A method for evaluating the genetic background of a backcross improved population

Abstract

The present application relates to the technical field of plant breeding, and particularly relates to a genetic background evaluation method of backcross improvement population. The present application divides chromosome intervals and molecular markers based on plant genetic recombination exchange rules, obtains typing results of the simplified markers, calculates background recovery rate of the backcross improvement population based on the typing results, combines the background recovery rate with the structure of the recovered fragments to evaluate the genetic background recovery degree of the backcross improvement population, and selects effective single plants with small genetic differences from the receptor parent and relatively concentrated unrecovered segments for pollination and protection, thereby greatly reducing field workload and accelerating the backcross breeding process.

Description

Technical Field

[0001] This invention relates to the field of plant breeding technology, and in particular to a method for evaluating the genetic background of a backcross improved population. Background Technology

[0002] Backcrossing is a commonly used genetic improvement technique that improves specific traits by introducing foreign genes into inbred lines. Traditional backcrossing relies on observing phenotypes and using a small number of molecular markers to assess genetic background. However, with the advent of single nucleotide polymorphism (SNP) marker technology and the gradual maturation of high-density genetic mapping technology, high-density SNP markers evenly distributed in the genome can be used to accurately assess the genetic background of individual plants in a population.

[0003] Currently, most laboratories use phenotypic observation and a small number of molecular markers for simple evaluation when developing genetic background reversion of backcross breeding populations. However, this method is not only time-consuming, but also has a large error in the evaluation results of genetic background reversion, which 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] To address the shortcomings of existing technologies, this invention provides a simplified method for assessing and screening the genetic background of backcross improved populations.

[0005] This invention uses the genotyping results of a single polymorphic marker selected from each parent within each region to preliminarily assess whether recombination events occurred on the chromosome and the location of such recombination. Combining the assessment results of 10 chromosomes with a simplified background assessment algorithm, the background recovery degree of the population sample can be statistically analyzed. This provides a new method for rapidly, accurately, and cost-effectively screening samples with high genetic background recovery in backcross breeding populations. This invention is the first to provide a method for assessing the genetic background of backcross populations by dividing chromosomes into regions based on plant genetic recombination principles.

[0006] Specifically, in a first aspect, the present invention provides a method for assessing the genetic background of a backcross improved population, comprising: Chromosomal regions are divided, and polymorphic markers of the chromosomal regions are obtained. Based on the genotyping results of the polymorphic markers, the background recovery rate of the backcross improved population is calculated. The background recovery rate is combined with the recovery fragment structure to assess the genetic background of the backcross improved population. Methods for dividing chromosome regions include: calculating the minimum points of the intervals in the genetic distance variation curve of the species; selecting one minimum point on each side of the telomere region of each chromosome as the interval division point of the telomere; selecting two minimum points in the centromere region of each chromosome as the division points of the central region, thus dividing the chromosome into two proximal regions and one proximal region. The polymorphic marker refers to a marker that exhibits polymorphism between the parents.

[0007] In crop backcrossing breeding, chromosome recombination and exchange, as the result of the rearrangement and combination of gene segments on chromosomes between parents in offspring, provide the basis for genotypic diversity and genetic improvement in offspring, but it is not evenly distributed on chromosomes.

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

[0009] This invention relates to a method for assessing the genetic background of backcrossed crop populations. This method is applicable to genetic background assessment and selection using molecular markers on various detection platforms. The method is not limited to specific molecular marker types or detection platforms, but is applicable to various molecular markers with interparental polymorphism located in two proximal regions and one proximal region of the chromosomes of the population to be tested.

[0010] Currently, these molecular markers mainly include single nucleotide polymorphisms (SNPs) and insertions / deletions (InDels). Furthermore, the genetic background assessment method of this invention is applicable to various detection platforms, including KASP, gel electrophoresis, real-time quantitative PCR, digital PCR, and gene chips. Using the method of this invention, the genetic background of crop populations can be flexibly assessed and selected to achieve efficient crop genetic improvement.

[0011] This invention uses a combination of background reversion rate and reversion fragment structure to evaluate the genetic background of a backcross improved population. The evaluation refers to: when the difference in genetic background reversion rate between two or more samples is small, selecting individual plants with a relatively concentrated distribution of reverted segments as the selected individual plants for the corresponding generation of that population.

[0012] In the genetic background assessment method provided by this invention, the background recovery rate of the backcross improved population is calculated by weighting the typing results of three polymorphic markers on each chromosome and the genetic distance of the chromosomes; if the typing results of the polymorphic markers are consistent with the parents, it is recorded as a recovery state, and if the typing results of the polymorphic markers are inconsistent with the parents, it is recorded as a non-recovery state.

[0013] When using simplified marker pools to assess the genetic background of backcross populations, considering that the chromosome segments that generally undergo recombination are large, there may be very small differences between some proximal and proximal regions of different groups. Therefore, some regions in the combinations between accepting groups may have no polymorphic markers. Another meaning of the absence of polymorphic markers in such regions is that the simplified marker genotyping results distributed in them are consistent. Therefore, in the simplified marker genetic background assessment process, it is assumed that the genomic genetic background of such regions is nearly 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, and the recombination and exchange events of chromosomes are assessed, as well as the location of the recombination and exchange events.

[0015] In a second aspect, the present invention provides a simplified method for whole-genome molecular markers of backcross improved populations, comprising: setting a recombination exchange frequency threshold based on recombination exchange data on chromosomes of a species genetic diversity population, and calculating the interval minimum point in the species genetic distance change curve; Each chromosome is divided into two proximal regions and one proximal region by selecting a minimum point on each side of the telomere region as the dividing point of the telomere region, and two minimum points are selected in the centromere region of each chromosome as the dividing points of the central region. Based on the molecular markers in 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 this invention can utilize various molecular markers from the whole genome of a species to perform a simplified genetic background assessment of backcross populations.

[0017] In the simplified method for whole-genome molecular markers of backcross improved populations provided by this 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 an SNP molecular marker, based on the gene chip, molecular markers with minor allele frequency ≥0.05, polymorphism information content ≥0.25, and heterozygosity ≤0.01 are screened in the two proximal regions and one proximal region, respectively, and sorted in descending order according to polymorphism information content and minor allele frequency to obtain a simplified molecular marker pool.

[0019] The simplified molecular marker pool obtained by the simplified method provided in this invention can be used for genetic background assessment of backcross improved populations.

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

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

[0022] Thirdly, the present invention provides a plant breeding method, which uses the above-mentioned genetic background assessment method to assess the genetic background of a backcross improved population; Alternatively, molecular markers can be selected from the obtained simplified marker pool and genotyping results can be obtained to assess the genetic background of the backcross improved population; Based on the evaluation results, individual plants with similar genetic backgrounds to the recipient parents were selected for pollination or protection.

[0023] Fourthly, the present invention provides an electronic device, including a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein the processor executes the program to implement the genetic background assessment method as described above or the simplified method for backcross improved population whole-genome molecular markers as described above.

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

[0025] Sixthly, a computer program product includes a computer program that, when executed by a processor, implements the genetic background assessment method as described above or the simplified method for backcross improved population whole-genome molecular markers as described above.

[0026] The beneficial effects of this invention are as follows: This invention is based on the recombination and exchange patterns in the maize genome. Specifically, the number of recombination events on chromosomes in a single generation is relatively stable and limited (1-2 times), with relatively fixed hotspots and non-hotspot regions. By analyzing the genotyping results of a single polymorphic marker selected from both parents within each region, a preliminary assessment of whether a recombination and exchange event occurred on that chromosome and its location can be made. Combining the assessment results of 10 chromosomes with a background assessment algorithm, the background recovery degree of the population samples can be statistically analyzed, assisting in the rapid screening out of the vast majority of samples with significant genetic differences from the recipient. This invention improves and maintains the accuracy of genetic background assessment results while using fewer markers. Attached Figure Description

[0027] To more clearly illustrate the technical solutions in this invention or the prior art, the drawings used in the description of the embodiments or the prior art will be briefly introduced below. Obviously, the drawings described below are some embodiments of this invention. For those skilled in the art, other drawings can be obtained from these drawings without creative effort.

[0028] Figure 1 This invention relates to the BASS strategy design and core locus pool screening. (A) Maize whole-genome HTP genetic distance variation curve. The horizontal axis represents the physical location of HTP loci on chromosomes, and the vertical axis represents the genetic distance length of HTPs. Purple lines represent centromere positions, red filled areas represent CTR regions, and blue filled areas represent CCR regions. (B) Genetic background assessment model based on the BASS strategy. The genotypes of simplified molecular markers in CCR and CTR regions determine the genetic background recovery results for chromosome intervals 1, 2, and 3. If the genotype of the simplified molecular marker is consistent with 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 locus statistics within CCR and CTR regions based on the Maize6H-60K chip. (D) Distribution density heatmap of 3000 simplified molecular markers in the core locus pool on the 10 maize chromosomes. (E) Distribution of 3000 simplified molecular markers in the core locus pool in maize gene regions and intergenetic regions. (F) Polymorphism analysis of 3000 simplified molecular markers in the core site pool.

[0029] Figure 2 This is a generalization analysis of the BASS strategy of this invention. (A) CDC IV design of 140 representative maize inbred lines from 7 heterotic groups. (B) Percentage of hybrid combinations in 8400 maize hybrid combinations under simplified marker regions with n(0-6) no polymorphic markers. (C) Analysis of the percentage of hybrid combinations applicable to the BASS strategy in 21 mating patterns. (D) Number density and statistical analysis of polymorphic molecular markers in the CCR, CTR-L, and CTR-R regions of 8400 maize hybrid combinations. (E) Statistical analysis of the number of hybrid combinations in the CCR, CTR-L, and CTR-R regions where the BASS strategy is not applicable.

[0030] Figure 3This is a comparative analysis of genetic background assessment between the BASS strategy and the Maize 6H-60K chip of this invention. (A) Example figure of genetic background assessment results of the Jing92 / Jing724 BC1F1 population based on the BASS strategy. (B) Correlation analysis of whole-genome genetic background assessment based on the BASS strategy and the Maize 6H-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 Maize 6H-60K chip. (D) Percentage of the top 10% of samples with the top 1%-10% genetic background recovery rate assessed by the 60K chip in the top 1%-10% of samples assessed based on the BASS strategy.

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

[0032] To make the objectives, technical solutions, and advantages of this invention clearer, the technical solutions of this invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some, not all, of the embodiments of this invention. All other embodiments obtained by those skilled in the art based on the embodiments of this invention without creative effort are within the scope of protection of this invention.

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

[0034] This invention, based on the recombination and exchange patterns of multiple maize NUM populations, divides each maize chromosome into three regions: the 'proximal region' near the centromere and the 'proximal region' near the telomeres. In the high-density SNP gene chip Maize6H-60K, which is evenly distributed throughout the genome, 100 SNP markers were screened for each region, resulting in a core locus pool (core locus pool) consisting of 3000 SNP markers.

[0035] Specifically, this invention, based on HTP recombination and exchange data on chromosomes of maize NUM populations, sets a minimum exchange frequency threshold of 0.01 and uses the Signal module in the scientific computing library SciPy to calculate the interval minimum points in the genetic distance variation curve. Figure 1(The red dashed line in A) Based on the recombination and exchange patterns on maize chromosomes, a minimum point was selected on each side of the telomere region of each chromosome as the telomere division point, and two minimum points near the centromere were selected as the central region division points. That is, two minimum points near the centromere and two minimum points near the telomeres were selected on each chromosome, thus dividing the chromosome into two proximal regions and one proximal region. The proximal and central regions were filled with light red and light blue, respectively. The boundary of the left proximal region of chromosome 8 did not produce a suitable data inflection point. To distinguish between the proximal and central regions, the boundary of the proximal region was defined as 6 Mb to the left of the central region boundary. Thus, the boundaries of the proximal and central regions of the 10 maize chromosomes were determined.

[0036] Based on the MAF, PIC, and heterozygosity indices evaluated on 5822 inbred lines, markers with MAF ≥ 0.05, PIC ≥ 0.25, and heterozygosity ≤ 0.01 were selected in each interval. These markers were then sorted in descending order by PIC and MAF, and the top 100 markers in each interval were chosen, resulting in a simplified marker pool of 3000 markers. A heatmap showing the distribution density of the 3000 simplified molecular markers in the core locus pool on the 10 maize chromosomes is shown below. Figure 1 The distribution of 3000 simplified molecular markers in the core site pool in maize gene regions and intergenic regions is shown in Figure D. Figure 1 Polymorphism analysis of 3000 simplified molecular markers in the E. core site pool, see [link to E. core site pool]. Figure 1 F.

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

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

[0039] Using 20 representative inbred lines from each of seven commonly used maize inbred line groups (including the Huanggai group, tropical group, Lancaster group, Lüda Honggu group, improved Ruide group, X group, and Ruide group), a complete diallel cross IV design (CDC IV) was used to simulate 8400 F1 hybrid combinations. Figure 2(A) The proportion of hybrid combinations in which more than one polymorphic marker could be screened in each of the three regions on each chromosome was calculated. 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 was clarified by identifying whether there are a sufficient number of simplified molecular markers in the CCR and CTR regions of the F1 generation for genetic background assessment. It was found that 8030 maize hybrid combinations, accounting for 95.60% of the total hybrid combinations, could screen for more than one polymorphic SNP marker in the core SNP locus pool in each of the 30 CTR and CCR regions. This result indicates that the BASS strategy can meet the genetic background assessment of the vast majority of hybrid combinations. Since chromosomal recombination and exchange usually involve large segments, it cannot be ruled out that there are significant differences between each chromosome in different groups, resulting in small differences in a few regions between some groups. Therefore, the screening criteria can be relaxed to the condition that more than one polymorphic marker can be screened in each of the 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 embodiment show that the BASS strategy has significant universality in assessing the genetic background of maize breeding populations, and the simplified marker can meet the genetic background assessment of most different parental combinations.

[0041] Example 3: Correlation Comparison of Genetic Background Assessment Results

[0042] To verify the reference value of simplified marker genetic background assessment results and their ability to assist in sample screening for backcross breeding populations, more specifically, to test whether the simplified marker genetic background assessment results can quickly and accurately screen a batch of individual plants with a high degree of background reversion required for the backcross population, this example is based on 727 J724 / J92 / / J92 accessions. 1. Correlation comparison of genetic background assessment results across multiple platforms for samples.

[0043] In this embodiment, the DNA extraction method was as follows: Leaves from 727 BC1 generation plants and the five-leaf stage of maize (from jointing to tasseling) of both donor and recipient plants were collected from the experimental site. These leaves were placed in numbered sulfuric acid paper bags, and a suitable amount of each leaf was individually placed in a 2 mL centrifuge tube containing small steel beads. After grinding with liquid nitrogen, DNA was extracted using a modified magnetic bead method. The DNA concentration and mass were measured using a Nanodrop 2000, and the concentration was homogenized to 50 ng / µL.

[0044] This embodiment demonstrates genotyping of the Maize 6H-60K microarray on the Affymetrix GeneTitan MC platform. To ensure accuracy and reproducibility, DNA sample pretreatment was performed according to the microarray operation manual, including denaturation, neutralization, amplification, fragmentation, precipitation, and resuspending. After pretreatment, each sample underwent quality control, and the size and concentration of the fragmented DNA bands were measured. Quality-controlled DNA samples were hybridized with the Maize 6H-60K microarray, followed by elution, single-base extension, staining, washing, and stabilization to obtain the raw microarray data. The experiment strictly followed the experimental guidelines (Axiom™ 2.0 Assay for 384HT Array Format Automated Workflow User Guide rev. 5), which ensured high-quality genotyping data and provided a reliable foundation for subsequent analysis and research.

[0045] The software genotyping method in this embodiment is as follows: 727 BC1 samples, homozygous recipients, and donor samples were loaded into 384-well plates, and genotyping was performed using Axiom Analysis Suite v5.1 software. During the processing, quality control standards were set, including Discrete Quality Control (DQC) and QC Call Rate. DQC measures the contrast distribution resolution of non-polymorphic markers in the AT and GC channels, requiring a DQC value ≥ 0.82 to ensure data reliability. The QC Call Rate requires ≥ 0.97 to guarantee quality standards. Samples meeting the standards proceed to the next analysis. SNP QC was performed using default parameters for diploid species to ensure high-quality and reliable final genotyping data, supporting subsequent research.

[0046] This embodiment 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 reversion rate of different backcross generations; D represents the number of polymorphic markers that are completely different between the parents (such as recipient AA, donor GG) that have completely reverted to the recipient genotype, but does not include the number of markers that are heterozygous; L represents the number of polymorphic markers that are completely different between the parents.

[0047] The simplified marker genetic background assessment results are calculated by weighting the genotyping results of the three markers on each chromosome and the genetic distance of the chromosomes. The simplified marker genotyping of CCR, CTR-L, and CTR-R on each chromosome represents, respectively, Figure 1In region B, the genetic background of regions 2, 1, and 3 is determined by whether it has recovered. Regions are separated by dashed lines. Region 2 represents the sum of the genetic distances on the left and right arms of the chromosome, which is equivalent to the length of half the genetic distance of the chromosome. Regions 1 and 3 represent the genetic distances on the left and right arms of the chromosome, respectively. If the marker typing result is consistent with the recipient parent, it is recorded as recovered. If the typing result is inconsistent with 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 this chromosome is the ratio of the genetic length of half the short arm to the total genetic length of the chromosome, which is 21.16% (104.89 / 2 / 247.58×100%). Similarly, if only the CCR or CTR-R region markers on this chromosome have recovered, the genetic background recovery rates are 50.00% and 28.84%, respectively. Extending this to the comprehensive determination of the degree of whole-genome genetic background recovery for a single sample, a weighted calculation is performed based on the length of each chromosome, centromere position, and the genotyping results of the three markers on each chromosome.

[0048] Within the proximal and acrosome regions of 10 chromosomes, one marker with high polymorphism was randomly selected from each region, for a total of 30 markers. Correlation analysis was performed between the background recovery rate of these 30 simplified markers and the microarray assessment results. The results showed that the correlation between the dual-platform whole-genome genetic background assessment results was 0.88, with a p-value of 6.39e. -237 The correlation is extremely significant; from Figure 3 In terms of the correlation of single-chromosome genetic background assessment results in C, the correlation between the two platforms of chromosome 10 was the strongest, reaching 0.98, with a p value of 0.0.

[0049] To evaluate the effectiveness of the simplified marker screening results, the genetic background assessment results of the Maize 6H-60K microarrays of the top 10% (70 / 727) Maize 6H-60K microarray BC1F1 individuals with the highest genetic background recovery rate selected by the BASS strategy were compared and analyzed. Statistical analysis also showed that among the samples with the top 1-10% genetic background recovery rate selected by the BASS strategy, the top 3% of samples were all within the top 10% of samples ranked from highest to lowest 60K-HTP genetic background recovery rate. Figure 3The three samples with the highest 60K-HTP genetic background reversion rate were ranked 1, 4, and 9 in the BASS strategy, meaning that the top 2% of samples screened by the BASS strategy included the three best samples for 60K-HTP screening.

[0050] Based on the principle of chromosome structure optimization, among the 727 samples in this backcross population, the simplified marker genetic background recovery rate ranked 3rd (M14_NP0571) and 4th (C08_NP0016) samples ( Figure 3 The percentages for A and B were 87.25% and 85.48%, respectively. Since the fourth-ranked sample had only three regions of chromosomes to be restored, while the third-ranked sample still had four regions to be restored, the fourth-ranked sample would be prioritized during the selection phase.

[0051] In summary, using simplified markers for background assessment can effectively reduce the size of maize backcross populations and help select samples with greater background recovery potential.

[0052] Example 4: Maize backcross breeding

[0053] This embodiment uses genetic background assessment based on the BASS strategy for maize backcross breeding. The flowchart for maize backcross breeding is shown below. Figure 4 . Figure 4 RP stands for recipient parent; DP stands for donor parent; sBC1F1 stands for selected BC1F1 individuals; sBC2F1 stands for selected BC2F1 individuals.

[0054] The specific genetic background assessment process in this embodiment is as follows: ① Using the parents of the backcross population as the research subjects, 30 simplified polymorphic molecular markers that differ between the parents are screened from a core pool containing 3000 SNP molecular markers. ② Using these 30 simplified molecular markers, genotyping is performed on individuals in the backcross population on the KASP platform or other molecular detection platforms. ③ The degree of genetic background reversion in the backcross population is assessed based on the genotyping results, and individuals with high genetic background reversion rates are screened from the large-scale backcross population. Simultaneously, the small-scale individuals selected are further precisely assessed using the Maize6H-60K chip, ultimately identifying the individual with the highest genetic background reversion.

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

[0056] The present invention provides an electronic device, including a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein the processor executes the program to implement a method for assessing the genetic background of a backcross improved population.

[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, implements a simplified method for performing whole-genome molecular markers of the backcross improved population or a method for evaluating the genetic background of the backcross improved population.

[0058] A simplified method for backcrossing improved population whole-genome molecular markers includes: setting a recombination exchange frequency threshold based on recombination exchange data on chromosomes of the species genetic diversity population, and calculating the interval minimum point in the species genetic distance change curve; Each chromosome is divided into two proximal regions and one proximal region by selecting a minimum point on each side of the telomere region as the dividing point of the telomere region, and two minimum points are selected in the centromere region of each chromosome as the dividing points of the central region. Based on molecular marker gene chips, molecular markers with minor allele frequencies ≥0.05, polymorphism information content ≥0.25, and heterozygosity ≤0.01 were screened in the two proximal regions and one proximal region, respectively. The markers were then sorted in descending order according to polymorphism information content and minor allele frequency to obtain a simplified molecular marker pool.

[0059] A method for assessing the genetic background of a backcross improved population includes: dividing chromosome regions, obtaining polymorphic markers for the chromosome regions, calculating the background recovery rate of the backcross improved population based on the genotyping results of the polymorphic markers, and combining the background recovery rate with the structure of the recovered fragments to assess the genetic background of the backcross improved population. In the genetic background assessment method provided by this invention, the background recovery rate of the backcross improved population is calculated by weighting the genotyping results of the polymorphic markers on each chromosome and the genetic distance of the chromosomes. If the genotyping results of the polymorphic markers are consistent with the parents, it is recorded as a recovery state; if the genotyping results of the polymorphic markers are inconsistent with the parents, it is recorded as a non-recovery state.

[0060] The present invention also provides a computer program product, the computer program product comprising a computer program that can be stored on a non-transitory computer-readable storage medium, wherein when the computer program is executed by a processor, the computer is capable of performing the simplified method for whole-genome molecular markers of the backcross improved population described above or performing the genetic background assessment method of the backcross improved population described above.

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

[0062] The device embodiments described above are merely illustrative. The units described as separate components may or may not be physically separate. The components shown as units may or may not be physical units; that is, they may be located in one place or distributed across multiple network units. Some or all of the modules can be selected to achieve the purpose of this embodiment according to actual needs. Those skilled in the art can understand and implement this without any creative effort.

[0063] Through the above description of the embodiments, those skilled in the art can clearly understand that each embodiment can be implemented by means of software plus necessary general-purpose hardware platforms, and of course, it can also be implemented by hardware. Based on this understanding, the above technical solutions, in essence or the part that contributes to the prior art, can be embodied in the form of a software product. This computer software product can be stored in a computer-readable storage medium, such as ROM / RAM, magnetic disk, optical disk, etc., and includes several instructions to cause a computer device (which may be a personal computer, server, or network device, etc.) to execute the methods described in the various embodiments 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, and not to limit them; although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art should understand that modifications can still be made to the technical solutions described in the foregoing embodiments, or equivalent substitutions can be made to some of the technical features; and these modifications or substitutions do not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. A method for assessing the genetic background of a backcross improved population, characterized in that, include: Chromosomal regions are divided, and polymorphic markers of the chromosomal regions are obtained. Based on the genotyping results of the polymorphic markers, the background recovery rate of the backcross improved population is calculated. The background recovery rate is combined with the recovery fragment structure to assess the genetic background of the backcross improved population. The background recovery rate of the backcross improved population is calculated by weighting the genotyping results of the three polymorphic markers on each chromosome and the genetic distance of the chromosomes; if the genotyping results of the polymorphic markers are consistent with the recipient parent, it is recorded as a recovery state; if the genotyping results of the polymorphic markers are inconsistent with the recipient parent, it is recorded as a non-recovery state. The method for dividing chromosome regions includes: setting a recombination and exchange frequency threshold based on recombination and exchange data on chromosomes of a species genetic diversity population; calculating the minimum value points of intervals in the genetic distance variation curve of the species, wherein the genetic diversity population is an artificially constructed genetic diversity population; selecting one minimum value point in each telomere region on both sides of each chromosome as the interval division point of the telomere; selecting two minimum value points in the centromere region of each chromosome as the division points of the central region; thus dividing the chromosome into two proximal regions and one proximal region. The polymorphic marker refers to a marker that exhibits polymorphism between the parents.

2. The genetic background assessment method according to claim 1, characterized in that, Select a polymorphic marker for each chromosomal region on each chromosome.

3. The genetic background assessment method according to any one of claims 1-2, characterized in that, The genotyping results of the polymorphic markers are obtained, and the presence and location of recombination events on the chromosomes are assessed.

4. A simplified method for backcrossing improved population whole-genome molecular markers, characterized in that, Based on recombination and exchange data on chromosomes of a species genetic diversity population, a recombination and exchange frequency threshold is set, and the minimum value point of the interval in the species genetic distance change curve is calculated. The genetic diversity population is an artificially constructed genetic diversity population. Each chromosome is divided into two proximal regions and one proximal region. A local minimum point is selected on each side of the telomere region as the telomere division point. Two local minimum points are selected in the centromere region of each chromosome as the centromere division points, thus dividing the chromosome into two proximal regions and one proximal region. Based on the molecular markers in the two proximal regions and the proximal region, a simplified marker pool for the backcross improved population is obtained.

5. The simplified method according to claim 4, characterized in that, The molecular markers are SNP molecular markers. Molecular markers with minor allele frequencies ≥0.05, polymorphism information content ≥0.25, and heterozygosity ≤0.01 in the two proximal regions and one proximal region of the Maize6H-60K chip are screened. The markers are then sorted in descending order according to polymorphism information content and minor allele frequency. The top 100 markers in each region are selected to obtain a simplified molecular marker pool.

6. An electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, characterized in that, When the processor executes the program, it implements the genetic background assessment method as described in any one of claims 1-3 or the simplified method as described in any one of claims 4-5.

7. 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, it implements the genetic background assessment method as described in any one of claims 1-3 or the simplified method as described in any one of claims 4-5.

8. A computer program product, comprising a computer program, characterized in that, When the computer program is executed by a processor, it implements the genetic background assessment method as described in any one of claims 1-3 or the simplified method as described in any one of claims 4-5.

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