基于黄麻转录组序列SNP位点的CAPS标记开发与验证

doi:10.3724/SP.J.1006.2020.94158

Abstract

Abstract:

Developing CAPS markers can provide a new and effective tool for genetic diversity analysis, germplasm identification and marker-assistant selection of jute. The transcriptional sequence analysis was carried out by Illumina HiSeq 4000 with jute 179 and the wild species in Aidian. Furthermore, the SNP loci were screened and primers related to lignin synthesis genes 4CL, COMT and transcription factor MYB were developed. CAPS markers were screened based on above SNP primers using dCAPS Finder2.0 and their polymorphism was verified. A total of 72,674 unigene sequences were got in jute transcriptome by assembly, with a length of 29,705,997 bp, a number of SNP loci of 67,567, and an average of 1 SNP per 440 bp. Thirty-nine pairs of SNP primers related to 4CL, COMT, and MYB were designed by Oligo8, of which 26 pairs of CAPS primers were screened, with a developing rate of 66.7%. Among the 26 pairs of CAPS markers, 11 pairs were polymorphic, with a polymorphic ratio of 43.2%. The screened CAPS markers could effectively distinguish 12 different accessions of jute germplasm, indicating CAPS is an ideal molecular marker which can lie a reliable tool used in genetic research of jute.

Key words: jute, transcriptome, SNP loci, CAPS markers, development

TAO Ai-Fen,YOU Zi-Yi,XU Jian-Tang,LIN Li-Hui,ZHANG Li-Wu,QI Jian-Min,FANG Ping-Ping. Development and verification of CAPS markers based on SNPs from transcriptome of jute (Corchorus L.)[J].Acta Agronomica Sinica, 2020, 46(7): 987-996.

Figures/Tables 7

Table 1

Fig. 1

Table 2

Table 3

Name and sequence of 39 pairs of SNP primers"

引物名称 Primer name	正向引物序列 Forward primer sequence (5′-3′)	反向引物序列 Reverse primer sequence (5′-3′)
4CL SNP1-1	GTGCTTTTCATCGGTGGTTT	TGTCGTAAAACTGCTGCTGG
4CL SNP1-2	CGATTTTCATCTCGGCATTT	GCCACCCATAGTTTTGGCTA
4CL SNP2-1	AGCTCCCATGAAAGCAAAGA	AGCTCCCATGAAAGCAAAGA
4CL SNP2-2	AGCTCCCATGAAAGCAAAGA	CGATTTTCATCTCGGCATTT
4CL SNP3-1	GAGCTTAGCGCGAGAAGTGT	TGTCGTAAAACTGCTGCTGG
4CL SNP3-2	TCTCGGCATTTCTAACCACC	GCCACCCATAGTTTTGGCTA
COMT SNP1F1	CACCGTTTTCCGTTGTTCTT	GTTGGAAAGCTAGCCAAACG
COMT SNP1F2	ACACTCCATCTTGGTTTGGC	GCTACCCATGGCGTTAAAAA
COMT SNP1F3	CCAGGTTTTCAACACTGCAA	GCATCTCCATTGGGAACACT
COMT SNP1F4	TGAAGATGACAATAAAGCGAAAA	GTGGACAATCAGTGTGTGGC
COMT SNP1F5	ATGCAAGAAAGCCGAGTTTG	GCAGGATTCCAAGGTTTCAA
COMT SNP2F1	AAGGTGATAGAAACACGCCG	GTTGGAAAGCTAGCCAAACG
COMT SNP2F2	ACTCCATCTTGGTTTGGCAC	GCTACCCATGGCGTTAAAAA
引物名称 Primer name	正向引物序列 Forward primer sequence (5′-3′)	反向引物序列 Reverse primer sequence (5′-3′)
COMT SNP2F3	GCTTAACCGGGTTGTTGATG	GCATCTCCATTGGGAACACT
COMT SNP2F4	TGAAGATGACAATAAAGCGAAAA	GCATCTCCATTGGGAACACT
COMT SNP2F5	ATGCAAGAAAGCCGAGTTTG	TTGATTGCATCATGTTGGCT
COMT SNP3F1	AATTTCACCGTTTTCCGTTG	GTTGGAAAGCTAGCCAAACG
COMT SNP3F2	ACTCCATCTTGGTTTGGCAC	AAAAACTGCGGTGGAGATTG
COMT SNP3F3	GCTTAACCGGGTTGTTGATG	CCATTGTCTGGAATGGCTTT
COMT SNP3F4	TGAAGATGACAATAAAGCGAAAA	TGGACAATCAGTGTGTGGCT
COMT SNP3F5	ATGCAAGAAAGCCGAGTTTG	CATAATCCGGGTGGAAAAGA
MYB SNP F1	TTGCAATGGATTTGTGCAAT	GATTCCCAGCAAATGGAAGA
MYB SNP F2	TGCCTTGTCCTCTCACTAAGC	TTGAGGCCACATGTTCTAATTG
MYB SNP F3	CCTTGCTATCATTGCCCATT	TTTATGGCCCTCAAAACTGG
MYB SNP F4	CAAAAGCTCATCCTCTTCCG	CAAACTGCTTGGCTCATCAA
MYB SNP F5	AAGTGTTCAAAGAGAAGCAGCA	TTATAGATGGCGATGGAGGC
MYB SNP F6	AAGCAGAAGCAAAATCCCAA	AAGTAGCCATGGAGGTGTGG
MYB SNP F7	GGCCATGAGTTTCAACGACT	GACGGGAAGAGAAAACCCTT
MYB SNP F8	CTGCGTTTGTAACCCCAGAT	GCTTCCTCTTCTGCTTCTCG
MYB SNP F9	CGACTCTTTCGGGACTCAAG	TCGTCGGCGTTTAAGAAGTT
MYB SNP F10	TTACACCACCGTAACCGACA	AGATGTGGATCGGATCAAGG
MYB SNP F11	AAGGAAGCCATGGAAGGACT	ATGCTTCTACCAATGCCAGG
MYB SNP F12	TCGATCATCAGCAACCAAAA	GCATTGAATTTTCCGTGGTT
MYB SNP F13	CCTGATCTTAAGCGTGGCTC	TTTGGTGACGGAGTTGATGA
MYB SNP F14	GGCCATTGGAAAACTCAAAA	TGGATGAAGAGCCTTTCACA
MYB SNP F15	ATCTTTGCCCAAAAATGCTG	GCAATTACCTGCTTCCCAAA
MYB SNP F16	GAGAAGGGAAATGGCATCAA	CTTTGGTGGAACTGGAAGGA
MYB SNP F17	TTCTTCAGCTCTCCAACGCT	GGCTTGTGGTATTGTGAGCA
MYB SNP F18	CCCTTTCTAGCATATGGGCA	AACATCCCTCCATATTCATGTGT

Table 3

Table 4

Fig. 2

Fig. 3

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编号 Number	名称 Name	品种类型 Type of accessions
1	梅峰4号 Meifeng 4	圆果种 Corchorus capsularis
2	越南圆果 Yuenanyuanguo	圆果种 Corchorus capsularis
3	广东独尾麻 Guangdongduweima	圆果种 Corchorus capsularis
4	中黄麻1号 Zhonghuangma 1	圆果种 Corchorus capsularis
5	日本大分青皮 Japanese Dafenqingpi	圆果种 Corchorus capsularis
6	福农1号 Funong 1	长果种 Corchorus olitoris
7	马里野生种 Maliyeshengzhong	长果种 Corchorus olitoris
8	广西长果 Guangxichangguo	长果种 Corchorus olitoris
9	日本5号 Japanese 5	长果种 Corchorus olitoris
10	翠绿 Cuilyu	长果种 Corchorus olitoris
11	龙溪长果 Longxichangguo	长果种 Corchorus olitoris
12	台湾加利麻 Taiwanjialima	圆果种 Corchorus capsularis

SNP位点的数目 Number of SNP loci	对应unigene序列的数目 Corresponding number of unigenes	所占比例 Ratio of SNP (%)
0-1	66,525	91.53
1-2	2092	2.88
2-3	1277	1.76
3-4	948	1.30
4-5	735	1.01
5-6	258	0.35
6-7	234	0.32
7-8	174	0.24
>8	431	0.59

序号 Code	引物名称 Primer name	unigene编号 unigene code	内切酶的名称 Endonuclease name
1	4CL CAPS1-1	unigene_17597	Ssp I
2	4CL CAPS2-1	unigene_17597	Ssp I
3	4CL CAPS3-1	unigene_17597	Ssp I
4	COMT CAPS1-1	unigene_04800	Cla I
5	COMT CAPS1-3	unigene_09002	Bsi YI
6	COMT CAPS1-5	unigene_08713	Ava III
7	COMT CAPS2-1	unigene_04800	Cla I
8	COMT CAPS2-3	unigene_09002	Bsi YI
9	COMT CAPS2-5	unigene_08713	Ava III
10	COMT CAPS3-1	unigene_04800	Cla I
11	COMT CAPS3-3	unigene_09002	Bsi YI
12	COMT CAPS3-5	unigene_08713	Ava III
13	MYB CAPS1	unigene_47261	Psi I
14	MYB CAPS2	unigene_17018	Mse I
序号 Code	引物名称 Primer name	unigene编号 unigene code	内切酶的名称 Endonuclease name
15	MYB CAPS3	unigene_53709	Mbo II
16	MYB CAPS5	unigene_64377	Mnl I
17	MYB CAPS6	unigene_10508	Mbo I
18	MYB CAPS7	unigene_21631	Mfe I
19	MYB CAPS8	unigene_31305	Sec I
20	MYB CAPS9	unigene_16840	Hpy99 I
21	MYB CAPS11	unigene_02399	Alu I
22	MYB CAPS12	unigene_02162	Asu I
23	MYB CAPS13	unigene_46122	Sec I
24	MYB CAPS14	unigene_10460	Tsp RI
25	MYB CAPS17	unigene_59879	Rsa I
26	MYB CAPS18	unigene_49512	Mae I

Development and verification of CAPS markers based on SNPs from transcriptome of jute (Corchorus L.)

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