CN102925435B - Molecular markers closely linked to tuberculate fruit gene Tu in cucumber - Google Patents

Molecular markers closely linked to tuberculate fruit gene Tu in cucumber Download PDF

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CN102925435B
CN102925435B CN201210382890.8A CN201210382890A CN102925435B CN 102925435 B CN102925435 B CN 102925435B CN 201210382890 A CN201210382890 A CN 201210382890A CN 102925435 B CN102925435 B CN 102925435B
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cucumber
seq
gene
fruit
knurl
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CN102925435A (en
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杨绪勤
潘俊松
何欢乐
蔡润
李月
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Shanghai Jiaotong University
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Shanghai Jiaotong University
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Abstract

The invention relates to two molecular markers closely linked to a tuberculate fruit gene Tu in a cucumber. The first molecular marker is named Y32 and is composed of a DNA (deoxyribonucleic acid) segment shown as SEQ ID NO.1 and a DNA segment shown as SEQ ID NO.2, wherein the DNA segment shown as SEQ ID NO.1 is linked to the tuberculate fruit gene Tu, and the DNA segment shown as SEQ ID NO.2 is linked to a non-tuberculate fruit gene tu; and the second molecular marker is named Y46 and is composed of a DNA segment shown as SEQ ID NO.3 and a DNA segment shown as SEQ ID NO.4, wherein the DNA segment shown as SEQ ID NO.3 is linked to the tuberculate fruit gene Tu, and the DNA segment shown as SEQ ID NO.4 is linked to the non-tuberculate fruit gene tu. Compared with the disclosed SCAR marker C-SC69 and SSR marker 16203, the two molecular markers Y32 and Y46 are linked to the Tu gene locus more closely, and the Tu gene has been located in the 50Kb interval, thereby being more helpful to establish a molecular marker-aided breeding system of cucumbers with/without tuberculate fruits.

Description

With the closely linked molecule marker of cucumber fruit tumor gene Tu
Technical field
The present invention relates to the molecule marker of gene engineering technology field, particularly two and the closely linked molecule marker of cucumber fruit tumor gene Tu.
Background technology
Cucumber (Cucumis sativus L.) is the herbaceous plant that Curcurbitaceae (Cucurbitaceae) Cucumis (Cucumis) is overgrow for a year, originate in the north India area of the southern foot, the Himalayas of warm and moist, import China's cultivation history of existing more than 2000 year into, China is the Secondary centers of origin of cucumber.Cucumber is as one of the world ten large important vegetable crops, one of Ye Shi China main cultivation vegetable crop.
Fruit is the most important parts of cucumber economic characters, and cucumber fruits belongs to Peponidium, is formed by ovary and common growth of holder.In cucumber fruits, having an important proterties is fruit knurl, and fruit knurl is the strumae on cucumber fruits surface.The research of fruit tumor gene starts from 1913, and having fruit knurl is the wild characters of cucumber, and fruit knurl proterties is by Tu(Tuberculate fruit) gene regulating, there is fruit knurl (Tu) for dominant, the knurl of having no result (tu) is for recessive.Zhang Weiwei in 2009 etc. utilize 247 F 2fruit tumor gene Primary Location is incited somebody to action between the 5th karyomit(e) SSR mark 16203 and SCAR mark C_SC933 by colony, genetic distance is respectively 1.4cM and 5.9cM, detailed results can be referring to: what Zhang W W etc. delivered at " Theoretical and Applied Genetics " (theoretical applied genetics) the 120th volume the 3rd phase 645-654 page in 2009 is entitled as " Identi cation and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.) " (cucumber fruit tumor gene compact linkage molecule mark Primary Location) literary composition, above-mentioned mark also exists analysis colony relatively little, the problems such as linkage distance is relatively far away.
In breed cucumber, find the equal spinosity of cucumber fruits, but on some kind fruit, there is no fruit knurl, thorn and knurl are two different proterties, the formation of thorn is gene-determined by Gl, and Tu gene determines the formation of knurl, although thorn and knurl proterties are by different gene-determined, but there are some researches show that thorn has Recessive epistatic effect for knurl, the genetic analysis result of the emerging segregating population of Cao Chen shows to control stem, leaf, the hairless gene of fruit surface hair proterties to control the fruit tumor gene of fruit knurl proterties exist Recessive epistatic effect (Cao Chenxing etc. cucumber cauline leaf stings the genetic affinity of proterties without hair proterties and fruit knurl. gardening journal, 2001, 28 (6): 565-566).Therefore, the research of fruit tumor gene Tu will contribute to disclose the molecular mechanism that cucumber fruit Ci Jiyin forms, for cucumber is hereditary and breeding work lays the foundation.
Along with the development of biotechnology level, the method of clone's goal gene also emerges in an endless stream, map based cloning method utilize the genetic linkage analysis of segregating population or chromosome abnormalty by the assignment of genes gene mapping to the basis of a chromosomal particular location, by building highdensity Molecular Linkage Map, find and the closely linked molecule marker of goal gene, constantly dwindle candidate region and then clone this gene.SSR (Simple Sequence Repeats) mark has advantages of that good stability, polymorphism are high and extensive applicable, finds the closely linked mark with fruit tumor gene Tu, can be this gene of next step map based cloning and lays a solid foundation.
Along with the raising of people's living standard, quality breeding has been mentioned critical positions.Cucumber fruits thorn knurl proterties belongs to sensible quality category.The cucumber of American-European greenhouse is have no result knurl, few pericarp stinging, and is called Fruit Cucumber, and the 2-3 that its market value is common cucumber doubly.Smooth in appearance cucumber pollutes few, easy to clean, and sanitary edible, is the desirable kind of pollution-free vegetable.Show after testing: sting less cucumber pulp pesticide residue without knurl lower by 27% than spinosity cucumber, pericarp pesticide residue is low by 18%.Cucumber fruit tumor gene Tu controls the formation of fruit knurl, and its research will promote quality breeding process.In cucumber genetic breeding, be highly effective method with carrying out marker assisted selection with the closely linked molecule marker of object proterties, molecule marker is on DNA level, objective trait to be selected, there is advantages such as efficiently, fast, not being subject to envrionment conditions restriction, can select in seedling stage, accelerate the process of breeding.
Summary of the invention
Object of the present invention, is to overcome the deficiencies in the prior art, and two and the more closely linked molecule marker of cucumber fruit tumor gene Tu are provided.
The present invention is achieved by the following technical solutions:
One and the closely linked molecule marker of cucumber fruit tumor gene Tu, called after Y32, is made up of the DNA fragmentation shown in the DNA fragmentation shown in SEQ ID NO.1 and SEQ ID NO.2; Wherein the DNA fragmentation shown in SEQ ID NO.1 is chain with fruit tumor gene Tu, and the DNA fragmentation shown in SEQ ID NO.2 is with chain without tumor gene tu.
The closely linked molecule marker of above-mentioned and cucumber fruit tumor gene Tu, is obtained by the downstream primer amplification shown in the upstream primer shown in SEQ ID NO.5 and SEQ ID NO.6.This primer is synthetic by the raw work in Shanghai.
One and the closely linked molecule marker of cucumber fruit tumor gene Tu, called after Y46, is made up of the DNA fragmentation shown in the DNA fragmentation shown in SEQ ID NO.3 and SEQ ID NO.4; Wherein the DNA fragmentation shown in SEQ ID NO.3 is chain with fruit knurl Tu, and the DNA fragmentation shown in SEQ ID NO.4 is with chain without tumor gene tu.
The closely linked molecule marker of above-mentioned and cucumber fruit tumor gene Tu, is obtained by the downstream primer amplification shown in the upstream primer shown in SEQ ID NO.7 and SEQ ID NO.8.This primer is synthetic by the raw work in Shanghai.
The present invention utilizes molecule marker and chromosome walking method, provide two with the more closely linked stable SSR molecule marker of cucumber fruit tumor gene Tu, fruit tumor gene Tu is between two molecule markers that provide, and genetic distance is within 0.5cM, and physical distance is 50Kb left and right only; Due to the exploitation of all two molecule markers all with known Cucumber germplasm Serial relation, the physical map between two molecule markers that obtain therefrom, by being conducive to the final clone of Tu gene, is convenient to the foundation of molecular mark system.Molecule marker of the present invention can be applied to breeding practice easy, quick, high-throughput.
Brief description of the drawings
Fig. 1 is the pcr amplification result queue figure of Y32; S52 is for there being knurl parent; S06 is without knurl parent; F 1represent two parent filial generations; F 2random amplification represents at F 2in colony, 19 of random choose have knurl or without knurl plant pcr amplification result.Band representative is below chain with fruit tumor gene Tu, and band representative is above with chain without tumor gene tu.
Fig. 2 is the pcr amplification result queue figure of Y46; S52 is for there being knurl parent; S06 is without knurl parent; F 1represent two parent filial generations; F 2random amplification represents at F 2in colony, 19 of random choose have knurl or without knurl plant pcr amplification result.Band representative is below chain with fruit tumor gene Tu, and band representative is above with chain without tumor gene tu.
Fig. 3 is the chromosome walking schematic diagram of cucumber fruit tumor gene Tu: Y32 and Y46 representative and the closely linked molecule marker of Tu gene, and SSR16203 and C-SC933 represent the mark of having announced.What use is the cucumber variety genome sequence (http://cucumber.vcru.wisc.edu/wenglab/gy14-9930/index.html) of having announced in splicing: use be the sequence in Scaffold02633, the Scaffold00154 of gy14 kind and Scaffold000083, the Scaffold000234 of 9930 kinds, spliced sequence total length is 1300kb.× represent F 2the remaining exchange strain of colony.
Embodiment
One, the structure of hereditary segregating population and the qualification that exchanges individual plant
1, F 2the structure of colony
Europe greenhouse self-mating system S06 (female parent), the smooth surface knurl of having no result, white thorn is more tiny; South China type self-mating system S52 (male parent), there is fruit knurl on surface, black thorn is thicker, S06 self-mating system and S52 self-mating system open in " natural science progress " 2005 " structure of cucumber SRAP genetic linkage map and the assignment of genes gene mapping of flower joint position of beginning " literary composition (Pan Junsong etc. the structure of cucumber SRAP genetic linkage map and the assignment of genes gene mapping of flower joint position of beginning. natural science progress, 2005,15,167-172).The present embodiment utilizes these two parents to prepare cross combination, F 1for there being fruit knurl, black thorn is thicker, F 1produce F for selfing 2for colony.At 2200 strain F 2in individuality, qualification is with/without fruit knurl phenotype, and chi-square analysis method is verified.
2, the screening of exchange individual plant
The extraction of 2.1 Cucumber germplasm DNA
Ordinary method--CTAB method is extracted parent and F 2the total DNA of blade of segregating population.
2.2 mark scanning F 2segregating population
Utilize two molecule markers (Y32, Y46) of developing in the molecule marker SSR16203 of disclosed and Tu gene linkage and SCAR mark C_SC933 and the present invention to scan the F of above-mentioned acquisition 2segregating population, finds the difference individual plant of marker genetype (obtaining by analyzing aobvious hidden parent) and the Characters type (have knurl/without knurl), obtains the exchange individual plant of mark and Tu gene.PCR system: genomic dna 30 ng, primer 0.2 μ mol/L, 200 μ mol/L dNTPs, 2mmol/L MgCl 2, 1 × Taq damping fluid, 0.5 U TaqDNA polysaccharase, total reaction system is 10 μ L, wherein TaqDNA polysaccharase is purchased from Promega company.Pcr amplification program is: 94 DEG C of 5 min; 35cycles, 94 DEG C of 30s; 55 DEG C of 30s; 72 DEG C of 30s; 72 DEG C of 5 min.Above-mentioned PCR product detection method is: mark C_SC933 uses 3% agarose gel electrophoresis to show result; All the other (SSR16203, Y32, Y46) PCR products use 6% denaturing polyacrylamide gel electrophoresis to separate.
Polyacrylamide gel electrophoresis damping fluid is 1 × TBE, the permanent power of 50 W, electrophoresis 1h.After electrophoresis, carrying out silver dyes.Silver staining method is: the sheet glass with glue is put into stationary liquid, shake gently to indicator color fade, wherein consisting of of stationary liquid on shaking table: the volume ratio of Glacial acetic acid, dehydrated alcohol, distilled water is 1:10:100; With ultrapure washing 1min~3min; Offset plate after rinsing is put into staining fluid and shake half an hour, wherein the component of staining fluid is 2g/L Silver Nitrate; After offset plate after dyeing is put into ultrapure water rinsing 5s, put into the plastics casing that developing solution is housed, it is clear to shake gently to band, puts into tap water and rinses 3min; Dry under room temperature, take pictures after dry, wherein developing solution adds 15g NaOH and 3ml formaldehyde to mix to obtain in 1L distilled water.
The recovery of 2.3 polymorphic bandses, Cloning and sequencing
Polymorphic bands is cut from polyacrylamide gel, be placed in centrifuge tube, smash to pieces with rifle head, add ultrapure water to rinse three times, then add 95 DEG C of water-bath 15min of 10 ul ultrapure water, fast centrifuging and taking supernatant liquor, carries out pcr amplification with corresponding SSR primer, and PCR reaction system is: target stripe DNA 5 ul, primer 0.5 umol/L, 200 umol/L dNTPs, 1 × Taq Buffer, 1.5mmol/L MgCl 2, 2U Taq archaeal dna polymerase, total reaction system is 50 ul, wherein TaqDNA polysaccharase is purchased from Promega company.Target stripe pcr amplification program is: 94 DEG C of 5 min; 35cycles, 94 DEG C of 30s; 50 DEG C of 30s; 72 DEG C of 1min; 72 DEG C of 5 min.Goldview fluorescence dye 3ul will be added in PCR product, at 4 DEG C, placing 10min allows dyestuff with DNA combination, then add sample-loading buffer 2 ul, after mixing, separate by 1% agarose gel electrophoresis, under ultraviolet lamp, cut target fragment and put into the centrifuge tube of 1.5ml, reclaim test kit with DNA and reclaim, wherein DNA recovery test kit is that Shanghai raw work UNIQ-10 pillar DNA glue reclaims test kit, and production number is Cat.No.SK1132.Be connected by reclaiming product the pUCm-T vector system that adopts Shanghai Shen Neng betting office with carrier.The T-vector that is connected with target fragment is transformed and enters E.coli DH5 α competent cell with electric shocking method, bacterium liquid is evenly coated on the flat board of LB solid medium, the flat-plate inverted coating is placed in 37 DEG C of incubator overnight incubation, chooses bacterium, shakes bacterium and the detection of PCR bacterium liquid, carries out the mensuration of correlated series.
Two, chromosome walking and marker development
1, the merger of Cucumber germplasm sequence splicing
Utilize cucumber variety 9331 and the gy14 Cucumber germplasm sequence (http://cucumber.vcru.wisc.edu/wenglab/gy14-9930/index.html) announced, to in SSR molecule marker 16203 sequence scanning Cucumber germplasm 9930 databases, obtain Scaffold000083, the end sequence scanning Cucumber germplasm gy14 database of Scaffold000083 is obtained to Scaffold02633, end sequence scanning Cucumber germplasm 9930 databases of Scaffold02633 are obtained to Scaffold000234, the end sequence scanning Cucumber germplasm gy14 database of Scaffold000234 is obtained to Scaffold00154.In Scaffold00154 sequence, contain SCAR mark C_SC69 sequence,, annex and splice the sequence that obtains total length 1300Kb between SCAR mark C_SC69 and SSR mark 16203 these 4 Scaffold sequence alignments with DNAMAN software.
2, the exploitation of genetic molecule mark
The present invention carries out surface sweeping analysis by ssr analysis software to the 1300Kb sequence obtaining, use primer-design software Primer Premier5.0 to design primer to the SSR site obtaining, between two parents, carry out pcr amplification and use 6% denaturing polyacrylamide gel electrophoresis to detect.Find out the mark with polymorphism, the exchange strain in the 2200 group of hill bodies that screening obtains with SSR mark 16203 and SCAR mark C_SC933 again.The direction step that the polymorphism mark that is positioned at gene both sides reduces gradually to exchange strain is moved, last length fruit 2 nearest SSR sites of tumor gene Tu both sides produce difference (Fig. 1 and Fig. 2) between two parents, subsequently it checked order and obtain the sequence information in SEQ ID NO.1 and SEQ ID NO.2 and SEQ ID NO.3 and SEQ ID NO.4, these two marks called after Y32 and Y46 respectively, mark Y32 and Y46 remaining exchange strain in 2200 strain large groups remains respectively 4 strains and 2 strains.All SSR mark PCR reaction systems are: cucumber DNA 20ng, the each 0.2 μ mol/L of two-way primer, 200 μ mol/L dNTPs, 2mmol/L MgCl 2, 1 × Taq damping fluid, 0.5U TaqDNA polysaccharase, total reaction system is 10 μ l, wherein TaqDNA polysaccharase is purchased from Promega company.Amplification program is: 94 DEG C of 3min; 35cycles, 94 DEG C of 20s, 55 DEG C of 30s, 72 DEG C of 30s; 72 DEG C of 5min.
Above two molecule markers newly developed are through segregating population checking, all with Tu gene locus close linkage (Fig. 3, in figure, X represents remaining exchange strain).Owing to being all specific PCR amplification, therefore these marks have high stable.The high-density heredity and the physical map that utilize these marks to build, will contribute to the final clone of cucumber fruit tumor gene Tu.
The present invention utilizes fruit knurl parent S52 and the knurl parent S06 hybridization of having no result obtains F 1, F 1selfing obtains 2200 strain F again 2segregating population.Utilize cucumber variety 9930 and the gy14 Cucumber germplasm sequence (http://cucumber.vcru.wisc.edu/wenglab/gy14-9930/index.html) announced, the sequence between SCAR mark C_SC933 and SSR mark 16203 can be annexed to splicing.Splicing gy14 Cucumber germplasm sequence used has: Scaffold02633, Scaffold00154, splicing 9930 Cucumber germplasm sequences used has: Scaffold000083, Scaffold000234, spliced sequence total length is 1300kb.First with the colony of the SCAR mark C_SC933 having announced and 16203 these expansions of screening of SSR mark, find out exchange strain.And then find out SSR site with ssr analysis software, design primer software, to 1300kb, sequential analysis has designed a large amount of primers, find out the primer that has polymorphism between parent, exchange strain is screened and chromosome walking, finally determine that nearest both sides are marked between Tu/tu gene locus and also have respectively 4 and 2 exchange individual plants.The details of above-mentioned cucumber chromosome walking as shown in Figure 3.
The molecule marker SSR mark 16203 and the SCAR mark C_SC933 that in the present invention, relate to are open.That delivers at " Theoretical and Applied Genetics " (theoretical applied genetics) the 120th volume the 3rd phase 645-654 page in 2009 referring to Zhang W W etc. in detail is entitled as " Identi cation and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.) " (cucumber fruit tumor gene compact linkage molecule mark location) literary composition.
The E.coli DH5 α bacterial strain using in PCR product cloning order-checking in the present invention document " Li Xin, etc.Electrotransformation is prepared the E.coli competent cell research of high transformation efficiency.Food and biotechnology journal, 2007,26(6) 48~51 " in open; The E.coli DH5 α bacterial strain relating in the present invention can be obtained by openly commercially available commercial channel, is purchased from precious biotechnology (Dalian) company limited, CompanyAddress: No. 19, two street, northeast, Dalian Economic and Technological Development District.

Claims (2)

1. one and the closely linked molecule marker of cucumber fruit tumor gene Tu, called after Y46, is made up of the DNA fragmentation shown in the DNA fragmentation shown in SEQ ID NO.3 and SEQ ID NO.4; Wherein the DNA fragmentation shown in SEQ ID NO.3 is chain with fruit tumor gene Tu, and the DNA fragmentation shown in SEQ ID NO.4 is with chain without tumor gene tu.
2. the according to claim 1 and closely linked molecule marker of cucumber fruit tumor gene Tu, is characterized in that: obtained by the downstream primer amplification shown in the upstream primer shown in SEQ ID NO.7 and SEQ ID NO.8, pcr amplification program is: 94 DEG C of 5min; 35cycles, 94 DEG C of 30s; 55 DEG C of 30s; 72 DEG C of 30s; 72 DEG C of 5min.
CN201210382890.8A 2012-10-10 2012-10-10 Molecular markers closely linked to tuberculate fruit gene Tu in cucumber Expired - Fee Related CN102925435B (en)

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101302564A (en) * 2008-05-27 2008-11-12 周口市农业科学院 Primer sequence for screening wheat brown leaf rust-resistance and use thereof
CN101481737A (en) * 2009-01-08 2009-07-15 上海交通大学 Molecular marker tightly linked with Cucumis sativus tumor gene Tu
CN101985620A (en) * 2010-11-22 2011-03-16 深圳华大基因科技有限公司 Molecular marker SIsv1223 closely linked with millet herbicide-resistant gene

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101302564A (en) * 2008-05-27 2008-11-12 周口市农业科学院 Primer sequence for screening wheat brown leaf rust-resistance and use thereof
CN101481737A (en) * 2009-01-08 2009-07-15 上海交通大学 Molecular marker tightly linked with Cucumis sativus tumor gene Tu
CN101985620A (en) * 2010-11-22 2011-03-16 深圳华大基因科技有限公司 Molecular marker SIsv1223 closely linked with millet herbicide-resistant gene

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