CN114592086A - SNP molecular marker related to resistance of ring spot virus PRSV and application - Google Patents
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Abstract
The invention relates to the field of molecular biology, in particular to an SNP molecular marker related to resistance of a ring spot virus PRSV and application thereof. The invention discovers an SNP molecular marker related to the papaya disease resistance (resistance to ring spot virus PRSV) based on a GWAS analysis method, wherein the molecular marker is located at the 26455183 th basic group (Cpa 04g015360 gene promoter region) of a Chr04 chromosome and is named as Cpa04g015360:928, and the nucleotide sequence of the molecular marker is shown as the 78 th position of SEQ ID No. 1. The SNP molecular marker can be used for detecting PRSV high-resistance papaya breeding materials, is beneficial to quickly detecting the PRSV high-resistance papaya breeding materials, assists in cross breeding, shortens the breeding period of new varieties, and has the advantages of low detection cost, no environmental limitation, high detection result accuracy and easiness in repetition.
Description
Technical Field
The invention relates to the field of molecular biology, in particular to an SNP molecular marker related to resistance of a ring spot virus PRSV and application thereof.
Background
Papaya is a tropical evergreen fruit tree, a perennial fleshy herbaceous plant of the genus papaya of the family Caricaceae, also known as cushaw, rock-melon, papaya, wax gourd, papaya, and lotus seed fruit. The strain is originally produced in Mexico and Central America, is widely cultivated in tropical and subtropical regions all over the world, is introduced into China from the 17 th century, is mainly produced in Guangdong, Hainan, Guangxi, Yunnan, Taiwan, Fujian, and is also cultivated in Sichuan Wenchang and Jiangxi. The fresh papaya has beautiful appearance, thin skin and thick meat, multiple tastes and sweetness, fragrant and sweet smell and rich nutrition. The ripe papaya flesh is yellow or red, and the carotene and lycopene are rich, so that the papaya flesh has excellent health-care effect and important edible value and industrial value. The development of papaya production greatly stimulates the development of related industries such as food processing, medicine and health, beauty and health care, breeding and the like, and has important significance.
Molecular breeding facilitates selection of a desired trait and then breeding of a new variety. With the development of genetics, genetic markers can be used as an aid to help people to select and improve the accuracy of breeding (Sunde et al, 2006, seeds, 25(12): 54-57). As for the antiviral breeding research of papaya, the genetic engineering technology has been greatly developed with the continuous improvement of tissue culture technology. In the research of Fitch et al (1990), transgenic papaya plants were developed by particle gun method, and then further cultured and successfully obtained callus with stable genetic characteristics. Zhongpeng et al (1997, Chi Dai Xue, 16(2): 66-69) studied the introduction of the bivalent gene of PRV-CP-SN into papaya and succeeded in obtaining transgenic plants. The transgenic plants obtained by Zhongpeng and Zheng's office (1996, the Collection of tropical crops, 17(2): 84-87) by the Agrobacterium-mediated method can successfully express the gene of the Sm strain CP. Zhao Shi Ying et al (1998, the report on tropical crops, 19(2): 20-26) successfully obtained transgenic plants by transferring the ribozyme-related gene of PRV RNA into papaya using genetic engineering techniques, and also carried out the corresponding challenge study by artificial inoculation. Transgenic papaya plants have also been successfully obtained by a number of studies in units such as the national institute of Life sciences of the university of Zhongshan (Mei et al, 2001). Kumar et al (2018) cultured papaya with CP and GFP fusion gene transferred based on sequence homology analysis of transgenic sources, and used for improving transgenic papaya strain to resist PRSV infection. The transgenic papaya strain produced by the experiments of Jia et al (2017) has certain application value to PRSV. The gene engineering method can be used as a better method for preventing and controlling the disease-resistant breeding in the breeding of the papaya, and the method makes the papaya capable of resisting various virus diseases (such as ringspot virus diseases) possible; the papaya tissue culture and rapid propagation technology (Chuan Yixingchun and Laishongong, 2003) not only provides an effective way for preserving papaya germplasm resources, but also successfully maintains the genetic stability of excellent varieties (disease-resistant, high-quality and high-yield), and simultaneously provides convenience for international germplasm exchange.
Single Nucleotide Polymorphism (SNP) mainly refers to DNA sequence polymorphism caused by variation of a single nucleotide at the genome level. Compared with molecular markers such as RAPD, AFLP, SSR and the like in the early stage, the SNP molecular marker has the advantages of wide distribution and more quantity on an individual genome, easiness in genotyping (binary SNP), suitability for rapid and large-scale screening and the like. Genome-wide association analysis (GWAS) is a method for mining candidate genes related to traits based on the relationship between high-throughput SNP molecular markers and the traits, and the basic principle of the method is the phenomenon of Linkage Disequilibrium (LD) among genes in a population. GWAS was first applied in human disease research, plays an important role in genetic basic analysis of complex quantitative traits, and has absolute advantages in mining real major genes or key mutation sites. Until 2010, the popularization of the second-generation sequencing technology and the large-scale development of high-throughput molecular markers, and the whole-genome association analysis method are applied to the research of complex traits of crops on a large scale, and have complete use methods and experiences in rice, wheat, corn, rape and cotton.
Disclosure of Invention
The technical problem to be solved by the invention is as follows: provides an SNP molecular marker related to the papaya disease resistance character (ring spot virus PRSV resistance) and application thereof.
The technical scheme adopted by the invention is as follows:
an SNP molecular marker related to resistance of the ring spot virus PRSV, wherein the SNP molecular marker is positioned on a nucleotide sequence shown as SEQ ID No.1, and the 78 th base from the 5' end of the sequence is an SNP locus; the SNP locus is at the 26455183 th base of the chromosome of Chr 04; the SNP molecular marker is very obviously related to the Cpa04G015360 gene related to papaya PRSV resistance (P < 0.01), has G/T polymorphism, and is very obviously related to a T allele and an anti-PRSV virus.
Further, the molecular marker is very significantly related to the Cpa04G015360 gene related to papaya PRSV resistance (P < 0.01), has G/T polymorphism, and is very significantly related to a T allele and an anti-PRSV virus.
The SNP molecular marker can be used for detecting PRSV high-resistance papaya breeding materials.
The SNP molecular marker can be used for detecting or predicting the papaya PRSV virus resistance.
The invention also provides a method for preparing the molecular marker, which comprises the steps of designing a primer pair by using the nucleotide sequence base sequence containing the SNP marker, carrying out PCR amplification by using papaya genomic DNA as a template, and converting the SNP marker into a 276bp molecular marker, wherein an upstream primer of the primer is as follows: caatcacctg gccacagtac, the downstream primer is: actctgaaga acatgaagct t are provided.
The SNP molecular marker Cpa04g015360:928 related to the papaya PRSV resistance is discovered based on a GWAS analysis method, is beneficial to quickly detecting PRSV high-resistance breeding materials, assisting in hybridization breeding, shortening the breeding period of new varieties, and has the advantages of low detection cost, no environmental limitation, high detection result accuracy and easiness in repetition.
Drawings
FIG. 1 Manhattan plot of SNP markers of the present invention that are very significantly associated with papaya PRSV resistance.
FIG. 2 is a Manhattan diagram of a Chr04 chromosome local interval in which an SNP marker which is extremely significantly related to papaya PRSV resistance is located and a linkage disequilibrium haplotype block diagram, wherein deepening marks in the interval are molecular markers screened by the invention.
FIG. 3 shows that the T allele is significantly related to PRSV high resistance by comparing the PRSV resistance difference among different genotypes of the SNP markers which are significantly related to the papaya PRSV resistance in the invention.
FIG. 4 is an agarose gel electrophoresis of the primers of the present invention, wherein the M lane: DNA Marker DL 1000; the right side of the lane M is sequentially provided with 2 genes of TT genotype and GT genotype.
Detailed Description
In order that the objects and advantages of the invention will be more clearly understood, the invention is further described in detail below with reference to examples. It should be understood that the specific embodiments described herein are merely illustrative of the invention and are not intended to limit the invention.
Papaya PRSV resistance assessment
340 parts of papaya collected from Mexico, south Africa, Guangxi, Hainan, etc. are sown in Wenchang base of Chinese tropical agricultural academy of sciences, and the soil fertility is moderate and the irrigation conditions are good. After the seedlings are planted for many years at multiple points and artificially inoculated with PRSV virus under natural conditions, the resistance of the varieties is scored according to the following standard evaluation.
The observation started at 10d from the day of inoculation, and the disease was recorded and graded every 10 d. And 45d after inoculation, the illness state of each treatment is basically stable, the number of diseased plants of each variety is counted, the diseased plant rate is calculated, and the resistance level of the test material to the PRSV virus is evaluated. Standard for the population resistance of papaya to PRSV reference is made to the standard described by Magdalita et al (1988) for PRSV rating 6 as follows:
level 0: the whole plant is disease-free, and the plant grows normally.
Level 1: the leaf has bright vein or slight flower leaf (yellow spot or chlorosis), and does not deform.
And 2, stage: 1/3-1/2 leaves, or a few leaves are deformed, shrunk and curled, or the veins are embrittled, and the plant growth is hindered.
And 3, level: 1/2 the leaf has severe deformation, and mild dwarfing.
4, level: the whole leaf is deformed seriously and the plant is dwarfed.
And 5, stage: the whole plant leaves are seriously flapped, deformed and even fallen off, the diseased plants are obviously dwarfed, and the growth potential is weak.
Disease index formula:
disease index = (number of diseased plant at each stage x disease grade value)/(total number of investigated plant x highest grade value) × 100
Division of population resistance:
high Resistance (High Resistance HR): disease refers to 0-10.0;
anti (Resistance R): disease refers to 10.1-35.0;
sensation (susceptable S): disease refers to 35.0-60.0;
high feeling (High susceptable HS): diseased finger > 60.0.
And (4) the phenotypic character data is processed by Excel2016 and then is used for subsequent analysis.
Papaya whole genome SNP marker development
Taking 1-2g of fresh young leaves from a papaya plant, grinding by liquid nitrogen, and extracting papaya material DNA by using a radix asparagi plant genome DNA extraction kit (DP 305). Detecting the quality and concentration of a DNA sample by using an ultramicro spectrophotometer and 1% agarose gel electrophoresis, and selecting the DNA sample with clear electrophoresis band, no obvious protein residue in a gel hole, OD260/OD280 of between 1.8 and 1.9 and the concentration of more than 100 ng/mu L for library construction and sequencing.
The DNA is randomly broken into fragments of about 300bp by adopting an ultrasonic wave breaking (or enzyme digestion) method, and the construction of a sequencing library is completed by the DNA fragments through end repair, 3' end adding A, sequencing joint coupling adding, purification and PCR amplification. Sequencing the library through an illumina platform after the library is qualified through quality inspection. After the sequencing data are off, the quality control of original data (Raw reads) is required according to a certain standard, and the filtering standard is as follows: (1) removing sequences with a linker (adapter), (2) removing a pair of sequences with a single-ended sequence nitrogen content >10%, and (3) removing a pair of sequences with a low-mass base number exceeding 50%. And removing the low-quality sequence, the linker sequence and the inaccurate sequence to carry out the next sequence alignment. Selecting a newly assembled papaya fruit material 'kamiya' genome from the subject group by referring to the genome, comparing Clean reads with a reference genome sequence by using BWA-mem software, sequencing results by using samtools software, removing PCR repetitive sequences by using GATK4.0 software, performing mutation detection, filtering a variation set by using hard standards of QD > 2.0, QUAL > 30.0, FS < 60.0 and MQ > 40.0, and reserving a variation site data set with statistical significance. And (4) filtering the mutation sites again by taking MAF (minor allele frequency) > = 0.05 and miss (deletion rate) < =0.2 as standards to obtain a high-quality mutation site collection.
Analysis of papaya PRSV resistance SNP site
And annotating the variation sites by using the genome DNA interval feature description file, and respectively counting the number of the variation sites which fall in a gene coding region, a non-coding region, an intergenic region, non-synonymous mutation and the like. After a population genetic relationship matrix is obtained through population structure analysis, a suitable GWAS model is selected by combining phenotypic character data to carry out genome-wide association analysis, a linkage disequilibrium region which is obviously related to papaya PRSV resistance (-log 10 (P-value) > 6) and has the size of 50kb is detected on a Chr04 chromosome, and a candidate gene Cpa04g015360 related to papaya PRSV resistance is determined.
Screening candidate markers
Based on SNP markers in the region related in GWAS analysis, allele frequency, character difference and gene expression quantity difference are compared, and SNP sites Cpa04G015360:928 (G/T) which are obviously related to papaya PRSV resistance are screened in the Cpa04G015360 gene promoter region.
TABLE 1 Cpa04g015360:928 different genotypic populations resistance profiles
After a 276bp DNA fragment is obtained by using the SNP marker primer through common PCR reaction, a sequencing result is compared and analyzed with a papaya related gene fragment SEQ ID No.1, and the genotype carried by the 78 th site of the SNP site of the sequence is detected, so that the detection or prediction of the PRSV resistance of a papaya variety can be realized, the papaya variety with high PRSV resistance can be effectively selected, and the process of the papaya PRSV high-resistance variety breeding is accelerated.
To verify the utility of the SNP markers described in the present invention, 30 papaya plants (excluding 340 papaya plants used for SNP marker development) were randomly selected from papaya growing areas of Wenchang base, Biotech institute of Chinese tropical agrology academy, and were genotyped and evaluated for papaya PRSV resistance after sequencing.
Table 230 papaya strains evaluation of different genotypes and PRSV resistance at Cpa04g015360:928
Statistics of resistance evaluation of papaya strains of Table 330 at Cpa04g015360:928 by different genotypes and PRSV
As can be seen from tables 2 and 3, the number of T alleles at Cpa04g015360:928 was significantly correlated with PRSV resistance.
The foregoing is only a preferred embodiment of the present invention, and it should be noted that those skilled in the art can make various improvements and modifications without departing from the principle of the present invention, and these improvements and modifications should also be construed as the protection scope of the present invention.
Sequence listing
<110> three colleges of tropical agricultural sciences in China
<120> SNP molecular marker related to resistance of ring spot virus PRSV and application
<160> 3
<170> SIPOSequenceListing 1.0
<210> 1
<211> 276
<212> DNA
<213> Artificial Sequence Artificial Sequence (caatcacctg gccacagtac tttgaggagt ttctgacggg 40 cgaattgaca cacccgtgct ttatactctt tattacarg/tcc 80 atcttgtata tatgtgtata tagaccatct atttctatac 120 atacaatcgc agatagtttt tatttgaagg atacagctac 160 tacttatata ttcagtctta taaatggcaa ctaacatccc 200 tataattgac aattaacatt tcaaatactg gtaattatgc 240 atggtaaaag tatttactct gaagaacatg aagctt 276)
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<212> DNA
<213> Artificial Sequence (caatcacctg gccacagtac 20)
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<212> DNA
<213> Artificial Sequence (actctgaaga acatgaagct t 21)
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Claims (6)
1. SNP molecular markers associated with resistance to the ring spot virus PRSV characterized by: the molecular marker is located at 26455183 th base of Chr04 chromosome and named as molecular marker Cpa04g015360:928, and the molecular marker is located at 78 th base of SEQ ID No. 1.
2. The SNP molecular marker as set forth in claim 1, wherein: the Cpa04G015360 gene related to papaya PRSV resistance of the molecular marker is remarkably related to P < 0.01, has G/T polymorphism, and is remarkably related to a T allele and an anti-PRSV virus.
3. Use of the SNP molecular marker according to any one of claims 1 to 2, wherein: can be used for detecting PRSV high-resistance papaya breeding materials.
4. Use of the SNP molecular marker according to any one of claims 1 to 2, wherein: can be used for detecting or predicting papaya PRSV virus resistance.
5. A method of preparing a molecular marker according to claim 1, wherein: designing a primer pair by taking a nucleotide sequence containing the SNP marker as a basic sequence, and carrying out PCR amplification by taking papaya genome DNA as a template so as to convert the SNP marker into a 276bp molecular marker.
6. The method of molecular labeling of claim 5: the method is characterized in that: the upstream primer of the primer is as follows: caatcacctg gccacagtac, the downstream primer is: actctgaaga acatgaagct t are provided.
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