Crops ›› 2020, Vol. 36 ›› Issue (5): 65-70.doi: 10.16035/j.issn.1001-7283.2020.05.010

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Genetic Diversity of Popcorn Landraces Based on SNP Markers

Zeng Yanhua(), Xie Hexia, Jiang Yufeng, Zhou Jinguo, Xie Xiaodong, Zhou Haiyu, Tan Xianjie, Qin Lanqiu(), Cheng Weidong()   

  1. Institute of Maize Research, Guangxi Academy of Agricultural Sciences/Guangxi Branch Center of National Maize Improvement Center, Nanning 530007, Guangxi, China
  • Received:2020-01-16 Revised:2020-05-08 Online:2020-10-15 Published:2020-10-12
  • Contact: Qin Lanqiu,Cheng Weidong E-mail:zengyanhua_12@163.com;lanqiuqin@sina.com;chengweidong1112@sina.com

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Abstract:

In order to evaluate the genetic variation of popcorn landraces in Guangxi, 45 popcorn landraces of Guangxi and two popcorn hybrids from China and six popcorn germplasm resources from South America were analyzed for SNP genotyping using the Illumina 56K iSelect SNP chip. The 14 338 polymorphic markers were obtained. Based on SNP markers, genotypes were divided into six types, of which a maximum of 5 805 was of type A/G, and the least of 149 was of type A/T, the number of which on chromosome 1 was the largest (2 302), and chromosome 10 was the least (848). The genetic similarity of 45 landraces ranged from 0.41 to 0.99 with an average value of 0.62. The varieties were classified into three groups by NJ-tree analyses. Most of the same regions of landraces belonged to a group. Principal component analysis showed that most of the landraces get together. There was no intersection between the South America varieties and the materials of the landraces and the hybrids. The results indicated the high genetic similarity of the landraces, and the genetic differences between landraces and the materials of hybrids and South America varieties was significant.

Key words: Popcorn, Germplasm resource, Landrace, SNP gene chip, DNA typing

Table 1

Information of popcorn landraces and hybrids from Guangxi"

序号Number 统一编号Uniform number 品种代号Variety code 品种名称Variety name 来源Source 主要特征Main characteristics
1 200393 PC1 爆裂糯 都安 籽粒白色米粒形
2 200571 PC2 爆裂种 来宾 籽粒红色米粒形
3 200572 PC3 爆裂玉米 来宾 籽粒黄色珍珠形
4 200628 PC4 多苞爆花玉米 兴安 籽粒黄色珍珠形
5 200689 PC5 东田爆 资源 籽粒红色米粒形
6 200715 PC6 爆米苞谷 恭城 籽粒黄色珍珠形
7 200720 PC7 狮子爆花米 恭城 籽粒红色米粒形
8 200721 PC8 黄紫爆花 恭城 籽粒黄、紫色珍珠形
9 200722 PC9 多苞黄玉米 恭城 籽粒黄色珍珠形
10 200771 PC10 爆玉米 龙胜 籽粒白色珍珠形
11 200781 PC11 黄爆玉米 阳朔 籽粒黄色珍珠形
12 200782 PC12 爆花玉米 阳朔 籽粒黄色珍珠形
13 200783 PC13 多苞黄 阳朔 籽粒黄色珍珠形
14 200838 PC14 刺苞谷 融水 籽粒红色米粒形
15 200839 PC15 爆玉米 融水 籽粒红色米粒形
16 200847 PC16 刺玉米 三江 籽粒白色珍珠形
17 200892 PC17 九子苞 南丹 籽粒黄、白色珍珠形
18 200893 PC18 苞谷爆 南丹 籽粒黄色珍珠形
19 201037 PC19 爆花玉米 钟山 籽粒黄、白色珍珠形
20 201045 PC20 开山水玉米 贺县 籽粒白色珍珠形
21 201055 PC21 黄石爆玉米 贺县 籽粒白色珍珠形
22 201092 PC22 平顶爆粟 玉林 籽粒黄、白色珍珠形
23 201093 PC23 卫东爆粟 玉林 籽粒白色珍珠形
24 201094 PC24 沙塘爆 玉林 籽粒白色珍珠形
25 201099 PC25 爆禄粟 玉林 籽粒黄色米粒形
26 201156 PC26 多苞红爆玉米 扶绥 籽粒红色米粒形
27 - PC27 爆花玉米 融水 籽粒红色米粒形
28 - PC28 爆花玉米 融水 籽粒红色米粒形
29 - PC29 爆花玉米 融水 籽粒红色米粒形
30 - PC30 爆花玉米 阳朔 籽粒黄、红色珍珠形
31 - PC31 五月黄 富川 籽粒黄色珍珠形
32 - PC32 爆裂玉米 隆安 籽粒黄色珍珠形
33 - PC33 爆玉米 龙胜 籽粒红色珍珠形
34 - PC34 爆裂玉米 西林 籽粒红色珍珠形
35 - PC35 爆裂玉米 隆林 籽粒黄色珍珠形
36 - PC36 爆玉米 融安 籽粒黄色珍珠形
37 - PC37 爆花玉米 田林 籽粒红色珍珠形
38 - PC38 爆花黄玉米 田林 籽粒黄色珍珠形
39 - PC39 爆花玉米 田林 籽粒红色米粒形
40 - PC40 爆裂玉米 三江 籽粒红、黄色米粒形
41 - PC41 爆裂玉米 三江 籽粒黄色珍珠形
42 - PC42 爆裂玉米 三江 籽粒白色珍珠形
43 - PC43 爆玉米 天等 籽粒黄、红色珍珠形
44 - PC44 爆玉米 田林 籽粒黄、红色珍珠形
45 - PC45 爆玉米 阳朔 籽粒黄、红色珍珠形
46 - CK1 沈爆3号 沈阳农业大学 籽粒黄色珍珠形
47 - CK2 沈爆8号 沈阳农业大学 籽粒黄色珍珠形

Table 2

Germplasm information of popcorn from South America"

序号Number 统一编号Uniform number 品种代号Variety code 品种名称Variety name 来源Source 主要特征Main characteristics
1 - Z1G10886 黄爆裂玉米 美国 籽粒橘黄色珍珠形
2 - Z1G17919 YJ003502 巴西 籽粒黄、白色珍珠形
3 - Z1G19295 YJ12245 阿根廷 籽粒黄色珍珠形
4 - Z1G19306 YJ12257 阿根廷 籽粒白色珍珠形
5 - Z1G19319 YJ12274 阿根廷 籽粒白色珍珠形
6 - Z1G19335 YJ12293 阿根廷 籽粒黄色珍珠形

Fig.1

Heterozygous ratio distribution of tested varieties"

Fig.2

Distribution of genetic similarity coefficients for the tested popcorn varieties"

Table 4

Genetic similarity coefficient of popcorn landraces from different regions of Guangxi"

地区
Region		 品种数
Variety
number		 遗传相似系数
Genetic similarity coefficient
变幅Range 均值Average
桂北Northern Guangxi 31 0.44~0.99 0.62
桂中Central Guangxi 5 0.61~0.99 0.74
桂东Eastern Guangxi 9 0.41~0.81 0.61

Fig.3

Phylogenetic tree for 53 popcorn germplasms Similar or suspected same varieties in box"

Fig.4

Principal component analysis for 53 popcorn germplasms"

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