东北春播区糜子核心种质及其DNA分子身份证构建

doi:10.3724/SP.J.1006.2024.34153

作物学报 ›› 2024, Vol. 50 ›› Issue (5): 1181-1192.doi: 10.3724/SP.J.1006.2024.34153

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

东北春播区糜子核心种质及其DNA分子身份证构建

丁艺冰¹^,²(), 辛旭霞², 冯智尊², 曹越², 郭娟², Dipak K SANTRA³, 王瑞云²^,^*(), 陈喜明¹^,⁴^,^*()

¹山西农业大学玉米研究所, 中国山西忻州 034000
²山西农业大学农学院, 中国山西太谷 030801
³内布拉斯加大学林肯分校农艺系小宗粮豆研究与推广中心, 美国内布拉斯加州斯克茨布拉夫 69361
⁴山西农业大学杂粮种质创新与分子育种山西省重点实验室, 中国山西太原 030000

收稿日期:2023-09-12 接受日期:2024-01-12 出版日期:2024-05-12 网络出版日期:2024-01-31
通讯作者: *陈喜明, E-mail: 516834898@qq.com; 王瑞云, E-mail: wry925@126.com
作者简介:E-mail: 2771284358@qq.com
基金资助:
山西农业大学杂粮种质创新与分子育种国家实验室(筹)项目(202204010910001);国家自然科学基金项目(31271791);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-06-14.5-A16);山西省现代农业产业技术体系建设专项资金项目(2023CYJSTX03-12);山西省重点研发项目(2022ZDYF110);山西农业大学杂粮种质创新与分子育种山西省重点实验室项目(K462202040);山西农业大学生物育种工程项目(YZGC069);山西农业大学农学院研究生教育改革项目(2023YJG05);山西省科技成果转化引导专项(201904D131056)

Core germplasm and DNA molecular identity card of proso millet in Northeast Spring sowing region in China

DING Yi-Bing¹^,²(), XIN Xu-Xia², FENG Zhi-Zun², CAO Yue², GUO Juan², Dipak K SANTRA³, WANG Rui-Yun²^,^*(), CHEN Xi-Ming¹^,⁴^,^*()

¹Corn Research Institute, Shanxi Agricultural University, Xinzhou 034000, Shanxi, China
²College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
³Panhandle Research and Extension Center, Department of Agronomy and Horticulture, University of Nebraska- Lincoln, Scottsbluff 69361, Nebraska, USA
⁴Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Taiyuan 030000, Shanxi, China

Received:2023-09-12 Accepted:2024-01-12 Published:2024-05-12 Published online:2024-01-31
Contact: *E-mail: 516834898@qq.com; E-mail: wry925@126.com
Supported by:
National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding(202204010910001);National Natural Science Foundation of China(31271791);China Agriculture Research System of MOF and MARA(CARS-06-14.5-A16);Special Fund for Construction of Modern Agricultural Industrial Technology System of Shanxi Province(2023CYJSTX03-12);Key Research & Development Project of Shanxi Province(2022ZDYF110);Shanxi Key Laboratory of Innovation and Molecular Breeding, Shanxi Agricultural University(K462202040);Biological Breeding Project of Shanxi Agricultural University(YZGC069);Graduate Education Reform Project of Agronomy College in Shanxi Agricultural University(2023YJG05);Shanxi Province Scientific and Technological Achievements Transformation and Guidance Project(201904D131056)

摘要/Abstract

摘要：

本研究以500份东北春播区糜子资源为材料, 利用169个SSR标记, 采用UPGMA聚类分组, 进行分层抽样, 构建核心种质, 同时应用ID Analysis 4.0软件构建分子身份证。利用等位基因数(Na)等遗传多样性衡量指标评估核心种质的遗传差异, 并利用PCOA分析核心种质。结果表明, 对169对SSR引物进行筛选, 发现30对多态性好, 利用30对SSR引物构建的糜子核心种质包含190份材料, 占全部种质的38%, 全部种质与核心种质的均检测出91个等位变异, 保留了100%等位基因; 有效等位基因数为2.2977~2.9975和2.2872~3.0173, 平均值分别为2.8198和2.8297; Shannon多样性指数为0.9532~1.0990和0.9535~1.1162, 平均值为1.0645和1.0667; 观测杂合度为0.3434~0.8037和0.3162~0.7849, 平均值为0.5399和0.5359; 期望杂合度为0.5654~0.6672和0.5645~0.6707, 平均值为0.6448和0.6473; Nei’s基因多样性指数为0.5648~0.6664和0.5628~0.6686, 平均值为0.6441和0.6452; 多态性信息含量为0.6657~0.8356和0.6493~0.8340, 平均值为0.7974和0.7944。全部种质与核心种质的分子标记的相关指标进行t检验, 结果无显著性差异, 且PCOA分析表明核心种质与全部种质具有相似的遗传多样性和群体结构, 同时发现8个SSR标记(RYW5、RYW8、RYW16、RYW28、RYW40、RYW53、RYW62和RYW67)可区分190份核心种质, 构建了东北糜子核心种质的分子身份证。

关键词: 糜子, 东北春播区, SSR, 核心种质, DNA分子身份证

Abstract:

In this study, 500 proso millet resources in Northeast Spring Sowing Region were used as the experimental materials, 169 SSR markers, UPGMA clustering, and stratified sampling were used to construct core germplasm, and ID Analysis 4.0 software was used to construct molecular identity card. The genetic diversity of the core collection was evaluated by genetic diversity metrics such as allele number (N_a), and the core collection was analyzed by PCOA. The results showed that 169 pairs of SSR primers were screened, and 30 pairs of SSR primers were found to have good polymorphism. The core collection of proso millet constructed by 30 pairs of SSR primers contained 190 materials, accounting for 38% of all germplasm. Ninety-one alleles were detected in all germplasm and core collection, and 100% alleles were retained. The number of effective alleles was 2.2977-2.9975 and 2.2872-3.0173, with an average of 2.8198 and 2.8297, respectively. The Shannon diversity index was 0.9532-1.0990 and 0.9535-1.1162, with an average of 1.0645 and 1.0667. The observed heterozygosity was 0.3434-0.8037 and 0.3162-0.7849, with an average of 0.5399 and 0.5359. The expected heterozygosity was 0.5654-0.6672 and 0.5645-0.6707, with an average of 0.6448 and 0.6473. Nei’s gene diversity index was 0.5648-0.6664 and 0.5628-0.6686, with an average of 0.6441 and 0.6452. The polymorphism information content was 0.6657-0.8356 and 0.6493-0.8340, with an average of 0.7974 and 0.7944. The results of t-test showed that there was no significant difference in the related indexes of molecular markers between all germplasm and core germplasm, and PCOA analysis showed that the core germplasm and all germplasm had similar genetic diversity and population structure. At the same time, 8 SSR markers (RYW5, RYW8, RYW16, RYW28, RYW40, RYW53, RYW62, and RYW67) were found to distinguish 190 core germplasms, and the molecular identity card of the core germplasms of Northeast proso millet was constructed, which providing a scientific basis for the efficient utilization and rapid traceability of proso millet germplasm.

Key words: Panicum miliaceum, the Northeast Spring sowing region, SSR, core collection, DNA molecular ID card

丁艺冰, 辛旭霞, 冯智尊, 曹越, 郭娟, Dipak K SANTRA, 王瑞云, 陈喜明. 东北春播区糜子核心种质及其DNA分子身份证构建[J]. 作物学报, 2024, 50(5): 1181-1192.

DING Yi-Bing, XIN Xu-Xia, FENG Zhi-Zun, CAO Yue, GUO Juan, Dipak K SANTRA, WANG Rui-Yun, CHEN Xi-Ming. Core germplasm and DNA molecular identity card of proso millet in Northeast Spring sowing region in China[J]. Acta Agronomica Sinica, 2024, 50(5): 1181-1192.

图/表 11

表1

表2

构建核心种质的30对SSR引物"

引物 Primer name	正向引物序列 Forward sequence (5′-3′)	反向引物序列 Reverse sequence (5′-3′)	退火温度 T_m (℃)	重复碱基 Repeat motif
RYW2	TTAGGGCTCTCCTGCATCC	CAGCGAGTTCACCGTCAAG	56.8	(CGAAGC)5
RYW3	GGAGGCGTGACAATAAAAC	GGCGTGAGGTGTTGTTTTT	52.5	(CTGCAA)5
RYW5	GACGATGCTCTTGACCTTGT	CACCGTGAAATGTCTCTGCT	55.0	(CCTTT)5
RYW6	AGCCGATTTGCTGTGGAGT	CTGCCTCCGATGAGTTGGT	57.4	(ACACC)5
RYW8	GGGTCAGAGAATACACAGCG	GTAGGGAAGGAGAAGTGGGT	55.9	(AATAG)5
RYW12	ACCATCCCAGCACAAACCA	TGCCTGAAGGAGAAGAGCG	57.5	(AGCT)5
RYW16	ATCTCCTCCGCCTTCTAACCC	TGGCAATGGTCGTACAAACT	56.7	(GAGC)5
RYW17	TCAGCTACTTCGAACGGC	GGATCATGCGATACATTTGG	53.0	(TTTC)5
RYW20	ACCTCTTGCCGCACACTAC	TTCTACATCCCCGAACCAC	56.2	(TTGG)6
RYW28	CCAAGGCTGAGCAGAAAGAT	ACAAGGTGAAACCCGAAGC	55.4	(AGGC)5
RYW29	CTTGATTTCTCACGCACCG	TGTCCAGCAGTAGTCGTTCCT	56.2	(GCAG)5
RYW30	TAGCCTTCTTTGCCACCACT	GCCCGTGATGATATTCGAC	54.9	(TTTC)5
RYW40	TGCTCTTCGGCTCTTCTCC	ATCAGCTCATCGTGACCCC	57.4	(CAGC)6
RYW42	AGACACCCTGGGCAACATC	CTGGACTGGGCTTCGTTCT	57.8	(GGCT)5
RYW43	GGAGATGCTTGCTTGGTTG	CAGGAATCGCAAGGAACAG	54.0	(GGAG)5
RYW47	TTGTTTTTGCTGCTGCCTC	TGCTGGACTTCTTTTTGCC	53.7	(GCCT)5
RYW50	CAAGGCAGATAGGGCAAGT	TCGTCTGCTGCTGGTTTGT	56.1	(GGAG)5
RYW52	AGTAGTCCTCCACCGCCAT	CTCTTCCTCGTTCTCGGCT	57.8	(TACC)5
RYW53	ATGCCTCCGATGTAGATGC	GCCGCCTTCTCTTCATTCT	54.9	(GAGG)5
RYW55	CTGGTGGTGGTAGTTAGCG	TTATGCCACCCACCGTAGC	56.9	(TAGC)5
RYW62	GTTTAGAGAGCAGGAGGCG	AGCCCTGTCCACCCTAATC	56.4	(GCTC)5
RYW67	GAAGGAAACGCACCAGAGT	TTGGGTTTGTGCTTGGAGT	54.9	(TGCG)5
RYW99	CGGAGTTCTTGGTGGCTT	GCGTTCGCCAAAGAGCAT	56.1	(CCA)5
RYW125	TTGACGACGACTGTGTGC	TGTTGGTGGAGTTGAGGAC	55.1	(GGC)5
RYW145	CTTTTTCTGCTGCTCCCT	TGATGCCATACCCAACTG	52.2	(GAC)6
RYW146	TGATGCTTCTTGGGTTCG	CGCCGTCCACTTCTGTAT	53.6	(GCG)6
RYW149	CAGGACTTGGGTGATTGC	GAGCGGAGGAGGAAACTA	53.7	(AGC)7
RYW156	TTTACAACCCTTCCCGCC	AGGACTTTCCGCCTCTACCC	57.5	(CCG)5
RYW158	GGTAGGGTTCAAGGTGGTT	CAGGCAATCTCTTCAGGC	54.0	(CCG)5
RYW164	AGACAGCCATTCAACCACG	CCATCTCCTCATCCACCA	54.6	(GA)6

表2

图1

图2

表3

种质资源与核心种质遗传参数的对比"

位点 Locus	N_a			N_e		I		H_o		H_e		Nei		PIC
位点 Locus	CC		EC	CC	EC	CC	EC	CC	EC	CC	EC	CC	EC	CC	EC
RYW2	3		3	2.8424	2.7698	1.0695	1.0561	0.4785	0.5023	0.6502	0.6397	0.6482	0.6390	0.8241	0.8202
RYW3	3		3	2.8456	2.8320	1.0705	1.0692	0.6785	0.7271	0.6506	0.6476	0.6486	0.6469	0.7663	0.7438
RYW5	3		3	2.9708	2.9804	1.0936	1.0953	0.3162	0.3434	0.6658	0.6655	0.6634	0.6645	0.7867	0.7830
RYW6	3		3	2.9285	2.9128	1.0864	1.0841	0.3791	0.3652	0.6607	0.6575	0.6585	0.6567	0.8213	0.8154
RYW8	3		3	2.7788	2.7895	1.0552	1.0576	0.4938	0.4635	0.6421	0.6423	0.6401	0.6415	0.7989	0.8133
RYW12	3		3	2.8112	2.7954	1.0654	1.0631	0.5875	0.5704	0.6463	0.6430	0.6443	0.6423	0.8100	0.8093
RYW16	3		3	2.7053	2.7785	1.0443	1.0562	0.3664	0.3610	0.6328	0.6410	0.6304	0.6401	0.7701	0.7703
RYW17	3		3	2.9691	2.9921	1.0933	1.0973	0.4908	0.5274	0.6652	0.6666	0.6632	0.6658	0.8340	0.8356
RYW20	3		3	2.9224	2.8151	1.0848	1.0634	0.4931	0.4558	0.6601	0.6456	0.6578	0.6448	0.8075	0.8130
RYW28	3		3	2.9102	2.8245	1.0828	1.0663	0.4522	0.4638	0.6587	0.6467	0.6566	0.6460	0.8227	0.8168
RYW29	3		3	2.8740	2.8909	1.0762	1.0803	0.5739	0.6388	0.6539	0.6548	0.6521	0.6541	0.7935	0.8021
RYW30	4		4	3.0173	2.9609	1.1162	1.0990	0.5380	0.5217	0.6707	0.6631	0.6686	0.6623	0.8307	0.8226
RYW40	3		3	2.7040	2.7078	1.0376	1.0385	0.6095	0.6147	0.6320	0.6314	0.6302	0.6307	0.7453	0.7762
RYW42	3		3	2.9503	2.9008	1.0904	1.0821	0.5944	0.6116	0.6629	0.6560	0.6610	0.6553	0.8119	0.8035
RYW43		3	3	2.5607	2.5420	1.0080	1.0029	0.6080	0.6122	0.6112	0.6073	0.6095	0.6066	0.7538	0.7616
RYW47		3	3	2.7607	2.7934	1.0534	1.0591	0.7849	0.8037	0.6395	0.6427	0.6378	0.6420	0.6493	0.6657
RYW50		3	3	2.9990	2.9975	1.0984	1.0982	0.5395	0.5205	0.6688	0.6672	0.6666	0.6664	0.8223	0.8245
RYW52		3	3	2.2872	2.2977	0.9535	0.9532	0.5868	0.5494	0.5645	0.5654	0.5628	0.5648	0.7468	0.7599
RYW53		3	3	2.9822	2.9776	1.0956	1.0949	0.4326	0.4820	0.6670	0.6651	0.6647	0.6642	0.7931	0.8051
RYW55		3	3	2.9655	2.9109	1.0927	1.0834	0.5385	0.5323	0.6649	0.6573	0.6628	0.6565	0.8253	0.8191
RYW62		3	3	2.7967	2.8045	1.0638	1.0651	0.6628	0.6645	0.6443	0.6441	0.6424	0.6434	0.7774	0.7773
RYW67		3	3	2.7732	2.8980	1.0596	1.0816	0.5148	0.5583	0.6413	0.6557	0.6394	0.6549	0.8114	0.8169
RYW99		3	3	2.4995	2.5108	1.0050	1.0073	0.4765	0.4834	0.6017	0.6024	0.5999	0.6017	0.7887	0.7958
RYW125		3	3	2.8868	2.8902	1.0796	1.0803	0.5723	0.5429	0.6556	0.6548	0.6536	0.6540	0.8132	0.8219
RYW145		3	3	2.9704	2.9767	1.0936	1.0946	0.6312	0.6320	0.6654	0.6649	0.6633	0.6641	0.8154	0.8223
RYW146		3	3	2.9161	2.9046	1.0841	1.0824	0.4324	0.3854	0.6593	0.6566	0.6571	0.6557	0.8156	0.8093
RYW149		3	3	2.5402	2.4947	1.0006	0.9880	0.5756	0.6000	0.6081	0.5998	0.6063	0.5991	0.7617	0.7645
RYW156		3	3	2.9045	2.8552	1.0824	1.0743	0.5893	0.5597	0.6577	0.6505	0.6557	0.6498	0.8085	0.8134
RYW158		3	3	2.8640	2.8123	1.0751	1.0663	0.5098	0.4975	0.6530	0.6452	0.6508	0.6444	0.8139	0.8195
RYW164		3	3	2.9527	2.9776	1.0905	1.0948	0.5765	0.6050	0.6633	0.6649	0.6613	0.6642	0.8128	0.8207
平均Mean		3.0333	3.0333	2.8297	2.8198	1.0667	1.0645	0.5359	0.5399	0.6473	0.6448	0.6452	0.6441	0.7944	0.7974
合计Total		91	91	—	—	—	—	—	—	—	—	—	—	—	—
St.Dev		0.1826	0.1826	0.1704	0.1661	0.0354	0.0350	0.0979	0.1047	0.0238	0.0232	0.0237	0.0232	—	—

表3

表4

表5

图3

表6

图4

图5

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材料编号 Serial number	统一编号 Unicode	名称 Name	来源 Source	备注 Remark
1	00000018	黑糜子 Heimeizi	黑龙江克山 Keshan, Heilongjiang	地方品种 Landrace
2	00000173	黄糜子 Huangmeizi	黑龙江穆棱 Muling, Heilongjiang
3	00000081	黄糜子 Huangmeizi	黑龙江富锦 Fujin, Heilongjiang
4	00000001	64黍120 64 Shu 120	黑龙江嫩江 Nenjiang, Heilongjiang
5	00000501	通辽高粱黍Tongliaogaoliangshu	内蒙古通辽 Tongliao, Inner Mongolia
6	00000413	昌图红糜子Changtuhongmeizi	辽宁昌图 Changtu, Liaoning
7	00000452	海城紧穗 Haichengjinsui	辽宁海城 Haicheng, Liaoning
8	00000423	黑山红黍 Heishanhongshu	辽宁黑山 Heishan, Liaoning
9	00000401	红糜子 Hongmeizi	吉林通化 Tonghua, Jilin
10	00000331	红糜子 Hongmeizi	吉林白城 Baicheng, Jilin
11	00000386	糜子 Meizi	吉林安图 Antu, Jilin
12	00006562	燕头黑黍 Yantouheishu	吉林吉林 Jilin, Jilin

指标 Index	群体 Group	黑龙江 Heilongjiang	吉林 Jilin	辽宁 Liaoning	内蒙古 Inner Mongolia
N_a	EC	3.0333±0.1826	3.0000±0.0000	3.0000±0.0000	2.9667±0.1826
N_a	CC	3.0333±0.1826	3.0000±0.0000	3.0000±0.0000	2.6333±0.4901
N_e	EC	2.7912±0.2025	2.8123±0.1458	2.7715±0.1611	2.4734±0.3518
N_e	CC	2.7958±0.1980	2.7720±0.1761	2.7665±0.2072	2.2392±0.3878
I	EC	1.0572±0.0465	1.0637±0.0287	1.0551±0.0326	0.9669±0.1148
I	CC	1.0582±0.0474	1.0560±0.0347	1.0526±0.0457	0.8568±0.1764
H_o	EC	0.5442±0.1137	0.5260±0.1182	0.5472±0.1475	0.5165±0.2476
H_o	CC	0.5387±0.1178	0.5106±0.1203	0.5576±0.1465	0.5461±0.3237
H_e	EC	0.6410±0.0298	0.6462±0.0196	0.6452±0.0220	0.6157±0.0728
H_e	CC	0.6446±0.0292	0.6441±0.0247	0.6484±0.0313	0.6013±0.0923
Nei	EC	0.6397±0.0297	0.6434±0.0194	0.6380±0.0215	0.5863±0.0700
Nei	CC	0.6403±0.0289	0.6378±0.0242	0.6363±0.0303	0.5400±0.0814
PIC	EC	0.7932	0.7896	0.7778	0.6715
PIC	CC	0.7805	0.7840	0.7610	0.5572

引物Primer	N_a	N_e	I	H_o	H_e	Nei	PIC
RYW5	3.0000	2.9335	1.0873	0.3841	0.6613	0.6591	0.8213
RYW8	3.0000	2.7817	1.0559	0.4969	0.6425	0.6405	0.7989
RYW16	3.0000	2.7052	1.0442	0.3643	0.6328	0.6303	0.7701
RYW28	3.0000	2.9053	1.0815	0.4452	0.6579	0.6558	0.8227
RYW40	3.0000	2.7007	1.0368	0.6048	0.6316	0.6297	0.7453
RYW53	3.0000	2.9793	1.0951	0.4317	0.6668	0.6644	0.7931
RYW62	3.0000	2.7981	1.0641	0.6588	0.6445	0.6426	0.7774
RYW67	3.0000	2.7664	1.0585	0.5150	0.6404	0.6385	0.8114
平均Mean	3.0000	2.8213	1.0654	0.4876	0.6472	0.6451	0.7925
合计Total	24	—	—	—	—	—	—
标准差SD	0.0000	0.1054	0.0208	0.1033	0.0132	0.0131	—

东北春播区糜子核心种质及其DNA分子身份证构建

Core germplasm and DNA molecular identity card of proso millet in Northeast Spring sowing region in China

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t检验 t-test	N_a	N_e	I	H_o	H_e	Nei	PIC
SSR	1.000	0.822	0.806	0.887	0.691	0.847	0.746
群体Group	1.000	0.680	0.614	0.715	0.862	0.658	0.575

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