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

Abstract

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

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.

Figures/Tables 11

Table 1

Table 2

30 SSR primer pairs for construction of the core germplasm"

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

Table 2

Fig. 1

Fig. 2

Table 3

Comparison of genetic parameters between germplasm resources and core collections"

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	—	—

Table 3

Table 4

Table 5

Fig. 3

Table 6

Fig. 4

Fig. 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	—

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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