CN113430299B - SNP molecular marker associated with castor stem color and application thereof - Google Patents

SNP molecular marker associated with castor stem color and application thereof Download PDF

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CN113430299B
CN113430299B CN202110929763.4A CN202110929763A CN113430299B CN 113430299 B CN113430299 B CN 113430299B CN 202110929763 A CN202110929763 A CN 202110929763A CN 113430299 B CN113430299 B CN 113430299B
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杨俊芳
王宏伟
曹越
王宙
王亚
赵宜婷
张宏斌
张红
申登高
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Abstract

The invention belongs to the technical field of molecular markers, and provides an SNP molecular marker associated with castor stem color and application thereof. The SNP molecular marker related to the color of the castor bean stem provided by the invention is as follows: one or more of mk5702, mk2560, mk2581 and mk 2988. According to the invention, the castor stem color of two groups of multi-generation genetic groups is subjected to genetic rule analysis, based on the result of the constructed high-density SNP genetic map, the QTL positioning is carried out on the castor stem color character through stem color phenotype value and marker linkage analysis, a main effect QTL cluster is positioned in the No. 2 linkage group, a group of SNP molecular markers associated with the castor stem color character is screened, and an effective basis is provided for the castor molecular marker assisted breeding.

Description

SNP molecular marker associated with castor stem color and application thereof
Technical Field
The invention relates to the technical field of molecular markers, in particular to an SNP molecular marker associated with the color of castor stems and application thereof.
Background
Castor is an important green energy crop (Ricinus communis,2n ═ 20), is an important energy oil crop, and is also one of irreplaceable strategic resource crops. Because of its special physical properties of high viscosity, high specific gravity, high combustion point and low freezing point, castor oil is widely used in several tens of fields such as aviation, aerospace, medical treatment, plastics and chemical engineering. The color of the stem is one of the important characters for breeding the castor-oil plant variety, and the stem is often dark red, light red, cyan, dark green, light green and the like.
At present, the basis of castor genetic breeding research is weak, and excellent varieties are bred mainly through hybridization, so that a long time is needed and the accuracy is lacked when plants with ideal traits, particularly multi-gene control traits, are selected, and the castor variety improvement process is slow. Molecular marker assisted breeding (MAS) methods can effectively address these problems. However, the research on the construction of the genetic spectrogram of castor beans starts late, the research is less, the research on the color traits of castor beans is less, and at present, no research report on the QTL positioning of the color of the castor beans and the development of molecular markers is seen.
Disclosure of Invention
According to the invention, the genetic rule analysis is carried out on the castor stem colors of two groups of multi-generation genetic groups, based on the constructed high-density SNP genetic map result, the QTL positioning is carried out on the castor stem color character through the stem color phenotype value and marker linkage analysis, a main effect QTL cluster is positioned in the No. 2 linkage group, a group of SNP molecular markers associated with the castor stem color character is screened, and an effective basis is provided for the castor molecular marker assisted breeding.
The invention provides an SNP molecular marker associated with the color of castor bean stalks, which is characterized in that: one or more of mk5702, mk2560, mk2581 and mk 2988;
the scafford position of mk5702 is 30101, the physical position is 24335, the reference genome base type is C, the variant genome base type is A, and the gene ID is 30101.t 000002;
the scaffold position of the mk2560 is 29916, the physical position is 51828, the reference genome base type is G, the variant genome base type is A, and the ID of the gene in which the variant genome base type is located is 29916.t 000004;
the scafford position of the mk2581 is 29916, the physical position is 135549, the reference genome base type is C, the variant genome base type is T, and the ID of the gene is 29916. T0000014;
the scafford position of the mk2988 is 27401, the physical position is 124144, the reference genome base type is T, the variant genome base type is A, and the gene ID is 27401. T000015.
The invention also provides application of the SNP molecular marker associated with the color of the castor bean stem in identifying the color of the castor bean stem.
Based on the result of the constructed high-density genetic map, the color traits of castor stems are positioned in the No. 2 linkage group, the QTL interval is 196.01-428.61 cM (the genetic distance is 232.cM), the peak interval of the highest reliability is 402.1-422.61 cM (the genetic distance is 20.51cM), and 4 SNP markers closely related to the color traits of the castor stems are screened to be mk5702, mk2581, mk2988 and mk2560 respectively.
Drawings
FIG. 1 shows that the color character of the stem is in QTL location cluster 1 of No. 1 linkage group;
FIG. 2 locating cluster 2 of QTL of No. 2 linkage group for the color character of the stem;
FIG. 3 is a QTL locating cluster 3 of the number 3 linkage group with the color character of the stem;
FIG. 4 shows that the color character of the stem is located in QTL location cluster 4 of linkage group No. 4;
FIG. 5 QTL locating cluster 5 of the stalk color character in No. 5 linkage group;
FIG. 6 is a QTL location cluster 6 with the stalk color character in No. 6 linkage group;
FIG. 7 QTL location cluster 7 of the stalk color trait in linkage group No. 7;
FIG. 8 is a QTL location cluster 8 with the stalk color character in No. 8 linkage group;
FIG. 9 QTL location cluster 9 with the stalk color trait in linkage group 9;
FIG. 10 stalk color trait is located in QTL location cluster 10 of linkage group No. 10.
Detailed Description
The technical solutions provided by the present invention are described in detail below with reference to examples, but they should not be construed as limiting the scope of the present invention.
Example 1
Cultivating two groups of multi-generation castor plants
In 2018, a homozygous dark green stalk amphibian strain SL1 male parent and dark red stalk mosaic female lines HCH1 and HCH3 are selected as female parents to be hybridized. Specifically, a combination SL1(P1) × HCH3(P2) is defined as combination 1, and a combination SL1(P1) × HCH1(P3) is defined as combination 2; cross-breeding in combination 1 to obtain orthogonal F 1 -1 and backcross F 1 -1; cross-breeding in combination 2 to obtain orthogonal F 1 -2 and backcross F 1 -2; 2019 planting parent and two groups of orthogonal F 1 -1 and orthogonal F 1 2, quadrature F of the two groups 1 -1 and orthogonal F 1 -2 respective selfing harvest F 2 -1 and F 2 -2; will obtain F 2 -1 and F 2 -2 backcrossing with parents to harvest BC respectively 1 P1-1、BC 1 P2-1 and BC 1 P1-2、BC 1 P3-2. Two groups of multi-generation genetic groups are obtained, and two groups of each generation group are planted in 2020. The experimental materials of this example were provided by the institute for commercial crop, academy of agricultural sciences, Shanxi province, and the planting of the materials of each generation was also completed. The row spacing of the material is 1m multiplied by 1m, and the test land requires uniform fertility and flat topography. When the mature period of the plants comes, the color of the stems of the plants of each generation group is investigated for use
Figure BDA0003210907990000032
Excel 2007 was used for data statistics, and SPSS 18.0 was used for chi-square test genetic analysis.
By carrying out positive and negative cross F on the parent and two groups 1 The investigation of the stem color of generations shows that the color of the filial generation whether orthogonal or reverse-crossed is intermediate type light purple, which indicates that the character is controlled by nuclear genes, and the allele is incompletely dominant, purple is dominant, and green is recessive. Two groups F 2 The progressive significance of the generation separation ratio is more than 0.05, which shows that F 2 The generation segregation ratio is not obviously different from the theoretical value of 1:2:1, and the result accords with the segregation ratio controlled by a pair of alleles, and is tested in a backcross populationAnd (4) evidence. Two groups F 1 The generation and the dark red-stalk female parent are backcrossed, the progeny does not have green plants, and the dark green-stalk male parent is backcrossed, the progeny has a separation ratio of light purple to green stalk of 1: 1. Through investigation and chi-square test analysis (as shown in table 1) on the stem color of two groups of different genetic generations, the stem color is the character controlled by a pair of incomplete dominant alleles, purple is dominant, and green is recessive.
TABLE 1 separation ratio of each generation and chi-square test
Figure BDA0003210907990000031
Figure BDA0003210907990000041
Note a: 0 cells (0%) have a desired frequency of less than 5.
Example 2
Performing whole genome sequencing
Through earlier analysis of SNP marker polymorphism between two groups of parents, the parent polymorphism of the hybrid combination SL1 xHCH 1 is better than that of SL1 xHCH 3. F constructed by SL1 XHCH 1 is randomly selected during sampling 2 In 150 single young leaves in the population, 0.1-0.5 g of leaf in each sample is taken, and the genome DNA of each sample is extracted by using a plant genome DNA extraction kit (solarBio). The DNA concentration and purity were determined using an Eppendorf AG 22331 protein/nucleic acid analyzer (Eppendorf Co., Germany) and the DNA quality was determined by electrophoresis on a 1.0% agarose gel. According to the requirement of high-throughput sequencing, the total amount of DNA of each sample is more than or equal to 1 mu g, and the concentration is more than or equal to 50 ng/mu L; the sample purity OD260/280 is 1.8-2.0, and A260/230 is 1.9-2.4. The main band of the electrophoresis result is clear, and the electrophoresis result is not degraded, so that the method can be used for high-throughput sequencing. Qualified DNA samples were sent to sequencing for pooling and whole genome sequencing using the illumina HiSeqTM PE 150.
Example 3
Construction of high Density genetic maps
Group SNP marker development: and (3) carrying out inter-parent polymorphism marker development based on the castor parent genotype detection result. And carrying out abnormal base inspection, integrity filtration and partial separation marker filtration on the classified filial generation markers.
Through alignment of sequencing data and population SNP marker development, labels of each linkage group are sequenced by using Joinmap4.1 for each linkage group (the linkage groups are sequenced by using a maximum likelihood algorithm, genetic distances are calculated by a Kosambi function), a high-density genetic map is constructed, the high-density genetic map comprises 10 linkage groups (shown in a table 2), the total length of the genetic distances is 3355.03cM, the total number of upper icons is 5713, the average genetic distance between the labels (the label distance is far lower than that of the traditional label genetic map) is 0.59cM, and the label distance is far lower than that of the traditional label genetic map. The marker density and the map resolution are far higher than those of the traditional SSR marker genetic map.
TABLE 2 statistics of genetic linkage group information
linkage Marker number length Average length Max gap
LG1 1949 1171.78 0.60 61.01
LG2 970 458.32 0.47 9.05
LG3 659 397.43 0.60 20.54
LG4 626 349.77 0.56 9.40
LG5 497 281.76 0.57 6.46
LG6 246 134.67 0.55 23.25
LG7 243 196.25 0.81 24.37
LG8 182 120.87 0.66 25.15
LG9 242 170.22 0.70 12.33
LG10 99 73.96 0.75 4.53
total 5713 3355.03 0.59 61.01
Note: linking age: a linkage group number; marker number: the number of markers; length is the genetic distance (cM) of the linkage group; average length: mean genetic distance (cM); max gap: maximum gap distance (cM).
Example 4
Stem color QTL localization analysis
Based on the results of the high density genetic map of example 3 above, in combination with 150F of Ricinus communis 2 The stem phenotype value of the colony is subjected to QTL analysis on the single female shape of the castor by using a CIM (common element mapping) method of MapQTL and WinQTL software. The LOD value threshold for the stem color phenotype was determined using PT (persistence test,1000 times) in MapQTL and the main stem color phenotype results are shown in table 3.
TABLE 3 QTL replacement test results, i.e. threshold values
Figure BDA0003210907990000051
Figure BDA0003210907990000061
Note: group, linkage Group number; GW denotes the entire genome; interval, LOD Interval; count, 1000 times of replacement and inspection, and the number of times of appearance of the LOD interval value; count, replacement test 1000 times, LOD occurrence times are less than or equal to; count, Count/total number of permutation tests (1000); sum, sum/total number of displacement tests.
Selecting an LOD threshold value of the experiment, wherein the LOD value corresponding to each linkage group is selected at 95% confidence (namely, the LOD of the second row corresponding to the sixth row at 0.95 is selected as the LOD threshold value of the linkage group, and when the sixth row does not have 0.95, the LOD threshold value is selected to be more than 0.95 and is closest to 0.95); on the genome-wide level, the LOD at 95% confidence Interval (i.e., the value in the Interval) was chosen as the phenotypic LOD threshold; finally, the LOD threshold value of the stem color positioning is determined to be 3.7.
QTL positioning analysis is carried out on the color characters of the stalks by using a CIM mapping method of WinQTL software, QTL sections with LOD values more than or equal to 3.7 are selected, and the results are shown in figures 1-10. Finally, a main QTL cluster (FIG. 2) is obtained in the linkage group No. 2, and the total number of QTL sites with continuous variation is 40, and the genetic distance between the QTL sites is 232.6cM (shown in a table 4). Wherein the interval is 402.01 cM-422.61 cM, the genetic distance is 20.6cM, the LOD value of the interval is more than 14 percent, the phenotypic variation rate is higher by 29 percent to 77 percent, and both the LOD value and the phenotypic variation rate are higher. And taking the peak interval as the most credible interval of the close association of the colors of the castor bean stalks.
TABLE 4 QTL analysis results
Figure BDA0003210907990000062
Figure BDA0003210907990000071
Figure BDA0003210907990000081
Note: and (6) wait: a trait; chromosome: a linkage group number; positon: genetic distance, in cM; LOD the LOD value of QTL; additive effect; the Dominant effect RIL or DH population Dominant effect value of the Dominant effect is 0; r 2 The ratio of QTL to accounted for phenotypic variation (decimal indicates that 0.63 indicates a 63% accounted phenotypic variation rate); confidence intervals for "LOD 1_ L" and "LOD 1_ R" 99%; confidence intervals of "LOD 2_ L" and "LOD 2_ R" 95%.
Through information comparison with a castor reference genome (a castor whole genome database TIGR (http:// cassette bean. jcvi. org/downloads. php)), 39 SNP markers in a peak interval with the highest reliability are subjected to gene annotation analysis, four nonsynonymous mutated SNP marker sites of mk5702, mk2581, mk2988 and mk2560 are obtained through screening, and according to reference gene information, candidate genes in which the three markers of mk5702, mk2581 and mk2988 are located all encode conservative hypothetical proteins and have unknown gene functions, and candidate genes in which the mk2560 is located encode recognized aspartyl-tRNA synthetase. The four genes are candidate genes closely related to the color trait of the castor stalk (see table 5 for specific information).
TABLE 5 closely related SNP marker information
Figure BDA0003210907990000082
The foregoing is only a preferred embodiment of the present invention, and it should be noted that, for those skilled in the art, various modifications and decorations can be made without departing from the principle of the present invention, and these modifications and decorations should also be regarded as the protection scope of the present invention.

Claims (1)

1. The application of the SNP molecular marker associated with the color of castor bean stalks in identifying the color of the castor bean stalks is characterized in that the SNP molecular marker is as follows: mk5702, mk2560, mk2581, and mk 2988;
the scafford position of mk5702 is 30101, the physical position is 24335, the reference genome base type is C, the variant genome base type is A, and the gene ID is 30101.t 000002;
the scafford position of mk2560 is 29916, the physical position is 51828, the reference genome base type is G, the variant genome base type is A, and the gene ID is 29916.t 000004;
the scaffold position of the mk2581 is 29916, the physical position is 135549, the reference genome base type is C, the variant genome base type is T, and the ID of the gene is 29916. T0000014;
the scafford position of the mk2988 is 27401, the physical position is 124144, the reference genome base type is T, the variant genome base type is A, and the gene ID is 27401. T000015;
the information of the scaffold positions, the physical positions, the reference genome basic types and the gene IDs of mk5702, mk2560, mk2581 and mk2988 are all derived from a castor plant whole genome database TIGR; the varieties of the castor-oil plant are SL1 and HCH 1.
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