CN103898105A - Stable soybean hundred-grain weight related QTL (quantitative trait loci) locus and close linkage mark satt281 thereof - Google Patents
Stable soybean hundred-grain weight related QTL (quantitative trait loci) locus and close linkage mark satt281 thereof Download PDFInfo
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Abstract
The invention relates to a stable soybean hundred-grain weight related QTL (quantitative trait loci) locus and a close linkage mark satt281 thereof, which belong to the technical field of crop selective breeding. The locus is located on a linkage group of soybean C2, the close linkage mark is an SSR primer satt 281 and located on a position of 40.3cm on a public map, and the close linkage mark satt281 can be detected in two generations and two environments by adopting four different location methods (double-tail and single marking square difference analysis adopts the P which is less than or equal to 0.01 as the standard, and CI and MICIM adopt LOD which is more than or equal to 3 as the standard). The trait related QTL is located by adequately utilizing different methods, the hundred-grain weight QTL detection situations are compared in different environments and different generations, and the stable soybean hundred-grain weight QTL locus can be determined. The stable soybean hundred-grain weight related QTL can be used for improving the hundred-grain weight traits by utilizing the molecular mark auxiliary selection and map-based cloning, so that powerful technical support can be provided for the breeding and improvement of the soybean crops.
Description
Technical field
The present invention relates to crop seed selection and cultivate technical field, refer more particularly to the relevant QTL site of a stable soybean 100-grain weight and close linkage mark satt281 thereof.
Background technology
Soybean is important oil crops and high protein crop, one of Ye Shi China 5 large staple crops.As the soybean country of origin, China was once maximum Soybean production state and export State in the world.But because soybean unit yield increasess slowly, soybean acreage and the output of nearly more than ten years of China decline continuously, along with the increase day by day of domestic Soybean demand amount, China has become one of maximum in the world Soybean import state.Soybean is compared with other high-yield crops at present, and fractional yield is on the low side, and improving Soybean Yield Potential is the vital task of soybean breeder.SOYBEAN IN HIGH-YIELD BREEDING is also the main direction of crop breeding always.Output is a Comprehensive Traits, is subject to the impact of multiple forms, physiology and economical character.100-grain weight is the important factor that soybean yields forms, and becomes positive correlation with output, is easily subject to the impact of environment, and the accuracy of Phenotypic Selection is not high, so detect the relevant QTL of soybean 100-grain weight, developer molecule marker assisted selection has great importance.
In recent years, DNA molecular marker technical development is comparatively rapid, and the soybean gene group mapping document from first piece of nineteen ninety based on RFLP mark is delivered the research of soybean Quantitative Trait Genes location so far and obtained greater advance.Up to the present on whole 20 karyomit(e)s of soybean, all there is the relevant QTL of soybean 100-grain weight to be distributed in.During this period QTL method for positioning analyzing also along with research deeply and the needs of different researchs had the development of each side, comprise that two methods, single mark variance analysis (ANOVA), Interval Mapping (IM) are to composite interval mapping method (CIM), complete Interval Mapping (ICIM) etc.And the existence that at present epistasis and environment are done mutually and plant genetic evolve and hybrid vigour in vital role think and studies confirm that in a large number, and in the QTL of soybean 100-grain weight proterties location, conventionally suppose that epistasis does not exist in early days.Just study the relative merits of several different localization methods as far back as favour great Feng in 1997 etc., although point out accurately Mapping of QTL of ANOVA, found that on QTL may be the most effective.The diligent grade of Li Jie in 2005 adopts diverse ways location Plant Height of Rice proterties in 4, finds that CIM has stronger ability of discovery, and adopts multiple drawing method when suggestion location.In soybean 100-grain weight QTL research, YingPeng Han etc. adopt the method for CIM in 3 colony's 5 environment, to detect 100-grain weight QTL for 2012, and wherein 3 colony's 5 environment all can detect to obtain QTL.And the research that epistasis and gene and environment are done mutually or little.Maugham in 1996 finds that in Liang Ge colony epistatic interaction 6 is right.Sun Ya man in 2012 waits and makes mutually QTL take charleston × eastern agriculture 594 RILs as material tests to 5 human and environment, 8 pairs of epistatic interaction sites, but the site that epistasis and environment are done mutually do not detected.
Summary of the invention
The object of the invention is to arrive the relevant QTL site of stable soybean 100-grain weight and close linkage mark satt281 by research detection and location, cause because Phenotypic Selection is subject to environmental factors interference the problem that breeding efficiency is low to overcome in conventional breeding.
The solution of the present invention is as follows:
Its close linkage of the relevant QTL of stable soybean 100-grain weight site is labeled as satt281, this site is positioned in soybean C2 linkage group, close linkage is labeled as SSR primer satt281, position on public collection of illustrative plates is 40.3cM place, adopt four kinds of different localization methods (two tails and single mark variance analysis are standard take P≤0.01, and CI and MICIM are take LOD >=3.0 as standard) all can detect in two generations, two environment.
(two tails and single mark variance analysis are standard take P≤0.01 to adopt four kinds of different localization methods, CI with MICIM take LOD >=3.0 as standard) 75 of the relevant QTL of soybean 100-grain weight and close linkage marks in two generations, two environment, can also be detected, wherein repeating the QTL that frequency is higher just has qSW-Gm06 (close linkage is labeled as satt281), and contribution rate is 11.68% to the maximum.
Under multiple environment, utilize multiple localization method detecting soybean 100-grain weight QTL, relatively 100-grain weight QTL detection case under varying environment different generations, specifically comprise the following steps: take the F8 of Ji beans 12 × black soya bean colony, F9 for RIL as material, under three environment, adopt respectively two tail methods, single mark variance analysis, composite interval mapping method and complete Interval Mapping, the relevant QTL of location soybean 100-grain weight.
The present invention utilizes multiple localization method detecting soybean 100-grain weight QTL under multiple environment, and inquire into epistasis effect and environment is made effect mutually, the relevant QTL site of stable soybean 100-grain weight and close linkage mark satt281 thereof are found, overcome in conventional breeding and caused breeding efficiency because Phenotypic Selection is subject to environmental factors interference, can utilize the primer special of satt281 mark to carry out early generation selection and shorten breeding cycle the high 100-grain weight related locus of soybean, thereby filter out quickly the high yielding soybeans material that seed is larger.The present invention can be applicable to high yield of soybean breeding, to improve breeding efficiency and soybean yields level, can be used for molecular marker assisted selection and map based cloning and improves 100-grain weight proterties, for seed selection cultivation, the crop improvement of soybean crops provide strong technical support.
Accompanying drawing explanation
Fig. 1 is the colony's 100-grain weight distribution frequency under F8 material, Shijiazhuang growing environment.
Fig. 2 is colony's 100-grain weight distribution frequency under F9 material, Shijiazhuang growing environment.
Fig. 3 is colony's 100-grain weight distribution frequency under F9 material, Sanya growing environment.
Embodiment
Specifically set forth the specific implementation process of this invention below with embodiment.
Embodiment:
Combine F8, F9 two generations restructuring self-fertilization family (sff)s (RIL) as material take the Ji beans 12 × black soya bean that comprises 216 familys.The improved variety of grain and oil institute of Ji Dou12Wei Hebei province, 100-grain weight size is 21g; Black soya bean is farmers''s semi-wild material.Two parents all have larger difference on geographic origin, genetic origin and economical character.Summer F8RIL in 2011 and parent design random district group 3 repeat sowings experiment centre on the dike of Shijiazhuang, the long 3m of row, line-spacing 0.5m; Winter in 2011 respectively by F9RIL and the random district of parent group 3 repeat sowings in Sanya experiment centre; It is consistent with 2011 that F9RIL and parent are seeded on the dike of Shijiazhuang the capable long line-spacing of experiment centre by summer in 2012.After material natural maturity, gather in the crops airing, measure 100-grain weight according to the criterion in " Soybean Germplasm is described standard and data standard ", get one of 100 complete seed percentages balance and weigh counting, each strain is got at random 5 strains and is measured.Adopt corresponding function and corresponding program analysis phenotypic data extreme difference, kurtosis, the degree of bias, standard deviation and heritability etc. in SPSS17.0 software.
By analyzing rear discovery, all there is significant difference in the 100-grain weight mean value between two parents in three environment, and beans 12 100-grain weights in Ji are apparently higher than black soya bean, as shown in table 1.RIL individual in population phenotypic number is worth between low parent's value between high parent, and is normal distribution, as shown in Figure 1, Figure 2, Figure 3 shows, wherein in the environment of Shijiazhuang, occurs in 2011 that ultralow parent separates.Phenotypic number to 216 RIL materials in three environment carries out two-way analysis of variance, and discovery phenotypic number in varying environment does not have the difference of significance, and under the 100-grain weight heritability calculating respectively under three environment and three environment, overall heritability is all greater than 85%.
100-grain weight phenotypic characteristic in table 1 F8 Shijiazhuang, F9 Shijiazhuang and F9 Sanya three environment
Utilize the F6 of this colony generation 216 RIL to build a genetic linkage maps, comprise 117 SSR marks of 21 karyomit(e)s, overall length 1501cM, between mark, mean distance is 15.6cM, each linkage group on average contains 6 of marks.Adopt take proterties as basic analytical procedure (Trait-based analysis, TBA, Lebowitz et al., 1987) and detect soybean 100-grain weight close linkage mark to be labeled as basic analytical procedure (Marker-based analysis, MBA).
1, take proterties as basic analytical procedure:
The method supposition increases because selection makes the QTL synergy allelotrope in the high phenotype individuality of quantitative character and the QTL in low phenotype individuality subtract the allelic frequency of effect, when the allelotrope of QTL and a certain marker gene are when chain, meeting is because of the interrelated difference that causes marker gene frequency between high and low phenotype individuality, as shown in table 2.
Table 2 detects the 100-grain weight SSR mark of being correlated with take proterties as basic single labeled analysis method
2, two tail methods
Two tail methods are specifically 30 parts of larger materials of 100-grain weight in F8 colony according to selecting respectively 30 materials to form the F8-Bswp of Liang Ge colony at two ends after phenotypic data sequence, F8-Sswp is 30 parts of less materials of 100-grain weight in F8, F9SHI-Bswp, F9SHI-Sswp is the large and 30 parts of little materials of 100-grain weight of 100-grain weight in the colony of F9 Shijiazhuang, F9SAN-Bswp, F9SAN-Sswp is respectively in F9 tri-subpopulations the large and 30 parts of little materials of 100-grain weight of 100-grain weight), the banding pattern of molecule marker in two colonies is added up, analyze A, the distribution of B banding pattern in Liang Ge colony, two groups of data are carried out to paired t-test, select the mark of P≤0.005 to infer and the 100-grain weight linkage of characters.The individual bill of material offset of high and low phenotype of choosing respectively in three environment is in table 3.Between the phenotypic number of the high and low phenotype material of selecting in the method as can be seen from Table 3,, there is larger difference.
The individual bill of material offset of the high and low phenotype of table 3
The method detects altogether 38 of the marks chain with 100-grain weight in three environment, wherein in Shijiazhuang environment in 2011, arrive and 11 of the closely linked marks of 100-grain weight altogether, be distributed on the 5th, 8,6,17,15,18,12,19, No. 7 karyomit(e)s explainable heritable variation; 17 of the marks relevant to 100-grain weight in Shijiazhuang environment in 2012, detected altogether, be positioned on the 5th, 14,4,6,2,17,18,12,16,7, No. 3 karyomit(e)s; 10 of the marks that 100-grain weight is relevant within 2011, in the environment of Sanya, detected altogether, lay respectively on 5,11,4,6,2,17,18,9, No. 19 karyomit(e)s.The significance mark enrichment region all detecting in 3 colonies has 3, is to be respectively positioned at A1 linkage group 30.93cM-52.32cM, C2 linkage group 40.3cM, D2 linkage group 107.49cM-120.3cM.Sat_333, the sat_022 of D2 linkage group, the sat_244 that is arranged in the satt442 of H linkage group and is positioned at M linkage group detect at two environment simultaneously.
3, single mark variance analysis
Utilize the proterties average difference between each marker site different genotype, test the significance of difference of studied quantitative character between marker genetype with traditional one-way analysis of variance method.For a mapping population, marker site has three kinds of genotype (F2 colony) or two kinds of genotype (backcross population, RIL, Doubled haploid line) arbitrarily, analyze the difference of the quantitative character average of each genotype individuality, and carry out variance analysis, in the time of P value≤0.05, show that this marker site may be chain with one or more QTL.When multiple significance marks (P≤0.05) appear in (20cM) in karyomit(e) certain limit region, in section, select the close linkage mark for navigating in this section of interpret table form variation maximum.
As shown in table 4, the method detects 22 of the extremely significant marks of P value altogether at Shijiazhuang in 2011, Shijiazhuang in 2012, Sanya three environment in 2011, is distributed in the 8th, 11,14,6,17,15,12,16, No. 19 karyomit(e)s.7 of 100-grain weight close linkage marks in Shijiazhuang environment in 2011, detected, explainable heritable variation is between 5.32%-11.68%, accumulative total is explained heritable variation 48.54%, and being wherein labeled as of soluble heritable variation value maximum (11.68%) is positioned at the satt281 on karyomit(e) No. 6; Relevant QTL5 of 100-grain weight in Shijiazhuang experiment in 2012, detected altogether, explainable heritable variation scope is in 4.74%-9.53%, and accumulative total is explained heritable variation 34.03%; Relevant QTL10 of 100-grain weight in Sanya experiment in 2011, detected altogether, explainable heritable variation scope is in 4.05%-10.06%, accumulative total is explained heritable variation 67.38%, and being wherein labeled as of soluble heritable variation value maximum is positioned at the satt281 on karyomit(e) No. 6.
The significance that all can be detected in three environment is marked with 1, is positioned at the satt281 at No. 6 karyomit(e) 40.3cM place.
Table 4 detects soybean 100-grain weight linked marker to be labeled as basic single mark variance analysis
4, QTL positioning analysis method
Use V.2.5 composite interval mapping (CIM) and ICIMaping of WinQTL Cartographer.
(1) CIM method is used standard model 6, and step-length is 1cM, adopts the Return Law forward to search QTL and common factor, and window size is made as 10cM, and the context marker of maximum 5 high P values is as its genetic background of concomitant variable control.Be more than or equal to 2.5 threshold values that exist as QTL using LOD value.Fiducial interval is determined according to each 1 the LOD value that declines in the peak value both sides of LOD value.1.4 make effect mutually adopts IciMapping2.0 to carry out 100-grain weight proterties QTL location, judges existing of QTL take LOD > 3.0 as threshold value.Needed file layout is by the requirement editor of Manual.Institute's analytical results is as table 5.
Table 5 composite interval mapping method detects soybean 100-grain weight QTL
(2) complete interval mapping (ICIM) method of IciMap-ping2.0 comprises two steps: first utilize markd information, selected important token variable and estimated its effect by successive Regression; Then utilize the linear model that successive Regression obtains to proofread and correct phenotypic data, locate by one-dimensional scanning and add (showing) property effect QTL, locate epistatic interaction QTL by two-dimensional scan.Acquired results is as table 6.
The complete Interval Mapping of table 6 detects soybean 100-grain weight QTL
Utilize CIM method 8 relevant QTL of 100-grain weight (table) to be detected altogether under 2011 Shijiazhuang environment, 2012 Shijiazhuang and three of 2011 Sanyas environment, synergy gene all comes from Ji beans 12.Wherein in the environment of F8 Shijiazhuang, navigating to 2, is respectively qSW-Gm06 and qSW-Gm17; In the environment of F9 Shijiazhuang, navigating to 2, is respectively qSW-Gm02 and qSW-Gm17; In the environment of F9 Sanya, navigate to 2, respectively qSW-Gm13 and qSW-Gm15.Do not find the QTL simultaneously occurring at three environment by the method, the QTL that all can detect in F8 Shijiazhuang environment and F9 Shijiazhuang environment has 1, to be positioned at the qSW-Gm06 between 33.40cM-47.20cM on No. 6 karyomit(e), its explainable genetic mutation rate is 11.57% to the maximum, and additive effect maximum value is 0.87.
Utilize ICIM method in three environment, to detect altogether QTL10, lay respectively on the 11st, 6,2,17,16, No. 9 karyomit(e)s, synergy gene is all from Ji beans 12.In Shijiazhuang environment in 2011, detect that 2 QTL are respectively qSW-Gm06 and qSW-Gm17, qSW-Gm17 genetic mutation rate more greatly 12.39%.In Shijiazhuang environment in 2012, detect that 4 QTL are respectively qSW-Gm06, qSW-Gm11, qSW-Gm17 and qSW-Gm02, qSW-Gm02 genetic mutation rate is 10.70% to the maximum.In Sanya environment in 2011, detect that 4 QTL are respectively qSW-Gm06, qSW-Gm16, qSW-Gm17 and qSW-Gm19, qSW-Gm19 genetic mutation rate is 11.82% to the maximum.The QTL that all can detect in three environment has 2, wherein has and is positioned at the qSW-Gm06 (close linkage is labeled as satt281) on karyomit(e) No. 6, and LOD scope is between 4.96-5.79, and explainable genetic mutation rate is 8.60%-9.92%.
In this embodiment, under three environment, adopt four kinds of methods 76 of the closely linked marks of soybean 100-grain weight to be detected altogether.In the environment of F8 Shijiazhuang, four kinds of methods detect closely linked mark or QTL22 altogether, are marked with 2 with the close linkage that four kinds of methods all can detect, wherein have and are positioned at the satt281 on karyomit(e) No. 6.In the environment of F9 Shijiazhuang, four kinds of methods detect close linkage mark or QTL28 altogether.QSW-Gm06 (linked marker is satt281) all can detect in single mark, CIMI, tri-kinds of methods of CIM, near Barcsoyssr-6-200 and this proterties close linkage at Cm place this mark detected in two tails, is speculated as same QTL.In the environment of F9 Sanya, four kinds of methods detect linked marker or QTL26 altogether, and the mark that four kinds of methods all can detect does not have, and what under three methods, can detect therein is marked with 3 simultaneously, wherein has and is positioned at the satt281 on karyomit(e) No. 6.In the present embodiment, the QTL qSW-Gm06 that three four kinds of environment methods all can detect, on No. 6 karyomit(e), between 33.4-47.2, close linkage is labeled as satt281.
It should be noted last that, above embodiment is only unrestricted in order to technical scheme of the present invention to be described, although the present invention is had been described in detail with reference to preferred embodiment, those of ordinary skill in the art is to be understood that, can modify or be equal to replacement technical scheme of the present invention, and not departing from the spirit and scope of technical solution of the present invention, it all should be encompassed in the middle of claim scope of the present invention.
Claims (2)
1. its close linkage of the relevant QTL of stable soybean 100-grain weight site is labeled as satt281, it is characterized in that: this site is positioned in soybean C2 linkage group, close linkage is labeled as SSR primer satt281, position on public collection of illustrative plates is 40.3cM place, adopt four kinds of different localization methods (two tails and single mark variance analysis are standard take P≤0.01, and CI and MICIM are take LOD >=3.0 as standard) all can detect in two generations, two environment.
2. its close linkage of the relevant QTL of a stable soybean 100-grain weight according to claim 1 site is labeled as satt281, it is characterized in that: (two tails and single mark variance analysis are standard take P≤0.01 to adopt four kinds of different localization methods, CI with MICIM take LOD >=3.0 as standard) 75 of the relevant QTL of soybean 100-grain weight and close linkage marks in two generations, two environment, can also be detected, wherein repeating the QTL that frequency is higher has qSW-Gm06 (close linkage is labeled as satt281), and contribution rate is 11.68% to the maximum.
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| CN104087580A (en) * | 2014-07-10 | 2014-10-08 | 山东农业大学 | Wheat 4B chromosome grain weight QGW4B-CAPS molecular marker and application thereof |
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| CN105543222A (en) * | 2016-02-29 | 2016-05-04 | 南京农业大学 | Molecular marker InDeL_33 of main-effect QTL (quantitative trait locus) of soybean hundred-grain weight and application of molecular marker InDeL_33 |
| CN108411021A (en) * | 2018-03-13 | 2018-08-17 | 山东省农业科学院作物研究所 | A kind of relevant molecule labelling method of soybean 100-grain weight and its label combination |
| CN114107550A (en) * | 2021-12-15 | 2022-03-01 | 吉林省农业科学院 | QTL (quantitative trait locus), molecular marker, amplification primer and application related to soybean hundred-grain weight |
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Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104087580A (en) * | 2014-07-10 | 2014-10-08 | 山东农业大学 | Wheat 4B chromosome grain weight QGW4B-CAPS molecular marker and application thereof |
| CN104087580B (en) * | 2014-07-10 | 2017-03-01 | 山东农业大学 | Semen Tritici aestivi 4B chromosome grain weight QGW4B CAPS molecular marker and its application |
| CN104673788A (en) * | 2014-07-24 | 2015-06-03 | 东北农业大学 | Tagged site Satt318 related to genetic characteristics of 100-seed weight of soybeans and application of tagged site Satt318 |
| CN105543222A (en) * | 2016-02-29 | 2016-05-04 | 南京农业大学 | Molecular marker InDeL_33 of main-effect QTL (quantitative trait locus) of soybean hundred-grain weight and application of molecular marker InDeL_33 |
| CN105543222B (en) * | 2016-02-29 | 2019-05-07 | 南京农业大学 | The molecular labeling InDeL_33 of soybean 100-grain weight main effect QTL and its application |
| CN108411021A (en) * | 2018-03-13 | 2018-08-17 | 山东省农业科学院作物研究所 | A kind of relevant molecule labelling method of soybean 100-grain weight and its label combination |
| CN114107550A (en) * | 2021-12-15 | 2022-03-01 | 吉林省农业科学院 | QTL (quantitative trait locus), molecular marker, amplification primer and application related to soybean hundred-grain weight |
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