Crops ›› 2020, Vol. 36 ›› Issue (2): 54-59.doi: 10.16035/j.issn.1001-7283.2020.02.009

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Genetic Diversity Analysis of Amomum tsao-ko in Jinping Based on Phenotypic Traits and SSR Markers

Ma Mengli,Wang Tiantao,Lei En,Meng Hengling,Zhang Wei,Zhang Tingting,Lu Bingyue()   

  1. College of Life Science and Technology/Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, Mengzi 661100, Yunnan, China
  • Received:2019-09-16 Revised:2019-10-16 Online:2020-04-15 Published:2020-04-13
  • Contact: Bingyue Lu E-mail:lby202@126.com

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Abstract:

Amomum tsao-ko is a common Chinese medicine and seasoning, mainly produced in Yunnan. In this study, the genetic diversity of Amomum tsao-ko (in Jinping County, Honghe Prefecture, Yunnan Province) was analyzed by phenotypic traits and SSR markers. The results showed that the coefficient of variation of 13 quantitative traits was 7.64%-50.00%, and the Shannon-Weaver diversity index (H') was 1.74-2.16. The coefficient of variation of fruiting rate was the largest, and the diversity level of fresh fruit length was the highest. The first four principal components could explain 81.615% of the variation, and the first principal component could explain 37.369% variation with the main contributions from dry fruit weight, fresh fruit weight, dry pericarp weight and seed number, which are related to the yield. A total of 23 bands were amplified by 5 pairs of SSR markers in 44 Amomum tsao-ko samples, with an average of 4.6 polymorphic loci per pair of primers. The shannon information index and the average polymorphism information content (PIC) were 1.266 and 0.672, respectively. Cluster analysis could divide 44 samples into two clusters. Cluster I consisted of 34 samples, and the Cluster II consisted of 10 samples. The results indicated that Jinping Amomum tsao-ko had abundant phenotypic variation and high genetic diversity at the molecular level.

Key words: Amomum tsao-ko, Genetic diversity, Phenotype, SSR

Table 1

List of SSR markers used"

引物
Primer		 正向引物(5'-3')
Forward primer (5'-3')		 反向引物 (5'-3')
Reverse primer (5'-3')		 重复序列
Repeat sequence		 退火温度(℃)
Annealing temperature
AT1 F: GCTTCACCTCCAGTTTCC R: GTCCTCCTTGTCCACCC (GA)14 59
AT5 F: AATGCAAATGGTGGACG R: GGATAAATCAAAGAGGAGGA (GA)16 58
AT29 F: GAGGAGGCGTGGACTTT R: GGGCTGCTTCTATTTCAT (GA)8 58
AT30 F: TAACGACGAAGGAAACG R: TGAGTAGGAAAGAAGAAAGAA (CT)9 55
AT56 F: AGTTTGAACCTCCCATTT R: ATCTTGAGCTTCGTGCC (CA)6 55

Table 2

Diversity analysis of quantitative traits of Amomum tsao-ko"

性状
Trait		 最小值
Minimum		 最大值
Maximum		 平均
Mean		 标准差
Standard deviation		 极差
Range		 变异系数(%)
Coefficient of variation		 Shannon-Weaver
多样性指数H′
每穗花数Number of flowers per ear 27.67 112.67 71.78 17.84 85.00 24.85 2.04
挂果率Fruiting rate (%) 1.47 42.11 15.96 7.98 40.64 50.00 1.93
鲜果重Fresh fruit weight (g) 6.80 15.61 10.39 1.97 8.81 18.92 1.97
鲜果长Fresh fruit length (mm) 26.03 36.10 30.98 2.57 10.08 8.28 2.16
鲜果宽Fresh fruit width (mm) 20.85 31.47 25.58 1.95 10.62 7.64 1.92
鲜果长宽比
Ratio of fresh fruit length to width		 0.98 1.64 1.22 0.14 0.66 11.77 1.95
干果长Dry fruit length (mm) 22.88 43.45 29.12 4.33 20.57 14.88 1.93
干果宽Dry fruit width (mm) 15.10 22.97 18.79 1.59 7.87 8.45 2.01
干果长宽比
Ratio of dry fruit length to width		 1.13 2.34 1.57 0.32 1.21 20.45 2.07
干果重Dry fruit weight (g) 1.35 4.83 3.24 0.65 3.48 20.02 1.94
干果皮重Dry fruit peel weight (g) 0.50 1.23 0.82 0.15 0.73 18.56 2.00
种子团重Seed regiment weight (g) 0.73 3.94 2.42 0.55 3.22 22.87 1.74
单果种子数Number of seeds per fruit 26.60 55.00 36.92 5.81 28.40 15.75 2.03

Table 3

Principal component analysis based on phenotypic traits of Amomum tsao-ko"

性状Trait 第1主成分
Principal component 1		 第2主成分
Principal component 2		 第3主成分
Principal component 3		 第4主成分
Principal component 4
每穗花数Number of flowers per ear 0.432 0.016 -0.772 0.043
挂果率Fruiting rate -0.193 0.353 0.313 0.723
鲜果重Fresh fruit weight 0.831 0.038 0.331 -0.296
鲜果长Fresh fruit length 0.449 0.821 0.209 -0.226
鲜果宽Fresh fruit width 0.751 -0.213 0.035 -0.308
鲜果长宽比Ratio of fresh fruit length to width -0.151 0.917 0.133 0.003
干果长Dry fruit length 0.460 0.842 0.132 -0.055
干果宽Dry fruit width 0.724 -0.573 0.067 -0.012
干果长宽比Ratio of dry fruit length to width -0.039 0.971 0.041 -0.040
干果重Dry fruit weight 0.786 -0.234 0.391 0.291
干果皮重Dry fruit peel weight 0.865 -0.004 0.033 -0.048
种子团重Seed regiment weight 0.656 -0.281 0.461 0.368
单果种子数Number of seeds per fruit 0.760 0.077 0.156 -0.099
特征值Eigen value 5.979 4.008 1.944 1.127
贡献率Contribution (%) 37.369 25.049 12.152 7.046
累积贡献率Accumulated contribution (%) 37.369 62.417 74.569 81.615

Table 4

Polymorphism analysis of Amomum tsao-ko with SSR primers"

引物
Primer		 多态带百分比(%)
Percentage of polymorphism bands		 观测等位
基因数 Na		 有效等位
基因数 Ne		 观测杂合度
Ho		 期望杂合度
He		 Shannon′s
信息指数 I		 多态性信息
含量 PIC		 解析度
Rp
AT1 100 4 3.305 0.697 0.708 1.289 0.730 2.606
AT5 100 5 3.940 0.487 0.756 1.417 0.763 2.757
AT29 100 6 4.418 0.731 0.789 1.581 0.723 3.385
AT30 100 6 3.738 0.150 0.742 1.462 0.738 2.200
AT56 100 2 1.646 0.390 0.398 0.582 0.405 1.122
平均值Mean value 100 4.6 3.410 0.491 0.679 1.266 0.672 2.414

Fig.1

Cluster diagram of 44 Amomum tsao-ko individuals based SSR markers"

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