Genetic Diversity and Population Structure Analysis of Currently Cultivated Rice Landraces from Hani’s Terraced Fields in Yunnan Province

doi:10.3969/j.issn.1001-7216.2015.01.004

Abstract

Abstract:

In order to provide useful information for protection and utilization of rice landraces from Hani’s Terraced Fields, the genetic diversity and population structure of the currently cultivated lines were determined by using molecular makers. In this study, 118 SSR markers were used to detect the polymorphism of 47 local rice materials, and their genetic diversity and population structure were analyzed. There were a total of 255 alleles, ranging from 2 to 4 per locus, with the mean of 2.161. Genetic diversity index varied from 0.043 to 0.656 with an average of 0.303. The polymorphic information content (PIC) ranged from 0.042 to 0.583 with the average of 0.256. There are two highly polymorphic loci (PIC> 0.5) and 66 moderately polymorphic loci (0.25 <PIC <0.5). All the landraces could be divided into two groups, partial indica group and partial japonica group, based on the genetic similarity coefficient and mathematical model of population structure. There was no obvious regularity between clustering results and altitude, but partial indica red rice group had two clusters coming from different altitudes. In conclusion, currently cultivated rice in Hani’s Terraced Fields had a majority of landraces belonging to indica type, and lower genetic diversity than that in previous reports.

Key words: Oryza sativa L., Hani’s Terraced Fields, SSR marker, genetic diversity, population structure

摘要：

利用118对SSR分子标记对2012年云南哈尼梯田的47份水稻材料进行多态性检测,分析其遗传多样性,并利用Structure 2.3.4软件进行群体结构分析。结果显示,118对SSR标记共检测到255个等位变异,变幅为2~4个,平均每个标记2.161个。基因多样性指数变异范围为0.043~0.656,平均0.303。多态信息含量(PIC)变异范围为0.042~0.583,平均0.256。其中高度多态位点(PIC>0.5)有2个,中度多态位点(0.25<PIC<0.5)有66个;通过遗传相似系数及基于数学模型的群体结构分析均将供试材料分为偏籼和偏粳2个类群;聚类结果和海拔高度总体上没有明显规律,但偏籼类群中的偏籼红米亚群按海拔高低分别聚在一起。研究表明,云南哈尼梯田现有栽培水稻以偏籼水稻为主,但本研究估测的遗传多样性低于前人报道。

关键词: 水稻, 哈尼梯田, SSR标记, 遗传多样性, 群体结构

CLC Number:

Cheng-chen LIU, Fu-wei ZHAO, Xiao-xia WU, Chang-quan ZHANG, Kong-zhi ZHU, Da-yuan XUE, Jian-yong WU, Shao-wen HUANG, Xiao-ying XU, Yin-gen JIN, Qiao-quan LIU. Genetic Diversity and Population Structure Analysis of Currently Cultivated Rice Landraces from Hani’s Terraced Fields in Yunnan Province[J]. Chinese Journal OF Rice Science, 2015, 29(1): 28-34.

刘承晨, 赵富伟, 吴晓霞, 张昌泉, 朱孔志, 薛达元, 武建勇, 黄绍文, 徐小颖, 金银根, 刘巧泉. 云南哈尼梯田当前栽培水稻遗传多样性及群体结构分析[J]. 中国水稻科学, 2015, 29(1): 28-34.

Figures/Tables 5

References 27

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取样地点与海拔 Collecting site and altitude/m	栽培品种名称(海拔/m) Name of cultivated rice varieties(Altitude/m)
元阳县下新城 Xiaxincheng, Yuanyang County, Yunnan Province
1223-1494	△黄壳糯(1223), 菠萝谷(1249), ※大老粳(1265), ※黄壳(1394), ※黄壳-1(1475), ※老粳(1475), △老粳糯(1307), △杂交稻-抗(1295), ※小白壳(1475), 香谷糯(1413), 838新品种(1494), △紫糯(1258),※晚稻(1244),杂交稻-感(1295),△杂交糯(1390),※麻线谷(1475)
元阳县小新街 Xiaoxinjie, Yuanyang County, Yunnan Province
1200-1450	※红谷(1250),※炮竹谷(1300),△黄壳糯-1(1372),※老粳-1(1304),△老粳糯-1(1321),△滑糯(1238),杂交糯-1(1342),香谷糯-1(1200),△老粳糯-2(1450)
元阳县爱春村 Aichuncun, Yuanyang County, Yunnan Province
1400-1964	※黑壳谷(1948),※漫车(1964),※红米谷(1400),※车然,狗爪谷(1924),△团棵糯(1947)
元阳县全福庄 Quanfuzhuang, Yuanyang County, Yunnan Province
1300-1789	※观音山谷(1742),※大老粳-1(1250),△白糯(1789),△冷水糯(1771),△老粳糯-3,※早稻(1751),※黄草岭谷(1730),△冷水糯-1(1751),※车然-1(1751),△杂交糯-2,※花谷,红脚小老粳(1300),※刺竹谷(>1600),※绿叶谷(1600)
元阳县箐口村 Jingkoucun, Yuanyang County, Yunnan Province
1600	※早稻-1,※黄草岭谷-1

取样地点与海拔 Collecting site and altitude/m	栽培品种名称(海拔/m) Name of cultivated rice varieties(Altitude/m)
元阳县下新城 Xiaxincheng, Yuanyang County, Yunnan Province
1223-1494	△黄壳糯(1223), 菠萝谷(1249), ※大老粳(1265), ※黄壳(1394), ※黄壳-1(1475), ※老粳(1475), △老粳糯(1307), △杂交稻-抗(1295), ※小白壳(1475), 香谷糯(1413), 838新品种(1494), △紫糯(1258),※晚稻(1244),杂交稻-感(1295),△杂交糯(1390),※麻线谷(1475)
元阳县小新街 Xiaoxinjie, Yuanyang County, Yunnan Province
1200-1450	※红谷(1250),※炮竹谷(1300),△黄壳糯-1(1372),※老粳-1(1304),△老粳糯-1(1321),△滑糯(1238),杂交糯-1(1342),香谷糯-1(1200),△老粳糯-2(1450)
元阳县爱春村 Aichuncun, Yuanyang County, Yunnan Province
1400-1964	※黑壳谷(1948),※漫车(1964),※红米谷(1400),※车然,狗爪谷(1924),△团棵糯(1947)
元阳县全福庄 Quanfuzhuang, Yuanyang County, Yunnan Province
1300-1789	※观音山谷(1742),※大老粳-1(1250),△白糯(1789),△冷水糯(1771),△老粳糯-3,※早稻(1751),※黄草岭谷(1730),△冷水糯-1(1751),※车然-1(1751),△杂交糯-2,※花谷,红脚小老粳(1300),※刺竹谷(>1600),※绿叶谷(1600)
元阳县箐口村 Jingkoucun, Yuanyang County, Yunnan Province
1600	※早稻-1,※黄草岭谷-1

引物 Primer	等位基因数 Allele number	基因多样性指数 Gene diversity	多态信息含量 PIC	引物 Primer	等位基因数 Allele number	基因多样性指数 Gene diversity	多态信息含量 PIC
RI02451	2	0.089	0.085	RI02791	2	0.335	0.279
RI02500	2	0.287	0.246	CS0700	2	0.117	0.110
RI02271	2	0.449	0.348	CS0703	2	0.405	0.323
CS0111	3	0.326	0.299	SD705	2	0.287	0.246
RM129	3	0.294	0.262	R7M20	2	0.278	0.239
chr101	2	0.400	0.320	CS0714	3	0.608	0.531
chr0114	2	0.287	0.246	RP296	2	0.127	0.119
Chr0111	2	0.049	0.048	R7M30	2	0.310	0.262
CHR0108	2	0.287	0.246	RI04064	2	0.396	0.317
RI02611	2	0.369	0.301	RI03064	2	0.369	0.301
RI03843	2	0.303	0.257	CS0730	3	0.322	0.283
RI04506	2	0.043	0.042	RM337	2	0.210	0.188
R2M10	2	0.310	0.262	RI04271	2	0.078	0.075
R2M24	2	0.263	0.228	RI03207	2	0.282	0.243
RP54	2	0.320	0.269	CHR801	2	0.254	0.221
chr202	2	0.298	0.253	R8M23	2	0.085	0.081
S006	2	0.287	0.246	RI04234	2	0.198	0.178
RI03629	2	0.444	0.346	CHR804	2	0.282	0.243
R2M50	2	0.424	0.334	RP12	2	0.282	0.243
RI04851	2	0.355	0.292	CHR805	2	0.287	0.246
RM523	2	0.282	0.243	CS0826	2	0.282	0.243
R3M10	2	0.258	0.225	CHR901	2	0.335	0.279
RP135	2	0.429	0.337	RI05321	2	0.223	0.198
CS0312	2	0.292	0.250	RI05260	2	0.292	0.250
RP188	2	0.310	0.262	R9M20	2	0.474	0.362
R3M30	2	0.310	0.262	RP62	2	0.315	0.265
RM16	3	0.397	0.360	CHR905	2	0.292	0.250
R3M37	3	0.441	0.362	RI04946	2	0.247	0.217
CS0330	3	0.360	0.326	CHR902	2	0.282	0.243
RP185	3	0.267	0.248	CS0920	2	0.500	0.375
CHR404	2	0.049	0.048	RM205	2	0.083	0.080
S016	2	0.253	0.221	CS1002	2	0.364	0.298
CS0408	2	0.303	0.257	CHR1001	2	0.456	0.352
R4M17	2	0.268	0.232	CHR1006	3	0.656	0.583
R4M30	2	0.452	0.350	CHR1011	2	0.296	0.252
RP288	2	0.375	0.305	CHR1013	2	0.308	0.261
RP207	2	0.315	0.265	CHR1002	2	0.298	0.253
CHR405	2	0.298	0.253	CHR1020	2	0.287	0.246
chr406	2	0.141	0.131	RP249	3	0.273	0.252
RP68	2	0.081	0.078	RI00310	2	0.310	0.262
chr501	2	0.156	0.144	CHR1004	2	0.386	0.311
CHR523	2	0.287	0.246	CHR1110	2	0.320	0.269
CHR543	2	0.494	0.372	CS1104	2	0.400	0.320
CHR530	3	0.293	0.268	R11M17	2	0.497	0.373
R5M20	3	0.524	0.441	CS1107	2	0.500	0.375
RM18484	3	0.386	0.350	CHR1103	2	0.310	0.262
chr507	2	0.263	0.228	CHR1106	2	0.500	0.375
RP329	2	0.201	0.181	R11M40	2	0.454	0.351
chr508	2	0.308	0.261	RI01700	2	0.320	0.269
RM480	3	0.388	0.341	RI01666	2	0.340	0.282
Chr601N	2	0.284	0.244	RI05612	2	0.346	0.286
RI02672	2	0.161	0.148	RM247	3	0.343	0.297
RM276	4	0.542	0.480	CHR1211	2	0.085	0.081
CS0610	3	0.198	0.185	CHR1209	2	0.198	0.178
RI02678	3	0.217	0.205	CHR1201	2	0.243	0.213
R6M30	2	0.254	0.221	CHR1211	2	0.418	0.331
CS0622	2	0.081	0.078	CHR1215	2	0.254	0.221
RM454	2	0.085	0.081	CHR1207	2	0.194	0.175
RI04969	2	0.301	0.256	CHR1208	2	0.340	0.282

引物 Primer	等位基因数 Allele number	基因多样性指数 Gene diversity	多态信息含量 PIC	引物 Primer	等位基因数 Allele number	基因多样性指数 Gene diversity	多态信息含量 PIC
RI02451	2	0.089	0.085	RI02791	2	0.335	0.279
RI02500	2	0.287	0.246	CS0700	2	0.117	0.110
RI02271	2	0.449	0.348	CS0703	2	0.405	0.323
CS0111	3	0.326	0.299	SD705	2	0.287	0.246
RM129	3	0.294	0.262	R7M20	2	0.278	0.239
chr101	2	0.400	0.320	CS0714	3	0.608	0.531
chr0114	2	0.287	0.246	RP296	2	0.127	0.119
Chr0111	2	0.049	0.048	R7M30	2	0.310	0.262
CHR0108	2	0.287	0.246	RI04064	2	0.396	0.317
RI02611	2	0.369	0.301	RI03064	2	0.369	0.301
RI03843	2	0.303	0.257	CS0730	3	0.322	0.283
RI04506	2	0.043	0.042	RM337	2	0.210	0.188
R2M10	2	0.310	0.262	RI04271	2	0.078	0.075
R2M24	2	0.263	0.228	RI03207	2	0.282	0.243
RP54	2	0.320	0.269	CHR801	2	0.254	0.221
chr202	2	0.298	0.253	R8M23	2	0.085	0.081
S006	2	0.287	0.246	RI04234	2	0.198	0.178
RI03629	2	0.444	0.346	CHR804	2	0.282	0.243
R2M50	2	0.424	0.334	RP12	2	0.282	0.243
RI04851	2	0.355	0.292	CHR805	2	0.287	0.246
RM523	2	0.282	0.243	CS0826	2	0.282	0.243
R3M10	2	0.258	0.225	CHR901	2	0.335	0.279
RP135	2	0.429	0.337	RI05321	2	0.223	0.198
CS0312	2	0.292	0.250	RI05260	2	0.292	0.250
RP188	2	0.310	0.262	R9M20	2	0.474	0.362
R3M30	2	0.310	0.262	RP62	2	0.315	0.265
RM16	3	0.397	0.360	CHR905	2	0.292	0.250
R3M37	3	0.441	0.362	RI04946	2	0.247	0.217
CS0330	3	0.360	0.326	CHR902	2	0.282	0.243
RP185	3	0.267	0.248	CS0920	2	0.500	0.375
CHR404	2	0.049	0.048	RM205	2	0.083	0.080
S016	2	0.253	0.221	CS1002	2	0.364	0.298
CS0408	2	0.303	0.257	CHR1001	2	0.456	0.352
R4M17	2	0.268	0.232	CHR1006	3	0.656	0.583
R4M30	2	0.452	0.350	CHR1011	2	0.296	0.252
RP288	2	0.375	0.305	CHR1013	2	0.308	0.261
RP207	2	0.315	0.265	CHR1002	2	0.298	0.253
CHR405	2	0.298	0.253	CHR1020	2	0.287	0.246
chr406	2	0.141	0.131	RP249	3	0.273	0.252
RP68	2	0.081	0.078	RI00310	2	0.310	0.262
chr501	2	0.156	0.144	CHR1004	2	0.386	0.311
CHR523	2	0.287	0.246	CHR1110	2	0.320	0.269
CHR543	2	0.494	0.372	CS1104	2	0.400	0.320
CHR530	3	0.293	0.268	R11M17	2	0.497	0.373
R5M20	3	0.524	0.441	CS1107	2	0.500	0.375
RM18484	3	0.386	0.350	CHR1103	2	0.310	0.262
chr507	2	0.263	0.228	CHR1106	2	0.500	0.375
RP329	2	0.201	0.181	R11M40	2	0.454	0.351
chr508	2	0.308	0.261	RI01700	2	0.320	0.269
RM480	3	0.388	0.341	RI01666	2	0.340	0.282
Chr601N	2	0.284	0.244	RI05612	2	0.346	0.286
RI02672	2	0.161	0.148	RM247	3	0.343	0.297
RM276	4	0.542	0.480	CHR1211	2	0.085	0.081
CS0610	3	0.198	0.185	CHR1209	2	0.198	0.178
RI02678	3	0.217	0.205	CHR1201	2	0.243	0.213
R6M30	2	0.254	0.221	CHR1211	2	0.418	0.331
CS0622	2	0.081	0.078	CHR1215	2	0.254	0.221
RM454	2	0.085	0.081	CHR1207	2	0.194	0.175
RI04969	2	0.301	0.256	CHR1208	2	0.340	0.282