Sequence Variation of Functional Fragment in Pita Gene for Rice Blast Resistance in Yunnan Rice Landraces

doi:10.16819/j.1001-7216.2016.5188

Abstract

Abstract:

Identification and analysis of the variations of rice blast resistance gene sequence is the basis to dig into the genetic resources of the rice blast resistance. In this paper, 609 bases in the second code functional region of the rice blast resistance gene Pita were analyzed using 218 rice landraces from 56 counties of Yunnan Province. A total of 18 nucleotide variations were found in the sequence and the ORFs of 218 rice accessions were grouped into 46 haplotypes and 28 proteins types. Pita-H1 (17.89%), Pita-H2(29.82%) and Pita-H6(20.18%) were high-frequency types in Yunnan, while other types were at low frequency (0.46%-3.67%). So the advantage haplotypes in Yunnan were Pita-H1, Pita-H2 and Pita-H6 (totally 67.89%). A total of 61 rice landraces carrying the resistance gene Pita, the base functional site 2752 was G with the rate of 27.98%. The sequence of Pita in 39 resistance varieties was identical with the sequence obtained from the Vietnamese resistance variety Tetep. The distribution of resistance gene Pita in rice subspecies or ecotypes was unbalanced. The distribution frequency of indica was 35.06%, japonica 24.11%, rice 31.03%, upland rice 21.92%, no-glutinous rice 30.77%, glutinous rice 18.37%. The distribution of blast resistance gene Pita in Yunnan Province featured wide distribution and small concentration. Pita gene was detected in 36 counties of Yunnan Province. The distribution frequency in southern Yunnan was higher than other area. Moreover, some counties were of high distribution frequency. The resistance gene Pita was not detected in seven rice varieties growing over 2200 m elevation.

Key words: rice, Yunnan, blast, Pita

摘要：

稻瘟病抗性基因序列变异的分析与认识是挖掘水稻抗稻瘟病基因资源的基础。对来源于云南省56个县(市)的218份地方稻品种稻瘟病抗性基因Pita第二编码区功能位点区段的609个碱基进行了测序分析。结果表明,所有供试品种在此序列上有18个变异位点,存在46种DNA单倍型和28种蛋白类型,其中DNA单倍型Pita-H1、Pita-H2、 Pita-H6频率较高,三者比例分别为17.89%、29.82%、20.18%,合计67.89%,是云南的优势单倍型,而其他单倍型频率较低,频率0.46%~3.67%。携带Pita抗性基因(编码区第2752位功能位点碱基为G)的品种共61个,占供试材料的27.98%,其中39个品种(占63.93%)与越南抗性品种Tetep序列一致。Pita抗性基因在水稻各亚种和生态型中的分布是不平衡的,籼稻中的频率为35.06%,粳稻中为24.11%,水稻中31.03%,陆稻中21.92%,黏稻中30.77%,糯稻中18.37%。Pita抗性基因在云南省广泛分布,36县(市)检测到了Pita抗性基因,但南部地区频率高于其他地区,且有的县频率较高,呈小集中的特点,海拔2200m以上的7个品种未能检测到Pita抗性基因。

关键词: 稻, 云南, 稻瘟病, Pita

CLC Number:

Ji-qiong MA, Yi YANG, Yi-ding SUN, Yan-yan WANG, Ming-hui XU. Sequence Variation of Functional Fragment in Pita Gene for Rice Blast Resistance in Yunnan Rice Landraces[J]. Chinese Journal OF Rice Science, 2016, 30(3): 265-272.

马继琼, 杨奕, 孙一丁, 王炎炎, 许明辉. 云南地方水稻品种抗稻瘟病基因Pita功能区段序列变异分析[J]. 中国水稻科学, 2016, 30(3): 265-272.

Figures/Tables 6

References 22

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单倍型 Haplotype	品种数 No. of accessions	比例 Percentage /%	2184	2249	2283	2291	2354	2373	2388	2395	2402	2466	2477	2495	2575	2584	2715	2726	2752^*	2766
Tetep			T	T	A	C	C	G	A	C	T	T	C	C	C	G	C	C	G	A
日本晴Nipponbare			.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.
H1	39	17.89	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H2	65	29.82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.
H3	3	1.38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.
H4	8	3.67	.	.	.	.	.	.		T	.	.	.	.	.	.	.	.	.	.
H5	8	3.67	.	.	.	.	.	.		T	.	.	.	.	.	.	.	.	T	.
H6	44	20.18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	G
H7	7	3.21	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	T	.
H8	1	0.46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	A	.	.
H9	1	0.46	.	.	.	.	.	.	.	T	.	.	.	.	T	.	.	.	.	.
H10	3	1.38	.	.	.	.	.	.	G	T	.	.	.	.	.	.	.	.	T	G
H11	2	0.92	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	A	T	G
H12	1	0.46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	T	.
H13	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	A	.	.
H14	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	.	.	.	A	.	.
H15	1	0.46	C	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	T	G
H16	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	.	A	T	.
H17	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	.
H18	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	.	.
H19	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	.	.
H20	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	A	T	G
H21	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H22	1	0.46	C	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	.	.
H23	1	0.46	C	.	.	.	.	.	G	T	C	.	.	.	T	.	.	.	.	.
H24	1	0.46	.	.	.	.	.	.	.	T	.	.	.	.	T	.	.	.	T	.
H25	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	.
H26	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	.	.	.	.	T	G
H27	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	.	T	G
H28	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	T	.
H29	2	0.92	C	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	T	.
H30	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	T	G
H31	1	0.46	.	C	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H32	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	.	.	G	.	T	G
H33	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H34	1	0.46	C	C	.	.	.	.	G	T	.	C	.	.	T	.	.	.	.	.
H35	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	T	.
H36	1	0.46	C	C	.	.	.	.	G	T	.	.	.	.	T	C	.	.	T	.
H37	2	0.92	C	.	.	.	.	C	G	T	C	.	.	.	T	C	.	.	T	.
H38	1	0.46	C	.	.	T	.	C	G	T	.	.	.	.	T	.	.	.	T	G
H39	1	0.46	C	C	.	.	.	C	G	T	.	C	.	.	T	.	.	.	T	G
H40	1	0.46	C	.	.	T	.	C	G	T	.	C	.	.	T	C	.	.	T	G
H41	1	0.46	C	.	T	.	T	C	G	T	.	.	G	.	T	.	.	.	T	G
H42	1	0.46	C	.	.	.	.	C	G	T	.	C	G	A	T	C	.	A	.	.
H43	1	0.46	C	C	.	.	.	C	G	T	.	C	G	A	T	.	G	A	.	.
H44	1	0.46	C	C	.	.	.	C	G	T	C	C	G	A	T	C	.	.	T	.
H45	1	0.46	C	.	T	T	T	C	G	T	C	C	.	A	T	C	.	.	T	.
H46	1	0.46	C	C	T	T	T	C	G	T	C	C	G	.	T	.	.	.	T	G
合计	218	100

单倍型 Haplotype	品种数 No. of accessions	比例 Percentage /%	2184	2249	2283	2291	2354	2373	2388	2395	2402	2466	2477	2495	2575	2584	2715	2726	2752^*	2766
Tetep			T	T	A	C	C	G	A	C	T	T	C	C	C	G	C	C	G	A
日本晴Nipponbare			.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.
H1	39	17.89	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
H2	65	29.82	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.
H3	3	1.38	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.
H4	8	3.67	.	.	.	.	.	.		T	.	.	.	.	.	.	.	.	.	.
H5	8	3.67	.	.	.	.	.	.		T	.	.	.	.	.	.	.	.	T	.
H6	44	20.18	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	G
H7	7	3.21	.	.	.	.	.	.	.		.	.	.	.	.	.	.	.	T	.
H8	1	0.46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	A	.	.
H9	1	0.46	.	.	.	.	.	.	.	T	.	.	.	.	T	.	.	.	.	.
H10	3	1.38	.	.	.	.	.	.	G	T	.	.	.	.	.	.	.	.	T	G
H11	2	0.92	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	A	T	G
H12	1	0.46	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	T	.
H13	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	A	.	.
H14	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	.	.	.	A	.	.
H15	1	0.46	C	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	T	G
H16	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	.	A	T	.
H17	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	.
H18	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	.	.
H19	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	.	.
H20	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	A	T	G
H21	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H22	1	0.46	C	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	.	.
H23	1	0.46	C	.	.	.	.	.	G	T	C	.	.	.	T	.	.	.	.	.
H24	1	0.46	.	.	.	.	.	.	.	T	.	.	.	.	T	.	.	.	T	.
H25	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	.
H26	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	.	.	.	.	T	G
H27	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	.	.	G	.	T	G
H28	1	0.46	.	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	T	.
H29	2	0.92	C	.	.	.	.	C	G	T	.	.	.	.	T	.	.	.	T	.
H30	1	0.46	.	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	T	G
H31	1	0.46	.	C	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H32	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	.	.	G	.	T	G
H33	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	.	T	G
H34	1	0.46	C	C	.	.	.	.	G	T	.	C	.	.	T	.	.	.	.	.
H35	1	0.46	C	.	.	.	.	.	G	T	.	.	.	.	T	.	.	A	T	.
H36	1	0.46	C	C	.	.	.	.	G	T	.	.	.	.	T	C	.	.	T	.
H37	2	0.92	C	.	.	.	.	C	G	T	C	.	.	.	T	C	.	.	T	.
H38	1	0.46	C	.	.	T	.	C	G	T	.	.	.	.	T	.	.	.	T	G
H39	1	0.46	C	C	.	.	.	C	G	T	.	C	.	.	T	.	.	.	T	G
H40	1	0.46	C	.	.	T	.	C	G	T	.	C	.	.	T	C	.	.	T	G
H41	1	0.46	C	.	T	.	T	C	G	T	.	.	G	.	T	.	.	.	T	G
H42	1	0.46	C	.	.	.	.	C	G	T	.	C	G	A	T	C	.	A	.	.
H43	1	0.46	C	C	.	.	.	C	G	T	.	C	G	A	T	.	G	A	.	.
H44	1	0.46	C	C	.	.	.	C	G	T	C	C	G	A	T	C	.	.	T	.
H45	1	0.46	C	.	T	T	T	C	G	T	C	C	.	A	T	C	.	.	T	.
H46	1	0.46	C	C	T	T	T	C	G	T	C	C	G	.	T	.	.	.	T	G
合计	218	100

蛋白类型 Protein type	DNA单倍型 Haplotypes	750	761	764	785	791	801	826	832	859	862	905	909	918^*
	Tetep	L	R	A	T	M	F	S	T	L	D	S	S	A
	日本晴Nipponbare	.	.	.	.	.	.	.	.	.	.	.	.	S
Pita-p1	Pita-H1, Pita-H4	.	.	.	.	.	.	.	.	.	.	.	.	.
Pita-p2	Pita-H2, Pita-H5, Pita-H 6, Pita-H7, Pita-H10, Pita-H15, Pita-H26	.	.	.	.	.	.	.	.	.	.	.	.	S
Pita-p3	Pita-H3	.	.	.	.	.	.	.	.	.	.	.	Y	.
Pita-p4	Pita-H9	.	.	.	.	.	.	.	.	F	.	.	.	.
Pita-p5	Pita-H11, Pita-H16	.	.	.	.	.	.	.	.	.	.	.	Y	S
Pita-p6	Pita-H8, Pita-H13	.	.	.	.	.	.	.	.	.	.	R	Y	.
Pita-p7	Pita-H12, Pita-H27, Pita-H32	.	.	.	.	.	.	.	.	.	.	R	.	S
Pita-p8	Pita-H17, Pita-H21, Pita-H24, Pita-H25, Pita-H33	.	.	.	.	.	.	.	.	F	.	.	.	S
Pita-p9	Pita-H18	.	.	.	.	.	.	.	.	F	.	.	Y	.
Pita-p10	Pita-H23	.	.	.	.	.	S	.	.	F	.	.	.	.
Pita-p11	Pita-H14	.	.	.	.	I	.	.	.	.	.	.	Y	.
Pita-p12	Pita-H19, Pita-H22	.	.	.	.	I	.	.	.	F	.	.	.	.
Pita-p13	Pita-H34	P	.	.	.	.	.	.	.	F	.	.	.	.
Pita-p14	Pita-H20	.	.	.	.	.	.	.	T	.	.	R	Y	S
Pita-p15	Pita-H30, Pita-H35	.	.	.	.	.	.	.	T	F	.	.	Y	S
Pita-p16	Pita-H28, Pita-H29	.	.	.	.	I	.	.	T	F	.	.	.	S
Pita-p17	Pita-H31	P	.	.	.	.	.	.	T	F	.	.	.	S
Pita-p18	Pita-H36	P	.	.	.	.	.	.	T	F	H	.	.	S
Pita-p19	Pita-H39	P	.	.	.	I	.	.	T	F	.	.	.	S
Pita-p20	Pita-H38	.	.	V	.	I	.	.	T	F	.	.	.	S
Pita-p21	Pita-H37	.	.	.	.	I	S	.	T	F	H	.	.	S
Pita-p22	Pita-H40	.	.	V	.	I	.	.	T	F	H	.	.	S
Pita-p23	Pita-H41	.	S	.	I	I	.	C	T	F	.	.	.	S
Pita-p24	Pita-H42	.	.	.	.	I	.	C	N	F	H	.	Y	.
Pita-p25	Pita-H43	P	.	.	.	I	.	C	N	F	.	R	Y	.
Pita-p26	Pita-H44	P	.	.	.	I	S	C	N	F	H	.	.	S
Pita-p27	Pita-H45	.	S	V	I	I	S	.	N	F	H	.	.	S
Pita-p28	Pita-H46	P	S	V	I	I	S	C	T	F	.	.	.	S

蛋白类型 Protein type	DNA单倍型 Haplotypes	750	761	764	785	791	801	826	832	859	862	905	909	918^*
	Tetep	L	R	A	T	M	F	S	T	L	D	S	S	A
	日本晴Nipponbare	.	.	.	.	.	.	.	.	.	.	.	.	S
Pita-p1	Pita-H1, Pita-H4	.	.	.	.	.	.	.	.	.	.	.	.	.
Pita-p2	Pita-H2, Pita-H5, Pita-H 6, Pita-H7, Pita-H10, Pita-H15, Pita-H26	.	.	.	.	.	.	.	.	.	.	.	.	S
Pita-p3	Pita-H3	.	.	.	.	.	.	.	.	.	.	.	Y	.
Pita-p4	Pita-H9	.	.	.	.	.	.	.	.	F	.	.	.	.
Pita-p5	Pita-H11, Pita-H16	.	.	.	.	.	.	.	.	.	.	.	Y	S
Pita-p6	Pita-H8, Pita-H13	.	.	.	.	.	.	.	.	.	.	R	Y	.
Pita-p7	Pita-H12, Pita-H27, Pita-H32	.	.	.	.	.	.	.	.	.	.	R	.	S
Pita-p8	Pita-H17, Pita-H21, Pita-H24, Pita-H25, Pita-H33	.	.	.	.	.	.	.	.	F	.	.	.	S
Pita-p9	Pita-H18	.	.	.	.	.	.	.	.	F	.	.	Y	.
Pita-p10	Pita-H23	.	.	.	.	.	S	.	.	F	.	.	.	.
Pita-p11	Pita-H14	.	.	.	.	I	.	.	.	.	.	.	Y	.
Pita-p12	Pita-H19, Pita-H22	.	.	.	.	I	.	.	.	F	.	.	.	.
Pita-p13	Pita-H34	P	.	.	.	.	.	.	.	F	.	.	.	.
Pita-p14	Pita-H20	.	.	.	.	.	.	.	T	.	.	R	Y	S
Pita-p15	Pita-H30, Pita-H35	.	.	.	.	.	.	.	T	F	.	.	Y	S
Pita-p16	Pita-H28, Pita-H29	.	.	.	.	I	.	.	T	F	.	.	.	S
Pita-p17	Pita-H31	P	.	.	.	.	.	.	T	F	.	.	.	S
Pita-p18	Pita-H36	P	.	.	.	.	.	.	T	F	H	.	.	S
Pita-p19	Pita-H39	P	.	.	.	I	.	.	T	F	.	.	.	S
Pita-p20	Pita-H38	.	.	V	.	I	.	.	T	F	.	.	.	S
Pita-p21	Pita-H37	.	.	.	.	I	S	.	T	F	H	.	.	S
Pita-p22	Pita-H40	.	.	V	.	I	.	.	T	F	H	.	.	S
Pita-p23	Pita-H41	.	S	.	I	I	.	C	T	F	.	.	.	S
Pita-p24	Pita-H42	.	.	.	.	I	.	C	N	F	H	.	Y	.
Pita-p25	Pita-H43	P	.	.	.	I	.	C	N	F	.	R	Y	.
Pita-p26	Pita-H44	P	.	.	.	I	S	C	N	F	H	.	.	S
Pita-p27	Pita-H45	.	S	V	I	I	S	.	N	F	H	.	.	S
Pita-p28	Pita-H46	P	S	V	I	I	S	C	T	F	.	.	.	S

地点 Location	材料数 No. of accessions	抗性基因数 No. of resistance genes	频率 Frequency /%	地点 Location	材料数 No. of accessions	抗性基因数 No. of resistance genes	频率 Frequency /%
西双版纳州Xishuangbanna	21	8	38.10	保山市Baoshan	14	5	35.58
勐腊县 Mengla	2	0		腾冲县 Tengchong	7	2
勐海县 Menghai	11	2		昌宁县 Changning	2	1
景洪市Jinghong	8	3		龙陵县 Longling	2	1
普洱市Pu'er	52	17	32.69	隆阳区Longyang	3	1
孟连县 Menglian	9	3		玉溪市 Yuxi	13	3	23.08
澜沧县 Lancang	8	1		新平县 Xinping	8	2
西盟县 Ximeng	5	3		峨山县 Eshan	2	1
江城县 Jiangcheng	5	1		江川县 Jiangchuan	2	0
宁洱县 Ning’er	3	1		易门县 Yimen	1	0
墨江县 Mojiang	21	8		昆明市Kunming	2	1	50.00
景东县 Jingdong	1	0		富民县 Fumin	2	1
红河州 Honghe	16	6	37.50	曲靖市Qujing	3	1	33.33
金平县 Jinping	4	2		富源县 Fuyuan	1	0
屏边县 Pingbian	7	2		师宗县 Shizong	1	0
红河县 Honghe	1	1		麒麟区Qilin	1	1
开远市Kaiyuan	3	1		昭通市Zhaotong	13	4	30.77
弥勒县 Mile	1	0		巧家县 Qiaojia	1	0
文山州Wenshan	12	5	41.67	镇雄县 Zhenxiong	1	0
富宁县 Funing	1	0		彝良县 Yiliang	2	1
文山县 Wenshan	5	2		大关县 Daguan	3	0
广南县 Guangnan	6	3		盐津县 Yanjin	3	2
临沧市Lincang	36	6	16.67	威信县 Weixin	3	1
沧源县 Cangyuan	2	0		大理市Dali	3	1	33.33
双江县 Shuangjiang	2	1		大理市Dali	1	1
耿马县 Gengma	12	2		剑川县 Jianchuan	1	0
镇康县 Zhenkang	4	1		云龙县 Yunlong	1	0
临翔区Linxiang	1	0		丽江市 Lijiang	12	3	25.00
永德县 Yongde	10	1		永胜县 Yongsheng	3	3
云县 Yunxian	3	1		宁蒗县 Ninglang	3	0
凤庆县 Fengqing	2	0		玉龙县 Yulong	3	0
德宏州Dehong	20	4	20.00	华坪县 Huaping	3	0
瑞丽县 Ruili	6	1		迪庆州Diqing	1	0	0
芒市Mangshi	2	0		维西县 Weixi	1	0
陇川县 Longchuan	2	0		总计 Total	218	61	27.98
盈江县 Yingjiang	5	2
梁河县 Lianghe	5	1