CN110317894B - SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof - Google Patents
SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof Download PDFInfo
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Abstract
The invention discloses an SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof. The invention provides application of SNP loci or substances for detecting single nucleotide polymorphism of SNP loci in pseudo-ginseng genome in identifying or assisting in identifying total root weight characters of pseudo-ginseng to be detected; the SNP loci are as follows: taking the pseudo-ginseng genome DNA as a template, and adopting a primer pair consisting of SEQ ID No.1 and SEQ ID No.2 to carry out PCR amplification to obtain an amplified product, wherein the 199 th nucleotide is from the 5' end; the nucleotide at the SNP site is C or T. According to the invention, through a sequencing technology, on the basis of researching germplasm resources of the pseudo-ginseng with different root weights, the total root weight gene locus is accurately positioned, and then SNP markers closely connected with the total root weight gene locus are developed. And further, the screening of high-yield plants is realized in the early stage of pseudo-ginseng planting, and the planting benefit of pseudo-ginseng is improved.
Description
Technical Field
The invention relates to the technical field of biology, in particular to a SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof.
Background
Notoginseng Panax notoginseng (burk.) f.h.chen also known as Notoginseng, yunnan Notoginseng, ginseng, sanchi, notoginseng etc., perennial cross pollinated herbs belonging to the genus Panax (Panax) of the family Araliaceae (2n=24). Distribution of pseudo-ginseng is limited to medium-high altitude areas around 23 DEG 30' north latitude. Because of excessive digging, the wild notoginseng resources are scarce, the existing notoginseng is mostly cultivated artificially, and the planting area and the yield of the regions such as Yunnan mountain, inkstone, maguan and the like in the main production area of the domestic notoginseng are all over 98 percent of the whole country.
Notoginseng has a medicinal history of over 600 years, and roots, stems, leaves and flowers of the Notoginseng can be used as medicines, so that the Notoginseng is one of the main components of common traditional Chinese medicine preparations such as compound red-rooted salvia drop pills, yunnan white drug powder, PIANZAIHUANG, compound Notoginseng oral liquid and the like, and the Notoginseng is used as a formulation to enter into the preparation of national basic medicinal catalogue and national Chinese medicine protection catalogue for over 20 kinds. As a traditional rare medicinal material in China, the study on the biological characteristics of pseudo-ginseng is also very detailed. The pharmacological actions of pseudo-ginseng are mainly reflected in the influence on the blood system, cardiovascular system, cerebrovascular system, nervous system, metabolism, immune regulation system and the like. In recent years, a plurality of relevant literature reports of pseudo-ginseng are provided, and the content is mainly focused on the separation and extraction of chemical components of the pseudo-ginseng and pharmacodynamic aspects.
The root is one of the main medicinal parts of pseudo-ginseng and contains various saponins. The pharmacological action of notoginseng and its chemical composition are inseparable, and the saponin compound is the main chemical composition of notoginseng and one of the main effective components accepted in notoginseng, and can be roughly classified into ginsenoside, notoginsenoside, aescine, etc. The ginsenoside amount in Notoginseng radix is ginsenoside Rg 1 And Rb 1 The highest quality standard is also based on ginsenoside Rg 1 、Rb 1 And notoginsenoside R 1 The sum of the amounts of (2) is not less than 5.0% as a standard for measuring the quality of pseudo-ginseng. The variety and amount of saponins contained in different parts of Notoginseng radix are different. The leaves and flowers of Notoginseng mainly contain PDS, while the roots of Notoginseng mainly contain PDS and PTS, such as ginsenoside Rb 1 、Rb 2 、Rd、Re、Rg 1 、Rg 2 、Rh 1 And notoginsenoside R 1 、R 2 、R 3 、R 4 、R 6 Aescin XVII, etc.
The amount of saponin component in notoginseng is affected by various factors. Ma Ni and the like discover that the sun shine and the drying at 50 ℃ are more suitable for the processing of pseudo-ginseng slices by researching the influence of different drying methods on the saponin content of pseudo-ginseng slices; along with the development of the drying technology, the radix notoginseng is dried by adopting a microwave drying method, and the results show that the microwave radiation with different intensities can reduce the amount of main saponin components in the radix notoginseng, which is lower than the 2010 edition standard of Chinese pharmacopoeia. Therefore, the drying method can influence the accumulation of the effective components in the pseudo-ginseng, and the traditional airing method can well keep the quantity of the effective components in the root of the pseudo-ginseng.
At present, the breeding research of pseudo-ginseng still belongs to the starting stage. Cui Xiuming the viability of the pseudo-ginseng pollen was measured, and it was found that the pseudo-ginseng pollen could be stored for 11-13 days at normal temperature. Sun Yuqin and the like observe the flowering time and the powder scattering time of pseudo-ginseng. Chen Zhongjian and the like have studied the differences in the properties of pseudo-ginseng such as green stems, purple stems, green tubers and purple tubers, and are considered to be genetically controlled.
The genetic background of pseudo-ginseng is evaluated by a learner by using an allelic enzyme, RAPD and AFLP method. The segment bearing and the like analyze 34 pseudo-ginseng samples in total of 7 personality variation types through a RAPD method, and find that the DNA polymorphism between the variation types of pseudo-ginseng and between different individuals of the same type is higher, namely 75.5% and 75.2%, respectively, which indicates that the pseudo-ginseng is a heterozygous colony from the aspect of genetic background, and has rich genetic diversity. Hong et al found that in one plant site, both the genetic composition of individuals and the saponin content of the root of pseudo-ginseng had variations by AFLP markers, and considered that the genetic diversity of pseudo-ginseng affected the saponin content of the root of pseudo-ginseng. Zhou et al studied Notoginseng radix and Panax schinseng from ITS and SFLP, and the results showed that the polymorphism of cultivated Notoginseng radix was smaller than that of wild Panax schinseng. Wang et al, by performing AFLP analysis on 92 samples from four populations, consider that the pseudo-ginseng cultivar has only moderate genetic diversity, and the genetic heterozygosity of the four populations are: 0.166, 0.093, 0.094 and 0.125, and the inter-group genetic distance is small (Nei genetic distances < 0.03). The isozyme labeling analysis of the genetic diversity in pseudo-ginseng species is adopted by the zodiac, and indicates that the genetic variation (81.01%) mainly exists in the middle of the colony and has small intra-colony differentiation. Zhang Jinyu and the like utilize EST-SSR markers to study the phenotypic character variation of 10 pseudo-ginseng cultivation communities in 4 pseudo-ginseng producing regions in the mountain area, and the mountain pseudo-ginseng communities are considered to have rich genetic diversity whether in the communities or among the communities, and the genetic variation of the mountain pseudo-ginseng communities mainly exists among individuals in the communities.
The development of SNP sites is mainly based on DNA sequencing and sequence alignment. Currently, strategies and techniques for SNP development, whether for model or non-model organisms, mainly include two classes, reference-based (ref-based) and reference-free (de novo). SNP development strategies with reference sequences mainly have resequencing (Re-sequencing), both high and low depth. Currently, relatively widely used reference-sequence-free SNP development strategies include simplified polymorphic sequence complexity (complexity reduction of polymorphic sequences, CRoPS), restriction-site-related DNA sequencing (RAD-seq), sequencing-based genotyping (genotyping by sequencing, GBS), and the like. In addition, transcriptome sequencing of different samples or SNP locus mining using a common sequence database is also an effective technical means based on development cost consideration.
The development and research of the pseudo-ginseng SNP markers are started later, but are increasingly paid attention to by researchers. Chen Zhongjian and the like screen a plurality of SNP loci related to root rot resistance by utilizing RAD-seq technology, and successfully select and breed a new disease-resistant variety of the first pseudo-ginseng. Wei Chen et al have first completed whole genome sequencing of Notoginseng radix while finding a large number of candidate genes for saponin biosynthesis. Root is one of the main medicinal parts of pseudo-ginseng, and total root weight directly affects the yield of pseudo-ginseng, which is a main factor restricting the development of pseudo-ginseng industry. The grade of Notoginseng radix is distinguished by the number of heads according to the national markers. The head number of Notoginseng radix refers to the relative number of Notoginseng radix in every 500 g (1 jin) of Notoginseng radix. In the terminal retail market, the price of pseudo-ginseng varies with the number of heads, and the lower the number of heads, the higher the level and the higher the price. In popular terms, the smaller the number of heads, the larger the number of heads of pseudo-ginseng is, the longer the growth year is, the more nutrient substances are abundant, and otherwise, the quality is slightly poorer. The size (total root weight) of the pseudo-ginseng root has important economic value, but few people analyze the characteristics by using a molecular means. The existing technology can only roughly judge the root size (root weight) according to the plant type in the mature period and is specific and clear after picking, and cannot be explained from the aspects of genetic background, physiological mechanism and the like. The completion of the whole genome sequencing of the pseudo-ginseng marks the possibility of developing high-precision SNP markers, and simultaneously improves the breeding efficiency of the pseudo-ginseng and accelerates the molecular breeding process of the pseudo-ginseng.
Disclosure of Invention
The invention aims to provide an SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof.
In a first aspect, the invention claims the use of the following SNP sites in the genome of panax notoginseng or a substance for detecting single nucleotide polymorphisms of the following SNP sites in the genome of panax notoginseng for the identification or assisted identification of the total root weight trait of panax notoginseng to be tested:
the SNP loci are as follows: taking the pseudo-ginseng genome DNA as a template, and adopting a primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No.2 to carry out PCR amplification to obtain an amplification product, wherein the 199 th nucleotide is from the 5' end; the nucleotide at the SNP site is C or T.
Further, the "amplified product obtained by PCR amplification of a primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2" is the 303 th to 876 th positions from the 5' end of the nucleotide sequence shown in SEQ ID No.3 (full-length sequence 1001 bp), and the SNP site is the 501 th position of the sequence shown in SEQ ID No.3, and is represented by Y, which represents C or T.
In a second aspect, the invention claims a reagent or kit for identifying or aiding in the identification of the total root weight trait of pseudo-ginseng to be tested.
The reagent for identifying or assisting in identifying the total root weight character of the pseudo-ginseng to be detected is a substance for detecting single nucleotide polymorphism of SNP loci in pseudo-ginseng genome; the kit contains the reagent. The SNP sites are as above.
In the first and second aspects, the "substance for detecting a single nucleotide polymorphism of a SNP site in a pseudo-ginseng genome" may be a primer pair as shown in (a) or (b) or (c) below:
(a) A primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2;
(b) Consists of two single-stranded DNA molecules shown in sequences obtained by substituting and/or deleting and/or adding one or more nucleotides of SEQ ID No.1 and SEQ ID No.2, and has the same function as the primer pair in (a).
(c) The primer pair obtained by designing the nucleotide sequence shown in SEQ ID No.3 has the same function as the primer pair described in (a).
In a third aspect, the present invention claims a molecular marker for identifying or aiding in identifying the total root weight trait of pseudo-ginseng to be tested.
The molecular marker for identifying or assisting in identifying the total root weight character of the pseudo-ginseng to be detected provided by the invention is an amplification product obtained by using the pseudo-ginseng genome DNA as a template and adopting the primer pair A for amplification.
Wherein, the primer pair A satisfies the following conditions: the amplified product obtained by PCR amplification with the genomic DNA of the pseudo-ginseng to be detected as a template contains the nucleotide at the SNP locus as follows. The SNP sites are as above.
Further, the primer pair a may be a primer pair as shown in (a) or (b) or (c) below:
(a) A primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2;
(b) Consists of two single-stranded DNA molecules shown in sequences obtained by substituting and/or deleting and/or adding one or more nucleotides of SEQ ID No.1 and SEQ ID No.2, and has the same function as the primer pair in (a).
(c) The primer pair obtained by designing the nucleotide sequence shown in SEQ ID No.3 has the same function as the primer pair described in (a).
In a fourth aspect, the invention claims the use of said agent or said kit or said molecular marker for the identification or assisted identification of the total root weight trait of pseudo-ginseng to be tested.
In a fifth aspect, the invention claims a method for identifying or aiding in identifying the total root weight trait of pseudo-ginseng to be tested.
The method for identifying or assisting in identifying the total root weight character of the pseudo-ginseng to be detected provided by the invention specifically comprises the following steps: detecting the nucleotide at the following SNP loci in the genome of the pseudo-ginseng to be detected to determine the genotype of the pseudo-ginseng to be detected, and determining the total root weight character of the pseudo-ginseng to be detected according to the genotype of the pseudo-ginseng to be detected according to the following rule: the total root weight of the pseudo-ginseng to be detected with the TT genotype is larger than or candidate is larger than that of the pseudo-ginseng to be detected with the CC genotype, and the total root weight of the pseudo-ginseng to be detected with the CT genotype is between the two. The SNP sites are as above.
The TT genotype is homozygote with the 199 th nucleotide from the 5' end of an amplification product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2.
The CC genotype is homozygote with 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2.
The CT genotype is heterozygous of the amplified product obtained by PCR amplification by taking pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No.2, wherein the 199 th nucleotide from the 5' end is C and T.
Further, the method of "detecting nucleotides at the following SNP sites in the genome of pseudo-ginseng to be detected" may be a sequencing analysis; the sequencing analysis may comprise two steps of PCR amplification and sequencing the products resulting from the PCR amplification; the template for PCR amplification is the genomic DNA of the pseudo-ginseng to be detected, and the primer pair meets the following conditions: and performing PCR amplification by taking the genomic DNA of the pseudo-ginseng to be detected as a template, wherein an amplification product obtained by performing PCR amplification contains the nucleotide at the SNP locus.
Still further, the primer pair may specifically be a primer pair as shown in (a) or (b) or (c) below:
(a) A primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2;
(b) A primer pair which consists of two single-stranded DNA molecules shown in sequences obtained by substituting and/or deleting and/or adding one or more nucleotides of SEQ ID No.1 and SEQ ID No.2 and has the same function as the primer pair in (a);
(c) The primer pair obtained by designing the nucleotide sequence shown in SEQ ID No.3 has the same function as the primer pair described in (a).
In a sixth aspect, the invention claims the use of said agent or said kit or said molecular marker or said method in pseudo-ginseng breeding.
In the application, the high-yield fine variety of the pseudo-ginseng can be cultivated by a molecular marker assisted breeding method.
In a seventh aspect, the invention claims a method of (a) or (B) as follows:
(A) The method for cultivating the variety of pseudo-ginseng with increased total root weight comprises the step of selecting pseudo-ginseng with TT or CT genotype for breeding;
the TT genotype is homozygote with the 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the CT genotype is heterozygous with C and T nucleotides from the 5' end of an amplification product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No.2 (the heterozygous can be subjected to selfing purification in offspring).
(B) The method for identifying and filtering the variety of the pseudo-ginseng with small total root weight comprises the step of filtering out the CC genotype of the pseudo-ginseng from the pseudo-ginseng population to be identified; the CC genotype is homozygote with 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2.
In one embodiment of the invention, the total root weight trait is embodied as fresh total root weight.
The invention accurately locates the total root weight gene locus based on researching the germplasm resources of the pseudo-ginseng with different root weights by a sequencing technology, further develops SNP markers closely connected with the total root weight gene locus, and tries to analyze the genetic mechanism behind the SNP markers, thereby locating and explaining the important characteristic of the total root weight of the pseudo-ginseng from a molecular level. And further, the screening of high-yield plants is realized in the early stage of pseudo-ginseng planting, and the planting benefit of pseudo-ginseng is improved.
The beneficial effects of the invention are as follows:
according to the embodiments of the present invention, the method of sequencing the PCR amplification product is not particularly limited as long as the sequence of the PCR amplification product, i.e., the fragment in which the SNP marker is located, can be efficiently obtained. According to some specific examples of the invention, the PCR amplification product may be sequenced using at least one selected from the group consisting of HISEQ2000, SOLiD, 454, and single molecule sequencing methods. Thus, the sequencing result can be obtained rapidly, efficiently and accurately with high flux.
According to the embodiment of the invention, based on a sequencing result, the genotype of the SNP marker carrying pseudo-ginseng to be detected can be effectively determined as TT or CC by comparing the pseudo-ginseng reference genome sequences.
According to an embodiment of the present invention, the fresh total root weight of the TT genotype individuals of the SNP markers is significantly higher than that of the CC genotype individuals. That is, the SNP markers of the invention are closely related to the fresh total root weight of the pseudo-ginseng. Therefore, based on the determined genotype of the SNP marker of the pseudo-ginseng to be detected, the fresh total root weight property of the pseudo-ginseng can be accurately and effectively judged, for example, when the genotype of the SNP locus is TT, the sample belongs to an individual with larger total root fresh weight. Furthermore, the method can be effectively used for molecular marker assisted breeding of the pseudo-ginseng, so that the method can assist early stage selection of excellent varieties of the pseudo-ginseng in a short time with low cost and high accuracy. It should be noted that the SNP marker provided by the invention is not limited by the plant size of the pseudo-ginseng, can be used for early breeding of the pseudo-ginseng, and obviously promotes the breeding process.
Detailed Description
The experimental methods used in the following examples are conventional methods unless otherwise specified.
Materials, reagents and the like used in the examples described below are commercially available unless otherwise specified.
Example 1 development and application of SNP molecular marker scaffold6086_33242 closely linked with total root weight of Panax notoginseng
1. Development of SNP molecular marker scanfold 6086_33242 closely linked with total root weight of pseudo-ginseng
1. Construction of pseudo-ginseng sample resource group
The pseudo-ginseng sample group adopted is obtained from different counties and cities of Miao nationality of Wenshan, yunnan province, wherein the county of Shang guan, the county of Zhuibei, the county of inkstone and other materials respectively have 179 parts, 150 parts, 386 parts and 803 parts, and 1518 single plants are obtained.
2. Simplified genome sequencing (Restriction site Associated DNA sequencing, RAD-seq)
Based on a Hiseq2000 high throughput sequencing platform, a RAD simplified genome sequencing method was used to sequence the DNA samples of 1518 individuals, resulting in an average data size of about 0.4G per individual, covering on average 1.6% of the Notoginseng genome.
3. Obtaining SNP markers related to fresh total root weight of pseudo-ginseng
The 1518 individuals were phenotypically identified for growth traits such as root weight. The data were screened using PLINK software and then analyzed by GWAS using EMMA software based on a hybrid linear model, finding 1 SNP locus significantly related to fresh total root weight from 254,083 SNPs. The SNP site is located at 33,242bp of the scafold 6086, and the base of the site is C or T (the SNP site is marked as scafold 6086_ 33242). The fresh total root weight of the pseudo-ginseng with the genotype of homozygous TT at the locus is obviously higher than that of the pseudo-ginseng with the genotype of homozygous CC at the locus, and the total root weight of the CT genotype is between homozygous CC and TT.
Further, SNP site scanfold 6086_33242 is the 501 st position of the sequence shown in SEQ ID No.3 in the genomic DNA of Notoginseng radix.
2. Application of SNP molecular marker scanfold 6086_33242 closely linked with total root weight of pseudo-ginseng
1. Extraction of genomic DNA from Notoginseng radix sample
The pseudo-ginseng sample to be detected is from the resource group containing 1518 samples in the description, 300 samples are randomly selected, and genome DNA is respectively extracted by a CTAB method, and the specific method is as follows:
(1) The leaves frozen at 20℃were placed in a mortar, ground with liquid nitrogen, then 3mL of 1.5 XCTAB was added, ground into homogenate, transferred to a 15mL centrifuge tube, then 1mL of 1.5 XCTAB was added to the mortar, rinsed and transferred to the centrifuge tube. Mixing, and slowly shaking in water bath at 65deg.C for 30 min.
Wherein the 1.5 XCTAB formulation is as follows (1L): 15g of CTAB; 1mol/L Tris.Cl (pH 8.0) 75mL; 30mL of EDTA at 0.5 mol/L; 61.4g of NaCl; deionized water was added to a volume of 1L, and mercaptoethanol was added to a final concentration of 0.2% (2 ml) prior to use.
(2) After cooling to room temperature, an equal volume of chloroform/isoamyl alcohol (24:1, volume ratio) was added and gently mixed until the lower layer became dark green.
(3) Centrifuge at 4200rpm for 10min, phase shift the supernatant to a new 15mL centrifuge tube, add 2 volumes of pre-chilled absolute ethanol, mix and rest for 5min. The DNA was precipitated by standing at-20℃for 30 min.
(4) Centrifuge at 4200rpm for 10min, discard supernatant, wash pellet 1 times with 1mL of 75% ethanol, invert centrifuge tube to dry DNA, add 200. Mu.L TE to dissolve DNA.
(5) Genomic DNA was detected with 0.8% agarose gel.
(6) The obtained genomic DNA was stored at-20℃for use.
2. Amplification of nucleotide fragments containing SNP loci
And amplifying the nucleotide fragments of the SNP markers to be detected by using the genomic DNA of each pseudo-ginseng to be detected obtained by the extraction as a template and using the forward primer F and the reverse primer R.
Forward primer F:5'-ACCCGTTGCTCTAATGCCTC-3' (SEQ ID No. 1);
reverse primer R:5'-ACTCTTCCGGACTCGAACAC-3' (SEQ ID No. 2).
The amplified product is 303-876 th from the 5 'end of the nucleotide sequence shown in SEQ ID No.3, and 501 st from the 5' end of the nucleotide sequence shown in SEQ ID No.3 is SNP locus scaffold6086_33242.
The PCR reaction (25. Mu.l) was as follows: 20.2 μl of sterile water; 10 XBuffer (containing Mg) 2+ ) 2.5 μl; dNTPs (25 mM) 0.15. Mu.l; taq enzyme (5U/. Mu.l) 0.15. Mu.l; forward primer 0.5 μl; reverse primer 0.5. Mu.l; template 1.0 μl.
The PCR reaction procedure was as follows: pre-denaturation at 94 ℃ for 5 min; denaturation at 94℃for 30 seconds, annealing at 60℃for 30 seconds, extension at 72℃for 40 seconds, and running 35 cycles; finally, the extension is carried out at 72 ℃ for 3 minutes. The PCR amplification product may be stored at 4 ℃.
3. Sequencing recognizes SNP locus genotypes
The PCR amplification products obtained in the above steps were subjected to unidirectional sequencing on an ABI3730 sequencer, and the genotype of SNP marker scafold 6086_33242 was identified.
Taking the pseudo-ginseng genome DNA as a template, and adopting a forward primer F and a reverse primer R (SEQ ID No.1 and SEQ ID No. 2) to carry out PCR amplification to obtain an amplification product, wherein the 199 th nucleotide from the 5' end of the amplification product is the SNP locus scaffold6086_33242; the nucleotide at the SNP site is C or T.
4. Correlation analysis of SNP locus genotype and fresh total root weight
The phenotype (fresh total root weight) profiles of the different genotypes (CC, TT and CT) were counted to give Table 1. The CC genotype is homozygous with the 199 th nucleotide (501 th nucleotide corresponding to SEQ ID No. 3) from the 5' end of an amplification product obtained by PCR amplification by using the pseudo-ginseng genomic DNA as a template and adopting a forward primer F and a reverse primer R (SEQ ID No.1 and SEQ ID No. 2). The TT genotype is homozygous with the 199 th nucleotide (501 th nucleotide corresponding to SEQ ID No. 3) from the 5' end of an amplification product obtained by PCR amplification by using the pseudo-ginseng genomic DNA as a template and adopting a forward primer F and a reverse primer R (SEQ ID No.1 and SEQ ID No. 2) as T. The CT genotype is the heterozygote of the amplified product obtained by PCR amplification by using the pseudo-ginseng genomic DNA as a template and adopting a forward primer F and a reverse primer R (SEQ ID No.1 and SEQ ID No. 2) and the 199 th nucleotide (501 th nucleotide corresponding to SEQ ID No. 3) from the 5' end is C and T.
As can be seen from Table 1, the average fresh total root weight of the TT homozygous individuals is greater than that of the CC homozygous individuals, while the average fresh total root weight of the CT heterozygous individuals is between the two.
TABLE 1 phenotypic distribution of different genotypes
| Genotype of the type | Mean value of | Standard deviation of | Number of samples |
| CC | 29.3595 | 8.22357 | 160 |
| TT | 46.2548 | 15.02478 | 58 |
| CT | 39.0117 | 11.04394 | 82 |
| Totals to | 35.2642 | 12.56897 | 300 |
Based on the results of table 1 above, the correlation of the genotype of the SNP site with fresh total root weight was analyzed using a single factor analysis method of the generalized linear model of SPSS software, wherein the phenotype value was represented by fresh total root weight at the time of analysis.
The correlation analysis results of the genotype of SNP locus and fresh total root weight are shown in Table 2 below.
TABLE 2 correlation analysis results of SNP genotype and fresh total root weight
The correlation analysis results shown in Table 2 indicate that the correlation of genotypes to the mean of fresh total root weights reaches a very significant level (P < 0.01). Furthermore, it was confirmed that the SNP locus was significantly correlated with fresh total root weight of Notoginseng radix, and was a SNP marker correlated with fresh total root weight of Notoginseng radix, and that the fresh total root weight of TT genotype individuals of the SNP marker was significantly higher than that of CC genotype individuals, and that the fresh total root weight of CT genotype individuals was intermediate between them.
<110> Shenzhen Hua Daagricultural application institute, shenzhen Hua Daliving science institute, yunnan Hua Dagenetic science and technology Co., ltd., wen mountain City Miao Xiang Notoginseng radix Co., ltd
<120> SNP molecular marker closely linked with total root weight of pseudo-ginseng and application thereof
<130> GNCLN180721
<160> 3
<170> PatentIn version 3.5
<210> 1
<211> 20
<212> DNA
<213> Artificial sequence
<400> 1
acccgttgct ctaatgcctc 20
<210> 2
<211> 20
<212> DNA
<213> Artificial sequence
<400> 2
actcttccgg actcgaacac 20
<210> 3
<211> 1001
<212> DNA
<213> Panax notoginseng
<220>
<221> misc_feature
<222> (501)..(501)
<223> y is c or t
<400> 3
ccggatccag acagaatggg aatatacacc tctggatgac cgtgctcttt gtagtctatc 60
agattagggt tatactcagg catgcgataa agcccttatt taagcccttt gggagcagat 120
aagggtatct cagttggatg cccaacgtga gtcaagccaa gataactcgg acaagagtga 180
gaccgaggat actcacatgg gagctctcca tttgcttaat gtcattcatt aaaggctatg 240
ccgatagcaa ggcaacaaaa caagcaacga ctttcgcgcg ctagtctagt agtagtacgc 300
tcacccgttg ctctaatgcc tcgttacgta aacaatggta accttgtcgg tttgccgaca 360
atacaccgag aattcacggt gtttcgatgt tacgcgtaac aaaagtgttt taggctaatc 420
acctaacagt acttcatgta gagtttcata gtctgtgact aatgaacact tggaaaagtt 480
tttaacattg tttaagaatt yattacctta tggtcattca gttatttgat attattcata 540
tcattggaaa gttgagccac aactgatgaa aatcatttca ttttgagtta tttactcttt 600
tattagttgt cgagttaaga gacaaagatt caagctttta ttattcctta gatccgggat 660
tctgaaatgt tacgatatat tttaaacgat aaattgtatt aattgttaat tattgagcta 720
taaaacttga tgaacaaatt tgttgctcac ttatacttat aggacctctt tcgagcaatt 780
tcagaatagg gtagagcact acccaacaga gataggtcag acaagttaca ctatcagcaa 840
gggtctgtct agctttgtgt tcgagtccgg aagagtacct agatgccata agagaagacc 900
tatgagactt ttgtgtgtgt gtgtgtgtgt gtctatatat atatatatat atggaaaatg 960
atctatagca agtatttgct atggatgaca aatatccatt g 1001
Claims (7)
1. The application of a reagent for detecting single nucleotide polymorphism of SNP loci in pseudo-ginseng genome or a kit containing the reagent in identifying or assisting in identifying the total root weight character of pseudo-ginseng to be detected;
the SNP loci are as follows: taking the pseudo-ginseng genome DNA as a template, and adopting a primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No.2 to carry out PCR amplification to obtain an amplification product, wherein the 199 th nucleotide is from the 5' end; the nucleotide at the SNP locus is C or T;
in the application, the total root weight of the pseudo-ginseng to be detected with the TT genotype is larger than or the candidate is larger than that of the pseudo-ginseng to be detected with the CC genotype, and the total root weight of the CT genotype is between the total root weight and the candidate;
the total root weight trait is embodied as fresh total root weight.
2. The use according to claim 1, characterized in that: the reagent for detecting the SNP locus single nucleotide polymorphism in the pseudo-ginseng genome is a primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2.
3. A method for identifying or assisting in identifying total root weight characteristics of pseudo-ginseng to be detected comprises the following steps: detecting the nucleotide at the following SNP loci in the genome of the pseudo-ginseng to be detected to determine the genotype of the pseudo-ginseng to be detected, and determining the total root weight character of the pseudo-ginseng to be detected according to the genotype of the pseudo-ginseng to be detected according to the following rule: the total root weight of the pseudo-ginseng to be detected with the TT genotype is greater than or candidate is greater than that of the pseudo-ginseng to be detected with the CC genotype, and the total root weight of the CT genotype is between the total root weight and the candidate;
the SNP loci are as follows: taking the pseudo-ginseng genome DNA as a template, and adopting a primer pair consisting of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No.2 to carry out PCR amplification to obtain an amplification product, wherein the 199 th nucleotide is from the 5' end; the nucleotide at the SNP locus is C or T;
the TT genotype is homozygote with the 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the CC genotype is homozygote with the 199 th nucleotide from the 5' end of an amplification product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the CT genotype is heterozygous with the genomic DNA of the pseudo-ginseng as a template and the 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the total root weight trait is embodied as fresh total root weight.
4. A method according to claim 3, characterized in that: the method for detecting the nucleotide at the SNP locus in the genome of the pseudo-ginseng to be detected is sequencing analysis; the sequencing analysis comprises two steps of PCR amplification and sequencing of a product obtained by the PCR amplification; the template for PCR amplification is the genomic DNA of the pseudo-ginseng to be detected, and the primer pair meets the following conditions: and performing PCR amplification by taking the genomic DNA of the pseudo-ginseng to be detected as a template, wherein an amplification product obtained by performing PCR amplification contains the nucleotide at the SNP locus.
5. The method according to claim 4, wherein: the primer pair consists of single-stranded DNA shown in SEQ ID No.1 and single-stranded DNA shown in SEQ ID No. 2.
6. The method for cultivating the variety of the pseudo-ginseng with increased total root weight comprises the step of selecting pseudo-ginseng with TT genotype or CT genotype for breeding; the TT genotype is homozygote with the 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2; the CT genotype is heterozygous with the genomic DNA of the pseudo-ginseng as a template and the 199 th nucleotide from the 5' end of an amplified product obtained by PCR amplification by adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the total root weight is fresh total root weight.
7. The method for identifying and filtering the variety of the pseudo-ginseng with small total root weight comprises the step of filtering the pseudo-ginseng with CC genotype from the pseudo-ginseng population to be identified; the CC genotype is homozygote with the 199 th nucleotide from the 5' end of an amplification product obtained by PCR amplification by using pseudo-ginseng genomic DNA as a template and adopting a primer pair consisting of single-stranded DNA shown as SEQ ID No.1 and single-stranded DNA shown as SEQ ID No. 2;
the total root weight is fresh total root weight.
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| WO2006016762A1 (en) * | 2004-08-13 | 2006-02-16 | Bio-Medic Research Center Daegu Hanny University | A method for genetic identification of ginseng species and the kit using thereby |
| CN106591459A (en) * | 2016-12-26 | 2017-04-26 | 中国医学科学院药用植物研究所 | SNP (Single Nucleotide Polymorphism) marker, kit and method for rapidly identifying panax traditional Chinese medicines including panax stipuleanatus and panax quinquefolius |
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| JP5163999B2 (en) * | 2007-11-14 | 2013-03-13 | 国立大学法人富山大学 | DNA microarray for identification of similar plants and herbal medicines |
| CN102888456B (en) * | 2012-09-21 | 2014-03-26 | 中国医学科学院药用植物研究所 | Method for quickly identifying pseudo-ginseng |
| CN104830969B (en) * | 2015-03-17 | 2017-10-17 | 中国医学科学院药用植物研究所 | A kind of pseudo-ginseng molecular identity card and authentication method |
| AU2015101752A4 (en) * | 2015-12-04 | 2016-01-14 | Fit-Bioceuticals Pty Ltd | Composition for mood and/or cognitive function support |
| CN106332628A (en) * | 2016-08-22 | 2017-01-18 | 文山苗乡三七科技有限公司 | Conservation method for pingpien gingseng rhizome |
| CN106383064B (en) * | 2016-08-25 | 2019-07-09 | 文山苗乡三七科技有限公司 | A kind of method of the quick selection of land in notoginseng planting region |
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| WO2006016762A1 (en) * | 2004-08-13 | 2006-02-16 | Bio-Medic Research Center Daegu Hanny University | A method for genetic identification of ginseng species and the kit using thereby |
| CN106591459A (en) * | 2016-12-26 | 2017-04-26 | 中国医学科学院药用植物研究所 | SNP (Single Nucleotide Polymorphism) marker, kit and method for rapidly identifying panax traditional Chinese medicines including panax stipuleanatus and panax quinquefolius |
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