Genetic background evaluation method of backcross improved population

Abstract

The invention relates to the technical field of plant breeding, in particular to a genetic background evaluation method of a backcross improved population. The method comprises the following steps: dividing chromosome intervals and molecular markers based on a plant genetic recombination exchange rule to obtain a typing result of a simplified marker, calculating a background recovery rate of a backcross improved population based on the typing result, and combining the background recovery rate with a recovery fragment structure to evaluate the genetic background recovery degree of the backcross improved population. Effective single plants which are small in genetic difference with receptor parents and relatively concentrated in non-recovery sections are screened for pollination and protection, so that the field workload is greatly reduced, and the backcross breeding process is accelerated.

Description

Technical Field

[0001] The present invention relates to the technical field of plant breeding, and in particular to a method for evaluating the genetic background of a backcross improved population. Background Art

[0002] Backcross breeding is a commonly used genetic improvement technology that improves specific traits by introducing foreign genes into inbred varieties. Traditional backcross breeding technology relies on observing phenotypes and a small number of molecular markers for genetic background assessment. With the emergence of single nucleotide polymorphism (SNP) marker technology and the gradual maturity of high-density genetic map construction technology, high-density SNP markers evenly distributed in the genome can be used to accurately assess the genetic background of individual plants in the population.

[0003] Currently, most laboratories use phenotypic observation and a small number of molecular markers for simple evaluation when developing genetic background recovery for backcross breeding populations. However, this method is not only time-consuming, but the evaluation results of genetic background recovery also have large errors, and cannot meet the needs of rapid evaluation and screening of large-scale backcross populations. High-density chips based on SNP markers are limited by factors such as sample throughput, detection time and cost, and can often only be applied to a small number of samples after target gene prospect evaluation and preliminary screening of genomic genetic background. Summary of the invention

[0004] In order to solve the defects of the prior art, the present invention provides a simplified genetic background evaluation and screening method for a backcross improved population.

[0005] The present invention can make a preliminary assessment of whether a recombination exchange event occurs on the chromosome and the position where the recombination exchange occurs by typing the polymorphic markers selected between one parent in each region, and can statistically analyze the background recovery degree of the population sample by combining the evaluation results of 10 chromosomes and a simplified background evaluation algorithm, thereby providing a new solution for quickly, accurately and low-costly screening samples with high genetic background recovery degree in backcross breeding populations. The present invention provides for the first time a method for evaluating the genetic background of a backcross population by partitioning chromosomes based on the law of plant genetic recombination.

[0006] Specifically, in a first aspect, the present invention provides a method for evaluating the genetic background of a backcross improved population, comprising: Dividing the chromosome intervals, obtaining polymorphic markers of the chromosome intervals, calculating the background recovery rate of the backcross improved population based on the typing results of the polymorphic markers, combining the background recovery rate with the recovery segment structure, and evaluating the genetic background of the backcross improved population; The method for dividing the chromosome interval includes: calculating the interval minimum value point in the species genetic distance change curve; selecting a minimum value point in the telomere region on both sides of each chromosome as the telomere interval division point, selecting two minimum value points in the centromere region of each chromosome as the center area division points, and dividing the chromosome into two proximal areas and one proximal area; The polymorphic marker is a marker that is polymorphic between parents.

[0007] In the process of crop backcross breeding, chromosome recombination and exchange is the result of the rearrangement of gene fragments on chromosomes between parents in offspring, which provides a basis for the genotype diversity and genetic improvement of offspring, but it is not evenly distributed on chromosomes.

[0008] In the genetic background assessment method provided by the present invention, genetic background assessment can be achieved by selecting a polymorphic marker in each chromosome interval of each chromosome.

[0009] The present invention relates to a genetic background assessment method for backcrossing improved crop populations, which is applicable to genetic background assessment and selection using molecular markers on a variety of detection platforms. The method is not limited to a specific molecular marker type or detection platform, but is applicable to various molecular markers with parental polymorphism located in two proximal regions and one proximal region of the chromosome of the population to be detected.

[0010] Currently, these molecular markers mainly include single nucleotide polymorphism (SNP), insertion / deletion (InDel) and other types. In addition, the genetic background assessment method of the present invention is applicable to a variety of detection platforms, including KASP, gel electrophoresis, real-time fluorescence quantitative PCR, digital PCR, gene chip, etc. Through the method of the present invention, the genetic background of crop populations can be flexibly assessed and selected to achieve efficient crop genetic improvement.

[0011] The present invention uses the background recovery rate combined with the recovery segment structure to evaluate the genetic background of the backcross improved population. The evaluation means that when the difference in the genetic background recovery rate of two or more samples is small, the single plant with a relatively concentrated distribution of the recovery segment is preferred as the selected single plant of the population in the corresponding generation.

[0012] In the genetic background assessment method provided by the present invention, the background recovery rate of the backcross improved population is weightedly calculated based on the typing results of the three polymorphic markers on each chromosome and the genetic distance of the chromosome; if the typing result of the polymorphic marker is consistent with that of the parent, it is recorded as a recovered state; if the typing result of the polymorphic marker is inconsistent with that of the parent, it is recorded as a non-recovered state.

[0013] When using the simplified marker pool to evaluate the genetic background of the backcross population, considering that the chromosome fragments that undergo recombination and exchange are generally large, there may be very small differences in some proximal and proximal regions between different groups. Therefore, it is accepted that there are individual regions without polymorphic markers in the inter-group combination. Another meaning of the absence of polymorphic markers in this region is that the typing results of the simplified markers distributed therein are all consistent. Therefore, in the process of simplified marker genetic background evaluation, it is assumed that the genomic genetic background of this region is almost the same and recorded as recovered.

[0014] In the genetic background assessment method provided by the present invention, the typing results of the polymorphic markers are obtained to assess whether a recombination exchange event occurs on the chromosome and the position where the recombination exchange occurs.

[0015] In a second aspect, the present invention provides a simplified method for backcrossing to improve the whole genome molecular markers of a population, comprising: setting a recombination exchange frequency threshold based on the recombination exchange data on the chromosomes of the species genetic diversity population, and calculating the interval minimum point in the species genetic distance change curve; Select one minimum point in the telomere region on both sides of each chromosome as the telomere interval division point, and select two minimum points in the centromere region of each chromosome as the central region division points, dividing the chromosome into two proximal regions and one proximal region; Based on the molecular markers of the two proximal regions and the proximal region, a simplified marker pool for the backcross improved population is obtained.

[0016] The simplified method provided by the present invention can use various molecular markers of the whole genome of the species to perform simplified genetic background assessment on the backcross population.

[0017] In the simplified method for whole genome molecular markers of backcross improved population provided by the present invention, the genetic diversity population is an artificially constructed genetic diversity population.

[0018] As a specific embodiment of the present invention, when the molecular marker is a SNP molecular marker, based on the gene chip, molecular markers with a minor allele frequency ≥0.05, a polymorphism information content ≥0.25 and a heterozygosity rate ≤0.01 are screened out in the two proximal regions and one proximal region, respectively, and they are sorted in descending order according to the polymorphism information content and the minor allele frequency to obtain a simplified molecular marker pool.

[0019] The simplified molecular marker pool obtained by the simplified method provided by the present invention is used in the genetic background assessment of the backcross improved population.

[0020] The molecular marker gene chip includes, but is not limited to, a high-density SNP gene chip with uniform distribution over the entire genome. The high-density SNP gene chip used in the present invention is a Maize 6H-60K chip.

[0021] Specifically, when simplifying the whole genome molecular markers of the maize backcross improved population, the minimum threshold of the recombination exchange frequency was set to 0.01, and the Signal module in the scientific computing library Scipy was used to calculate the interval minimum point in the species genetic distance change curve.

[0022] In a third aspect, the present invention provides a plant breeding method, using the above-mentioned genetic background assessment method to perform genetic background assessment of a backcross improved population; Or select molecular markers from the obtained simplified marker pool and obtain typing results to evaluate the genetic background of the backcross improved population; Based on the evaluation results, individual plants with genetic backgrounds that are less different from the recipient parent are selected for pollination or protection.

[0023] In a fourth aspect, the present invention provides an electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein when the processor executes the program, the method for assessing genetic background as described above or the simplified method for whole genome molecular markers for backcrossing improved populations as described above is implemented.

[0024] In a fifth aspect, the present invention provides a non-transitory computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, implements the genetic background assessment method as described above or the simplified method for whole genome molecular markers of a backcross improved population as described above.

[0025] In a sixth aspect, a computer program product comprises a computer program, which, when executed by a processor, implements the genetic background assessment method as described above or the simplified method for improving whole genome molecular markers of a backcross population as described above.

[0026] The beneficial effects of the present invention are: The present invention is based on the law of recombination exchange in the corn genome, that is, the number of chromosomes that undergo recombination in a single generation is relatively stable and limited (1-2 times), the hot spots where exchange occurs, and the non-hot spots are relatively fixed. Through the typing results of a polymorphic marker selected between one parent in each region, a preliminary assessment can be made on whether the recombination exchange event on the chromosome occurs and the location where the exchange occurs. Combining the assessment results of 10 chromosomes with the background assessment algorithm, the background recovery degree of the population sample can be statistically analyzed to assist in the rapid screening of the vast majority of samples with large genetic differences from the recipient. While using fewer markers, the present invention improves and ensures the accuracy of the genetic background assessment results. BRIEF DESCRIPTION OF THE DRAWINGS

[0027] In order to more clearly illustrate the technical solutions in the present invention or the prior art, the following briefly introduces the drawings required for use in the embodiments or the description of the prior art. Obviously, the drawings described below are some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying creative work.

[0028] Figure 1 The BASS strategy design and core site pool screening of the present invention. Wherein (A) HTP genetic distance change curve of the whole corn genome. The horizontal axis represents the physical position of the HTP site on the chromosome, and the vertical axis represents the genetic distance length of the HTP. The purple line represents the centromere position, the red filled area represents the CTR area, and the blue filled area represents the CCR area. (B) Genetic background evaluation pattern diagram based on the BASS strategy. The genotypes of the simplified molecular markers in the CCR and CTR regions determine the results of the genetic background recovery of chromosome intervals 1, 2 and 3. If the genotype of the simplified molecular marker is consistent with that of the recipient parent, it indicates that the chromosome interval corresponding to the marker has been restored to the genomic background of the recipient parent. (C) SNP site statistics in the CCR and CTR regions based on the Maize6H-60K chip. (D) Distribution density heat map of 3000 simplified molecular markers in the core site pool on 10 chromosomes of corn. (E) Distribution of 3000 simplified molecular markers in the core site pool in the gene region and intergenic region of corn. (F) Polymorphism analysis of 3000 simplified molecular markers in the core locus pool.

[0029] Figure 2 This is a universal analysis of the BASS strategy of the present invention. (A) CDC IV design of 140 representative maize inbred lines from 7 heterotic groups. (B) Among 8400 maize hybrid combinations, the proportion of hybrid combinations with n (0-6) simplified marker regions without polymorphic markers. (C) Analysis of the proportion of hybrid combinations suitable for the BASS strategy in 21 combination modes. (D) Density and statistical analysis of the number of polymorphic molecular markers in 8400 maize hybrid combinations in CCR, CTR-L and CTR-R regions. (E) Statistics of the number of hybrid combinations that are not suitable for the BASS strategy in CCR, CTR-L and CTR-R regions.

[0030] Figure 3This is a comparative analysis of genetic background assessment between the BASS strategy of the present invention and the Maize6H-60K chip. (A) Example diagram of genetic background assessment results of the Jing 92 / Jing 724 BC1F1 population based on the BASS strategy. (B) Correlation analysis of whole genome genetic background assessment based on the BASS strategy and the Maize6H-60K chip. The horizontal axis represents the genetic background assessment results of the chip, and the vertical axis represents the genetic background assessment results of the BASS strategy. (C) Correlation analysis of single chromosome genetic background assessment based on the BASS strategy and the Maize6H-60K chip. (D) The proportion of samples in the TOP10% of the genetic background recovery rate of the 60K chip assessment among the TOP1%-10% samples assessed based on the BASS strategy.

[0031] Figure 4 Genetic background assessment based on BASS strategy was used for maize backcross breeding. RP, recipient parent; DP, donor parent; sBC1F1, selected BC1F1 individuals; sBC2F1, selected BC2F1 individuals. DETAILED DESCRIPTION

[0032] In order to make the purpose, technical solution and advantages of the present invention clearer, the technical solution of the present invention will be clearly and completely described below in conjunction with the drawings of the present invention. Obviously, the described embodiments are part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0033] Example 1 Simplified marker pool (core site pool) screening

[0034] The present invention combines the recombination exchange rules of multiple corn NUM populations to divide each chromosome of corn into three regions, namely the 'proximal region' close to the centromere and the 'proximal region' close to the telomeres on both sides. 100 SNP markers were screened for each region in the high-density SNP gene chip Maize6H-60K evenly distributed throughout the genome, and a core site library (core site pool) consisting of 3,000 SNP markers was obtained.

[0035] Specifically, based on the HTP recombination exchange data on the chromosomes of the maize NUM population, the present invention sets the minimum exchange frequency threshold of 0.01, and uses the Signal module in the scientific computing library Scipy to calculate the interval minimum point in the genetic distance change curve ( Figure 1(red dotted line in A of Figure 1), according to the recombination exchange rules on corn chromosomes, a minimum point is selected in the telomere region on both sides of each chromosome as the telomere interval division point, and two minimum points are selected near the centromere as the division points of the central region. That is, each chromosome selects 2 minimum points near the centromere and 2 minimum points near the telomere, thereby dividing the chromosome into two proximal regions and one proximal region, and the proximal region and proximal region are filled with light red and light blue respectively. Among them, the boundary of the proximal region on the left side of chromosome 8 did not produce a suitable data inflection point. In order to distinguish the proximal region and the proximal region, the 6Mb position on the left side of the proximal region boundary was defined as the proximal region boundary. So far, the positions of the proximal and proximal region boundaries of 10 corn chromosomes have been determined.

[0036] Combined with the MAF, PIC and heterozygosity indexes evaluated by markers on 5822 inbred line materials, markers with MAF ≥ 0.05, PIC ≥ 0.25 and heterozygosity ≤ 0.01 were screened in each interval and sorted in descending order according to PIC and MAF. Finally, the top 100 markers in each interval were selected, and a total of 3000 markers were selected as the simplified marker pool. The distribution density heat map of 3000 simplified molecular markers in the core locus pool on 10 chromosomes of maize is shown in Figure 1 D. The distribution of 3000 simplified molecular markers in the core locus pool in maize gene regions and intergenic regions is shown in Figure 1 E. polymorphism analysis of 3000 simplified molecular markers in the core locus pool, see Figure 1 F.

[0037] Based on the simplified method for whole genome molecular markers of backcross improved populations provided by the present invention, whole genome molecular markers of other species can be simplified.

[0038] Example 2 Verifying whether simplified markers can satisfy genetic background assessment of different parental combinations

[0039] Using 20 representative inbred lines from each of the seven commonly used maize inbred line groups (including Huanggai group, Tropical group, Lancaster group, Luda Honggu group, Improved Reed group, X group and Reed group), a complete diallel hybrid IV design (CDC IV) was used to simulate 8400 F1 hybrid combinations ( Figure 2A), calculate the proportion of hybrid combinations that can screen more than one polymorphic marker in the three intervals of each chromosome. Since the genotype of the F1 generation is directly inherited from its parents and can directly reflect the genetic differences between the parents, the universality of the BASS strategy in genetic background assessment is clarified by identifying whether there are sufficient simplified molecular markers in the CCR and CTR regions of the F1 generation for genetic background assessment. It was found that there were 8030 corn hybrid combinations that could screen more than one polymorphic SNP marker in the core SNP site pool in the 30 CTR and CCR regions, accounting for 95.60% of the total hybrid combinations. This result shows that the BASS strategy can meet the genetic background assessment of most hybrid combinations. Since the recombination exchange of chromosomes usually occurs in larger fragments, it cannot be ruled out that there are large differences between each chromosome between different groups, resulting in small differences in a few regions between some groups. Therefore, the screening conditions can be relaxed to the condition that more than one polymorphic marker can be screened in all 29 simplified marker regions. The results showed that the number of hybrid combinations that met this condition increased to 8323, accounting for 99.08% of the total hybrid combinations.

[0040] The results of this example show that the BASS strategy has obvious universality in the genetic background assessment of corn breeding populations, and the simplified markers can meet the genetic background assessment of most parent combinations between different groups.

[0041] Example 3 Comparison of correlation of genetic background assessment results

[0042] In order to verify whether the simplified marker genetic background assessment results have reference value and whether they can assist in sample screening of backcross breeding populations, more specifically, the test is whether the simplified marker genetic background assessment results can quickly and accurately screen a batch of individual plants with a high degree of background recovery required by the backcross population. This example is based on 727 samples of J724 / J92 / / J92 1. Comparison of correlation of the results of multi-platform genetic background assessment of samples.

[0043] The DNA extraction method in this embodiment is as follows: 727 BC1 generation plants and 5-leaf corn leaves from the donor and recipient jointing to tasseling stages were collected from the test site, and were packed in serial numbered sulfuric acid paper bags. A proper amount of leaves were taken out by a puncher and placed in a 2 mL centrifuge tube containing small steel balls. After grinding with liquid nitrogen, DNA was extracted using a modified magnetic bead method. The DNA concentration and quality were measured using Nanodrop 2000, and the concentration was normalized to 50 ng / µL.

[0044] In this example, the genotyping test of Maize 6H-60K chip was performed on Affymetrix GeneTitan MC platform. To ensure accuracy and repeatability, DNA sample pretreatment was performed according to the chip operation manual, including denaturation, neutralization, amplification, fragmentation, precipitation and resuspension, etc. After completion, each sample was quality controlled to detect the size and concentration of the DNA band after fragmentation. DNA samples with qualified quality control were selected for hybridization with Maize 6H-60K chip, and elution, single base extension, staining, washing and stabilization were performed after completion to obtain the raw data of the chip. The experiment strictly followed the experimental guidance (Axiom™ 2.0 Assay for 384HT Array Format Automated Workflow User Guiderev.5), which ensured high-quality typing data and provided a reliable basis for subsequent analysis and research.

[0045] The method of software typing in this embodiment is: 727 BC1 samples, homozygous recipient and donor samples are loaded into 384-well plates, and genotyping is performed using Axiom Analysis Suite v5.1 software. During the processing, quality control standards were set, including DQC and QC Call Rate. DQC is used to measure the contrast distribution resolution of non-polymorphic markers in the AT and GC channels, and the DQC value is required to be ≥0.82 to ensure data reliability. The QC Call Rate is required to be ≥0.97 to ensure quality standards. Samples that meet the standards will enter the next step of analysis. SNP QC is performed using the default parameters for diploid species to ensure that the final genotyping data is of high quality and reliable, supporting subsequent research.

[0046] This example is based on the genetic background assessment results of the Maize6H-60K high-density SNP chip, and the following formula is used for calculation: B = D / L × 100%. B represents the background recovery rate of different backcross generations; D represents the number of polymorphic markers that are completely different between the parents (such as the recipient AA, the donor GG) that have completely recovered to the recipient genotype, but does not include the number of markers with heterozygous genotypes; L represents the number of polymorphic markers that are completely different between the parents.

[0047] The genetic background assessment results of simplified markers are weighted based on the typing results of the three markers on each chromosome and the genetic distance of the chromosome. The simplified marker typing of CCR, CTR-L and CTR-R on each chromosome represents Figure 1In B, the genetic background of Region 2, Region 1 and Region 3 is recorded as recovered or not. The regions are separated by dotted lines. Region 2 represents the sum of the genetic distance lengths of 1 / 2 on the left arm and the right arm of the chromosome, which is equivalent to the length of 1 / 2 genetic distance of the chromosome. Region 1 and Region 3 represent the genetic distance lengths of 1 / 2 on the left arm and the right arm of the chromosome, respectively. When the marker typing result is consistent with that of the recipient parent, it is recorded as recovered, and if the typing result is inconsistent with that of the recipient parent, it is recorded as unrecovered. Taking maize chromosome 1 (genetic distance 247.58 cM, left short arm genetic distance 104.89 cM, right long arm genetic distance 142.68 cM) as an example, when only the CTR-L region marker on chromosome 1 has recovered, the genetic background recovery rate of the chromosome is the ratio of the genetic length of 1 / 2 short arm to the total genetic length of the chromosome, 21.16% (104.89 / 2 / 247.58×100%). Similarly, if only the CCR or CTR-R region marker on the chromosome has recovered, the genetic background recovery rates are 50.00% and 28.84%, respectively. Extended to the comprehensive judgment of the degree of genetic background recovery of the whole genome of a single sample, it is weighted based on the length of each chromosome, the centromere position and the typing results of the three markers on each chromosome.

[0048] In the proximal and proximal regions of 10 chromosomes, one highly polymorphic marker was randomly selected, totaling 30. The background recovery rate of the 30 simplified markers was analyzed with the chip evaluation results. The results showed that the correlation between the dual-platform whole genome genetic background evaluation results was 0.88, and the p value was 6.39e -237 , showing an extremely significant positive correlation; Figure 3 From the correlation of the single chromosome genetic background assessment results in C, the correlation between the two platforms of chromosome 10 was the strongest, reaching 0.98, and the p value was 0.0.

[0049] In order to evaluate the effectiveness of the simplified marker screening results, the genetic background assessment results of the Maize 6H-60K chip of the Maize 6H-60K chip BC1F1 individuals with the top 10% (70 / 727) of the genetic background recovery rate screened by the BASS strategy were compared and analyzed. At the same time, according to statistics, among the samples with the top 1-10% genetic background recovery rate screened by the BASS strategy, the top 3% of the samples are in the top 10% of the samples ranked from high to low in the 60K-HTP genetic background recovery rate ( Figure 3D), among which the three samples with the highest 60K-HTP genetic background recovery rate were ranked 1, 4, and 9 in the BASS strategy, that is, the top 2% samples screened by the BASS strategy included the three samples with the best 60K-HTP screening.

[0050] According to the principle of chromosome structure optimization, the simplified marker genetic background recovery rate ranked third (M14_NP0571), fourth (C08_NP0016) and fourth (C08_NP0017) among the 727 samples in this round of backcross population. Figure 3 ), are 87.25% and 85.48% respectively. Since the chromosome of the 4th ranked sample has only 3 regions to be restored, while the 3rd ranked sample still has 4 regions to be restored, the 4th ranked sample will be given priority in the selection stage.

[0051] In summary, the use of simplified markers for background assessment can effectively reduce the size of maize backcross populations and assist in selecting samples with greater background recovery potential.

[0052] Example 4 Maize Backcross Breeding

[0053] In this embodiment, corn backcross breeding is performed based on the genetic background assessment of the BASS strategy. The flowchart of corn backcross breeding is shown in Figure 4 . Figure 4 RP, recipient parent; DP, donor parent; sBC1F1, screened BC1F1 individual; sBC2F1, screened BC2F1 individual.

[0054] The specific genetic background assessment process of this embodiment is as follows: ① Taking the parents of the backcross population as the research objects, 30 polymorphic simplified molecular markers with differences between the parents are screened out from the core site pool containing 3000 SNP molecular markers. ② Using 30 simplified molecular markers, genotype the individuals in the backcross population on the KASP platform or other molecular detection platforms. ③ According to the genotyping results, the degree of genetic background recovery of the individuals in the backcross population is evaluated, and individuals with a higher genetic background recovery rate are screened out in the large-scale backcross population. At the same time, the Maize6H-60K chip is combined to further accurately evaluate the small-scale individuals screened out, and finally the individuals with the highest genetic background recovery are identified.

[0055] Example 5 Device or product for evaluating the genetic background of a backcross improved population

[0056] The present invention provides an electronic device, comprising a memory, a processor and a computer program stored in the memory and executable on the processor. When the processor executes the program, a method for evaluating the genetic background of a backcross improved population is implemented.

[0057] The present invention also provides a non-transitory computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, is implemented to execute the simplified method for whole-genome molecular markers of the backcross improved population or to execute the genetic background assessment method of the backcross improved population.

[0058] A simplified method for whole genome molecular markers of backcross improved populations, including: setting a recombination exchange frequency threshold based on the recombination exchange data on chromosomes of species genetic diversity populations, and calculating the interval minimum point in the species genetic distance change curve; Select one minimum point in the telomere region on both sides of each chromosome as the telomere interval division point, and select two minimum points in the centromere region of each chromosome as the central region division points, dividing the chromosome into two proximal regions and one proximal region; Based on the molecular marker gene chip, molecular markers with minor allele frequency ≥ 0.05, polymorphism information content ≥ 0.25 and heterozygosity rate ≤ 0.01 were screened out in the two proximal regions and one proximal region, and sorted in descending order according to polymorphism information content and minor allele frequency to obtain a simplified molecular marker pool.

[0059] The invention discloses a method for evaluating the genetic background of a backcross improved population, comprising: dividing a chromosome interval, obtaining polymorphic markers of the chromosome interval, calculating the background recovery rate of the backcross improved population based on the typing results of the polymorphic markers, combining the background recovery rate with the recovery segment structure, and evaluating the genetic background of the backcross improved population; in the genetic background evaluation method provided by the present invention, the background recovery rate of the backcross improved population is weightedly calculated based on the typing results of the polymorphic markers on each chromosome and the genetic distance of the chromosome; if the typing results of the polymorphic markers are consistent with those of the parents, it is recorded as a recovered state, and if the typing results of the polymorphic markers are inconsistent with those of the parents, it is recorded as a non-recovered state.

[0060] The present invention also provides a computer program product, which includes a computer program. The computer program can be stored on a non-transitory computer-readable storage medium. When the computer program is executed by a processor, the computer can execute the simplified method for whole-genome molecular markers of a backcross improved population or execute the genetic background assessment method of the backcross improved population.

[0061] More specifically, in response to the needs of simplified marker selection and genetic background assessment, a GUI analysis tool of BAS-Tools was developed using PyQT5. It consists of two functional modules, namely Simplified Marker Design and Background Assessment. The former is responsible for designing simplified markers, and the latter is responsible for background assessment and mapping of population typing data of simplified markers.

[0062] The device embodiments described above are merely illustrative, wherein the units described as separate components may or may not be physically separated, and the components displayed as units may or may not be physical units, that is, they may be located in one place, or they may be distributed on multiple network units. Some or all of the modules may be selected according to actual needs to achieve the purpose of the scheme of this embodiment. Ordinary technicians in this field can understand and implement it without paying creative labor.

[0063] Through the description of the above implementation methods, those skilled in the art can clearly understand that each implementation method can be implemented by means of software plus a necessary general hardware platform, and of course, can also be implemented by hardware. Based on this understanding, the above technical solution is essentially or the part that contributes to the prior art can be embodied in the form of a software product, and the computer software product can be stored in a computer-readable storage medium, such as ROM / RAM, a disk, an optical disk, etc., including a number of instructions for a computer device (which can be a personal computer, a server, or a network device, etc.) to execute the methods described in each embodiment or some parts of the embodiments.

[0064] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit it. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements do not deviate the essence of the corresponding technical solutions from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. A method for evaluating the genetic background of a backcross improved population, characterized in that: include: Dividing the chromosome intervals, obtaining polymorphic markers of the chromosome intervals, calculating the background recovery rate of the backcross improved population based on the typing results of the polymorphic markers, combining the background recovery rate with the recovery segment structure, and evaluating the genetic background of the backcross improved population; The method for dividing chromosome intervals includes: calculating the interval minimum value point in the species genetic distance change curve; selecting an interval minimum value point in the telomere region on both sides of each chromosome as the telomere interval division point, selecting two interval minimum value points in the centromere region of each chromosome as the center area division points, and dividing the chromosome into two proximal areas and one proximal area; The polymorphic marker is a marker that is polymorphic between parents.

2. The genetic background assessment method according to claim 1, characterized in that: One polymorphic marker is selected in each chromosomal interval on each chromosome.

3. The genetic background assessment method according to any one of claims 1-2, characterized in that: The background recovery rate of the backcross improved population is weightedly calculated based on the typing results of the three polymorphic markers on each chromosome and the genetic distance of the chromosome; if the typing result of the polymorphic marker is consistent with that of the recipient parent, it is recorded as a recovered state; if the typing result of the polymorphic marker is inconsistent with that of the recipient parent, it is recorded as a non-recovered state.

4. The genetic background assessment method according to any one of claims 1-2, characterized in that: The typing results of the polymorphic markers are obtained to evaluate whether a chromosome recombination exchange event occurs and the position where the recombination exchange occurs.

5. A simplified method for backcross improvement of whole genome molecular markers, characterized in that: The recombination exchange frequency threshold is set based on the recombination exchange data on the chromosomes of the species genetic diversity population, and the interval minimum point in the species genetic distance change curve is calculated; Select one interval minimum point in the telomere region on both sides of each chromosome as the telomere interval division point, and select two interval minimum points in the centromere region of each chromosome as the central region division points, so as to divide the chromosome into two proximal regions and one proximal region; Based on the molecular markers of the two proximal regions and the proximal region, a simplified marker pool for the backcross improved population is obtained.

6. The simplified method according to claim 5, characterized in that: Genetically diverse populations are artificially constructed genetically diverse populations; Preferably, the molecular marker is a SNP molecular marker, and the molecular markers with a minor allele frequency ≥0.05, a polymorphism information content ≥0.25 and a heterozygosity rate ≤0.01 in the corresponding regions of the Maize6H-60K chip are screened out in the two proximal regions and one proximal region, respectively, and are sorted in descending order according to the polymorphism information content and the minor allele frequency, and the first 100 markers in each interval are taken to obtain a simplified molecular marker pool.

7. A plant breeding method, characterized in that: Use the genetic background assessment method described in any one of claims 1 to 4 to conduct genetic background assessment of a backcross improved population; Or selecting molecular markers from the simplified molecular marker pool obtained by the simplified method according to any one of claims 5 to 6 and obtaining typing results to conduct genetic background assessment of the backcross improved population; Select individual plants whose genetic background is less different from that of the recipient parent for pollination or protection.

8. An electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein: When the processor executes the program, the genetic background assessment method as described in any one of claims 1 to 4 or the simplified method as described in any one of claims 5 to 6 is implemented.

9. A non-transitory computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the genetic background assessment method according to any one of claims 1 to 4 or the simplified method according to any one of claims 5 to 6 is implemented.

10. A computer program product, comprising a computer program, characterized in that When the computer program is executed by a processor, the genetic background assessment method according to any one of claims 1 to 4 or the simplified method according to any one of claims 5 to 6 is implemented.

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