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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (1): 80-93.doi: 10.3724/SP.J.1006.2021.04022

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

Establishment of DNA molecular fingerprint of applied core germplasm in jute (Corchorus spp.)

GUO Yan-Chun1,2,3(), ZHANG Li-Lan1,2,3, CHEN Si-Yuan1,2,3, QI Jian-Min1,2, FANG Ping-Ping1,2, TAO Ai-Fen1,2, ZHANG Lie-Mei1,*(), ZHANG Li-Wu1,2,3,*()   

  1. 1Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    2Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Public Platform of Fujian for Germplasm Resources of Bast Fiber Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    3Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2020-02-03 Accepted:2020-04-15 Online:2021-01-12 Published:2020-12-16
  • Contact: ZHANG Lie-Mei,ZHANG Li-Wu E-mail:565358452@qq.com;zhangliemei@126.com;lwzhang@fafu.edu.cn;zhang_liwu@hotmail.com
  • Supported by:
    National Natural Science Foundation of China(31771369);China Agriculture Research System(CARS-19-E06)

Abstract:

It is important to construct and study the applied core collection in order to promote jute genetic breeding and explore excellent genes. In this study, the applied core collection in jute, including 61 accessions divided into 16 application-oriented features, such as high yield, high quality, disease resistance and so on, was established based on the field performance from 300 jute germplasm. 12 fluorescent core primers were screened from 46 pairs of core primers. Fluorescence labeled capillary electrophoresis was used to analyze the polymorphism of these 12 pairs of primers, and a total of 140 polymorphism sites were detected. The precise DNA molecular ID cards were constructed by the combination of the 12 core primer pairs from the data coded in the form of numbers and English letters. Bar code and quick response code DNA molecular were established and can be quickly scanned and recognized by electric gadget. These results could be beneficial to increase the application efficiency and rapid molecular identification in jute germplasm resources.

Key words: jute, applied core collection of germplasm, SSR, fluorescent molecular markers, DNA molecular identification

Table S1

Information of 46 pairs of primer used in this study"

SSR引物
SSR primer
对应染色体
Corresponding chromosome
SSR重复基元
SSR repeat type
上游引物序列
Forward primer
(5°-3°)
下游引物序列
Reverse primer
(5°-3°)
CcSSR008 1 (CAT)6 CCACACCCATGAGCAACTCCCC CCCACACAATATTTTACCAGGGGGCA
CcSSR031 1 (CAT)6 GCCACACCCATGAGCAACTCCC CCAGGGGGCATGCAAATTTTTCAATCA
CcSSR039 1 (TCT)9 TGCTAAGCCTCTCTTCTGTTCTGCT ACAAAGCAGCAAGCTGGGCACT
CcSSR045 1 (TGC)4.3 AGCTCGCATACCCGACCCGT GCATCGGTTTGGGGCGGACA
CoSSR049 1 (TCTTT)3 GGCACGAGGGAACATCAACCA AAAGGAGCCGCCATAGATCTCCA
CoSSR121 1 (ACA)9.3 TGACAATGATTACGCCAAGCTTCTGA AGGTTCAGTTGTGGTTGGTGTGGT
CoSSR122 1 (AGA)9.3 ACAGCCATTACCACCACACCAACA GGTGGTGGGACACCTGGTGGA
CoSSR133 1 (CAA)32.3 GCCATTGCCTTCCCCTCCTCC TGGATCCAAATCGTAGCATTCCCCT
CcSSR011 2 (TCA)7.3 CCGCCGGTTTCTTACCATCCTCC TCCCGGCGGAGGAAACCTGA
CcSSR015 2 (TTCT)3.3 GCTTTGTGATTGTTTCAAAGGTGGCT AGGCATTAGGCCTTGTAGAGAAACCA
CcSSR029 2 (GAA)4.3 CCAGAGCAACTGCTTCTGAAAGCG CCGATTGTATAAAGTGCAAGGCCGA
CcSSR038 2 (CCT)4.3 GGCCCACTGATTCTCCCGACG TGCTGATTTCGCCAGGGTCG
CoEMS217 2 (GGA)4 TTCGCCTCCACCCCTAACCCT TGCTGCTGCAACCGTGGCTT
CoEMS250 2 (ATT)6.3 CCCCCAAAGTTGGCCATCCCA GGAACCAAAGGGAAAAGCCAAAGCA
CoSSR136 2 (CAA)15.3 GGCGCGGACAATGGCAGGAT ACGCACGGCCTGTAAGAGCG
CoSSR244 2 (TTC)12 GCGCCGTCGATCTCTCTGGC AAGGATTGGCCCCACCCCCA
CoSSR254 2 (AAG)6.7 CTGCCAGCTCCCCACAAGCC TGCCTCATAGGAGCCAATGGGAAGT
CcSSR007 3 (ATG)9 TCCGCAGCAACCCCACCAAC ACACAAGGGAGCAAGAGCTAACAACA
CcSSR014 3 (TA)7.5 TGGCACCGGTGATCCTCTTTGGA CCCCTGGGGATCTCTTCTTCCTTCC
CcSSR036 3 (GAT)5.7 CCGCCCGGGCAGGTACTACT TCCTCCTCTCCTTCCTCCCCTT
CoSSR087 3 (CTT)5.3 ACGACGCCATTTTGACCCAAGC TGGGATCATCGAAGGGTGAAGCGT
CoSSR146 3 (TTC)7.7 CCACCAAGCAAGGTGAATGCCC ACACTCTAGATACCTTGATGGGGCTC
CcID167 4 A/AAAG AGAACTCGTCGGATTTTATC ACTCTTTGTCTCCCACACTG
CcSSR019 4 (CCG)4.7 CCACCACCACCACCACCAGC GGCCTGCTTCTGAGCCCTGC
CcSSR020 4 (CTT)5.7 GGGTTCAGTCCGTTCTGGACTCTT CGTCGGAAATGGTTTTTGATTGACGG
CcSSR024 4 (GTG)5.3 GGGGATTACCGATGCCGCGA CACCACCCACCACCGCACAA
CoEMS474 4 (ACA)5.3 TGGTGGTGGTGGTGGAGGGT AGCTTGCATTTGTCCAAACGGCG
CoSSR068 4 (TG)21 AGGTTTATCGGTTTCTGCAGGGGT TGCGGTGGGATTTGGGTGCC
CoSSR119 4 (GA)13 ACCAAATCGGAAGCATCAAACAAACAG TCTTGACAACACTGGTCCTCTGCAT
CcSSR027 5 (CT)8 ACAGCCGTGCATGGCGAAGT TGAGGCTTGCAAACAGGAGGGT
CoEMS333 5 (GT)13 TGCCGCGGCTTCATCTAGACC GGGAACGCCTTACGCTCCCT
CoEMS523 5 (TTG)6.3 AGTGGCGGCAGAGGCACAAG CAGCAGCGGCTCCTCCATGA
CoSSR083 5 (GA)6 TGCAGGGCTGTTGTGGCTGC TGGTGGTGGTGGGTTGAAATGTCC
CoSSR094 5 (GAA)5 ACGCCTCCTAAGAGGGATGCCA TGTGGCCTTTTGAGGAGGTGC
CcSSR001 6 (AAAAG)3.4 TGAAAGGAGCCGCCATAGATCTCC GGATCTTTCGAGCTCTGGAGTCTGC
CoSSR072 6 (CAA)7 TGCCGCACCAAACAATGAGCA TCCGCAGGTGTCCTTCTCCCA
CoSSR086 6 (ACC)7.3 ACCATGATGCAAAGAATGGATGCCT TGTCCTCCAGCCTCTTGTTCCCT
CoSSR100 6 (TTTA)7.5 AAGCAACCAATATAGTCGCACTTGTCA TGAAATGGGCCCAAGCCCAAG
CcID066 7 C/CCCTGA AAGTCTTGCTATTAATGCCC TTCAACAGTATGGTGCTCAA
CcID071 7 G/GACAAAGCT CTCTCAACCCAAAGCAAAAG CTGAAATGAAAAAAGCAACA
CcID109 7 A/ACTGC TGAGTGTATAGAGGCGCAGC CATTTCATCATCAAAGGCAT
CoSSR090 7 (CT)12 TCGCGGAAACCACCTGCACA AGCCCCAATTCTTGATGGAAGGGA
CoSSR092 7 (CT)7.5 GGCGAGGGGAGATGAATGGGGA TGCCGAGTGTGTGTATGTGGGGA
CoSSR099 7 (AAG)4.7 GCAGCCTGCGGTCGACTCTG CTTGCGCGTTGGGCCATGCT
CoSSR164 7 (TG)14 CCCCCATATCTCCCATTGTACCTGC AGGGTCGGCCAAACCCACCA
CoSSR179 7 (AG)30 GGGAGAGAGAGAGAGAGAGAGAGAGAG ACAACACGTACCCCACCTTACGC

Table 1

Applied core collection of jute"

组Group 序号Number 产地或来源
Origin
种质名称
Name
特性
Characteristics
1 1 中国广东省广州市
Guangzhou, Guangdong, China
广东独尾麻
Guangdongduweima
高秆
Tall plant height
2 中国福建省龙海市
Longhai, Fujian, China
古农红皮
Gunonghongpi
高秆
Tall plant height
3 中国福建省福州市
Fuzhou, Fujian, China
梅峰4号
Meifeng 4
高秆
Tall plant height
4 中国福建省福州市
Fuzhou, Fujian, China
福黄麻2号
Fuhuangma 2
高秆
Tall plant height
5 中国福建省漳州市
Zhangzhou, Fujian, China
粤引长果1号
Yueyinchangguo 1
高秆
Tall plant height
6 中国湖南省长沙市
Changsha, Hunan, China
中长黄1号
Zhongchanghuang 1
高秆
Tall plant height
7 中国贵州省
Guizhou, China
甜麻
Tianma
高秆
Tall plant height
2 8 中国福建省三明市
Sanming, Fujian, China
闽麻273
Minma 273
茎粗
Large stem diameter
9 中国福建省
Fujian, China
闽麻737
Minma 737
茎粗
Large stem diameter
10 中国湖南省长沙市
Changsha, Hunan, China
中黄麻1号
Zhonghuangma 1
茎粗
Large stem diameter
11 中国福建省福州市
Fuzhou, Fujian, China
福农4号
Funong 4
茎粗
Large stem diameter
12 中国贵州省
Guizhou, China
甜麻
Tianma
茎粗
Large stem diameter
3 13 中国湖南省沅江市
Yuanjiang, Hunan, China
淡红皮10号
Danhongpi 10
鲜皮厚
Large fresh bark thickness
14 中国福建省福州市
Fuzhou, Fujian, China
福黄麻2号
Fuhuangma 2
鲜皮厚
Large fresh bark thickness
15 中国湖南省长沙市
Changsha, Hunan, China
中黄麻1号
Zhonghuangma 1
鲜皮厚
Large fresh bark thickness
16 巴基斯坦
Pakistan
巴长4号
Bachang 4
鲜皮厚
Large fresh bark thickness
4 17 中国四川省罗江县
Luojiang, Sichuan, China
圆子麻
Yuanzima
单株鲜皮重
Large fresh bark weight per plant
18 中国福建省福州市
Fuzhou, Fujian, China
福黄麻2号
Fuhuangma 2
单株鲜皮重
Large fresh bark weight per plant
19 中国湖南省长沙市
Changsha, Hunan, China
中黄麻1号
Zhonghuangma 1
单株鲜皮重
Large fresh bark weight per plant
20 马里
Mali
807元引马里
807 yuanyinmali
单株鲜皮重
Large fresh bark weight per plant
5 21 中国广东省广州市
Guangzhou, Guangdong, China
广东独尾麻
Guangdongduweima
高纤维素
High cellulose
22 中国湖南省长沙市
Changsha, Hunan, China
D-154 高纤维素
High cellulose
23 中国台湾省
Taiwan, China
新隆黄麻
Xinlonghuangma
高纤维素
High cellulose
24 中国福建省漳州市
Zhangzhou, Fujian, China
粤引长果1号
Yueyinchangguo 1
高纤维素
High cellulose
25 中国福建省福州市
Fuzhou, Fujian, China
福农1号
Funong 1
高纤维素
High cellulose
26 中国福建省福州市
Fuzhou, Fujian, China
福农4号
Funong 4
高纤维素
High cellulose
6 27 中国广东省广州市
Guangzhou, Guangdong, China
广东独尾麻
Guangdongduweima
低木质素
Low lignin
28 中国湖南省长沙市
Changsha, Hunan, China
D-154 低木质素
Low lignin
29 中国台湾省
Taiwan, China
新隆黄麻
Xinlonghuangma
低木质素
Low lignin
30 中国福建省漳州市
Zhangzhou, Fujian, China
粤引长果1号
Yueyinchangguo 1
低木质素
Low lignin
31 中国福建省福州市
Fuzhou, Fujian, China
福农1号
Funong 1
低木质素
Low lignin
32 中国福建省福州市
Fuzhou, Fujian, China
福农4号
Funong 4
低木质素
Low lignin
7 33 中国福建省龙海市
Longhai, Fujian, China
古农红皮
Gunonghongpi
高纤维强力
High fiber strength
34 中国福建省
Fujian, China
闽麻737
Minma 737
高纤维强力
High fiber strength
35 中国福建省漳州市
Zhangzhou, Fujian, China
闽麻429
Minma 429
高纤维强力
High fiber strength
36 中国湖南省沅江市
Yuanjiang, Hunan, China
宽叶长果
Kuanyechangguo
高纤维强力
High fiber strength
37 印度
India
翠绿
Cuilyu
高纤维强力
High fiber strength
8 38 中国台湾省
Taiwan, China
早生赤
Zaoshengchi
高纤维支数
High fiber fineness
39 中国湖南省沅江市
Yuanjiang, Hunan, China
琼粤青
Qiongyueqing
高纤维支数
High fiber fineness
40 中国台湾省
Taiwan, China
台湾8号
Taiwan 8
高纤维支数
High fiber fineness
41 中国台湾省
Taiwan, China
台湾9号
Taiwan 9
高纤维支数
High fiber fineness
42 巴基斯坦
Pakistan
巴麻72-1
Bama 72-1
高纤维支数
High fiber fineness
43 肯尼亚
Kenya
SM/034 高纤维支数
High fiber fineness
44 巴基斯坦
Pakistan
巴长4号
Bachang 4
高纤维支数
High fiber fineness
9 45 中国湖南省长沙市
Changsha, Hunan, China
中黄麻1号
Zhonghuangma 1
抗病
Disease-resistant
46 中国台湾省
Taiwan, China
55台露
55 Tailu
抗病
Disease-resistant
47 中国广西壮族自治区
Guangxi, China
爱店野生种
Aidianyeshengzhong
抗病
Disease-resistant
48 巴基斯坦
Pakistan
巴麻72-1
Bama 72-1
抗病
Disease-resistant
49 中国湖南省沅江市
Yuanjiang, Hunan, China
广巴矮
Guangba’ai
抗病
Disease-resistant
50 肯尼亚
Kenya
SM/034 抗病
Disease-resistant
10 51 中国广东省紫金县
Zijin, Guangdong, China
紫金黄麻
Zijinhuangma
抗盐
Salt resistance
52 中国福建省福州市
Fuzhou, Fujian, China
三元吉口
Sanyuanjikou
抗盐
Salt resistance
53 中国福建省南靖县
Nanjing, Fujian, China
南靖青皮
Nanjingqingpi
抗盐
Salt resistance
54 中国湖南省长沙市
Changsha, Hunan, China
摩维1号
Weimo 1
抗盐
Salt resistance
55 中国福建省福州市
Fuzhou, Fujian, China
福农5号
Funong 5
抗盐
Salt resistance
56 中国贵州省
Guizhou, China
甜麻
Tianma
抗盐
Salt resistance
11 57 中国台湾省
Taiwan, China
台湾8号
Taiwan 8
抗旱
Drought resistance
58 中国台湾省
Taiwan, China
55台露
55 Tailu
抗旱
Drought resistance
59 缅甸
Burma
缅甸圆果
Miandianyuanguo
抗旱
Drought resistance
60 中国湖南省沅江市
Yuanjiang, Hunan, China
宽叶长果
Kuanyechangguo
抗旱
Drought resistance
61 中国福建省福州市
Fuzhou, Fujian, China
福农3号
Funong 3
抗旱
Drought resistance
62 中国贵州省
Guizhou, China
甜麻
Tianma
抗旱
Drought resistance
12 63 中国福建省南安市
Nan’an, Fujian, China
红铁骨
Hongtiegu
抗倒伏
Lodging resistance
13 64 中国福建省福州市
Fuzhou, Fujian, China
福农4号
Funong 4
生育期适宜
Suitable growth period
65 中国海南省
Hainan, China
海南黄麻
Hainanhuangma
生育期适宜
Suitable growth period
66 中国广东省广州市
Guangzhou, Guangdong, China
广东独尾麻
Guangdongduweima
生育期适宜
Suitable growth period
67 中国广东省广州市
Guangzhou, Guangdong, China
粤圆5号
Yueyuan 5
生育期适宜
Suitable growth period
68 中国湖南省沅江市
Yuanjiang, Hunan, China
琼粤青
Qiongyueqing
生育期适宜
Suitable growth period
69 中国湖南省长沙市
Changsha, Hunan, China
湘黄麻3号
Xianghuangma 3
生育期适宜
Suitable growth period
14 70 中国福建省福州市
Fuzhou, Fujian, China
闽革9号
Minge 9
高发芽率
High germination rate
71 中国福建省浦城县
Pucheng, Fujian, China
浦城黄麻
Puchenghuangma
高发芽率
High germination rate
72 越南
Vietnam
越南圆果
Yuenanyuanguo
高发芽率
High germination rate
73 中国广东省广州市
Guangzhou, Guangdong, China
粤引1号
Yueyin 1
高发芽率
High germination rate
74 中国台湾省
Taiwan, China
台湾8号
Taiwan 8
高发芽率
High germination rate
75 中国河南省
Henan, China
河南野生圆果
Henanyeshengyuanguo
高发芽率
High germination rate
76 马里
Mali
807元引马里
807 yuanyinmali
高发芽率
High germination rate
77 中国贵州省
Guizhou, China
甜麻
Tianma
高发芽率
High germination rate
78 中国福建省福州市
Fuzhou, Fujian, China
福农3号
Funong 3
高发芽率
High germination rate
15 79 中国广东省广州市
Guangzhou, Guangdong, China
粤圆2号
Yueyuan 2
抗种子老化
Seed aging resistance
80 中国福建省邵武市
Shaowu, Fujian, China
邵武黄麻
Shaowuhuangma
抗种子老化
Seed aging resistance
81 中国福建省闽侯县
Minhou, Fujian, China
闽侯白皮
Minhoubaipi
抗种子老化
Seed aging resistance
82 日本
Japan
日本长分青皮
Ribenchangfenqingpi
抗种子老化
Seed aging resistance
83 中国海南省海口市琼山区
Qiongshan District, Haikou, Hainan, China
海南琼山圆果
Hainanqiongshanyuanguo
抗种子老化
Seed aging resistance
84 中国广东省
Guangdong, China
紫苏麻
Zisuma
抗种子老化
Seed aging resistance
85 中国福建省南安市
Nanan, Fujian, China
南安蒿麻
Nananhaoma
抗种子老化
Seed aging resistance
86 中国广西壮族自治区梧州市
Wuzhou, Guangxi, China
梧州绿
Wuzhoulyu
抗种子老化
Seed aging resistance
87 巴基斯坦
Pakistan
巴麻72-2
Bama72-2
抗种子老化
Seed aging resistance
88 中国
China
长果红茎
Changguohongjing
抗种子老化
Seed aging resistance
16 89 印度
India
D154 骨干亲本
Elite parent
90 中国福建省福州市
Fuzhou, Fujian, China
卢滨圆果
Lubinyuanguo
骨干亲本
Elite parent
91 中国广东省广州市
Guangzhou, Guangdong, China
粤圆1号
Yueyuan 1
骨干亲本
Elite parent
92 印度
India
JRC-212 骨干亲本
Elite parent
93 孟加拉国
Bangladesh
选46
Xuan 46
骨干亲本
Elite parent
94 中国湖南省沅江市
Yuanjiang, Hunan, China
广丰长果
Guangfengchangguo
骨干亲本
Elite parent

Table 2

Information of 12 core pairs of SSR primes and their characteristic values of polymorphism"

Fig. 1

Characteristic band features of the primer of CcID071 detected by capillary electrophoresis"

Fig. 2

Characteristic band features of the primer CcSSR024 detected by capillary electrophoresis"

Table 3

Amplification results and code typing of 12 pairs of core primers detected with capillary electrophoresis"

引物名称Primer 荧光基团Fluorescent group 毛细管电泳多态性位点Observed number of alleles (na) 毛细管电泳多态性片段及编码
Code of capillary electrophoresis polymorphism fragments (bp)
CcID071 FAM (blue) 19 104/113 (1), 108/129 (2), 112/128 (3), 113 (4), 113/117 (5), 113/125 (6), 113/126 (7), 113/128 (8), 113/129 (9), 114 (A), 114/126 (B), 114/129 (C), 116/125 (D), 117 (E), 119/126(F), 122 (G), 125 (H), 126 (I), 129 (J)
CoSSR083 FAM (blue) 17 204 (1), 205 (2), 205/228 (3), 205/230 (4), 205/233 (5), 205/234 (6), 206/229 (7), 206/231 (8), 206/233 (9), 206/235 (A), 206/236 (B), 207/231 (C), 207/234 (D), 207/236 (E), 219/360 (F), 234/309(G), 359(H)
CoSSR146 FAM (blue) 7 199/216 (1), 200 (2), 201 (3), 210 (4), 217 (5), 218 (6), 219 (7)
CoSSR179 FAM (blue) 16 234 (1), 234/236 (2), 234/238 (3), 234/242 (4), 235/237 (5), 235/239 (6), 236 (7), 238/240 (8), 246/253 (9), 250/286 (A), 253 (B), 253/286 (C), 253/287 (D), 253/288 (E), 286/289 (F), 287/290 (G)
CoSSR049 FAM (blue) 7 193 (1), 194 (2), 195 (3), 196 (4), 197 (5), 202 (6), 203 (7)
CcSSR001 FAM (blue) 8 240 (1), 241 (2), 242 (3), 243 (4), 248 (5), 249 (6), 252 (7), 255 (8)
CoSSR119 HEX (green) 15 470 (1), 470/477 (2), 470/494 (3), 471 (4), 474/495(5), 477 (6), 489 (7), 490 (8), 491 (9), 492 (A), 493 (B), 494 (C), 495 (D), 496 (E), 497 (F)
CoSSR133 HEX (green) 9 202/219 (1), 218 (2), 218/222 (3), 218/223 (4), 219 (5), 219/222 (6), 222 (7), 222/238 (8), 223 (9)
CoSSR136 HEX (green) 19 262 (1), 291/323 (2), 292/323 (3), 295 (4), 295/407 (5), 317/322 (6), 317/323 (7), 323 (8), 323/402 (9), 323/407 (A), 355 (B), 357 (C), 398 (D), 398/407 (E), 399/432 (F), 402/407 (G), 403/407 (H), 422/425 (I), 422/434 (J)
CcSSR024 HEX (green) 4 196 (1), 197 (2), 199 (3), 200 (4)
CcSSR015 HEX (green) 5 193 (1), 194 (2), 195 (3), 203 (4), 204 (5)
CoEMS333 HEX (green) 14 231/311 (1), 231/326 (2), 234/345 (3), 237/326 (4), 310/326 (5), 311/326 (6), 319 (7), 319/326 (8), 319/344 (9), 326 (A), 326/344 (B), 327/345 (C), 344 (D), 345 (E)

Fig. 3

Bar code and quick response (QR) code of the applied core collection germplasm A: bar code DNA molecular identification of Yueyuan 5; B: bar code DNA molecular identification of Bachang 4; C: quick response (QR) code DNA molecular identification of Yueyuan 5; D: quick response (QR) code DNA molecular identification of Bachang 4."

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