Development and Application of VEGMarkerDB：a Molecular Marker Database for Brassica Vegetable Crops

doi:10.16420/j.issn.0513-353x.2025-0204

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (5): 1285-1300.doi: 10.16420/j.issn.0513-353x.2025-0204

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Development and Application of VEGMarkerDB：a Molecular Marker Database for Brassica Vegetable Crops

YANG Baoju¹^,², HE Xiaoning³, CHEN Haixu², CAI Xu², HOU Jiawei², LI Yufang², WANG Hui¹, WANG Xiaowu²^,^*(), WU Jian²^,^*()

¹ College of Horticulture，Qingdao Agricultural University，Qingdao，Shandong 266000，China
² State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China
³ Institute of Plant Sciences Paris-Saclay (IPS2)，Orsay 91405，France

Received:2025-03-06 Revised:2025-05-06 Online:2025-05-23 Published:2025-05-21
Contact: WANG Xiaowu, WU Jian

Abstract

Abstract:

As a direct characterization of genetic polymorphisms at DNA level，molecular markers have important application value in vegetable genetic research. Aiming at the problems of complex operation and low efficiency of primer design in existing molecular marker analysis tools，in this study，VEGMarkerDB，a molecular marker database for Brassica vegetables，was developed based on SNP and InDel markers with integrated data storage and high-throughput primers design. The system adopts B/S architecture，builds back-end services based on Django framework，and combines MySQL database management system. Resequencing data and VCF variation files of cabbage（Brassica rapa），cabbage（B. oleracea），rapeseed（B. napus）and mustard（B. juncea）were integrated. The database provides mutation site retrieval services，which can be queried according to the location of chromosomes to realize the rapid location of molecular marker information. This system provides real-time feedback on candidate primer parameters（e.g.，Tm value，GC content，amplicon length）via an interactive visual interface，while automatically generating standardized experimental reports. Experimental validation using laboratory materials demonstrated a KASP primer design success rate exceeding 95%. The system’s technical innovations include：(1) Establishment of an integrated management platform for multispecies molecular marker resources in Brassica vegetables；(2) Implementation of web-based parallel primer design architecture；(3) Development of a closed-loop optimization mechanism integrating experimental validation with algorithmic refinement. As a modular technical platform accessible at VEGMarkerDB（vegmarker.top/），this system not only advances molecular breeding research in vegetable crops but also demonstrates extensibility to other agricultural systems through its adaptable framework.

Key words: Brassica, molecular marker, database, high-throughput on-line primer design, KASP

YANG Baoju, HE Xiaoning, CHEN Haixu, CAI Xu, HOU Jiawei, LI Yufang, WANG Hui, WANG Xiaowu, WU Jian. Development and Application of VEGMarkerDB：a Molecular Marker Database for Brassica Vegetable Crops[J]. Acta Horticulturae Sinica, 2025, 52(5): 1285-1300.

Figures/Tables 18

References 34

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工具/系统 Tool/system	是否支持批量引物设计 Batch primer design	平均响应时间/s Average response time
Primer3	否No	10.0
Primer-BLAST	否No	16.0
BatchPrimer3	是Yes	12.0
VEGMarkerDB	是Yes	6.7

工具/系统 Tool/system	是否支持批量引物设计 Batch primer design	平均响应时间/s Average response time
Primer3	否No	10.0
Primer-BLAST	否No	16.0
BatchPrimer3	是Yes	12.0
VEGMarkerDB	是Yes	6.7

系统和软件 System and software	版本 Version	系统和软件 System and software	版本 Version
操作系统	Red Hat Enterprise Linux (RHEL) 7	Python	3.9
MySQL	8.0.36 MySQL Community Server	Django	4.2.11
Nginx	1.20.1	Sratoolkit	2.10.8
BLAST	2.16.0	Element UI	2.15.14
muscle	5.1.linux64	Openpyxl	3.1.2
vue/cli	5.0.8

系统和软件 System and software	版本 Version	系统和软件 System and software	版本 Version
操作系统	Red Hat Enterprise Linux (RHEL) 7	Python	3.9
MySQL	8.0.36 MySQL Community Server	Django	4.2.11
Nginx	1.20.1	Sratoolkit	2.10.8
BLAST	2.16.0	Element UI	2.15.14
muscle	5.1.linux64	Openpyxl	3.1.2
vue/cli	5.0.8

字段名Field name	字段类型Field type	说明Instructions
Chr	varchar	物种染色体 Species chromosome
Pos	int	变异位点位置 Variant position
Ref	longtext	参考基因序列或碱基 Reference allele
Alt	longtext	变异基因序列或碱基 Alternative allele
PRODUCT_LEN	varchar	PCR产物长度 PCR product length
Tm_L	varchar	左引物 T_m 值 Forward primer T_m
GC_L	varchar	左引物 GC 含量 Forward primer GC content
SEQ_L	varchar	左引物序列 Forward primer sequence
Tm_R	varchar	右引物 T_m 值 Reverse primer T_m
GC_R	varchar	右引物 GC 含量 Reverse primer GC content
SEQ_R	varchar	右引物序列 Reverse primer sequence
Gene_id	varchar	该位点所在基因ID Gene ID at variant site
Diff_Tm	varchar	左右引物T_m差值 T_m difference between primers
Marker_Type	varchar	变异类型 Variant type
Num_id	int	物种ID Species ID

Development and Application of VEGMarkerDB：a Molecular Marker Database for Brassica Vegetable Crops

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Figures/Tables 18

References 34

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物种ID字段枚举值 Enumeration values of species ID field	物种 Species
1	白菜 Brassica rapa
2	甘蓝 B. oleracea
3	甘蓝型油菜 B. napus
4	芥菜 B. juncea
5	黄瓜 Cucumis sativus

染色体 Chromosome	SNP位置 Position	参考等位基因型引物 Ref allele primer	变异等位基因型引物 Alt allele primer	反向通用引物 Common primer
A02	8 898 094	TGGATCTAAGGCCTTCTCAAGTTC	TGGATCTAAGGCCTTCTCAAGTTA	CCACCAATCTCAACTCTTGGCTT
A09	37 693 232	GATCCGAACTCTGCTGGTCCAA	GATCCGAACTCTGCTGGTCCAT	ATGCATTGGATTGTTCCCTTCCG
A05	4 048 250	GAGAAGACAGAGGAGATTGAGA	GAGAAGACAGAGGAGATTGAGG	TCCATTGCCATCTTCTGCTCTT
A07	28 025 341	AGTCTTCACAGGCTTTTACCAGGGCC	AGTCTTCACAGGCTTTTACCAGGGCG	GGGGTTTTCTCCAATCCCGGTTATAGA
A10	18 732 379	TGTAACCTCCAACGACAAATACA	TGTAACCTCCAACGACAAATACT	TTCTCTAGGCAGAACACCAGGAA
A10	8 561 457	TTCTCCCTCCCTGTAAACTCCTC	TTCTCCCTCCCTGTAAACTCCTT	TGGTTTCATGCTACAGATCTTGCA
A07	19 593 473	TATTTACCTCTCATTGCTACTGT	TATTTACCTCTCATTGCTACTGG	TAGGCACTCTTTTCACTATAAGCC
A02	589 526	GCCATGAGCTTTTCCCTTCCTT	GCCATGAGCTTTTCCCTTCCTC	TGGATCTCAACCCTAGGCTTTGA
A06	9 709 533	GGGCACATTATTGACTGGAGATATCA	GGGCACATTATTGACTGGAGATATCT	CATCTCCTGCACAGCTAACTCAG
A03	8 320 577	CGCAGAAGGGAAGAGGAGTTTAAT	CGCAGAAGGGAAGAGGAGTTTAAG	TTCTTGCTCCTCTTCCTCACTCA

染色体 Chromosome	SNP位置 Position	参考等位基因型引物 Ref allele primer	变异等位基因型引物 Alt allele primer	反向通用引物 Common primer
C02	662 742	AGGACAGAAACGAATGGAGGTTC	AGGACAGAAACGAATGGAGGTTG	CAAGCTCTCTTATCAGCAGGTGG
C02	1 174 749	CCGGTATATGCACACAATTATTA	CCGGTATATGCACACAATTATTC	ACAACGCCATAAAAGAGATAG
C02	1 845 663	CTCCTCGTCGAGCTCGGA	CTCCTCGTCGAGCTCGGC	AACGCCAAAGTCCAAATCGAGAA
C02	1 859 262	AAGAATCTCAAGCCTTATAGGGAACT	AAGAATCTCAAGCCTTATAGGGAACC	CTCGCATAGTTCAGAAACTTGGG
C02	1 931 270	GGTTTTGATTGTTTCGGTTGGGT	GGTTTTGATTGTTTCGGTTGGGA	GGGCAAAACACCAGAACCAAAAA
C02	1 949 652	GAGAGGAAACCGGCAAGGTCTAT	GAGAGGAAACCGGCAAGGTCTAC	AAACCTTCCTCGGATGTTCAACC
C02	2 533 572	TTACTGCCTGCACACGTCGGAGAAC	TTACTGCCTGCACACGTCGGAGAAG	ACAGATTTGGAGAAGCCGTTGAGG
C02	2 534 457	CACTTTTGTTGCTTCGATACGCA	CACTTTTGTTGCTTCGATACGCG	AGATTACAGGAACGGGAACTTCG
C02	2 542 265	GTAACTTATTTTTGTTTTTAGTCACT	GTAACTTATTTTTGTTTTTAGTCACA	GACAGATCTCTGACATCAATTG
C02	2 543 737	AGAAGTTTAATGTAGACTTGCGAGC	AGAAGTTTAATGTAGACTTGCGAGT	CTTGTGTCGAGAGCCTCAAAACT

引物参数Primer parameter	说明Instruction
product_size	PCR产物长度 PCR product length
type	引物类型（左引物/右引物）Primer type（Forward/Reverse）
start	引物起始位置 Primer start position
end	引物终止位置 Primer end position
3'diffall	引物3' 端错配评分 3' End mismatch score
Tm	引物T_m值 T_m value
GCcontent	引物GC碱基的含量百分比 GC content
end_stability	引物3'端稳定性 3' End stability（ΔG，kcal · mol^-1）
hairpin	引物自身发夹结构评分 Hairpin structure score
primer_seq	引物序列 Primer sequence
ReverseComplement	反向引物的互补序列 Reverse primer complementary sequence
penalty	引物惩罚值 Primer penalty score
compl_any	引物间任意位置的互补性评分 Complementarity score at any position between primers
compl_end	引物3'端互补性评分 3' End complementarity score
score	引物综合得分 Overall primer score

引物名称 Primer name	DNA样品总数 Total DNA sample	SNP分型正确数 Correct number of SNP type	SNP分型正确率/% SNP typing accuracy rate
662 742	84	84	100
1 174 749	84	83	98.8
1 845 663	84	84	100
1 859 262	84	84	100
1 931 270	84	84	100
1 949 652	84	84	100
2 533 572	84	82	97.6
2 534 457	84	84	100
2 542 265	84	84	100
2 543 737	84	84	100

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