CN111394509B - Molecular marker linked with pepper reverse thermosensitive sterile gene and application thereof - Google Patents
Molecular marker linked with pepper reverse thermosensitive sterile gene and application thereof Download PDFInfo
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Abstract
The invention discloses a molecular marker linked with a capsicum reverse thermosensitive genic male sterile gene and application thereof. Benefit (benefit)Construction of F with wild-type and mutant capsicum materials 2 A population. And (3) obtaining a chromosome region closely linked with the capsicum reverse thermosensitive sterile gene by using a BSA population positioning method, and developing a molecular marker in a candidate region. 1 KASP molecular marker was designed based on single base mutation, and the marker pair F was used 2 Genotyping is carried out on 220 single plants in the population, and the coincidence rate reaches 100%. The research result is not only helpful for the identification and auxiliary breeding of the pepper reverse temperature-sensitive sterility, but also provides a basis for the map-based cloning of the reverse temperature-sensitive sterility gene and the analysis of the molecular mechanism of the reverse temperature-sensitive sterility, and has a wide popularization value.
Description
Technical Field
The invention belongs to the field of pepper breeding molecular biology, and relates to a molecular marker linked with a temperature-sensitive sterile gene of pepper (Capsicum annuum L) and application of the molecular marker in pepper temperature-sensitive sterile identification and breeding.
Background
The plant male sterility has an important role in heterosis utilization, has been widely applied to the production of commercial hybrid seeds of crops such as rice, wheat, corn, rape, cotton and the like, wherein the temperature-sensitive sterility is one of important types of male sterility, and the two-line breeding method based on the temperature-sensitive male sterility line has obvious advantages, is not restricted by restoring and maintaining relations, has two purposes of free and one-line matching, has simple production process, and has no potential risks caused by cytoplasmatic negative effects and cytoplasmatic singleness. The most widely applied forward temperature-sensitive male sterile lines at present are 10 forward temperature-sensitive male sterile lines such as 64S, norin PL12, TGMS-VN and 5460S and the like in rice. For example, the sterility critical temperature of the temperature-sensitive male sterile line 64S of the rice is 23.3 ℃, the rice can be self-propagated under the condition of lower temperature, and the seeds can be produced under the condition of higher temperature. The forward thermosensitive male sterile lines of crops such as cotton, corn, wheat, barley, rape, soybean, sorghum and the like are also discovered successively, such as TMS-2 thermosensitive male sterile line (27-28 ℃) of cotton, 6Qms thermosensitive male sterile line (31 ℃) of corn and the like.
The reverse thermosensitive male sterile line has opposite fertility to the forward thermosensitive male sterile line and shows high-temperature fertility and low-temperature sterility characteristics. The reverse thermosensitive male sterile line can be self-propagated under the high temperature condition, and can be used for seed production under the conditions of higher latitude or higher altitude area and lower latitude and lower temperature. At present, the rice reverse temperature-sensitive male sterile line mainly comprises Yunnan nong S-2, kunzing S-1, heng S-3, IVA, go543S, J S, DIS and G20S and the reverse temperature-sensitive male sterile line FHS obtained by physical mutagenesis. The research shows that the fertility transition temperature of the reverse thermosensitive male sterile line go543S is 28-30.5 ℃, the fertility is only regulated and controlled by the temperature, namely, the fertility is higher than 30.5 ℃ and the fertility is low at 28 ℃. The fertility transition temperature of the reverse thermosensitive male sterile line FHS is 25-26 ℃ (Wang Huifeng, 2005). In wheat, the fertility characteristics of reverse thermosensitive male sterile lines such as ES series, C49S and C86S series, YM3314, A3017 and 337S and the like are also reported successively. The discovery and breeding of the reverse thermosensitive male sterile line expands a new application space for two-line cross breeding and heterosis utilization.
Capsicum (Capsicum annuum l.) is a annual or limited perennial herb of the family solanaceae, genus Capsicum. In recent years, the annual sowing area of the chillies in China is 150 to 200 ten thousand hm 2 At present, the total sowing area of the vegetables in China is 8 to 10 percent. At present, no related report on the reverse thermosensitive genic male sterility of the capsicum exists, so that the thermosensitive genic male sterile mutant of the capsicum is taken as an important germplasm resource and is favored by breeders in the future. Through developing molecular markers linked with the capsicum reverse thermosensitive sterile genes, the thermosensitive sterile genes and other excellent trait genes are rapidly introduced into plants by adopting technologies such as hybridization, backcrossing and the like, and gene resources are provided for breeding high-quality new varieties. Developing molecular markers linked with reverse thermosensitive sterile genes, which is favorable for breeding of thermosensitive male sterility of capsicum and is a cloned capsicum reverse thermosensitive sterile geneThe sterile gene lays a foundation for researching the molecular mechanism of reverse thermosensitive sterility.
Disclosure of Invention
The primary purpose of the invention is to provide a molecular marker Pe_K_1200003 (G-to-A at the positions of the whole genome Chr12:12,852,132bp of the capsicum) linked with a capsicum reverse thermosensitive sterile gene aiming at the male thermosensitive sterile phenomenon (fertility is shown at 28 ℃ and above and sterility is shown at below 28 ℃) occurring in the development of the capsicum flower buds. Provides a new way for screening, identifying and assisting in screening the temperature-sensitive sterile character of the capsicum, breeding of male temperature-sensitive sterile of the capsicum and the like.
The genotypes corresponding to the molecular markers comprise: g and A are the fertility genotypes with pollen activity and A is the sterility genotype without pollen activity.
The pollen viability of the invention is shown to be pollen-free, and the pollen has sufficient fertility (28 ℃ and above), and the pollen viability is not shown to be completely pollen-free, or the pollen viability is shown to be very little, and the pollen has no fertility (28 ℃ and below).
The primer designed for the pepper reverse thermosensitive sterile mutation comprises two forward primers and one reverse primer,
forward primer X: AAAATATCAAACCAATTCCAACTAG, shown in SEQ ID No. 1;
forward primer Y: AAAATATCAAACCAATTCCAACTAA, SEQ ID No. 2.
The two forward primers were each ligated to a different fluorescent linker sequence (FAM or HEX linker sequence from LGC Co.)
Preferably:
FAM: GAAGGTGACCAAGTTCATGCT, shown in SEQ ID No. 3;
HEX: GAAGGTCGGAGTCAACGGATT, SEQ ID No. 4.
The primer sequences after the different fluorescent linker sequences were ligated respectively were as follows:
forward primer pe_k_1200003X: GAAGGTGACCAAGTTCATGCTAAAATATCA AACCAATTCCAACTAG, shown in SEQ ID No. 5;
forward primer pe_k_1200003Y: GAAGGTCGGAGTCAACGGATTAAAATATCA AACCAATTCCAACTAA, shown in SEQ ID No. 6;
reverse primer pe_k_1200003C: TCACATGTTAGAAATTGTTTGTCA, shown in SEQ ID No. 7;
the second purpose of the invention is to provide the application of the molecular marker, which is favorable for breeding of the fertility of the pepper pollen and lays a foundation for cloning the temperature-sensitive sterility and researching the molecular mechanism of the temperature-sensitive sterility.
The method specifically comprises the following steps: is used for identifying and assisting in screening pepper fertility.
Further, the method is used for identifying, screening or breeding the temperature-sensitive sterility of the capsicum.
When the molecular marker is applied, the detection is carried out by adopting a PCR reaction.
When the molecular marker is applied, the method specifically comprises the following steps: (1) Taking genomic DNA of a sample to be detected as a template, and amplifying by using a molecular marked amplification primer to obtain an amplification product; (2) detecting and analyzing the amplified product.
When the amplified product is subjected to fluorescence detection, if the sample PCR product only detects a fluorescence signal corresponding to the primer Pe_K_1200003X, the detection site is G genotype, and the single plant of the chilli with pollen viability phenotype is judged; if the sample PCR product only detects a fluorescent signal corresponding to the primer Pe_K_1200003Y, the detection site is A, the genotype A is determined to be a single plant with a sterile phenotype of the capsicum pollen; if two fluorescent signals are detected at the same time, the detection site is A G genotype, and the single plant of the capsicum with pollen vitality phenotype is judged.
When the molecular marker is applied, the TouchDown PCR is adopted, and the amplification program is as follows: 94 ℃ for 15min;95 ℃ for 20s; 60s at 65-56 ℃ for 10 cycles, and the annealing extension temperature of each cycle is reduced by 0.8 ℃;94 ℃ for 20s;57 ℃ 60s,26 cycles.
The invention utilizes a BSA positioning method to position a new SNP variation for controlling the development of the pepper pollen, and develops a KASP molecular marker related to the pepper pollen development gene according to the mutation site of the gene. Can be directly used for identifying fertility and corresponding genotype of pepper pollen, and further relies on the molecular marker for auxiliary breeding, so that the problems of long conventional breeding period and easiness in environmental influence can be effectively solved. The molecular marker can be used for rapidly screening satisfactory plants in early stage, so that the planting scale is effectively reduced, and the workload of later stage identification is reduced. The efficiency and the accuracy of selection are improved. Can be used for identifying various varieties of capsicum, and has great significance for researching the formation mechanism of reverse thermosensitive sterility. Therefore, the invention has important significance on the breeding practice of the male temperature-sensitive sterility of the capsicum and the theoretical research of the temperature-sensitive sterility.
Drawings
FIG. 1 shows F of the Pe_K_1200003 molecular marker of the invention constructed in Wild Type (WT) and Mutant (MT) 2 Partial results of genotyping in the population;
the A represents: the PCR product is a fluorescent signal corresponding to a primer Pe_K_1200003Y and is a sterile homozygous single plant;
and B represents: the PCR product is a fluorescent signal corresponding to a primer Pe_K_1200003X and is a fertile homozygous single plant;
and C represents: the PCR product has two corresponding fluorescent signals of the primer Pe_K_1200003X, Y, and is a fertile heterozygous single plant.
FIG. 2 is 2 parents of BSR population localization: 6421 (A), E6421S (B).
FIG. 3 shows the BSA localization results for the 6421 and E6421S construct populations;
chr01-Chr12 represents chromosome number, and the male temperature-sensitive sterile gene is located on chromosome 12, with a region between about 11-20M.
FIG. 4 shows the fine localization of mutation of temperature sensitive sterile gene of the present invention.
Detailed Description
The invention will be further illustrated with reference to specific examples, but the invention is not limited to the examples. The materials, reagents, instruments and methods used in the examples below, without any particular description, are conventional in the art and are commercially available. The capsicum germplasm related to the invention is provided by Hunan province vegetable institute, and can be sold for at least 20 years.
Example 1 method for obtaining BSA positioning by molecular marker BSA molecular marker linked with capsicum temperature sensitive sterile gene
1. Construction of populations
And (3) hybridizing the fertile parent and the temperature sensitive sterile parent to obtain an F1 generation and obtaining an F2 population after the F1 generation selfing by using the fertile material '6421' (shown in fig. 2A) and the reverse temperature sensitive sterile material 'E6421S' which are obtained through multi-generation selfing as parents (shown in fig. 2B).
2. Pollen fertility identification
And (5) observing and identifying whether pollen exists or not when the F2 generation population is in the full bloom stage, and determining the fertility of individual plants in the population.
3. Initial localization of temperature sensitive sterile gene
F at 6421 XE 6421S 2 And respectively selecting 25 pollen plant leaves and 25 pollen-free plant leaves from the population, and equally mixing the plant leaves to construct a fertility/sterility DNA mixing pool. The total DNA of 4 pools was extracted by CTAB method. 4 pooled DNA was pooled using TruSeq DNA LT Sample Prep Kit (Illumina corporation), sequenced by Illumina HiSeq2000 platform, genomic sequencing was performed, the obtained data extracted polymorphic SNPs using samtools software and autonomously developed Perl scripts, and the maximum allele frequency of the recessive pool (SNP-index) was calculated, as well as the frequency of the genotype in the dominant pool, and the euclidean distance (ED value) for each SNP site was calculated. Sites with sequencing depths of both pools lower than 10 reads and SNP-index larger than 0.7 are filtered, linear regression fitting and mapping are carried out after the ED value is exponentiated, the median value of all site exponentiated fitting values and 3 times of the sum of standard deviation are taken as threshold lines, the section higher than the threshold lines is taken as a candidate section, namely, the gene for controlling temperature sensitive sterility is positioned in the 11-20M section on chromosome 12, as shown in figure 3.Chr01-Chr12 represents chromosome number, and the thermo-sensitive sterile major QTL is located on chromosome 12.
4. Fine localization of temperature sensitive sterile genes
Obtaining a chromosome region for controlling temperature-sensitive sterility through the step 3, analyzing DNA sequence variation in a section for further shrinking a candidate region for controlling temperature-sensitive sterility gene, developing InDel and KASP markers, and utilizing the developed InDel and KASP molecular markersRecord F pair 2 Genotyping the individual plants of the population, and determining the exchange individual plants. Based on the phenotype investigation data of pollen and the determined genotype of the exchange individual, the temperature sensitive sterile gene is positioned in the 11-13M interval, and KASP marking type capsicum is carried out according to SNP in the interval.
Finally, the whole genome of the capsicum Chr12 is obtained by sequencing: the G-to-A mutation at 12,852,132bp is shown in FIG. 4.
220 individuals of the F2 population constructed by 6421 and E6421S were genotyped using the Pe_K_1200003 marker. There are 3 fluorescent signals, wherein the fluorescent signal of A: A has 65 individuals, the fluorescent signal of A: G has 105 individuals, and the fluorescent signal of G: G has 50 individuals. The phenotype investigation data are combined to find that the genotype is highly consistent with the pollen fertility phenotype, and the coincidence rate reaches 100%. The result fully shows that the Pe_K_1200003 marker has universality and accuracy, and can be applied to prediction, identification and screening of pepper temperature-sensitive sterile plants.
When the molecular marker is applied, the method specifically comprises the following steps: (1) Taking genomic DNA of a sample to be detected as a template, and amplifying by using a molecular marked amplification primer to obtain an amplification product; (2) detecting and analyzing the amplified product.
Reverse primer pe_k_1200003C: TCACATGTTAGAAATTGTTTGTCA
Forward primer pe_k_1200003X: GAAGGTGACCAAGTTCATGCTAAAATATCAAACCAATTCCAACTAG.
Forward primer pe_k_1200003Y: GAAGGTCGGAGTCAACGGATTAAAATATCAAACCAATTCCAACTAA.
The primer has specificity through sequencing verification of the whole genome sequence of the capsicum.
When the amplified product is subjected to fluorescence detection, if the sample PCR product only detects a fluorescence signal corresponding to the primer Pe_K_1200003X, the detection site is G genotype, and the single plant of the chilli with pollen viability phenotype is judged; if the sample PCR product only detects a fluorescent signal corresponding to the primer Pe_K_1200003Y, the detection site is A, the genotype A is determined to be a single plant with a sterile phenotype of the capsicum pollen; if two fluorescent signals are detected at the same time, the detection site is A G genotype, and the single plant of the capsicum with pollen vitality phenotype is judged.
When the molecular marker is applied, the TouchDown PCR is adopted, and the amplification program is as follows: 94 ℃ for 15min;95 ℃ for 20s; 60s at 65-56 ℃ for 10 cycles, and the annealing extension temperature of each cycle is reduced by 0.8 ℃;94 ℃ for 20s;57 ℃ 60s,26 cycles.
The detection sample is leaf, and pollen fertility detection is carried out at about 22 ℃.
Table 1 shows the Pe_K_1200003 markers of part of the individual sterility and genotypes of F2 populations constructed from 6421 and E6421S.
The identification result shows that the material of the male temperature-sensitive sterility of the capsicum can be bred by molecular marker identification and screening and retaining the material of the A fluorescent signal corresponding to the primer Pe_K_1200003Y (figure 1). The material of the B fluorescence signal corresponding to the primer Pe_K_1200003X (figure 1) is remained, so that the fertility homozygous material can be bred. The materials with the fluorescence signals (including the fluorescence signals corresponding to the two primers) of the C in the figure 1 are remained, so that the fertile hybrid materials can be bred, the workload of later screening and identification can be reduced through the screening of the early molecular markers, and the breeding process is accelerated.
Sequence listing
<110> Hunan province vegetable institute
<120> molecular marker linked with pepper reverse thermosensitive sterile gene and application thereof
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Claims (8)
1. A molecular marker linked with a capsicum reverse thermosensitive sterile gene, which is characterized in that: is chilli Chr12:12,852,132bp, said molecular marker primer comprising two forward primers and one reverse primer,
forward primer X: AAAATATCAAACCAATTCCAACTAG;
forward primer Y: AAAATATCAAACCAATTCCAACTAA;
reverse primer: TCACATGTTAGAAATTGTTTGTCA;
the genotypes corresponding to the molecular markers comprise: g is a genotype with pollen activity, A G is a genotype with pollen activity; a is a genotype without pollen activity.
2. The molecular marker according to claim 1, wherein: the two forward primers are respectively connected with different fluorescent joint sequences: FAM: GAAGGTGACCAAGTTCATGCT; HEX: GAAGGTCGGAGTCAACGGATT.
3. Use of a molecular marker according to any one of claims 1-2 for the identification and assisted screening of pepper fertility.
4. The use according to claim 3, for identification, screening or breeding of temperature-sensitive sterile mutants of capsicum.
5. The use according to claim 4, wherein the detection is performed by a PCR reaction.
6. The use according to claim 5, characterized in that it comprises in particular the following steps:
(1) Taking genomic DNA of a sample to be detected as a template, and carrying out PCR (polymerase chain reaction) amplification by using a molecular marked amplification primer to obtain an amplification product;
(2) And detecting and analyzing the amplified product.
7. The method according to claim 6, wherein the amplified product is detected by fluorescence, and the amplified product is a homozygous wild individual with pollen viability; if the genotype A is A, judging that the pollen viability homozygous mutant single plant does not exist; if the genotype A is G, the heterozygous single plant with pollen activity is judged.
8. The use according to claim 7, characterized in that Touchdown PCR is used; the touch hdown PCR amplification procedure was: 94 ℃ for 15min;95 ℃ for 20s; 60s at 65-56 ℃ for 10 cycles, and the annealing extension temperature of each cycle is reduced by 0.8 ℃;94 ℃ for 20s;57 ℃ 60s,26 cycles.
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| CN108754013A (en) * | 2018-06-24 | 2018-11-06 | 华中农业大学 | A kind of and capsicum cytoplasmic male sterility restoring gene close linkage molecular labeling and its preparation method and application |
| CN109207622A (en) * | 2018-10-24 | 2019-01-15 | 湖南省蔬菜研究所 | A kind of molecular labeling and application with the stagnant green gene linkage of capsicum |
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| CN108754013A (en) * | 2018-06-24 | 2018-11-06 | 华中农业大学 | A kind of and capsicum cytoplasmic male sterility restoring gene close linkage molecular labeling and its preparation method and application |
| CN109207622A (en) * | 2018-10-24 | 2019-01-15 | 湖南省蔬菜研究所 | A kind of molecular labeling and application with the stagnant green gene linkage of capsicum |
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