A method for detecting plant polyploidy advantage

Abstract

The application discloses a plant polyploidy advantage detection method, which comprises the following steps: (1) material selection, including a diversity natural population or an artificial population; (2) phenotype identification: target traits are identified; (3) genotype identification: high-density SNP markers, chips or resequencing SNPs can be used, and part of homologous genes are combined to form a new genotype; (4) polyploidy advantage locus detection: part of homologous alleles are used to perform association analysis on phenotypes to obtain polyploidy advantage loci HQTL; and (5) polyploidy advantage genotype selection: polyploidy advantage alleles are detected from the polyploidy advantage loci. The method combines part of homologous genes of the polyploidy into a new haplotype, and performs whole genome association analysis in the form of haplotype combination, thereby breaking through the limitation of traditional single analysis of each gene at each subgenomic locus.

Description

TECHNICAL FIELD

[0001] The application belongs to the technical field of polyploid breeding, and particularly relates to a plant polyploid heterosis detection method. BACKGROUND

[0002] In a broad sense, the main crops in the world are polyploids. Polyploid heterosis is a ubiquitous phenomenon and has been widely recognized. However, there is no accurate and effective method to detect polyploid heterosis so far.

[0003] Common wheat is an allohexaploid with A, B and D subgenomes, and is a natural hybrid. Based on the analysis of common wheat genome structure, gene expression and epigenetic modification, we found that the diploidization and differentiation of homoeologous genes in each subgenome are the basis of polyploid heterosis, and homoeologous genes coordinate and jointly regulate phenotypic traits. On this basis, we proposed a method for detecting polyploid heterosis, HGWAS.

[0004] Traditional QTL and genome-wide association analysis (GWAS) are based on diploid genomes and cannot detect the interaction effects of homoeologous genes / paralogous genes. SUMMARY

[0005] In view of the above problems in the prior art, the application provides a plant polyploid heterosis detection method, which is a new method for detecting gene interaction at the whole genome level, i.e. heterosis, and is named HGWAS (homoeologous GWAS).

[0006] In order to achieve the above-mentioned application purposes, the technical scheme adopted by the application is

[0007] The application provides a plant polyploid heterosis detection method HGWAS, which comprises the following steps:

[0008] S1, selecting materials: selecting more than 100 natural or artificial populations with diversity;

[0009] S2, phenotypic identification: performing phenotypic identification on the target traits of the test population;

[0010] S3, genotypic identification: obtaining high-density SNPs of the test population by high-density SNP chip, exon capture sequencing and resequencing methods; and recombining homoeologous allele haplotypes by using the high-density SNPs of the test population according to the physical positions of the homoeologous genes.

[0011] S4, using the recombinant partial homologous allelic haplotype as the genotype of the test population, combining the phenotype to perform whole genome association analysis, and obtaining a partial homologous HQTL site, i.e., a polyploidy advantage site;

[0012] S5, calculating the effect value of each polyploidy advantage site containing various partial homologous allelic haplotypes in the test population, and obtaining an optimal polyploidy advantage genotype;

[0013] S6, comparing the optimal polyploidy advantage genotype obtained with the mid-parent value and the high-parent value to calculate the polyploidy advantage.

[0014] Further, in S1, 300-500 natural or artificial populations with diversity are selected.

[0015] Further, in S2, yield is the most important polyploidy advantage trait, and the yield trait should be based on a material plot, and the area of the plot is not less than 4*1.5 square meters.

[0016] Further, in S6, the mid-parent value of the natural population is the average value of the test materials, and the mid-parent value of the artificial population is the average value of the parents; and the high-parent value is the value of an excellent variety.

[0017] Further, the method is suitable for polyploidy advantage detection of all existing polyploid or partial polyploid species, wherein the polyploid plants are wheat, cotton, rapeseed, peanut, soybean and corn; the partial polyploid is rice; and the polyploid animals are polyploid fish.

[0018] The present application has the following beneficial effects:

[0019] 1. The present application combines partial homologous genes of polyploidy into new haplotypes, and performs whole genome association analysis in the form of haplotype combination, thereby breaking through the limitation of traditional analysis of each gene at each sub-genomic site.

[0020] 2. The HGWAS can show the effect of partial homologous gene haplotypes on traits, and clearly determine the polyploidy advantage sites and the action size. DETAILED DESCRIPTION

[0021] The specific embodiments of the present application are described below to facilitate the understanding of the present application by those skilled in the art, but it should be clear that the present application is not limited to the scope of the specific embodiments, and for those skilled in the art, it is obvious that all kinds of changes within the spirit and scope of the present application defined and determined by the appended claims are within the scope of protection.

[0022] Example 1

[0023] This embodiment takes 400 parts of hexaploid wheat artificial population F2 population as an example to illustrate the calculation method of polyploidy advantage detection method HGWAS and its ability to detect polyploidy heterosis. In the F2 population, the genotypes of parents P1 and P2 are a and c respectively, and the genotype of the hybrid individual is h.

[0024] The specific detection method is as follows:

[0025] First, HGWAS determines the chromosome interval significantly related to the trait.

[0026] Phenotypic identification is performed on hexaploid wheat, of which yield is the most important polyploidy heterosis trait. Yield traits should be based on material plots, and the planting area should be no less than 4x1.5 square meters.

[0027] Genotype data is sorted according to homologous / partially homologous genes. For example, the gene gene1 of hexaploid wheat subgenome A (named gene1A), the gene gene1 of subgenome B (named gene1B), and the gene gene1 of subgenome D (named gene1D) are homologous genes. According to their physical positions, each subgenome homologous gene is combined with closely linked markers (represented by SNP markers). Assuming that the closely linked marker of gene1A is SNP-gene1A, the closely linked marker of gene1B is SNP-gene1B, and the closely linked marker of gene1D is SNP-gene1D, then all homologous genes have their representative marker combination SNP-gene1A_SNP-gene1B_SNP-gene1D. Then, HGWAS analysis is performed based on the homologous gene haplotype combination formed by the SNP markers.

[0028] Preferably, high-density SNPs of the test population can be obtained by high-density SNP chips, exon capture sequencing, resequencing, etc.

[0029] Second, determine the polyploidy advantage site HQTL.

[0030] Taking F2 population as an example, first, the mid-parent value is calculated. In the traditional QTL definition, the mid-parent value (MP value) is the intermediate value of the trait of two parents in the F1 population; when the HGWAS analysis is performed on the wheat F2 population, the genotype of parent 1 (P1) is defined as a, the genotype of parent 2 (P2) is defined as c, the genotype of a heterozygous individual in the F2 population is defined as h, and the three subgenomes A, B and D correspond to three genotypes of a, h and c homologous genes respectively, and the MP value is defined as the average value of all genotypes. Then, the trait value of each haplotype combination is calculated. Specifically, for a certain trait locus, there are 27 genotypic combinations in all F2 populations (parent P1 genotype aaa, parent P2 genotype ccc, homozygous genotypic combinations aac, aca, acc, cca, cac, caa; heterozygous genotypes aha, aah, ahh, haa, hah, hha, chc, cch, chh, hcc, hch, hhc, ach, ahc, hac, hca, cah, cha, hhh). The triallelic genotype represents the genotype of three subgenomic homologous genes, for example, aaa indicates that the gene in the three subgenomic homologous genes is the same as the genotype of parent P1, aac indicates that the A and B subgenomic homologous genes are the same as the genotype of parent P1, and the D subgenomic genotype is the same as parent P2, aha indicates that the A and D subgenomic homologous genes are the same as the genotype of parent P1, and the B subgenomic genotype is a heterozygous genotype. Each genotypic combination is a haplotype. After determining the haplotype, the average trait value of the F2 individual haplotype and the significance of the difference from the mid-parent value are calculated, and the polyploidy dominant haplotype is determined accordingly.

[0031] The process is summarized in the following table: As can be seen from the table, the mid-parent value of the spike length (SL) locus SL_G5_473.7_489.9 is 8.7 cm, the average spike length of the parent P1 haplotype aaa and the parent P2 haplotype ccc in the F2 population is 8.4 cm and 8.0 cm respectively, and the homozygous haplotypes aca, caa and cca have a spike length of 9.2 cm, 9.3 cm and 9.3 cm respectively, which is significantly longer than the mid-parent phenotype, showing polyploidy heterosis.

[0032]

[0033]

[0034] Example 2

[0035] The example takes natural population as an example, calculates the trait value of each sub-genome haplotype, and records the method in Example 1. Since it is a natural population, there is no parent, and the mid-parent value is the average value of each sub-genome genotype. Taking the ear length locus SL_G5_473.7_489.9 as an example, each sub-genome part homologous gene haplotype has 2, 3, 1, respectively, named A-1, A-2; B-1, B-2, B-3; D-1, then three sub-genomes, the gene will appear the following haplotype combination: A-1_B-1_D-1, A-1_B-2_D-1, A-1_B-3_D-1, A-2_B-1_D-1, A-2_B-2_D-1, A-2_B-3_D-1, that is, 2x3x1=6 haplotype combinations. The number of diverse alleles is increased compared with GWAS, such as gene1D, which has only one haplotype, which is an invalid marker in marker-trait association analysis; but it is an effective marker in HGWAS analysis. Then, the average value of the phenotype corresponding to each haplotype and its significance test are calculated to determine the polyploidy dominant haplotype of the trait in the natural population. As can be seen from the table, the haplotype A-1_B-2_D-1 haplotype ear length is 9.2 cm on average, which is significantly longer than the mid-parent value of 8.7 cm, and is a polyploidy dominant haplotype.

[0036]

[0037] HGWAS is suitable for all existing polyploid crops such as cotton, rapeseed, peanut, and ancient polyploid crops such as soybean, rice, corn, millet, and polyploidy advantage detection. The method has been used to analyze all agronomic traits of rapeseed, peanut, soybean, and corn, and polyploidy advantage / heterosis sites have been detected, and the advantage rate is significantly higher than the mid-parent value and the high-parent value.

[0038] The polyploidy advantage site detection method HGWAS combines the partial homologous genome into a haplotype, and performs whole genome association analysis in the form of haplotype combination, breaking through the limitation of traditional analysis of each sub-genome site and each gene. HGWAS shows the effect of partial homologous gene haplotype on traits, and clearly shows the polyploidy advantage site and its effect size; while ordinary GWAS can only reflect the effect of a single sub-genome unit point on the trait.

[0039] This technology can be used for both conventional breeding and heterosis utilization.

[0040] It will be apparent to those skilled in the art that the application is not limited to the details of the above-exemplified embodiments and that the present application can be implemented in other particular forms without departing from the spirit or essential characteristics of the present application. The presently disclosed embodiments are, therefore, to be considered in all respects as illustrative and not restrictive, the scope of the application being indicated by the appended claims rather than by the foregoing description, and all changes which come within the meaning and range of equivalency of the claims are therefore intended to be embraced therein. No feature of the application is to be construed as a limitation thereon unless it is expressly stated to be such.

[0041] Furthermore, it should be understood that although the description above refers to particular embodiments, the description can include more than one independent technical solution, and the description is presented herein in such a way for the sake of clarity only. Those skilled in the art should consider the description as a whole and combine the technical solutions in each embodiment to form other embodiments that can be understood by those skilled in the art.

Claims

1. A method for detecting plant polyploidy advantage, characterized by, The method comprises the following steps: S1, selecting materials: selecting more than 100 natural or artificial populations with diversity; S2, phenotypic identification: phenotypic identification of target traits of the test population; S3, genotypic identification: obtaining high-density SNPs of the test population by high-density SNP chip, exon capture sequencing, and resequencing method; according to the physical position of the partial homologous gene, the recombination of the partial homologous allele haplotype is utilized; S4, using the recombination of the partial homologous allele haplotype as the genotype of the test population, and combining the phenotype for whole genome association analysis, obtaining the partial homologous site HQTL, i.e. the polyploidy advantage site; S5, calculating the effect value of each polyploidy advantage site in the test population, and obtaining the optimal polyploidy advantage genotype; S6, comparing the optimal polyploidy advantage genotype with the mid-parent value and the high-parent value to calculate the polyploidy advantage. The plant is wheat, rapeseed, peanut, soybean or corn. In S6, the mid-parent value of the natural population is the average value of the test material, and the mid-parent value of the artificial population is the average value of the parent; the high-parent value is the value of the excellent variety.

2. The method of claim 1, wherein the plant polyploidy advantage is determined by the step of: In S1, 300-500 natural or artificial populations with diversity are selected.

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