CN114540536B - QTL (quantitative trait locus) related to low temperature resistance of soybean in sprout period, molecular marker, amplification primer and application - Google Patents
QTL (quantitative trait locus) related to low temperature resistance of soybean in sprout period, molecular marker, amplification primer and application Download PDFInfo
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Abstract
The invention relates to the field of soybean molecular breeding, in particular to a QTL, a molecular marker, an amplification primer and application related to low temperature resistance in a soybean sprout period. The QTL is located in a 38426868bp-38983456bp interval of a soybean chromosome 9, the molecular marker is SSR-09-1126, the molecular marker is located in a 38701572bp-38701609bp interval of the soybean chromosome 9, and the nucleotide sequence of the molecular marker is shown in SEQ ID NO. 1. The molecular marker SSR-09-1126 can be used for molecular marker assisted selective breeding and related functional genes excavation, and can also utilize wild resources to widen the genetic basis of cultivated soybeans.
Description
Technical Field
The invention relates to the field of soybean molecular breeding, in particular to a QTL, a molecular marker, an amplification primer and application related to low temperature resistance in a soybean sprout period.
Background
Seed germination is one of the most important stages in the plant life cycle. Typically, the appearance of a radicle indicates the completion of seed germination. The low temperature stress is one of main abiotic stress factors in the growth and development of plants and the formation process of yield, soybean seeds germinate and are often subjected to the low temperature stress, so that the emergence rate and the emergence uniformity of the soybeans are affected, and the yield of the soybeans is further affected. At present, the effect of low temperature on soybean seed germination molecular mechanism is largely unknown. The method is significant for improving the low temperature resistance in the bud period and improving the yield and quality of soybeans. However, the low temperature resistance in bud period belongs to complex quantitative characters, is controlled by multiple genes, and has long traditional breeding period, great difficulty and great consumption of manpower and material resources. With the development of molecular genetics, molecular marker assisted selective breeding provides a new approach for people to accelerate the breeding process. Marker assisted selection breeding refers to indirect selection of a target trait by molecular markers linked to functional genes during breeding selection. The localization of the molecular marker to the digital trait loci (quantitative trait locus, QTL) is an important means for marker-assisted selection breeding. At present, the soybean sprout period low temperature resistant QTL which is positioned by scientific researchers at home and abroad is fewer, and the QTL positioning of the soybean sprout period low temperature resistant QTL is mainly primary positioning, the distance between a mark and a target property is overlarge, and the positioning accuracy is poor. QTL random localization is a recombination process that is diversified under different genetic backgrounds of different combinations, so that the localized QTL has hybridization combination specificity, a marker interval is too large, and the QTL may be lost along with the change of generation and genetic backgrounds, which is unfavorable for application. Molecular assisted selection is difficult.
Disclosure of Invention
The invention provides a QTL (quantitative trait locus) related to low temperature resistance in a soybean sprout period, a molecular marker, an amplification primer and application thereof, wherein the QTL site has a marker interval of 0.56Mb, an LOD value of 4.18 and a contribution rate of 10.59%, and a molecular marker SSR-09-1126 related to low temperature resistance in the soybean sprout period is identified.
In order to achieve the above purpose, the invention adopts the following technical scheme:
the first object of the present invention is to provide a QTL associated with low temperature tolerance in soybean sprout period, which QTL is located in the 38426868bp-38983456bp interval of chromosome 9 of soybean.
The second object of the invention is to provide an SSR molecular marker of the QTL related to low temperature resistance of soybean in the sprout period, wherein the molecular marker is SSR-09-1126, the 38701572bp-38701609bp interval of soybean chromosome 9, and the nucleotide sequence of the molecular marker is shown as SEQ ID NO. 1.
A third object of the present invention is to provide an amplification primer of the SSR molecular marker, which is as follows:
SSR-09-1126F：5′-CTCAATCGCGAACCCTAAAC-3′；
SSR-09-1126R：5′-GTGCTCCGAAGGCTGTCTAC-3′。
the fourth object of the invention is to provide the application of the amplification primer in the identification of the low temperature resistance of soybean sprouts.
The fifth object of the present invention is to provide a method for identifying low temperature resistance of soybean sprouts using the amplification primers, comprising the steps of:
s1, extracting genomic DNA of soybean materials to be identified;
s2, performing PCR amplification on soybean materials to be identified by using SSR-09-1126 amplification primers;
s3, carrying out electrophoresis analysis on the amplified product, if the electrophoresis band type of the soybean material amplified product to be identified belongs to the No.1 band type in SSR-09-1126, identifying the soybean sprout period low temperature resistant material, and if the electrophoresis band type of the soybean material amplified product to be identified belongs to the No. 2 band type in SSR-09-1126, identifying the soybean sprout period low temperature sensitive material.
The sixth purpose of the invention is to provide the application of the SSR molecular marker in low-temperature-resistant shape breeding in the soybean sprout period.
Compared with the prior art, the invention has the following beneficial effects:
1. the invention constructs genetic group by taking cultivated soybean and wild soybean as parents, locates 1 QTL locus related to low temperature resistance in soybean sprout period, has a marking interval of 0.56Mb and LOD value of 4.18, has a contribution rate of 10.59 percent, identifies molecular marker SSR-09-1126 related to low temperature resistance in soybean sprout period, and can be used for molecular marker assisted selective breeding and related functional gene excavation. And meanwhile, wild resources can be utilized, so that the genetic basis of the cultivated soybeans is widened.
2. The invention utilizes the incubator to carry out low-temperature stress treatment on the soybean sprout period, and takes the germination rate of the soybean seeds subjected to low-temperature treatment as an index for evaluating the low-temperature resistance of the soybean sprout period. And the complete genome introduced line (Chromosome Segment Substitution Lines, CSSLs) group is constructed by taking the Heilongjiang main cultivated variety seism 14 as a recurrent parent, the wild bean variety ZYD00006 as a donor parent, and carrying out multi-generation backcross and selfing after hybridization. Each plant row only contains a few wild bean introduction fragments, so that the QTL interval can be reduced, the positioning accuracy and the accuracy can be improved, and the molecular markers related to the low temperature resistance of the soybeans can be identified in the interval, which is very necessary for the auxiliary selection breeding of the molecular markers in the low temperature resistance state of the soybeans and the functional gene research, and has important significance for enriching the genetic diversity of soybean cultivars.
Drawings
FIG. 1 is a diagram of a mapping population construction process.
FIG. 2 is a flow chart of population resequencing.
Fig. 3 is a maternal chromosome coverage depth profile.
FIG. 4 is a distribution density chart of SNP markers and Bin markers of each chromosome.
FIG. 5 is a diagram of polyacrylamide gel electrophoresis of materials used to develop molecular markers;
wherein, the chart A is an electrophoresis chart of SSR-09-1126 primer resistant material, and each lane from left to right respectively represents public field 03-7239, celebration An Xiao golden yellow, black pears 24, tea beans, jiyu 39, public field 03-5570, changjisoybean, iron pod four yellow, huang Baozhu, golden full soybean, jiyu 93, public field 04L-141, jilin 20, gold ingot, iron pod black, soyabean, tongnong 13, cyclobalanopsis glabra, jiyu 71, public field 04-L15, huang Jinyuan, bai Pidou, tender Fengfeng 11, ji Yo 97, jack yellow, small soybean, jiyu 406, jiyu 66, five-ordinary soybean and cat eye soybean;
FIG. B is an electrophoretogram of SSR-09-1126 primer-sensitive material, lanes from left to right represent black river 25, male P06-12, tongnong 15, heinong 69, J2512, jiyu 69, male P06-6, jiyu 441, jiyu 303, mongolian 31, heinong 29, changnong 14, heinong 35, changinong 25, heinong 11, heinong 31, jiyu 299, hefeng 37, heinong 14, jiunong 36, heinong 13, changinong 30, suinong 15, ji Nong, swan egg, changinong 29, heinong 43, sueinong 28, suiufei No. 2, respectively.
Detailed Description
The present invention will now be described in detail with reference to the drawings and specific examples, which should not be construed as limiting the invention. Unless otherwise indicated, the technical means used in the following examples are conventional means well known to those skilled in the art, and the materials, reagents, etc. used in the following examples are commercially available unless otherwise indicated.
Example 1
QTL (quantitative trait locus) related to low temperature resistance of soybean in sprout period, molecular marker, amplification primer and application
1. Acquisition of QTL, molecular marker and amplification primer related to low temperature resistance of soybean in sprout period
1. Construction of mapping populations
In 2006, full genome introduced line population is constructed by taking the seism 14 (SN 14) as recurrent parent and the wild soybean ZYD00006 as donor parent through continuous backcrossing and selfing. See fig. 1 for a specific generation.
2. Group genotype detection
The population was re-sequenced to detect genotypes (flow scheme shown in fig. 2), comprising the steps of:
(1) And extracting parent and offspring strain DNA by using a CTAB method. After the sample is detected to be qualified, DNA is randomly broken by an ultrasonic breaking method, and the construction of a sequencing library is completed by end repair, addition of A at the 3' end, addition of a sequencing joint, purification and PCR amplification of the DNA fragment. And sequencing the library through an Illumina HiSeqTM sequencing platform after the library is qualified in quality inspection.
(2) The sequencing reads obtained by re-sequencing are relocated to a reference genome for subsequent mutation analysis. The short sequences obtained by the second generation high throughput sequencing were aligned to the reference genome using BWA software. By comparing and positioning the position of the clear Reads on the reference genome, the information such as sequencing depth (figure 3), genome coverage and the like of each sample is counted, and mutation is detected.
(3) For the results obtained from BWA alignment, the Mark duplex tool of Picard was used to remove duplicates, shielding the effects of PCR-multiplexing. The GATK is used for InDel Realignment, namely, the local realignment is carried out on the sites near the comparison result with the insertion deletion, and the error of the comparison result caused by the insertion deletion is corrected. Base substrate value recalibration (Base Recalibration) was performed using GATK, and base mass values were corrected. Mutation detection (variant rolling) was performed using GATK, mainly including SNP and InDel. Stringent filtration of SNPs: SNP cluster filtration (if there are 2 SNPs in 5 bp), SNP filtration near InDel (SNP filtration in 5bp near InDel); and adjacent INDEL filtering (two INDEL distances less than 10bp filtering out). The final screening was 580524 for available SNP tags.
(4) And using the obtained 580524 SNP, taking 17 SNP as a window, taking 1 SNP as a step length, sliding and scanning on a chromosome, carrying out genotype filling and correction on the SNP with aa in the sliding window when the SNP with aa in the sliding window is more than 12 SNP with aa in the sliding window, and carrying out genotype filling and correction on the SNP with bb in the sliding window when the SNP with bb in the sliding window is more than 14 SNP with bb in the sliding window.
(5) And after the mark filling and correction are completed, carrying out Bin division according to the recombination condition of the offspring. The samples were aligned according to the physical location of the chromosome, and when the typing transformation occurred in any sample, the recombination breakpoints were considered to occur, then the SNPs between the recombination breakpoints were classified into bins, and after Bin screening, 3196 bins were finally used as mapped markers for localization (fig. 4).
3. Phenotype data acquisition
In the embodiment, the germination rate of the soybeans after the low-temperature treatment is used as an evaluation index of low temperature resistance in the soybean sprout period.
The germination percentage phenotype acquisition test is as follows: 3 times of repetition are arranged on each material, seeds which are consistent in size, round, full, free of diseases and insect pests are selected, sterilized by a 1% sodium hypochlorite solution, rinsed by distilled water for three times, each 40 grains are placed in a sterilized 9cm culture dish, a layer of sterilizing filter paper is respectively paved on the upper side and the lower side, the sterilized filter paper is placed in a 20 ℃ incubator to be inflated for 12 hours, and then the seeds are taken out to be changed into a 6 ℃ incubator. The germination number was investigated on day 6 after the end of the swelling.
4. Low temperature resistant QTL analysis in soybean sprout period
And carrying out QTL positioning on low temperature resistance of the colony bud phase by using an ICIM (complete interval mapping) method in ICIMAGPYRING 4.1 software, selecting an ICIM-ADD module for analysis, and adopting a CSL template for the introduced line colony. And setting the LOD value to be more than or equal to 2.5, and carrying out QTL analysis on the low temperature resistance of the soybean sprouts. The low temperature resistant QTL interval of the soybean sprout period is found on chromosome 9, and the physical position is 38426868bp-38983456bp, as shown in table 1.
TABLE 1 Low temperature resistant QTL intervals for soybean sprout period
5. Molecular marker identification
The molecular marker related to the low temperature resistance of soybean sprouts is identified in the interval by 60 parts of the existing soybean varieties, one molecular marker is identified to be related to the low temperature resistance of soybean sprouts, the molecular marker is located in the interval of 38701572bp-38701609bp of soybean chromosome 9, and is named SSR-09-1126, and the nucleotide sequence of the molecular marker is shown as SEQ ID NO. 1.
SEQ ID NO.1：
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA the phenotype data of the 60 soybean varieties are shown in Table 2;
TABLE 2 development of phenotypes of materials used for molecular markers
The amplification primer of the molecular marker SSR-09-1126 is as follows:
SSR-09-1126F：5′-CTCAATCGCGAACCCTAAAC-3′(SEQ ID NO.2)；
SSR-09-1126R：5′-GTGCTCCGAAGGCTGTCTAC-3′(SEQ ID NO.3)。
2. application of molecular marker SSR-09-1126 and amplification primer thereof
1. Identification of low temperature resistant material in soybean sprout period
S1, extracting genomic DNA of soybean materials to be identified;
the method for extracting the soybean leaf genome DNA by the CTAB method comprises the following steps:
(1) Putting 2-4g of soybean leaves into a 1.5ml centrifuge tube, adding 4 steel balls with the diameter of 2 mm, putting into liquid nitrogen for freezing, and grinding for 30 times/s for one minute;
(2) After finishing grinding, 700 mu L of CTAB extracting solution preheated at 65 ℃ in advance is added and fully and uniformly mixed;
(3) Placing the centrifuge tube added with CTAB into a water bath kettle with the temperature of 65 ℃, carrying out water bath for 60 minutes, and uniformly mixing the centrifuge tube with the water bath kettle upside down every 15 minutes;
(4) Adding 700 mu L of chloroform solution into the centrifuge tube after the water bath is completed, reversing and uniformly mixing, and centrifuging at 12000rpm/min for 15min;
(5) The supernatant is sucked and put into another prepared 1.5mL centrifuge tube, 700 mu L of chloroform is added again, after being mixed up and down gently, the mixture is centrifuged at 12000rpm/min for 15min;
(6) Adding 700 μl of pre-chilled isopropanol at-20deg.C into a new 1.5ml centrifuge tube, collecting supernatant, slowly dripping into the centrifuge tube containing isopropanol solution, centrifuging at 8000rpm/min for 2min;
(7) The supernatant was decanted and the precipitate was retained. Adding 700 mu L of absolute ethyl alcohol, blowing for several times, sucking out the absolute ethyl alcohol, adding 700 mu L of 75% ethyl alcohol, blowing for several times, sucking out 75% ethyl alcohol, and airing DNA at a ventilation place;
(8) 100 mu L of sterilized water is added into the dried DNA, and the DNA is put into a refrigerator at 4 ℃ until the DNA is completely dissolved and transferred into a refrigerator at-20 ℃ for preservation.
S2, performing PCR amplification on soybean materials to be identified by using SSR-09-1126 amplification primers;
the PCR reaction system is shown in Table 3, and the PCR reaction procedure is shown in Table 4;
TABLE 3 PCR reaction System
TABLE 4 PCR reaction procedure
S3, carrying out electrophoresis analysis on the amplified product, if the electrophoresis band type of the soybean material amplified product to be identified belongs to the No.1 band type in SSR-09-1126, identifying the soybean sprout period low temperature resistant material, and if the electrophoresis band type of the soybean material amplified product to be identified belongs to the No. 2 band type in SSR-09-1126, identifying the soybean sprout period low temperature sensitive material.
The amplified products are detected by polyacrylamide gel electrophoresis, and the result is shown in figure 5, wherein figure A is an electrophoresis diagram of SSR-09-1126 primer resistant materials (public field 03-7239, celebration An Xiao golden yellow, black peas 24, tea beans, jiyu 39, public field 03-5570, changji soybeans, iron pod four yellow, huang Baozhu, jinman soybeans, jiyu 93, public field 04L-141, jilin 20, gold ingot, iron pod black, white eyebrows, tongnong 13, cyclobalanopsis glauca four tops, jiyu 71, public field 04-L15, huang Jinyuan, bai Pidou, tender feng 11, ji Yo 97, jack yellow, small soybeans, jiyu 406, jiyu 66, five beans and cat eye beans);
FIG. B is an electrophoresis pattern of SSR-09-1126 primer-sensitive material (Heihe 25, male P06-12, tongnong 15, heihong 69, J2512, jiyu 69, male P06-6, jiyu 441, jiyu 303, mongolian 31, heihong 31, heihe 29, changnong 14, heihe 35, changnong 25, heihe 11, heihe 31, jiyu 299, hefeng 37, heihe 14, jinong 36, heihe 13, changfei 30, suilnong 15, ji Nong 32, swan egg, changnong 29, heihe 43, suilnong 28, suilnon-fishy bean No. 2).
The phenotype genotyping results of the materials used to develop the molecular markers are shown in Table 5;
TABLE 5 phenotypic genotyping results for materials used to develop molecular markers
The SSR-09-1126 molecular marker has obvious difference of single-factor analysis of variance of germination rates of the No.1 band type and the No. 2 band type, as shown in Table 6;
TABLE 6SSR-09-1126 molecular markers No.1 banding pattern and No. 2 banding pattern single factor analysis results
While preferred embodiments of the present invention have been described, additional variations and modifications in those embodiments may occur to those skilled in the art once they learn of the basic inventive concepts. It is therefore intended that the following claims be interpreted as including the preferred embodiments and all such alterations and modifications as fall within the scope of the invention.
It will be apparent to those skilled in the art that various modifications and variations can be made to the present invention without departing from the spirit or scope of the invention. Thus, it is intended that the present invention also include such modifications and alterations insofar as they come within the scope of the appended claims or the equivalents thereof.
Claims (2)
1. The application of a pair of amplification primers in the low temperature resistance identification of soybean sprouts is characterized in that the amplification primers are as follows:
SSR-09-1126F：5′-CTCAATCGCGAACCCTAAAC-3′；
SSR-09-1126R：5′-GTGCTCCGAAGGCTGTCTAC-3′。
2. the application of the SSR molecular marker in low temperature resistance breeding in the soybean sprout period is characterized in that the molecular marker is SSR-09-1126, the molecular marker is positioned in the 38701572bp-38701609bp interval of soybean chromosome 9, and the nucleotide sequence of the molecular marker SSR-09-1126 is shown as SEQ ID NO. 1.
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