Identification and QTL Mapping of Rice Germplasm Resources with Low Amylose Content

doi:10.16819/j.1001-7216.2023.221109

Abstract

Abstract:

【Objective】 Amylose content (AC) is one of the most critical factors that determine the eating and cooking quality (ECQ) of rice. Therefore, it holds great significance to screen rice germplasm resources with low amylose content and elucidate the genetic control mechanism for breeding new varieties with excellent ECQ. 【Method】 We determined AC in 22 restorer lines of three-line hybrid rice and analyzed the QTL locus controlling amylose content using a double haploid (DH) population derived from the cross between Fan 38 and Shenhui 26. 【Result】 Two rice germplasms with low AC, Fan 32 and Fan 38, were discovered among the 22 restorer lines. Their AC was found to be 11.39%±0.01% and 10.58%±0.13%, respectively. In contrast to other low AC varieties carrying Wx^mp alleles, Fan 32 and Fan 38 carried Wx^b alleles. A total of five QTLs, namely qAC1.1, qAC1.2, qAC5, qAC6.1, and qAC6.2, related to amylose content, were identified in the DH population. Among these, qAC6.1 and qAC6.2 were consistently detectable over two years. qAC6.2 emerged as a major QTL, contributing to over 30% of the phenotypic variation. 【Conclusion】 These findings suggest that the low AC in Fan 38 is likely primarily controlled by the qAC6.2 locus. This establishes a foundation for further research into the regulatory mechanism of amylose synthesis in rice and for the development of new rice varieties with low AC using marker-assisted selection technology.

Key words: rice, eating and cooking quality, low amylose, Wx, QTL

摘要：

【目的】 稻米直链淀粉含量（amylose content, AC）是决定稻米食味品质最为重要的因素之一。筛选具有低直链淀粉含量的水稻种质资源并探究其遗传机制，对于选育具有优质食味品质的水稻新品种具有重要意义。【方法】 测定了22个三系杂交稻的恢复系品种的直链淀粉含量，并利用一个来源于恢复系繁38和申恢26杂交后代的双单倍体（Doubled haploid，DH）群体，分析了控制直链淀粉含量的QTL位点。【结果】 在22个恢复系中发现了2个低直链淀粉含量的品系繁32和繁38，其直链淀粉含量分别为11.39%±0.01%和10.58%±0.13%。与其他携带Wx^mp等位基因的低直链淀粉材料不同，繁32和繁38携带Wx^b等位基因。利用DH群体进行QTL分析，结果共检测到了5个控制直链淀粉含量的QTL 位点（qAC1.1、qAC1.2、qAC5、qAC6.1和qAC6.2）。其中qAC6.1和qAC6.2两年均能检测到。qAC6.2是一个主效QTL位点，其表型贡献率超过30%。【结论】 这些结果表明，繁38中低直链淀粉含量的表型可能主要由qAC6.2位点控制，可为深入研究水稻直链淀粉合成调节机理，及利用分子标记辅助选择技术选育低直链淀粉含量的水稻新品种奠定了基础。

关键词: 水稻, 食味品质, 低直链淀粉, Wx, QTL

XIE Kaizhen, ZHANG Jianming, CHENG Can, ZHOU Jihua, NIU Fuan, SUN Bin, ZHANG Anpeng, WEN Weijun, DAI Yuting, HU Qiyan, QIU Yue, CAO Liming, CHU Huangwei. Identification and QTL Mapping of Rice Germplasm Resources with Low Amylose Content[J]. Chinese Journal OF Rice Science, 2023, 37(6): 609-616.

谢开珍, 张建明, 程灿, 周继华, 牛付安, 孙滨, 张安鹏, 闻伟军, 代雨婷, 胡启琰, 邱越, 曹黎明, 储黄伟. 低直链淀粉含量水稻种质资源的鉴定与QTL定位分析[J]. 中国水稻科学, 2023, 37(6): 609-616.

Figures/Tables 9

References 29

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名称 Name	引物序列 Primer sequence	PCR产物 PCR product/bp
Wx-1F	CAATGCAACGTACGCCAAGCCGA	1911
Wx-1R	GTACACGACGACGGAGGGGAACCT	1911
Wx-2F	ACAACCACCATGTCGGCTCTCACCA	1687
Wx-2R	GGTGAGCACCCTGTCGGCTTCCA	1687
Wx-3F	GAGCTGACAACCCTGCACTACTGTCCA	2005
Wx-3R	AACCACTGGTTCATTCGTCTCTCATCCA	2005

名称 Name	引物序列 Primer sequence	PCR产物 PCR product/bp
Wx-1F	CAATGCAACGTACGCCAAGCCGA	1911
Wx-1R	GTACACGACGACGGAGGGGAACCT	1911
Wx-2F	ACAACCACCATGTCGGCTCTCACCA	1687
Wx-2R	GGTGAGCACCCTGTCGGCTTCCA	1687
Wx-3F	GAGCTGACAACCCTGCACTACTGTCCA	2005
Wx-3R	AACCACTGGTTCATTCGTCTCTCATCCA	2005

序号 Number	名称 Name	直链淀粉含量 Amylose content/%	序号 Number	名称 Name	直链淀粉含量 Amylose content/%
1	C45	15.43±0.30	12	繁35 Fan 35	13.86±0.00
2	繁1 Fan 1	14.50±0.04	13	繁38 Fan 38	10.58±0.13
3	繁3 Fan 3	18.12±0.34	14	繁42 Fan 42	16.54±0.13
4	繁6 Fan 6	17.82±0.21	15	繁43 Fan 43	16.80±0.21
5	繁15 Fan 15	17.61±0.34	16	申CR1 Shen CR1	15.69±0.21
6	繁16 Fan 16	18.46±0.17	17	申CR2 Shen CR2	9.64±0.04
7	繁17 Fan 17	17.95±0.09	18	申CR3 Shen CR3	18.50±0.04
8	繁24 Fan 24	15.82±0.17	19	申CR4 Shen CR4	10.20±0.09
9	申恢26 Shenhui 26	17.48±0.13	20	申CR5 Shen CR5	14.07±0.13
10	繁29 Fan 29	16.50±0.09	21	申CR6 Shen CR6	13.39±0.13
11	繁32 Fan32	11.39±0.00	22	申CR7 Shen CR7	14.33±0.13

序号 Number	名称 Name	直链淀粉含量 Amylose content/%	序号 Number	名称 Name	直链淀粉含量 Amylose content/%
1	C45	15.43±0.30	12	繁35 Fan 35	13.86±0.00
2	繁1 Fan 1	14.50±0.04	13	繁38 Fan 38	10.58±0.13
3	繁3 Fan 3	18.12±0.34	14	繁42 Fan 42	16.54±0.13
4	繁6 Fan 6	17.82±0.21	15	繁43 Fan 43	16.80±0.21
5	繁15 Fan 15	17.61±0.34	16	申CR1 Shen CR1	15.69±0.21
6	繁16 Fan 16	18.46±0.17	17	申CR2 Shen CR2	9.64±0.04
7	繁17 Fan 17	17.95±0.09	18	申CR3 Shen CR3	18.50±0.04
8	繁24 Fan 24	15.82±0.17	19	申CR4 Shen CR4	10.20±0.09
9	申恢26 Shenhui 26	17.48±0.13	20	申CR5 Shen CR5	14.07±0.13
10	繁29 Fan 29	16.50±0.09	21	申CR6 Shen CR6	13.39±0.13
11	繁32 Fan32	11.39±0.00	22	申CR7 Shen CR7	14.33±0.13

年份 Year	位点 Locus	染色体 Chromosome	遗传区间 Genetic range	物理区间 Physical range/bp	LOD值 LOD value	贡献率 PVE/%	加性效应 Additive effect/%
2020	qAC1.1	1	ch1-336—ch1-344	27 294 708—27 633 625	4.03	10.76	―0.64
	qAC6.1	6	ch6-42—ch6-44	4 722 458—5 120 945	5.00	13.81	0.73
	qAC6.2	6	ch6-143—ch6-200	7 984 061—9 393 696	11.04	33.80	1.14
2021	qAC1.2	1	ch1-357—ch1-359	27 973 902—28 090 735	4.75	9.24	―0.64
	qAC5	5	ch5-56—ch5-59	7 001 034—7 208 572	4.35	8.41	0.61
	qAC6.1	6	ch6-42—ch6-44	4 722 458—5 120 945	6.10	12.44	0.75
	qAC6.2	6	ch6-143—ch6-200	7 984 061—9 393 696	13.87	32.14	1.20