CN110273019B - Molecular marker for rapidly identifying self-compatibility of citrus and application thereof - Google Patents

Molecular marker for rapidly identifying self-compatibility of citrus and application thereof Download PDF

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CN110273019B
CN110273019B CN201910506486.9A CN201910506486A CN110273019B CN 110273019 B CN110273019 B CN 110273019B CN 201910506486 A CN201910506486 A CN 201910506486A CN 110273019 B CN110273019 B CN 110273019B
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citrus
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柴利军
胡健兵
梁梅
邓秀新
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Huazhong Agricultural University
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Abstract

The invention relates to a molecular marker for rapidly identifying self-compatibility of citrus and application thereof, wherein the molecular marker is an Sm gene, and the coding region sequence of the Sm gene is SEQ ID NO:1, the detection primer pair sequence of the Sm gene is SEQ ID NO:2 and SEQ ID NO: 3; also relates to application of the Sm gene in identifying the self-compatibility of the citrus plants, and a kit and a method for identifying the self-compatibility of the citrus plants. The invention designs a specific amplification primer based on the Sm mutation site sequence, can stably detect the existence of the Sm gene in citrus plants, and further can rapidly identify the self-compatibility of citrus, thereby providing effective guidance for citrus compatible variety breeding and cultivation production. The method can quickly identify the self-compatibility of the citrus according to the PCR detection result, has short time consumption, does not need pollination observation, only needs to collect young citrus leaves, and is convenient and quick.

Description

Molecular marker for rapidly identifying self-compatibility of citrus and application thereof
Technical Field
The invention relates to the field of molecular biological marker application of rutaceae citrus fruit trees, in particular to a molecular marker for rapidly identifying self-compatibility of citrus and application thereof.
Background
Self-incompatibility (SI) is a ubiquitous reproductive isolation mechanism formed by flowering plants in the long-term natural evolution process, and aims to prevent close-breeding and species degeneration and maintain species genetic diversity. However, in plant production, particularly in fruit trees, plants with self-incompatibility need to be provided with proper pollinator trees in the cultivation process, which is a big disadvantage for production. Citrus belongs to the family Rutaceae, is a perennial woody fruit tree of tropical and subtropical regions, is widely cultivated and planted in the world, is the first acknowledged fruit in the world, and has important position in national economy. Many of the existing main citrus cultivars have self-incompatibility characteristics, such as Yamashita and Tanimoto (1985), sunshiny summer (Honsho et al, 2009), seedless sugar oranges (Ye et al, 2009), shatian pomelo (Chai et al, 2010), kremen orange (caroso et al, 2012), w.mer kott (Gambetta et al, 2013), perfume lemon (Zhang et al, 2015), and "Kagzi Kalan" lemon (kakakakade et al, 2017). Self-incompatibility is one of the important factors for restricting the improvement of the yield and the quality of citrus fruits. Taking shatian pomelo as an example, in actual production, because the shatian pomelo has a typical gametophytic self-incompatibility characteristic, the self-fertilization fruit setting rate is only 0.3%, so that a grapefruit pollination tree is configured or artificial pollination is carried out in production practice to improve the fruit setting rate, time and labor are wasted, fruit seeds are abundant (Bupleurum military, 2012), and the fruit quality requirement of a consumer is continuously improved in the current due to the shortage of labor force, so that the fruit setting rate becomes an important problem which restricts the sustainable development of the industry.
In the previous study, we confirmed that S-RNase is a key style determinant for controlling citrus self-incompatibility, 16 pistil determinant S-RNase multiple alleles for controlling citrus self-incompatibility have been discovered and identified, and a self-compatible mutant gene Sm (SEQ ID NO:1) which has an adenine (A) deletion at position 442 of ORF (open reading frame) and thus results in frame shift mutation and premature termination is found and identified in self-compatible mutant materials by using affinity mutant resources of lemon, Nanfeng mandarin orange, sweet orange and kumquat series and combining genome resequencing and style transcriptome information, resulting in 498bp coding sequence (FIG. 1), deletion of C5 conserved domain and 4 conserved cysteine residues at C-terminus of mutant Sm, and three-dimensional structure prediction shows that Sm protein lacks 4 beta-sheets at C-terminus, the activity of the protein is predicted to be affected. And detecting in natural citrus resource, and finding that the mutation site is closely linked with the self-compatible phenotype.
Disclosure of Invention
The invention aims to overcome the defects of the prior art and provide a molecular marker for rapidly identifying the self-affinity of citrus and application thereof.
The technical scheme for solving the technical problems is as follows:
a molecular marker for rapidly identifying self-compatibility of citrus is a Sm gene, wherein the coding region sequence of the Sm gene is SEQ ID NO: 1.
further, the detection primer pair sequence of the Sm gene is SEQ ID NO:2 and SEQ ID NO: 3.
the molecular marker is applied to the preparation of a kit for identifying the self-compatibility of citrus.
A kit for identifying the self-compatibility of citrus is used for detecting a molecular marker in a citrus plant, wherein the molecular marker is an Sm gene.
Further, the kit further comprises a pair of detection primers for the Sm gene of claim 2.
Further, the kit is a PCR-based kit.
A method for identifying self-compatibility of citrus plants comprises the step of identifying a molecular marker for self-compatibility in citrus plants.
The method comprises the following steps:
step 1: collecting tissue from said citrus plant carrying a complete set of genetic material;
step 2: extracting a genome from the tissue as a template, and amplifying by using a detection primer pair of the Sm gene;
and step 3: and judging whether the citrus plant is self-compatible or not according to the result of the amplification product, and if the Sm gene is positive as shown in the amplification result, judging that the citrus plant is self-compatible.
The tissue with the complete set of genetic material in the step 1 is leaf tissue.
The detection primer pair sequence of the Sm gene in the method is shown as SEQ ID NO. 2 and SEQ ID NO. 3.
The invention has the beneficial effects that: the invention designs a specific amplification primer based on the Sm mutation site sequence, and the primer can stably detect the existence of the Sm gene in citrus plants, so that the self-compatibility of citrus can be rapidly identified, and effective guidance is provided for citrus compatible variety breeding and cultivation production. The invention provides an effective means suitable for rapidly identifying the self-compatibility of citrus, and the self-compatibility of citrus can be basically judged according to the PCR detection result. The method has short time consumption, does not need pollination observation, only needs to collect the young leaves of the citrus, and is convenient and rapid.
Drawings
FIG. 1 is a diagram showing an intron/exon structure of the Sm gene and a mutation site;
FIG. 2 is a diagram showing the alignment of Sm and CgRNS1 gene sequences;
FIG. 3 is an electrophoresis photograph of 16 citrus germplasm Sm PCR amplified fragments;
FIG. 4 is a photograph of Sm genotype containing citrus varieties stained with aniline blue by selfing pollination.
Detailed Description
The principles and features of this invention are described below in conjunction with examples which are set forth to illustrate, but are not to be construed to limit the scope of the invention.
The technical scheme for solving the technical problems is as follows:
1. discovery and identification of citrus affinity mutation Sm genotype
Leaves of Yunnan Ruili lemon (Ulike) and 2 different flower organ tissue materials (including anther and style) in the day before flowering are adopted. Quickly freezing with liquid nitrogen, and storing at-80 deg.C. RNA from all tissue material was extracted by the method of Liu et al (Liu Y, Liu Q. effective isolation of RNA from fruit peel and pulp of pending novel orange [ D ]. Journal of Huangzhong Agricultural university.2006), and extracted quality of flower columns and pollen RNA were subjected to library construction and sequencing by Anouda, Beijing, with 3 biological replicates per sample. The clean data obtained by sequencing is assembled and spliced by using Trinity to respectively obtain the information of flower columns and anther transcripts, and then local Blastn comparison analysis is carried out on 16 citrus self-incompatibility control S-RNase genes previously obtained by the applicant, so that two transcripts (TRINITY _ DN14124_ c0_ g1_ i 1; TRINITY _ DN2385_ c0_ g1_ i1) in the clean data are higher in sequence homology with known CgRNS1 and CgRNS2, and reach 86% and 94% respectively. The nucleotide _ DN14124_ c0_ g1_ i1 and nucleotide _ DN2385_ c0_ g1_ i1 were amplified by PCR to obtain the complete sequence information (SEQ ID NO: 4; SEQ ID NO:5), and they were identified as ribonuclease genes. Wherein TRINITY _ DN2385_ C0_ g1_ i1 can translate the complete S-RNase protein, and TRINITY _ DN14124_ C0_ g1_ i1 has an adenine (A) deletion at position 442 of ORF (open reading frame) resulting in a frameshift mutation and premature termination, resulting in a 498bp coding sequence lacking the C5 conserved domain and the 4 conserved cysteine residues at the C-terminus, and three-dimensional structure prediction shows that the encoded protein lacks 4 β -sheets at the C-terminus, which is predicted to be affected, thus the ORF of TRINITY _ DN14124_ C0_ g1_ i1 is named Sm (SEQ ID NO: 1).
Through resequencing and analysis of floral tissue transcriptome data, Sm genotypes are found in 19 identified and compatible lemon varieties in Yunan Raidi, and the sequences are relatively conservative and widely exist in citrus fruit trees. Self-pollination observation is carried out on the citrus germplasm resources identified to contain the Sm genotype so as to determine the compatible phenotype, and the result shows that the oranges containing the Sm genotype all show self-compatibility.
2. Sm sequence analysis and spatial Structure analysis
And designing a full-length amplification primer according to sequence information obtained by the transcriptome, and respectively amplifying by taking the leaf DNA of the lemon of Eulegor and the cDNA of the style as templates. The amplification primers are respectively:
Sm-Full-length-F:5’--ATGAAGATTAATTTCTGCATTTTCA--3’(SEQ ID NO:6)
Sm-Full-length-R:5’--TTATTTATGCCGGGGGAAGCTGATA--3’(SEQ ID NO:7)
the product obtained by amplification is subjected to recovery, vector construction and sequencing to obtain a sequence, the DNA sequence of Sm is shown as SEQ ID NO. 4, and the CDS sequence is shown as SEQ ID NO. 1.
The size and isoelectric point of the protein encoded by the candidate gene are predicted by the ProtParam tool of the ExPASy website. Sm has a CDS sequence with the full length of 501bp, encodes a 19.6kDa protein and has an isoelectric point predicted to be 7.74. The intron/exon structure of the gene was mapped using GSDS, and Sm had only one intron and the position of the intron was around 300bp in the sequence as shown in FIG. 1.
Sm was aligned with the CgRNS1 sequence using clustalx software and the alignment was mapped using Genedoc, as shown in FIG. 2, 2 candidate genes all contained the conserved domains C1-C4, and two hypervariable regions HVa, HVb, where Sm did not have the C5 conserved domain. In addition, 2 ribonucleases all have two conserved histidine active sites, 6 cysteine sites.
3. Sm functional verification
As shown in FIG. 3, specific amplification primers are designed to amplify different citrus germplasms, and the result shows that the specific primers can stably detect the existence of Sm genotypes in the citrus germplasms.
Specific amplification primer sequence:
Sm-F:5’--TTACACCGTTCTAATGTTGCGA--3’(SEQ ID NO:2)
Sm-R:5’--TTGGCTGATCTCCGTTCTGC--3’(SEQ ID NO:3)
and randomly selecting the citrus germplasm containing Sm and the citrus germplasm without Sm genotypes according to the amplification result, and carrying out selfing pollination observation. Randomly selecting 10 mature flowers from each citrus germplasm, pollinating and bagging, respectively taking flower columns of different citrus varieties 3-9 days after pollination according to the experience of an earlier-stage subject group, placing the flower columns in a fixing solution for fixation, softening by NaOH, dyeing by water-soluble aniline blue, and observing the growth state of a pollen tube under a fluorescence microscope. As shown in FIG. 4, the results show that the Sm genotype of the citrus variety was shown to be compatible in self-pollination. Therefore, the Sm gene is closely related to the self-compatibility phenotype of the citrus, and a marker developed aiming at the Sm mutation site is suitable for rapidly identifying the self-compatibility of the citrus.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.
Sequence listing
<110> university of agriculture in Huazhong
<120> molecular marker for rapidly identifying self-affinity of citrus and application thereof
<160> 7
<170> SIPOSequenceListing 1.0
<210> 1
<211> 501
<212> DNA
<213> orange (Citrus)
<400> 1
atgaagatta atttctgcat tttcattgtt ctgtttgttt actgcatttc ctctgtagaa 60
aataattctg gttttgacca cttttggctg gtcctgagct ggccacctgt ctattgccta 120
caaatccgct gcgaaagaaa accaacagat ttcgtcctac acggtctctg gccagtaaac 180
tctaccgggc acagtttgaa aaattccacc aacggcaccc ctaatttcta ctcgatgcta 240
cgcaatcatt cttttggtat cgaaatggat gaacactggc caagtctcgg ttccaaagaa 300
ggacgagatc cgtacaaaca tattcgtttc tgggagcatg agtgggaaga gcatggcagc 360
ggccaacctt acggagatac atattatctc caatcagcta tcagactaag gaaaagtgtg 420
aacctgctga gaatactaag aatcaaggaa tatttccaga tggaaggagt tactgggaaa 480
ctgggtacgt ggatgcaata a 501
<210> 2
<211> 22
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 2
ttacaccgtt ctaatgttgc ga 22
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ttggctgatc tccgttctgc 20
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atgaagatta atttctgcat tttcattgtt ctgtttgttt actgcatttc ctctgtagaa 60
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caaatccgct gcgaaagaaa accaacagat ttcgtcctac acggtctctg gccagtaaac 180
tctaccgggc acagtttgaa aaattccacc aacggcaccc ctaatttcta ctcgatggta 240
ctcccgctcc tttttttttt tttaaaaaaa aaattaggag tcagtttgct agctttgttt 300
ttcaaacttt ttacaccgtt ctaatgttgc gaaaatttat ttgctattgg ttctcaagct 360
acgcaatcat tcttttggta tcgaaatgga tgaacactgg ccaagtctcg gttccaaaga 420
aggacgagat ccgtacaaac atattcgttt ctgggagcat gagtgggaag agcatggcag 480
cggccaacct tacggagata catattatct ccaatcagct atcagactaa ggaaaagtgt 540
gaacctgctg agaatactaa gaatcaagga atatttccag atggaaggag ttactgggaa 600
actgggtacg tggatgcaat aaaagacgca tacggttatc cagtacttaa gtgcttcaat 660
ggttatctgc taaaggaggt gactatatgc gttgacggtc aagcaagaag tttcatttca 720
tgcagtcccg cagaacggag atcagccaat tgccataacg ttatcagctt cccccggcat 780
aa 782
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<213> orange (Citrus)
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atgaaggcga ccaacctctt ttgctttgct cttcttgtaa tcaacgttac gtatggcaca 60
gctcaaaaca cctcacaggt gttcgaccac tattggctag tccaagtgtg gccacatggc 120
tattgcttgg agcgtgattg tgcccggcgt tcagatattt tcatcctaca tgggctttgg 180
ccggtgacct ctgaggggaa aactttggaa ggtgacaaaa taaataacac aacccacaac 240
aagattctaa aattggtact cccctcttct ttttgctgac catgagttaa ttctctaatt 300
tccttcatat actgatctaa ctatatcctt attgttactt ctgtagctga agcgagataa 360
atctcttgag ggtgatttga tgaaatattg gctaagtctc actactgtta atgagaatta 420
cattgcaggt ttttggattc atgagtggga aaaacatggc agtgctagaa aaggcatgga 480
tccgctagat tatttccgaa gagctgtcga actagcaaaa acaacggacc ttaggagcac 540
actagcagag aagggagtgt tgcctaatgg agctagttac cctaaattta attacatgaa 600
ggcaataatg gccaaaactg gtcaccttcc aatgcttaga tgcgttaaaa aaggtggtca 660
taatcattta aaggaggtaa ttatatgcgt aggtctccaa gcaaaaaatt tcaggtcatg 720
caattacgga gtggattcac ggcgctgtaa gggagaatat atcaagttcc ctgagccgac 780
caatgagtaa 790
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<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 6
atgaagatta atttctgcat tttca 25
<210> 7
<211> 25
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 7
ttatttatgc cgggggaagc tgata 25

Claims (5)

1. The molecular marker for rapidly identifying the self-compatibility of the citrus is characterized in that the molecular marker is a Sm gene, and the sequence of the Sm gene is SEQ ID NO: 4.
2. use of the molecularly imprinted detection reagent according to claim 1 for preparing a kit for identifying self-affinity of citrus.
3. A kit for identifying citrus self-affinity, which is characterized by comprising the Sm gene detection primer pair of claim 1, wherein the Sm gene detection primer pair has a sequence shown in SEQ ID NO:2 and SEQ ID NO: 3.
4. a method of identifying self-compatibility of citrus plants, comprising the steps of:
step 1: collecting tissue from said citrus plant carrying a complete set of genetic material;
step 2: extracting a genome from the tissue as a template, and amplifying the extracted genome using the Sm gene detection primer set of claim 1; the detection primer pair sequence of the Sm gene is shown as SEQ ID NO. 2 and SEQ ID NO. 3;
and step 3: and judging whether the citrus plant is self-compatible or not according to the result of the amplification product, and if the amplification result is positive, judging that the citrus plant is self-compatible.
5. The method of identifying self-affinity of a citrus plant according to claim 4, wherein the tissue bearing the full set of genetic material in step 1 is leaf tissue.
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Isolation and differential expression analysis of self-compatibility-related genes from mature pistils of "Shatangju" mandarin (Citrus reticulata Blanco);Miao,HX 等;《JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY》;20111231;第86卷(第6期);第575-582页 *
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