	○	√○
YC	7	BG2/GE	Increasing grain size	√	○	√	○	√○
OT	7	Sdr4	Controlling seed dormancy	√	○	√	○	√○
YC	8	GW8/OsSPL16	Increasing grain width	√	○	√	√	√
ABS	9	Sub1A	Submergence tolerance	√	○	√	√	√
BS	11	STV11	Increasing resistance to rice stripe virus	√	○	√	√	√
PA	1	D2/SMG11	Decreasing plant height	○	√	√	○	√○
YC	1	Rf3/OsMADS3	Fertility restoration	○	√	√	√	√
OT	3	BOC1	Callus browning	○	√	√	○	√○
BS	4	Xa1	Increasing blight resistance	○	√	√	○	√○
HD	7	Ghd7/Hd4	Promoting HD under long days	○	√	√	○	√○
BS	11	Xa3/Xa26	Increasing blight resistance	○	√	√	○	√○
YC	1	NOG1	Increasing grain number	√	√	○	√	√○
YC	1	LAX1	Increasing grain number	√	√	√	○	√○
BS	4	Pi21	Increasing blast resistance	○	√	○	√	√○
BS	4	Bph3	Increasing brown planthopper resistance	√	○	○	√	√○
YC	5	PTB1	Increasing seed-setting rate	√	○	○	√	√○
YC	5	GW5/GSE5	Increasing grain width	○	○	√	○	√○
BS	6	Bph29	Increasing brown planthopper resistance	√	○	○	√	√○
BS	6	Pi9	Increasing blast resistance	○	○	○	√○	√○
HD	7	Ghd7.1	Promoting HD under long days	√	√	√	○	√○
YC	8	Ghd8	Promoting HD under long days	○	○	○	√	√○
PA	8	TIG1	Smaller tiller angle	√	√	√	○	√○
BS	9	Pi5	Increasing blast resistance	○	○	○	√	√○
BS	9	Pi56	Increasing blast resistance	○	○	○	√	√○
YC	10	Rf4	Fertility restoration	○	○	○	√	√○
YC	10	Rf1b	Fertility restoration	○	○	○	√	√○
BS	11	Pi-ta	Increasing blast resistance	○	○	○	√	√○

Ecological growing region	Cultivar	Plot yield (kg)	Blast resistance	Bacterial blight resistance	White backed planthopper resistance	Brown planthopper resistance	Grain quality
Early-season indica in South China	Quanyousimiao	10.77 ± 0.29	3.8	7	7	/	II
Early-season indica in South China	Tianyouhuazhan	10.49 ± 0.12	4.1	7	7	/	NO
Late-season indica in South China	Quanyousimiao	9.35 ± 0.19*	3.3*	7	9	/	II
Late-season indica in South China	Boyou 998	8.95 ± 0.10	7.1	7	9	/	NO
Mid-season indica in the upper reaches of the Yangtze River	Quanyousimiao	12.75 ± 0.15	3.3*	/	/	7	II
	F-You 498	12.55 ± 0.24	8.2	/	/	9	NO
Mid-season indica in the middle and lower reaches of the Yangtze River	Quanyousimiao	12.71 ± 0.04***	3.1***	5	/	7	III
	Fengliangyou 4	11.75 ± 0.15	7.2	9	/	9	NO

Ecological growing region	Cultivar	Plot yield (kg)	Blast resistance	Bacterial blight resistance	White backed planthopper resistance	Brown planthopper resistance	Grain quality
Early-season indica in South China	Quanyousimiao	10.77 ± 0.29	3.8	7	7	/	II
Early-season indica in South China	Tianyouhuazhan	10.49 ± 0.12	4.1	7	7	/	NO
Late-season indica in South China	Quanyousimiao	9.35 ± 0.19*	3.3*	7	9	/	II
Late-season indica in South China	Boyou 998	8.95 ± 0.10	7.1	7	9	/	NO
Mid-season indica in the upper reaches of the Yangtze River	Quanyousimiao	12.75 ± 0.15	3.3*	/	/	7	II
	F-You 498	12.55 ± 0.24	8.2	/	/	9	NO
Mid-season indica in the middle and lower reaches of the Yangtze River	Quanyousimiao	12.71 ± 0.04***	3.1***	5	/	7	III
	Fengliangyou 4	11.75 ± 0.15	7.2	9	/	9	NO