Chin Bull Bot ›› 2019, Vol. 54 ›› Issue (6): 723-732.doi: 10.11983/CBB19037

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

The Genetic Diversity of Common Millet (Panicum miliaceum) Germplasm Resources Based on the EST-SSR Markers

He Jieli1,Shi Tiantian2,Chen Ling3,Wang Haigang3,Gao Zhijun4,Yang Meihong1,Wang Ruiyun2,3,*(),Qiao Zhijun3,*()   

  1. 1 College of Arts and Science, Shanxi Agricultural University, Taigu 030801, China
    2 College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
    3 Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, China
    4 Erdos Institute of Agriculture and Animal Husbandry, Erdos 017200, China
  • Received:2019-02-24 Accepted:2019-06-18 Online:2020-07-09 Published:2019-11-01
  • Contact: Wang Ruiyun,Qiao Zhijun E-mail:wry925@126.com;nkypzs@126.com

Abstract:

The EST-SSR molecular markers of common millet (Panicum miliaceum) were developed by high-throughput sequencing. Using these markers, we assessed the genetic diversity in a panel of 144 common millet accessions collected from different ecotopic regions in China and abroad. It was shown that 80 pairs of these markers were polymorphic, with the efficiency of approximately 40%. The resolution power (Rp) was 0.67-4.67 (mean 2.00) and the amplified product sizes ranged from 50 to 500 bp. Among the examined 144 accessions, 206 allelic variations were identified in 80 loci, with 2-3 alleles at each locus. The Shannon’s diversity index (I) ranged from 0.659 3 (RYW108) to 1.087 2 (RYW124) with an average of 0.859 9. The range of polymorphism information content (PIC) was 0.222 9 (RYW98) -0.717 2 (RYW124) with an average of 0.457 3. Based on UPGMA, these 144 accessions were classified into 3 groups, two of which belonged to the the Northern China spring-sowing ecotopes and one group was mainly from the Loess Plateau spring-summer-sowing ecotopes. Based on Structure (K=4), all the accessions were divided into four groups, of which two groups represented the gene pool originated from the Northern China, whereas the other two groups from the Loess Plateau and abroad accessions. Based on principal component analysis (PCA), the accessions were clustered into seven groups, consistent with their geographic origins.

Key words: Panicum miliaceum, genetic diversity, PCA, EST-SSR markers

Table 1

Distribution of common millet accessions in different ecotopes of China and abroad"

Ecotope/abroad Origin Number of accession Total
Northwest spring and summer-sowing ecotope (NWSS) Xinjiang 4 4
Northern spring-sowing ecotope (NSP) Qinghai 13 48
Gansu 11
Inner Mongolia 14
Shanxi 10
Loess Plateau spring and summer-sowing ecotope (LPSS) Shanxi 18 37
Shaanxi 8
Ningxia 11
Northeast spring-sowing ecotope (NES) Heilongjiang 5 9
Jilin 3
Liaoning 1
Northern summer-sowing ecotope (NSU) Hebei 9 13
Shandong 2
Anhui 1
Henan 1
Southern autumn and winter-sowing ecotope (SAW) Hainan 2 2
Abroad Former Soviet Union 2 31
Poland 2
India 27
Total 144

Table 2

Screening of SSR primers for common millet"

Number Unicode Accession name Origin
1 00000177 Hongmizi Ningan, Heilongjiang
2 00000750 Baimizi Shawan, Xinjiang
3 00006653 Jinshu Hainan
4 00007238 Dahongmizi Bameng, Inner Mongolia
5 00007478 Baigedami Huangzhong, Qinghai
6 No unicode Hongshuzi Anyang, Henan

Figure 1

Distribution of resolving power values of 80 EST- SSR markers"

Table 3

Parameters of genetic diversity in different ecotope of common millet"

Ecotope/ abroad Accessions Na Ne I Ho He PIC
NWSS 4 2.3375±0.5017 2.1517±0.4194 0.7644±0.2178 0.8042±0.2688 0.5944±0.1193 0.3551
NSP 48 2.5750±0.4975 2.3106±0.3211 0.8604±0.1576 0.8228±0.1308 0.5655±0.0604 0.4536
LPSS 37 2.5750±0.4975 2.2803±0.3110 0.8506±0.1534 0.8384±0.1166 0.5615±0.0595 0.4203
NES 9 2.5125±0.5030 2.2435±0.3929 0.8289±0.1823 0.7937±0.1732 0.5737±0.0909 0.4212
NSU 13 2.5625±0.4992 2.2815±0.3527 0.8496±0.1632 0.7946±0.1608 0.5712±0.0667 0.4304
SAW 2 2.2375±0.5092 2.0608±0.4387 0.7347±0.2316 0.7812±0.3265 0.6813±0.2006 0.2156
Domestic 113 2.5750 ±0.4975 2.3122±0.3086 0.8628±0.1554 0.8200±0.1188 0.5625±0.0584 0.4651
Abroad 31 2.5750±0.4975 2.2464±0.2909 0.8387±0.1449 0.8540±0.1193 0.5571±0.0561 0.3896

Table 4

Parameters of Nei’s genetic distance and Nei’s genetic agreement in common millet populations"

Population NWSS NSP LPSS NES NSU SAW Abroad
NWSS 0.9560 0.9614 0.9487 0.9380 0.8694 0.9477
NSP 0.0449 0.9884 0.9678 0.9794 0.9110 0.9864
LPSS 0.0394 0.0117 0.9716 0.9830 0.9116 0.9865
NES 0.0527 0.0327 0.0288 0.9675 0.8974 0.9587
NSU 0.0640 0.0208 0.0171 0.0331 0.9023 0.9762
SAW 0.1400 0.0932 0.0926 0.1083 0.1029 0.9102
Abroad 0.0537 0.0137 0.0136 0.0422 0.0240 0.0941

Figure 2

Cluster analysis chart of common millet accessions based on UPGMA NWSS, NSP, LPSS, NES, NSU and SAW are the same as Table 1."

Table 5

Genetic diversity of common millet groups based on UPGMA cluster analysis"

Group Accessions Na Ne I Ho He PIC
A 33 2.5750±0.4975 2.3226±0.3374 0.8654±0.1620 0.8055±0.1417 0.5696±0.0636 0.4716
B 15 2.5125±0.5030 2.2471±0.3383 0.8330±0.1627 0.8153±0.1530 0.5651±0.0686 0.3993
C 96 2.5750±0.4975 2.2922±0.2894 0.8571±0.1495 0.8363±0.1111 0.5599±0.0553 0.4380
C1 70 2.5750±0.4975 2.3136±0.3098 0.8635±0.1551 0.8291±0.1199 0.5643±0.0584 0.4531
C2 26 2.5625±0.4992 2.1912±0.2797 0.8163±0.1391 0.8555 ±0.1212 0.5477±0.0558 0.3420
C11 37 2.5750±0.4975 2.3014±0.3143 0.8589±0.1561 0.8332±0.1182 0.5664±0.0603 0.4382
C12 33 2.5750±0.4975 2.3028±0.3224 0.8583±0.1571 0.8255±0.1383 0.5654±0.0610 0.4348

Figure 3

Population modeling of 144 common millet accessions based on Structure"

Figure 4

Genetic structure of common millet based on Structure Color represents group; bar and the horizontal coordinate represent origin and its serial number, respectively."

Table 6

Genetic diversity analysis of different cluster based on genetic structure (K=2 and K=4)"

Cluster Accessions Na Ne I Ho He PIC
K=2 Red 68 2.5750±0.4975 2.2446±0.2626 0.8407±0.1403 0.8602±0.1056 0.5528±0.0520 0.3773
Green 76 2.5750±0.4975 2.3396±0.3329 0.8711±0.1620 0.7975±0.1315 0.5679±0.0619 0.5031
K=4 Red 47 2.5750± 0.4975 2.3496±0.3944 0.8745±0.1768 0.7439±0.1668 0.5785±0.0743 0.5296
Green 31 2.5750± 0.4975 2.2844±0.3202 0.8516± 0.1549 0.8225±0.1399 0.5635±0.0607 0.4414
Blue 19 2.5750±0.4975 2.2973±0.3199 0.8575±0.1568 0.8190±0.1311 0.5628±0.0608 0.4450
Yellow 47 2.5750±0.4975 2.2238±0.2723 0.8312±0.1387 0.3634±0.2702 0.4984±0.1050 0.3543

Figure 5

Principal component analysis on SSR genotypes of common millet accessions"

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