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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (1): 42-49.doi: 10.3724/SP.J.1006.2021.04067


Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil

SUN Qian1,2(), ZOU Mei-Ling2, ZHANG Chen-Ji2,4, JIANG Si-Rong2,5, Eder Jorge de Oliveira6, ZHANG Sheng-Kui7, XIA Zhi-Qiang2,3,4,*(), WANG Wen-Quan2,3,4,5,*(), LI You-Zhi1,*()   

  1. 1College of Life Science and Technology / State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, Guangxi, China
    2Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
    3Tropical Bio-omics and Big-Data Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
    4Hainan University, Haikou 570203, Hainan, China
    5Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
    6Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
    7Qilu University of Technology, Jinan 250306, Shandong, China
  • Received:2020-03-13 Accepted:2020-08-19 Online:2021-01-12 Published:2020-09-15
  • Contact: XIA Zhi-Qiang,WANG Wen-Quan,LI You-Zhi E-mail:sunqian9595@163.com;xiazhiqiang@itbb.org.cn;wangwenquan@itbb.org.cn;dyzl@gxu.edu.cn
  • Supported by:
    National Key Research and Development Project(2019YFD1001100);National Natural Science Foundation of China-CG Joint Fund(31861143005);Key Technology Integration Demonstration Project of Characteristic Crop Industry Development in the Rocky Desertification Area of Yunnan, Guangxi and Guizhou(SMH2019-2021);Special Fund for Basic Scientific Research Operating Expenses of the Chinese Academy of Tropical Agricultural Sciences(1630052019022)


As a typical tropical crop, cassava (Manihot esculenta Crantz) has the characteristics of drought resistance, barren resistance, high biomass and so on. In addition to being used for food and forage, it can also be used for production, processing and starch extraction. Due to highly heterozygous cassava genome, breeding is more difficult. Enriching the genetic diversity of cassava germplasm, comprehensively evaluating its genetic background and traits, and discovering superior alleles that control excellent traits are of great significance for cassava breeding in the future. In order to analyze the genetic diversity, genetic relationship and population structure of cassava germplasm in Brazil, 7946 SNPs and 1997 InDels molecular markers were used. Population structure analysis was performed by ADMIXTURE software, and principal component analysis was performed by GCTA software. Brazilian cassava was divided into nine subgroups, and was roughly consistent with the results of cluster analysis using PHYLIP. Among them, subgroup 1, subgroup 2, subgroup 4, subgroup 6, and subgroup 8 could be clustered together respectively, while the samples of other subgroups could be roughly clustered, and there was a certain cross between the samples. The genetic diversity of cassava germplasm in Brazil (0.274) was higher than the genetic diversity level of cassava germplasm in China and Nigeria. Subgroup 5 of Brazil cassava had a relatively high genetic diversity (0.29). The genetic differentiation of subgroups was low (the genetic differentiation vary from 0.03 to 0.15), but higher than domestic cassava germplasm. The genetic distance between cassava accessions varied from 0.084 to 0.297, with the average of 0.228. The results of this study can provide a basis for subsequent association analysis to identify great alleles and introduction.

Key words: cassava, SNP, InDel, genetic diversity, population structure

Table 1

List of 192 cassava cultivars"

001 9624-09 033 BGM0400 065 BGM0783 097 BGM1291 129 BGM1608 161 BGM1942
002 98150-06 034 BGM0405 066 BGM0788 098 BGM1313 130 BGM1615 162 BGM1957
003 BGM0020 035 BGM0408 067 BGM0807 099 BGM1324 131 BGM1622 163 BGM2022
004 BGM0042 036 BGM0425 068 BGM0886 100 BGM1327 132 BGM1626 164 BGM2028
005 BGM0045 037 BGM0428 069 BGM0889 101 BGM1328 133 BGM1640 165 BGM2041
006 BGM0073 038 BGM0436 070 BGM0896 102 BGM1364 134 BGM1662 166 BGM2047
007 BGM0087 039 BGM0443 071 BGM0905 103 BGM1370 135 BGM1667 167 BGM2052
008 BGM0103 040 BGM0451 072 BGM0917 104 BGM1376 136 BGM1668 168 BGM2061
009 BGM0135 041 BGM0452 073 BGM0930 105 BGM1387 137 BGM1672 169 BGM2062
010 BGM0145 042 BGM0467 074 BGM0972 106 BGM1396 138 BGM1679 170 BGM2063
011 BGM0152 043 BGM0495 075 BGM0976 107 BGM1409 139 BGM1682 171 BGM2071
012 BGM0163 044 BGM0501 076 BGM0982 108 BGM1412 140 BGM1684 172 BGM2078
013 BGM0179 045 BGM0507 077 BGM0989 109 BGM1429 141 BGM1690 173 BGM2081
014 BGM0188 046 BGM0523 078 BGM0993 110 BGM1437 142 BGM1697 174 BGM2082
015 BGM0206 047 BGM0540 079 BGM1042 111 BGM1440 143 BGM1698 175 BGM2083
016 BGM0209 048 BGM0542 080 BGM1050 112 BGM1458 144 BGM1704 176 BRS Amansa Burro
017 BGM0211 049 BGM0543 081 BGM1081 113 BGM1485 145 BGM1706 177 BRS Caipira
018 BGM0213 050 BGM0544 082 BGM1106 114 BGM1487 146 BGM1715 178 BRS Dourada
019 BGM0226 051 BGM0550 083 BGM1110 115 BGM1490 147 BGM1722 179 BRS Formosa
020 BGM0250 052 BGM0551 084 BGM1127 116 BGM1495 148 BGM1728 180 BRS Gema Ovo
021 BGM0261 053 BGM0562 085 BGM1153 117 BGM1510 149 BGM1732 181 BRS Jari
022 BGM0264 054 BGM0564 086 BGM1164 118 BGM1524 150 BGM1750 182 BRS Kiriris
023 BGM0269 055 BGM0574 087 BGM1165 119 BGM1535 151 BGM1757 183 BRS Mulatinha
024 BGM0283 056 BGM0600 088 BGM1171 120 BGM1537 152 BGM1760 184 BRS Tapioqueira
025 BGM0288 057 BGM0620 089 BGM1174 121 BGM1539 153 BGM1761 185 BRS Verdinha
026 BGM0331 058 BGM0624 090 BGM1178 122 BGM1549 154 BGM1763 186 Cascuda
027 BGM0336 059 BGM0640 091 BGM1180 123 BGM1552 155 BGM1794 187 Corrente
028 BGM0338 060 BGM0654 092 BGM1193 124 BGM1576 156 BGM1814 188 Eucalipto
029 BGM0352 061 BGM0670 093 BGM1202 125 BGM1581 157 BGM1835 189 Fécula Branca
030 BGM0361 062 BGM0678 094 BGM1226 126 BGM1590 158 BGM1850 190 IAC90
031 BGM0390 063 BGM0726 095 BGM1252 127 BGM1593 159 BGM1883 191 Olho Junto
032 BGM0394 064 BGM0752 096 BGM1281 128 BGM1596 160 BGM1884 192 Valencia

Table 2

Summary of SNPs and InDels"

Intergenic region
Upstream gene region
Downstream gene region
5' prime UTR variant
Missense variant
Synonymous variant
Frame shift variant
Other types
9443 3287 4005 471 2 845 745 417 171

Fig. 1

Population genetic structure of 192 cassava cultivars a: ADMIXTURE was used to analyze the population structure of 192 cassava materials, and the cross-validation error was calculated when K was 1-12. b: The population structure at K = 9, in this population structure, each individual is represented by a line with multiple different colors, and the subgroup to which the individual belongs is inferred based on the proportion of the color, the nine color regions arranged from left to right in order represent subgroups 1 to 9, respectively. c: Principal component analysis (PCA) of the group, one point represents an individual, nine colors and their corresponding shapes represent different subgroups."

Fig. 2

Phylogenetic tree of 192 cassava cultivars from Brazil Light blue, dark blue, grass green, dark green, flesh, orange, fuchsia, red, and purple represent subgroup 1 to 9, respectively."

Table 3

Statistics of genetic diversity index (π)"

1 0.192
2 0.281
3 0.261
4 0.221
5 0.289
6 0.264
7 0.284
8 0.209
9 0.234
整体Entirety 0.274
平均Average 0.248

Table 4

Statistics of population differentiation index (Fst)"

亚群Subgroup 1 2 3 4 5 6 7 8 9
2 0.065
3 0.081 0.061
4 0.152 0.073 0.112
5 0.053 0.032 0.069 0.062
6 0.058 0.045 0.033 0.086 0.041
7 0.059 0.038 0.054 0.078 0.031 0.045
8 0.139 0.085 0.076 0.119 0.084 0.056 0.080
9 0.058 0.043 0.046 0.083 0.048 0.034 0.038 0.061
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