Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (9): 1475-1477.doi: 10.3864/j.issn.0578-1752.2019.09.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic Diversity and Population Structure of Broomcorn Millet in China Based on Fluorescently Labeled SSR

KOU ShuJun1,HUO AHong1,FU GuoQing1,JI JunJian1,WANG Yao1,ZUO ZhenXing1,LIU MinXuan2(),LU Ping2   

  1. 1 Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou 075000, Hebei
    2 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081
  • Received:2018-01-08 Accepted:2019-03-05 Online:2019-05-01 Published:2019-05-16
  • Contact: MinXuan LIU E-mail:liuminxuan@caas.cn

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Abstract:

【Objective】Genetic diversity and population genetic structure of 131 broomcorn millet accessions in China were analyzed based on fluorescently labeled SSR markers for variety improvement and germplasm innovation as well as effective utilization of broomcorn millet germplasm.【Method】Six broomcorn millet accessions with phenotypical diversity from different geographical origins were used to select SSR markers with highly polymorphism by denaturing polyacrylamide gel electrophoresis. The polymorphic markers were labeled with four fluorescent dyes: 6-FAM, HEX, ROX and TAMRA at the 5' end of forward primers which used in subsequent analyses. The size of each allele locus was determined by DNA Analyzer to estimate the genetic diversity and genetic population structure of the tested accessions. 【Result】 Twenty-two polymorphic and stably amplifying markers were selected for both traditional denaturing PAGE electrophoresis detection and fluorescent SSR labeling-automatic analysis technology. A total of 128 alleles were detected with an average of 5.82 alleles per locus, the gene diversity index, polymorphism information content and Shannon's information index ranged from 0.3572 to 0.8132, 0.2934 to 0.8150 and 0.5427 to 1.7681, respectively, with an average of 0.6284, 0.5874 and 1.2062 respectively. Genetic distance and genetic identity of accessions from different ecotypes were 0.0764-0.7251 (average value is 0.3121) and 0.4843-0.9265 (average value is 0.7465), respectively, the smallest genetic distance was found between NSP ecotype and LPSS ecotype. UPGMA cluster analysis showed that NSP ecotype and LPSS ecotype were clustered into one group. The clustering result of the cultivars and landraces from NES ecotype was consistent, the cultivars from LPSS ecotype were divided into different groups. By plotting the relationship between K and ΔK, ΔK is the largest when K=4. Based on K and △K values, 131 broomcorn millet accessions were grouped four genotypes by the population genetic structure analysis. Group Ⅰ is composed of NSP ecotype. Group Ⅱ consist of NES ecotype. Most accessions of group Ⅲ are from NSP ecotype. Group Ⅳ mainly contain LPSS ecotype. Most of the accessions in same group have same genetic component while only a few accessions contained genetic component of other groups. The analysis result of population genetic structure was consistent with the UPGMA clustering, indicating that the genetic diversity is related to geographical region. 【Conclusion】 There have more abundant genetic diversity in NSP and LPSS ecotype than other regions. The cultivars of NES ecotype were bred mainly from the landraces. The cultivars of LPSS ecotype were introduced from a wide range of resources during the breeding process, harboring genetic exchanges with other ecological regions.

Key words: broomcorn millet, SSR fluorescently labeled markers, genetic diversity, population structure

Table 1

Genetic parameters of the 22 SSR markers used in this study"

位点
Locus		 等位基因数目
Allele number		 主要等位基因 Major allele 稀有基因数
Rare gene number		 基因多样性指数
H		 多态性信息含量
PIC		 Shannon信息指数
I
片段大小
Size (bp)		 频率
Frequency
BM552 7 240 0.4427 5 0.7403 0.7124 1.4924
BM637 5 167 0.3382 1 0.7373 0.6897 1.3527
BM787 5 290 0.6908 1 0.4874 0.4530 0.8807
BM2654 7 206 0.3015 1 0.7835 0.7525 1.6300
BM2715 6 227 0.3893 4 0.7324 0.6914 1.3745
BM2717 7 284 0.5916 5 0.6109 0.5825 1.2828
BM2729 4 122 0.6107 4 0.5593 0.5064 0.9212
BM2766 5 194 0.6450 1 0.5285 0.4817 1.0270
BM2792 5 132 0.4084 1 0.6626 0.5991 1.1651
BM6414 7 270 0.4618 5 0.7149 0.6814 1.3771
BM6573 2 118 0.7672 2 0.3572 0.2934 0.5427
BM6598 6 210 0.6450 1 0.5364 0.4964 1.0300
LMX503 5 226 0.6336 1 0.5489 0.5081 1.0867
LMX780 5 229 0.5076 1 0.6278 0.5659 1.1080
LMX836 8 224 0.4275 1 0.7562 0.7310 1.6617
LMX1553 6 192 0.7061 4 0.4788 0.4560 0.8776
LMX1959 5 266 0.4847 3 0.6584 0.6043 1.1549
LMX2019 8 250 0.3321 2 0.8132 0.7918 1.7681
LMX2068 8 289 0.7405 1 0.4411 0.4294 0.9994
LMX2281 5 248 0.6718 0 0.5140 0.4818 0.9819
LMX2382 8 195 0.2710 6 0.8350 0.8150 1.7779
LMX2734 4 210 0.4733 1 0.6826 0.6351 1.2678
合计Total 128 51
平均Average 5.8 0.5189 2.3 0.6284 0.5874 1.2062

Fig. 1

Alleles of 45 broomcorn millet accessions at marker locus BM2654 M: DNA molecular weight standard;Number 61-105 is the serial number of varieties listed in supplement table 1; The vertical arrow indicates heterozygous sites band patterns; The horizontal arrow indicates six different alleles"

Fig. 2

Peak patterns detected in seven broomcorn millet accessions at fluorescent marker locus BM2654 Two alleles were detected in variety 71049 because of heterozygosity at this locus. The Y axis indicates the intensity of fluorescent signals. The X axis indicates six different sizes of amplified fragment(bp)"

Table 2

Evaluation of genetic diversity of different ecotypes of broomcorn millet"

生态区
Ecotype		 类型
Type		 资源数
Accessions		 等位基因数
Allele number		 基因多样性指数
H		 多态性信息含量
PIC		 Shannon信息指数
I
东北春糜子区
NES		 育成品种 Cultivars 20 3.8636 0.5474 0.4953 0.9848
农家种 Landraces 11 3.3636 0.5373 0.4901 0.9225
材料数 Number 31 4.3182 0.5732 0.5291 1.0562
华北夏糜子区
NSU		 育成品种 Cultivars 0
农家种 Landraces 3 2.0455 0.3838 0.3197 0.4402
材料数 Number 3 2.0455 0.3838 0.3197 0.4402
北方春糜子区
NSP		 育成品种 Cultivars 32 4.4091 0.5521 0.5042 1.1074
农家种 Landraces 26 4.5455 0.6221 0.5725 1.1114
材料数 Number 58 5.0455 0.6083 0.5607 1.1283
黄土高原春夏糜子区 LPSS 育成品种 Cultivars 20 4.3636 0.5808 0.5337 1.0379
农家种 Landraces 16 4.0000 0.5250 0.4993 0.9290
材料数 Number 36 5.1364 0.6020 0.5576 1.1222
西北春夏糜子区 NWSS 育成品种 Cultivars 0
农家种 Landraces 3 2.1818 0.4621 0.3811 0.5001
材料数 Number 3 2.1818 0.4621 0.3811 0.5001

Table 3

Genetic distance and genetic identity of broomcorn millet accessions with different ecotypes"

生态区
Ecotype		 东北春糜子区
NES		 北方春糜子区
NSP		 华北夏糜子区
NSU		 西北春夏糜子区
NWSS		 黄土高原春夏糜子区
LPSS
东北春糜子区 NES — 0.8548 0.6408 0.7078 0.8814
北方春糜子区 NSP 0.1569 — 0.5993 0.8552 0.9265
华北夏糜子区 NSU 0.4451 0.5120 — 0.4843 0.6463
西北春夏糜子区 NWSS 0.3456 0.1564 0.7251 — 0.8684
黄土高原春夏糜子区 LPSS 0.1263 0.0764 0.4364 0.1411 —

Fig. 3

Cluster diagram of broomcorn millet accessions with different ecotypes based on genetic distance"

Fig. 4

Cluster diagram of 131 broomcorn millet accessions based on data from 22 SSR markers"

Fig. 5

Graphical relationship between K and Δk for 131 broomcorn millet accessions"

Fig. 6

Population genetic structure of 131 broomcorn millet accessions"

Table 4

Distribution of 131 broomcorn millet accessions based on STRUCTURE analysis(K=4)"

省份 Province 红色 Red 绿色 Green 蓝色 Blue 黄色 Yellow
山西省Shanxi 3 3 15 6
甘肃省Gansu 8 2 2
内蒙古自治区Inner Mongolia 7 9 1
青海省Qinghai 7 1
宁夏回族自治区Ningxia 6 1 4 4
黑龙江省Heilongjiang 3 10 2 1
陕西省Shaanxi 1 1 2 5
辽宁省 Liaoning 1 2 1
吉林省 Jilin 3 1 6
河北省 Hebei 6 3
新疆维吾尔自治区 Xinjiang 1 2
山东省 Shandong 1
合计 Total 35 21 43 32

Table 5

Distribution of Q-value of four groups"

类群
Group		 各群体品种数量
Number of varieties in each group		 品种数量Number of varieties
Q<0.6 Q≥0.6 Q≥0.8 Q≥0.9
1 35 1 34 26 21
2 21 3 18 15 14
3 43 12 31 18 14
4 32 7 25 18 15
合计 Total 131 24 107 76 63
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