黄麻应用核心种质的DNA分子身份证构建

doi:10.3724/SP.J.1006.2021.04022

Abstract

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

GUO Yan-Chun, ZHANG Li-Lan, CHEN Si-Yuan, QI Jian-Min, FANG Ping-Ping, TAO Ai-Fen, ZHANG Lie-Mei, ZHANG Li-Wu. Establishment of DNA molecular fingerprint of applied core germplasm in jute (Corchorus spp.)[J].Acta Agronomica Sinica, 2021, 47(1): 80-93.

Figures/Tables 7

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 S1

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 1

Table 2

Fig. 1

Fig. 2

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)

Table 3

Fig. 3

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

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