CN107090450B - Molecular marker related to millet ear length character and detection primer and application thereof - Google Patents

Molecular marker related to millet ear length character and detection primer and application thereof Download PDF

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CN107090450B
CN107090450B CN201710183552.4A CN201710183552A CN107090450B CN 107090450 B CN107090450 B CN 107090450B CN 201710183552 A CN201710183552 A CN 201710183552A CN 107090450 B CN107090450 B CN 107090450B
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millet
snp marker
length
primer
ear length
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CN107090450A (en
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赵治海
冯小磊
范光宇
王峰
魏玮
宋国亮
李双东
邹洪峰
任全军
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ZHANGJIAKOU ACADEMY OF AGRICULTURAL SCIENCES
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/13Plant traits
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

Abstract

The invention discloses a molecular marker related to the ear length property of millet as well as a detection primer and application thereof, wherein the molecular marker is PL-02-016 which is positioned at the 38395016bp position of the sequence of No. 2 chromosome of millet and has a basic group of C/T. The molecular marker and the detection primer thereof can predict the ear length of the millet and provide molecular auxiliary technical support for early identification and screening breeding of the ear length character of the millet.

Description

Molecular marker related to millet ear length character and detection primer and application thereof
Technical Field
The invention relates to the technical field of millet breeding, in particular to a molecular marker related to the ear length character of millet and a detection primer and application thereof.
Background
China is the country with the largest cultivation area and the highest yield in the native place of millet and the world, and the yield accounts for about 80 percent of the total amount of the world. Meanwhile, China is also the country with the largest quantity of millet genetic resources and the most abundant diversity.
The ear length, the plant height and the like are important factors influencing the millet yield, and the research on the gene position, the function and the like related to the yield characters such as controlling the ear length and the like of the millet has important significance for guiding the genetic breeding of the millet.
Single Nucleotide Polymorphism (SNP) is a DNA sequence polymorphism caused by variation of a single nucleotide base at the genome level, and is large in number, widely distributed, and good in genetic stability in the genome. With the development of gene sequencing technology and the reduction of cost, the same gene or gene fragment of different individuals is directly sequenced and compared with the sequence, and whether the base has variation or not can be determined. Therefore, SNP detection is beneficial to genotyping and is suitable for rapidly and massively screening the relation between unknown or known SNP and certain genetic traits.
At present, QTL (quantitative trait locus) positioning and SNP (single nucleotide polymorphism) marker research related to the quantitative traits of the millet mainly focuses on ways such as development and utilization of SSR (simple sequence repeat) markers, and development, application and research for detecting Single Nucleotide Polymorphism (SNP) molecular markers by genome sequencing of a population inbred line are not reported. Therefore, the development of the quantitative character SNP molecular marker of the millet is developed, and an auxiliary breeding system is established, so that the method has important significance for improving the yield of the millet and saving the breeding cost.
Disclosure of Invention
The invention provides a molecular marker related to the ear length property of millet, a detection primer and application thereof, which can predict the ear length of millet and provide molecular auxiliary technical support for early identification and screening breeding of the ear length property of millet.
According to the first aspect of the invention, the SNP marker related to the ear length trait of millet is PL-02-016 which is located at 38395016bp position of the sequence of chromosome 2 of millet and has a base C/T.
Further, the sequence of the PL-02-016 site is shown as SEQ ID NO: 3, the PL-02-016 site is SEQ ID NO: 3 from the 5' -end to the 148 th base.
Further, for the SNP markers, a composite interval mapping method is utilized, the total significance level is 5%, the LOD value detected by QTL is 3.7556, and the interpretation rate of phenotypic variation is 3.35%.
According to a second aspect of the present invention, there is provided a primer pair for detecting the SNP marker as set forth in the first aspect, comprising:
upstream primer 7_ 2F: 5'-GTATGCTCCACGCCCTTTA-3' (SEQ ID NO: 1) and
the downstream primer 7_ 2R: 5'-TTGCGATTACCACTTGATT-3' (SEQ ID NO: 2).
According to a third aspect of the present invention, the present invention provides a kit for detecting a SNP marker as described in the first aspect, comprising a primer pair as described in the second aspect, and optionally reagent components for PCR amplification, which may include PCR buffers, dNTPs, DNA polymerase, and the like.
According to a fourth aspect of the present invention, there is provided a method for detecting an SNP marker as defined in the first aspect, wherein the genomic DNA of millet to be detected is subjected to PCR amplification using a primer set as defined in the second aspect, and the base status of the PL-02-016 site is analyzed by sequencing the amplified product.
According to a fifth aspect of the present invention, the present invention provides the use of a primer pair as in the second aspect for detecting a SNP marker as in the first aspect.
According to a sixth aspect of the present invention, there is provided a method for predicting ear length of millet, comprising the steps of performing PCR amplification of millet genomic DNA using the primer set of the second aspect, and sequencing the amplified product to analyze the base condition of PL-02-016 site, thereby predicting ear length of millet.
According to a seventh aspect of the present invention, the present invention provides the use of the SNP markers of the first aspect in predicting ear length of millet, or in early identification of ear length traits of millet, or in assisted breeding of millet molecules.
According to an eighth aspect of the present invention, the present invention provides the use of the primer set according to the second aspect in prediction of ear length of millet, or early identification of ear length trait, or assisted breeding of millet molecules.
The invention has the beneficial effects that: the SNP marker related to the millet panicle length character provided by the invention can be used for molecular marker assisted breeding of the millet panicle length character, can predict the millet panicle length through the SNP marker, provides molecular assisted technical support for realizing early identification and screening breeding of the millet panicle length character, and has important theoretical and practical guiding significance for accelerating genetic breeding and improvement process of millet varieties. The specific primer of the invention can well type the ear length of the millet and detect the difference of SNP expression.
Drawings
FIG. 1 is a DNA electrophoresis gel of parental genome of millet in an example of the present invention, wherein lane M represents DL2000 marker; lane 1 shows Zhanggu No. three genomic DNA; lane 2 shows A2 genomic DNA.
FIG. 2 is an electrophoresis gel diagram of PCR products of parental genome of foxtail millet in the embodiment of the present invention, wherein A7-2 represents a PCR product with A2DNA as a template and 7-2 as a primer, 37-2 represents a PCR product with Zhang Gu No. three DNA as a template and 7-2 as a primer, and M represents the size of a fragment of DNA marker, which is 100bp, 250bp, 500bp, 750bp, 1000bp, 2000bp sequentially from bottom to top.
FIG. 3 is a diagram showing the alignment result of the sequences of the female and male SNP markers PL-02-016 according to the embodiment of the invention, wherein the SNP marker PL-02-016 is located on chromosome No. 2 at position 38395016bp, the female parent base is C, and the male parent base is T.
Detailed Description
The present invention will be described in further detail with reference to the following detailed description and accompanying drawings.
The embodiment of the invention provides a molecular marker related to the ear length property of millet, a primer and application thereof. The SNP marker PL-02-016 closely linked with the millet ear length in the embodiment of the invention is located at the 38395016bp position (the base number on a reference genome, Yugu genome) of the sequence of No. 2 chromosome of millet, and the base is C/T.
It is to be noted that Bin in the present invention refers to Bin mapping (Bin map), and the minimum unit (Recombination Bin) constituting a Recombination event is obtained using information on all Recombination sites in the mapped population. The obtained bin is used as a marker for subsequent linkage map construction and QTL positioning.
In the present embodiment, the genetic map (genetic map or linking map) refers to a linear arrangement diagram of the relative positions between markers constructed on the basis of the recombination rate between genetic markers. Sequencing parent and filial generation populations of the mapping population based on a high-throughput resequencing technology, and taking a certain number of continuous SNPs as a basis for judging recombination sites of the filial generation to obtain a whole genome physical recombination map of each filial generation. Using all Recombination site information in the mapped population, the minimum units (Recombination bins) and Bin maps (Bin maps) that constitute the Recombination events were obtained and the resulting bins were used as markers for subsequent linkage map construction and QTL mapping.
The embodiment of the invention provides a millet male parent Zhang Gu III and a female parent A2 (which is obtained by hybridizing a millet sterile line 1066A with a millet photo-thermo-sensitive sterile line 821 and then carrying out multi-generation breeding), an F1 generation hybridized material and an F2 group 441 parts of selfed 13 generation material. Planting the materials in the mouth of a family in the North Hebei province, and recording and finishing the property data such as spike length and the like. And after carrying out degenerate genome re-sequencing on each material, completing comparison and reference genome splicing to obtain the SNP marker. And (3) obtaining related SNP markers by analyzing the ear length character data, and verifying the SNP markers by clone sequencing.
The technical solutions and technical effects of the present invention are described in detail by the following examples, and it should be understood that the examples are only exemplary and are used for illustrating the feasibility of the present invention and the obtained results, and should not be construed as limiting the scope of the present invention.
Example 1: high throughput sequencing and SNP marker information analysis
In this embodiment, the materials of the male parent "Zhang miscellaneous cereal No. 3" and the female parent "A2", the F1 generation material obtained by hybridization of the two, and the F2 population 441 parts of the material obtained by selfing the F1 generation for 13 generations, i.e. Recombinant Inbred Lines (RILs), are used. Planting the materials in the mouth of a family in the North Hebei province, and recording and finishing the property data such as spike length and the like. And after carrying out degenerate genome re-sequencing on each material, completing comparison and reference genome splicing to obtain the SNP marker. And (3) obtaining related SNP markers by analyzing the ear length character data, and verifying the SNP markers by clone sequencing.
In this example, the RADseq method is used to extract the genomic DNA of each sample individual (441 RILs, 2 parents, 1F 1 individual) and perform DNA quality detection, the qualified DNA is digested, the DNA fragments are recovered by electrophoresis, and a linker is added to prepare a cluster (cluster), and finally the sequencing is performed on the machine.
The specific steps of this example are as follows:
(1) weighing 1.0g of fresh leaves, shearing, putting into a mortar, grinding with liquid nitrogen, adding 3mL of 1.5 xCTAB, grinding into homogenate, transferring into a 15mL centrifuge tube, adding 1mL of 1.5 xCTAB into the mortar for washing, and transferring into the centrifuge tube. Mixing, and slowly shaking at 65 deg.C in water bath for 30 min.
Wherein 1.5 × CTAB formulation (1L) is as follows in Table 1:
TABLE 1
Composition (I) Dosage of
CTAB 15g
1mol/L Tris.Cl (pH 8.0) 75mL
0.5mol/L EDTA 30mL
NaCl 61.4g
Deionized water was added to a volume of 1L, and mercaptoethanol was added to a final concentration of 0.2% (2ml) before use.
(2) After cooling to room temperature, an equal volume of chloroform/isoamyl alcohol (24: 1) was added and mixed gently until the subnatant turned dark green.
(3) Centrifuging at 4200rpm for 10min, transferring the upper water phase into a new 15mL centrifuge tube, adding 2 times volume of precooled absolute ethyl alcohol, mixing and standing for 5 min; the DNA was precipitated by standing at-20 ℃ for 30 min.
(4) Centrifuging at 4200rpm for 10min, discarding the supernatant, adding 1mL of 75% ethanol to wash the precipitate 1 time, inverting the centrifuge tube to dry the DNA, and adding 50. mu.L of TE to dissolve the DNA.
(5) The concentration of DNA was measured and adjusted to 20 ng/. mu.L with water.
(6) The cleavage with PstI enzyme breaks the genomic DNA, and the reaction system is shown in the following table 2:
TABLE 2
(7) The ligation reaction was carried out as follows in Table 3:
TABLE 3
(8) mu.L of each reaction product was taken from each sample and added to a new centrifuge tube in a total volume of 12. mu.L. One set of 12 samples each.
(9) Electrophoresis was performed on a 3% recovery gel for 1h, and the 300-and 700 bp-sized fragment was excised after EB staining. Gel purification was performed with QIAquick kit and recovered, and the recovered product was dissolved in 30. mu.L of EB solution.
(10) The PCR reaction was carried out as follows in Table 4:
TABLE 4
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 for 10 cycles; final extension at 72 ℃ for 3 min.
(11) And (5) magnetic bead purification to complete library construction. The specific purification method comprises the following steps: first, 1.2 times the volume of the magnetic beads was added after PCR and the mixture was allowed to stand for 10 min. Then, the mixture was adsorbed on a magnetic frame, and the supernatant was removed. Then, 500. mu.L of 70% ethanol was added and washed twice. After drying to dryness on a dry heat instrument, 15 μ L of EB solution was added and dissolved for 5 min. Finally, the supernatant was transferred to a 1.5ml centrifuge tube by adsorption on a magnetic rack.
(12) And (5) performing on-machine sequencing after the detection reaches the on-machine standard.
Results library sequencing of 444 samples (of 441 RILs, 2 parents, 1F 1 individuals) resulted in 75.99Gb raw data, and 171.54 Mb. on average per individual aligned the sequenced sequences to the reference genome (i.e., the Yugu genome, from which the sequence of the Yugu genome can be obtained: https:// www.ncbi.nlm.nih.gov/genome/? term ═ Setaria + italica + (foxtail + millet)), with 86.326% average alignment, 8.226% average coverage, and 3.655X average sequencing depth.
33771 SNP markers with polymorphism between parents are obtained by sequencing and information analysis. According to the window sliding method, a plurality of SNPs are selected as a window, and the genotype of each window and the crossover site of each individual are determined by sliding one SNP at a time. Finally, the bin genotype is generated. According to the bin genotype data, MSTMap software is used for constructing a genetic map, 2022 bins are positioned on 9 chromosomes, and then the genetic map data are introduced into MapChart software to integrate a genome genetic linkage map.
And carrying out QTL analysis on the long character phenotype of the millet ears by using the constructed high-density genetic map of the millet and adopting composite interval mapping analysis (CIM). QTL detection adopts 5% of total significance level, and according to 500 times of arrangement test results, critical LOD value of QTL analysis of spike length trait phenotype data is determined, and prediction bin interval and SNP locus information related to the spike length are obtained through analysis.
The result shows that the molecular marker PL-02-016 related to the ear length trait of millet is located on 237.81 centimorgans (cM) of chromosome 2, 201 bin to 202 bin (chr2_ bin201-chr2_ bin202) of a genetic linkage map, and the LOD value detected by QTL is 3.7556, the phenotypic variation interpretation rate is 3.35% and the additive effect value (additive effect, A) is-0.8594 by using a composite interval mapping method and adopting an overall significance level of 5%.
Example 2: SNP marker validation
And (3) comparing the reference genome according to the predicted bin interval and the SNP locus to obtain a gene sequence of a related region, selecting about 300bp before and after the SNP locus, designing and developing SNP marker primers, and performing PCR amplification by taking the DNA of male parent and female parent materials as templates. And selecting a marker primer with normal amplification and PCR product according with the predicted size, recovering the product and sequencing, and selecting the marker primer with the SNP locus difference in the male parent material amplification gene sequence and the female parent material amplification gene sequence.
The predicted bin marker contains multiple SNP sites, which are screened according to the PCR results.
Firstly, according to the sequencing result after PCR product recovery, selecting a marker with SNP locus difference in the amplified gene sequences of male parent and female parent materials. The method comprises the following specific steps:
(1) parental genomic DNAs were each extracted by the CTAB method according to the steps (1) to (4) in example 1.
(2) The genomic DNA was examined on a 0.8% agarose gel, and the electrophoretic gel image of the parental genomic DNA from millet is shown in FIG. 1.
(3) The parental genomic DNA obtained was stored at-20 ℃ until use.
(4) Respectively taking the extracted genomic DNA of the male parent and the extracted genomic DNA of the female parent as templates, and performing amplification reaction by using a DNA sequence of 7_ 2F: 5'-GTATGCTCCACGCCCTTTA-3' (SEQ ID NO: 1) and 7_ 2R: 5'-TTGCGATTACCACTTGATT-3' (SEQ ID NO: 2) amplification primers were used for PCR amplification.
The PCR reaction system is shown in Table 5 below:
TABLE 5
Reagent Dosage of
Sterile water 20.2μL
10 Xbuffer (containing Mg)2+) 2.5μL
dNTPs(25mM) 0.15μL
Taq enzyme (5U/. mu.l) 0.15μL
Forward primer (10. mu. mol/L) 0.5μL
Reverse primer (10. mu. mol/L) 0.5μL
Form panel 1.0μL
Total volume 25μL
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 for 35 cycles; final extension at 72 ℃ for 3 min. The PCR amplification product was purified and stored at 4 ℃. A portion of each PCR amplification product was detected by 1% agarose gel electrophoresis, and the results are shown in FIG. 2.
Sequencing the PCR amplification product, wherein the sequencing sequence of the maternal amplification product obtained by amplification of the primers 7_2F and 7_2R is shown as SEQ ID NO: 3, PL-02-016 of SEQ ID NO: 3 from the 5' -end to the 148 th base. The sequencing sequence alignment of the maternal and paternal amplification products is shown in FIG. 3, where the bases marked with gray represent the bases of the PL-02-016 site.
Then, screening according to the sample ear length data: the ear length of the male parent is 26cm, the ear length of the female parent is 19cm, among 441 samples, the minimum value is 17cm, the maximum value is 47cm, and in 50 samples with the shortest ear length, the SNP is more than 70 percent which is the same as that of the female parent, and in 50 samples with the longest ear length, the number of samples which is the same as that of the male parent SNP is more than 80 percent.
The foregoing is a more detailed description of the present invention that is presented in conjunction with specific embodiments, and the practice of the invention is not to be considered limited to those descriptions. For those skilled in the art to which the invention pertains, several simple deductions or substitutions can be made without departing from the spirit of the invention, and all shall be considered as belonging to the protection scope of the invention.
SEQUENCE LISTING
<110> Zhang Kouzhou agricultural science and academy
<120> molecular marker related to millet ear length trait, detection primer and application thereof
<130> 16I23502
<160> 3
<170> PatentIn version 3.3
<210> 1
<211> 19
<212> DNA
<213> upstream primer for detecting PL-02-016
<400> 1
gtatgctcca cgcccttta 19
<210> 2
<211> 19
<212> DNA
<213> downstream primer for detecting PL-02-016
<400> 2
ttgcgattac cacttgatt 19
<210> 3
<211> 281
<212> DNA
<213> PL-02-016 site
<220>
<221> SNP site
<222> (148)..(148)
<223> n is C or T
<400> 3
ccctttagca gagcgattgc acgaaacaaa agcctcgtat ccttcagcca ttatgacatc 60
tgcagacagg tcctgcctcg acaatttggt ctcctacata caacgcagaa ggcattgata 120
cagtttggca aatgaatcac aaaccaancc ccatttcacc cagttttact atttgcattt 180
gactgaacaa acgatccaat aacatcccac cacagaaccg acaatttgat cagcattaaa 240
cgagatacac taattttttt ctgaaatcaa gtggtaatcg c 281

Claims (10)

1. The SNP marker related to the ear length character of the millet is characterized in that the male parent of the millet is Zhangchong No. 3 male parent, and the female parent is millet A2 material; the SNP marker is PL-02-016, and the sequence of the SNP marker is shown as SEQ ID NO: 3, the 148 th base from the 5' end of the sequence is C/T.
2. The SNP marker related to the ear length trait of millet as claimed in claim 1, wherein the SNP marker is characterized in that a composite interval mapping method is adopted, the total significance level is 5%, the LOD value detected by QTL is 3.7556, and the phenotypic variation interpretation rate is 3.35%.
3. A primer set for detecting the SNP marker according to claim 1 or 2, comprising:
upstream primer 7_ 2F: 5'-GTATGCTCCACGCCCTTTA-3' (SEQ ID NO: 1) and
the downstream primer 7_ 2R: 5'-TTGCGATTACCACTTGATT-3' (SEQ ID NO: 2).
4. A kit for detecting the SNP marker according to claim 1 or 2, comprising the primer set according to claim 3.
5. The kit of claim 4, wherein the kit further comprises reagent components for PCR amplification.
6. A method for detecting the SNP marker according to claim 1 or 2, wherein the genomic DNA of the millet to be detected is subjected to PCR amplification using the primer set according to claim 3, and the base status of the PL-02-016 site is analyzed by sequencing the amplified product.
7. Use of the primer pair according to claim 3 for detecting the SNP marker according to claim 1 or 2.
8. A method for predicting the length of a millet ear, comprising the steps of carrying out PCR amplification on millet genomic DNA by using the primer set according to claim 3, and analyzing the base condition of the PL-02-016 site by sequencing the amplified product, thereby predicting the length of the millet ear.
9. Use of the SNP marker according to any one of claims 1 or 2 for prediction of ear length of millet, or for early identification of ear length traits of millet, or for molecular assisted breeding of millet.
10. The primer pair as claimed in claim 3, wherein the primer pair is used for predicting the length of the millet ears, or early identifying the trait of the length of the millet ears, or assisting in breeding of millet molecules.
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CN108707683B (en) * 2018-04-16 2021-12-21 张家口市农业科学院 SNP (Single nucleotide polymorphism) marker related to grain ear length character as well as detection primer and application thereof
CN109136399B (en) * 2018-04-16 2021-12-21 张家口市农业科学院(河北省高寒作物研究所) SNP (Single nucleotide polymorphism) marker related to weight of millet ears as well as detection primer and application thereof
CN108715900B (en) * 2018-04-16 2021-12-21 张家口市农业科学院 SNP (Single nucleotide polymorphism) marker related to weight of millet ears as well as detection primer and application thereof
CN114317810B (en) * 2022-02-25 2023-07-14 山西农业大学 SNP locus for identifying folic acid character of millet, KASP molecular marker primer group and application thereof

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