CN101974620A - Method for positioning quantitative trait loci (QTL) of rice - Google Patents
Method for positioning quantitative trait loci (QTL) of rice Download PDFInfo
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Abstract
The invention discloses a method for positioning the quantitative trait loci (QTL) of rice, which aims to guide a user to accurately, highly-efficiently and reliably detect major QTL. The method comprises the following steps of: selecting the permanent groups of recombinant inbred lines (RILs), significantly different in biparental agronomic traits, of the rice as QTL positioning groups; constructing a molecular genetic linkage map by selecting molecular simple sequence repeat (SSR) markers; inspecting trait phenotypic values of 5 completely-random single strains in high-trait lines of the permanent groups of the rice and 26 sets of trait phenotypic data of the completely-random combinations of 2, 3, 4 and 5 single strains of the 5 single strains; and by utilizing the molecular genetic linkage map, performing QTL mapping on high-trait genes of control strains by using a composite interval mapping (CIM) method of WinQTLCart 2.5-version software, the 5 single strains in the lines and the 26 sets of trait phenotypic data of the completely-randomly combined strains, and verifying the existence, detected by the CIP method, of the major QTL by using a multiple interval mapping (MIM) method. The method can be used for the positioning of the quantitative trait loci of the rice.
Description
Technical field
The present invention relates to the localized method of a kind of paddy rice quantitative trait locus (QTL), particularly relate to a kind of method that the quantitative character phenotypic data is analyzed when utilizing the permanent group expansion QTL of paddy rice location.
Background technology
Paddy rice is most important in the world first food crop, also is one of most important food crop of China.Paddy rice overwhelming majority economical character such as output, quality, resistance etc. all are subjected to quantitative trait locus (QTL) control of polygenic system.Current, paddy rice QTL location, separation, map based cloning strategy are that parsing controlled by multiple genes quantitative character is a single Mendelian inheritance factor effective means the most, also are the important channels of paddy rice quantitative character gene excavating and functional study.
As everyone knows, make up rice molecular genetic map, development statistical model and accurately to measure the quantitative character phenotypic number be to carry out requisite three important steps of quantitative trait locus (QTL) Position Research.In recent years, the structure of the more concern molecular genetic linkage maps of report of existing rice molecular quantitative character genetic research and the development of statistical model.So far, seldom when utilizing permanent group expansion QTL such as paddy rice recombinant inbred lines (RIL) or doubled haploid (DH) location in the strain system sample drawn amount of capacity influence the localized relevant report of main effect QTL.Generalized case is utilized paddy rice F
2Or BC
1F
2Every class proterties was only measured an individual plant character value when segregating population carried out the QTL location.But this class segregating population can not be used for experimental study under many environment simultaneously and seldom be used to carry out the QTL Position Research.At present, most of paddy rice QTL Position Research project is selected RIL or the permanent colony of DH for use.Normal conditions, when selecting the permanent group expansion QTL of paddy rice location for use, it is that the proterties phenotypic number carries out the QTL location that interior investigation 5 or 10 strains of every class proterties strain system are averaged as this strain.Yet, measure in the every class proterties strain system too much individual plant will be extraordinarily the workload measured of character value.As everyone knows, the height of measuring character value efficient directly affects QTL Position Research process, more particularly be difficult to carry out the quantitative character that the proterties phenotypic number is measured, for example root surface area, root diameter, tip of a root number, and some important physical or biochemical indicator character value.If the too much individual plant of single property determination in the strain system, the best period of property determination will be missed so, and this will have a strong impact on the QTL progress, even is difficult to obtain the complete localized phenotypic character data of QTL that are used for of a cover.Therefore, we are badly in need of understanding the interior best sample drawn capacity of every class proterties strain system when utilizing the permanent group expansion QTL of paddy rice location, and this size of a sample can be used for the QTL Position Research accurately, reliably, efficiently.
Utilize the permanent group expansion QTL of paddy rice Position Research to be of long duration, this types of populations can satisfy the needs of different goals in research and research environment simultaneously, at present already by rice genetic scholar and breeding scholar are extensive use of both at home and abroad.Utilizing the permanent group expansion QTL of paddy rice Position Research, accurately measuring character value will be one of important step of carrying out efficient QTL Position Research.But do not influence at present, the relevant information report of stably express main effect QTL Position Research as yet relevant for sample drawn amount of capacity in the strain system.
Summary of the invention
The present invention will solve current people and utilize the permanent colony of paddy rice to carry out causing the interior too much individual plant of mensuration of strain system when quantitative trait locus (QTL) is located easily and missing best proterties probation, the problem that is difficult to obtain a cover localized proterties phenotypic data of the complete QTL of being used for and then has a strong impact on QTL Position Research process.The invention provides the localized method of a kind of paddy rice quantitative trait locus (QTL) for this reason, result of study by method of the present invention is implemented and obtained can instruct people to detect the main effect QTL of stably express under varying environment accurately, efficiently, reliably well.
5 individual plants of completely random investigation in the every strain of the permanent colony of the paddy rice plant height proterties system, called after pha, phb, phc, phd, phe.Obtaining a series of strains of 26 covers altogether is that interior 5 individual plant completely randoms make up 2 strains, 3 strains, 4 strains and 5 strain proterties mean phenotypic values, and completely random combination 2 or 3 strains obtain 10 cover proterties phenotypic datas respectively in the strain system.Called after phab, phac, phad, phae, phbc, phbd, phbe, phcd, phce, phde; Phacd, phabe, phabd, phabc, phbcd, phbde, phade, phcde, phace, phbce; The interior completely random of strain system makes up 4 strains and 5 strains ask average proterties phenotypic number to be respectively phabde, phacde, phabcd, phabce, phbcde and phabcde.
Utilizing molecular genetic linkage map, composite interval mapping method (CIM), strain is that interior 5 individual plants and 26 cover completely random combined trait phenotype averages are carried out QTL location, the checking of selecting for use graphing method between multi-region (MIM) that whether the detected main effect QTL of CIM graphing method is existed to control plant height proterties.
Described main effect QTL can be that the proterties phenotypic number that interior 5 individual plants and 26 cover completely randoms make up detects respectively by strain under the varying environment condition simultaneously.
Described main effect QTL location is not subjected to the influence of sample drawn amount of capacity in the strain system.We when utilizing the permanent group expansion QTL of paddy rice location in the strain system sample drawn amount of capacity do not influence the detected result of the main effect QTL of stably express.Measure an individual plant in the every class proterties strain system and measure a plurality of individual plant character values simultaneously and average and carry out main effect QTL respectively and locate, its positioning result does not have significant difference.
Above-mentioned one step other guide is a known technology, does not repeat them here.
The invention has the beneficial effects as follows, utilize the localized method of paddy rice quantitative trait locus (QTL), the method analyzed of quantitative character phenotypic data is particularly well explored when utilizing the permanent group expansion QTL of paddy rice location in the every class proterties strain system sample drawn amount of capacity to the influence of main effect QTL positioning result.The size that result of study shows size of a sample in the strain system to the main effect QTL positioning result without any influence, this will the field phenotype experimental design when utilizing the permanent group expansion QTL of paddy rice location provide guidance for geneticist and breeding scholar, help to utilize accurate, efficient, the reliable paddy rice QTL Position Research of permanent group expansion.
Description of drawings
The main effect QTL that Fig. 1 represents to be positioned on paddy rice the 3rd karyomit(e) is that 5 individual plants and 26 cover completely random combined trait phenotypic datas detected under two varying environment conditions at 2006 and 2009 by the strain of paddy rice recombinant inbred lines simultaneously;
The main effect QTL that Fig. 2 represents to be positioned on paddy rice the 7th karyomit(e) is that 5 individual plants and 26 cover completely random combined trait phenotypic datas detected under an envrionment conditions in 2006 by the recombinant inbred lines strain simultaneously;
Embodiment is made description below to term wherein earlier before the explanation embodiment:
The molecular genetic linkage collection of illustrative plates: chromosomal exchange is the theoretical basis of genetic map construction with reorganization, and the ultimate principle of utilizing molecule marker to make up genetic map is to determine that according to being marked at being divided into from situation in the segregating population their linkage relationship sets up linkage group.Concrete steps comprise: select parent and molecule marker, structure genetic group, make up linkage group.Genetic linkage maps is not with the relative position between genetic distance expressive notation and the mark (being the actual physical distance), it is to be based upon on the basis of statistical study, by calculating the crossover value of two marks in segregating population, crossover value is converted into genetic distance (centimorgan cM).
Little satellite (SSR) mark: be the tumor-necrosis factor glycoproteins that reaches tens Nucleotide that repeating unit forms by a class by several Nucleotide (1-5), length is shorter, extensively is distributed on the karyomit(e).Because the different or degree of repetition of repeating unit's number of times is incomplete same, caused the height variability of SSR length, produce SSR mark or SSLP mark therefrom.Though the position of SSR on genome is not quite similar, mostly its two terminal sequence is the single-copy sequence guarded.Therefore, can be designed to primer,,, can show that the SSR site is in interindividual polymorphism through polyacrylamide gel electrophoresis by round pcr with little satellite region particular order.Advantage: 1) mark quantity is abundant, has more allelic variation, is distributed widely on each bar karyomit(e); 2) codominant marker is the Mendelian inheritance law of segregation; 3) technology good reproducibility, easy handling, reliable results; 4) the mark result can be directly used in the breeding of rice molecular marker assisted selection.
Composite interval mapping method (CIM): the CIM method is multiple labeling QTL localization method again, be a kind of based on full genome the drawing method of the underlined QTL of carrying out location and effect analysis.The CIM method is based on the IM method, still adopt QTL likelihood figure to show possible position and the significance degree of QTL, do not exist under the condition of epistasis effect in supposition, other marks outside the specific markers interval are fitted in the model, make full use of the label information of whole genome, controlled the hereditary effect of background largely; With the method that is similar to single interval mapping, calculate the LOD value and the significance of each parameter, draw each chromosomal likelihood collection of illustrative plates, mark the possible position of each QTL, can handle the chain situation of many QTL preferably, improved the precision and the efficient of mapping.
Quantitative trait locus (QTL): the position of quantitative gene in linkage group of accusing the performance of system quantitative character.The variation of quantitative character is continuity, and the segregating generation after the hybridization can not clearly divide into groups.Quantitative character is general to be subjected to the influence of envrionment conditions and to morph easily, and this variation generally can not heredity.The gene of the proterties of controlling the size is expressed under specific space-time condition, and the degree of genetic expression may be different under the varying environment condition, so the quantitative character ubiquity genotype by environment interaction.
Method specific implementation process of the present invention:
1, materials and methods
(1) for the examination material
Select China first commercial super hybridized rice combination " assisting excellent 9308 " parents preparation " the blue or green B (plant height 94.6cM) early of association * in extensive 9308 (plant height 119.3cM) " cross combination in 2002 for use and obtain F
1Containing 226 strains through the single seed descent structure is recombinant inbred lines.The plant height proterties is remarkable phenotypic genetic difference and shows continuous distribution in recombinant inbred lines parents, and this proterties ratio is easier to accurate mensuration simultaneously.Selected target group and location quantitative character all are adapted to the enforcement of present method." assist excellent 9308 " simultaneously and be the super hybrid rice of China Paddy Rice Inst's seed selection, the plant type compactness, it is medium on the weak side to tiller, cane is sturdy, and fertilizer resistance anti-lodging, sword-like leave are very, blue or green bar yellow maturity of later stage, annesl is good, in the first batch one of Super Hybrid rice varieties of being assert by the national Ministry of Agriculture.
(2) molecular genetic linkage map
Present method is implemented used molecular genetic linkage map, and to make up molecular genetic linkage map with " the blue or green B early of association * in extensive 9308 " 281 strains systems of recombinant inbred lines serve as to locate for collection of illustrative plates.This collection of illustrative plates comprises 199 SSR marks, flag sequence is published in (http://www.gramene.org/), the SSR mark is uniformly distributed in 12 karyomit(e)s of paddy rice, collection of illustrative plates covers rice genome total length 1765.6cM, the mean chart distance is 8.87cM between adjacent marker, this collection of illustrative plates is fit to the QTL Position Research, and the used software of drawing is MapMaker/EXP3.0Version.
(3) QTL mapping software and method
It is 2.5 editions softwares of WinQTLCart that present method is implemented the software that adopts.Use between composite interval mapping method (CIM) and multi-region that the main effect QTL location is carried out in mapping (MIM) and whether it is existed and verify, estimate the genetic parameter of main effect QTL.
Divided " the blue or green B early of association * in extensive 9308 " recombinant inbred lines and the parents that to contain 226 strains systems year to plant 2006,2009 summer in Fuyang, Zhejiang China Paddy Rice Inst test base, select the even field of fertility piece, specification experiment material according to plant spacing 20cM * 23cM, every strain is plantation 4 row, every row 6 strains.The quantitative character that is used for present method enforcement research is the paddy rice plant height.
Completely random is measured 5 individual plants in the recombinant inbred lines proterties plant height strain system; Called after pha, phb, phc, phd, phe.Obtaining a series of strains of 26 covers altogether is that interior 5 individual plant completely randoms make up 2 strains, 3 strains, 4 strains and 5 strain proterties average phenotypic data, completely random combination 2 or 3 strains can obtain 10 cover proterties phenotypic datas, called after phab, phac, phad, phae, phbc, phbd, phbe, phcd, phce, phde respectively in the strain system; Phacd, phabe, phabd, phabc, phbcd, phbde, phade, phcde, phace, phbce; Completely random makes up 4 strains and 5 strains in the strain system, obtains 6 cover proterties phenotypic datas, is phabde, phacde, phabcd, phabce, phbcde and phabcde.Utilizing structure RIL molecular genetic linkage map, composite interval mapping method (CIM), strain is that interior 5 individual plants and 26 cover completely random combined trait phenotypic datas carry out the QTL location respectively to the plant height proterties, selects for use graphing method between multi-region (MIM) whether the existence of the detected main effect QTL of CIM is verified.Found that, be the main effect QTL (Fig. 1, Fig. 2) that interior 5 individual plants and 26 cover completely random combined trait phenotypic datas detect 2 control plant heights simultaneously by strain respectively on the 3rd, the 7th karyomit(e).Being positioned at Qph3 on the 3rd karyomit(e) (RM148-RM85) can be detected under two varying environment conditions at 2006,2009 by 31 cover plant height phenotypic datas simultaneously.Being positioned at the 7th karyomit(e) control plant height Qph7a (RM3670-RM2) can be detected under an environment in 2006 by 31 cover plant height phenotypic datas simultaneously.The main effect QTL positioning result of finding stably express simultaneously is not subjected to the interior influence of extracting the sample amount of capacity of strain system.Therefore, present method has well been annotated when utilizing the permanent group expansion QTL of paddy rice location the problem that sample drawn amount of capacity in the strain system influences the QTL positioning result.
The present invention adopts the QTL plotting technique, utilize the assignment of genes gene mapping of the permanent group expansion quantitative character of paddy rice, the novel method that field proterties phenotypic data is analyzed when having created a kind of quantitative trait locus QTL Position Research, enriched QTL Position Research institute phenotypic character phenotypic data, improve accuracy, the reliability of QTL Position Research, will accelerate QTL Position Research process.
At last, what also pay particular attention to is that what more than to enumerate only is specific embodiments of the invention.Obviously, the present invention is not limited only to above examples of implementation, and the situation of many accommodations can also be arranged.Those skilled in the art all thinks protection scope of the present invention from all flexible situations that content direct derivation disclosed by the invention goes out or associates.
Claims (2)
1. the localized method of a paddy rice quantitative trait locus (QTL) is characterized in that:
Select for use parents' economical character to exist the permanent colony of paddy rice RIL (RILs) of significant difference as QTL target group; Select for use the little satellite of molecule (SSR) mark to make up the molecular genetic linkage collection of illustrative plates; 5 individual plants of completely random in the plant height proterties strain system of the permanent colony of investigation paddy rice, this individual plant proterties phenotypic number is called after pha, phb, phc, phd, phe respectively, obtaining 26 cover strains altogether is that interior 5 individual plant completely randoms make up 2 strains, 3 strains, 4 strains and 5 strain proterties phenotypic datas, wherein completely random makes up 2 strains and averages and obtain 10 cover proterties phenotypic datas, called after phab, phac, phad, phae, phbc, phbd, phbe, phcd, phce, phde in the strain system; Completely random makes up 3 strains and also obtains 10 cover phenotypic datas, called after phacd, phabe, phabd, phabc, phbcd, phbde, phade, phcde, phace, phbce; Completely random makes up 4 strains and 5 strains obtain 6 cover phenotypic datas, called after phabde, phacde, phabcd, phabce, phbcde and phabcde altogether;
Utilize described molecular genetic linkage collection of illustrative plates, composite interval mapping method (CIM) with 2.5 editions softwares of WinQTLCart, and strain is interior 5 individual plants and 26 cover completely random combination plant height proterties phenotypic datas, control plant height character gene is carried out the QTL mapping, and whether the existence of the main effect QTL that the CIM graphing method is detected with graphing method between multi-region (MIM) is verified.
2. the localized method of a kind of paddy rice quantitative trait locus as claimed in claim 1 (QTL) is characterized in that: described main effect QTL can be that the proterties phenotypic data that interior 5 individual plants and 26 cover completely randoms make up detects respectively simultaneously by strain under the varying environment condition simultaneously.
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Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104561348A (en) * | 2015-01-26 | 2015-04-29 | 中国水稻研究所 | Specific PCR molecular markers for detecting rice high-grain weight alleles |
| CN104830967A (en) * | 2015-03-10 | 2015-08-12 | 中国农业科学院作物科学研究所 | Positioning method of rice selected introgression lines QTL |
| CN107142317A (en) * | 2017-06-02 | 2017-09-08 | 中国水稻研究所 | A kind of method excavated and verify the Plant Height of Rice allele with cumulative effect |
| CN108197435A (en) * | 2018-01-29 | 2018-06-22 | 绥化学院 | Localization method between a kind of multiple characters multi-region for containing error based on marker site genotype |
| CN108841993A (en) * | 2016-02-04 | 2018-11-20 | 山东省农业科学院生物技术研究中心 | SSR molecular marker L10 and application with the high bar QTL close linkage of rice |
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| CN1448515A (en) * | 2002-04-02 | 2003-10-15 | 浙江大学 | Quantitative character gene site locating method based genomic exon chip |
| CN101760540A (en) * | 2008-12-19 | 2010-06-30 | 李祥 | Method for positioning quantitative trait locus (QTL) |
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Patent Citations (2)
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| CN1448515A (en) * | 2002-04-02 | 2003-10-15 | 浙江大学 | Quantitative character gene site locating method based genomic exon chip |
| CN101760540A (en) * | 2008-12-19 | 2010-06-30 | 李祥 | Method for positioning quantitative trait locus (QTL) |
Non-Patent Citations (3)
| Title |
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| 《中国水稻科学》 20091231 沈希宏等 超级杂交稻协优9308重组自交系群体的穗部性状QTL分析 354-362 第23卷, 第4期 * |
| 《作物学报》 20061031 张启军等 利用已测序水稻品种分析其农艺性状基因座 1503-1510 第32卷, 第10期 * |
| 《分子植物育种》 20041231 马大鹏等 利用重组自交系群体对水稻产量相关性状的QTL分析 507-512 第2卷, 第4期 * |
Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN104561348A (en) * | 2015-01-26 | 2015-04-29 | 中国水稻研究所 | Specific PCR molecular markers for detecting rice high-grain weight alleles |
| CN104830967A (en) * | 2015-03-10 | 2015-08-12 | 中国农业科学院作物科学研究所 | Positioning method of rice selected introgression lines QTL |
| CN104830967B (en) * | 2015-03-10 | 2018-03-09 | 中国农业科学院作物科学研究所 | A kind of rice selection introgressive line QTL localization method |
| CN108841993A (en) * | 2016-02-04 | 2018-11-20 | 山东省农业科学院生物技术研究中心 | SSR molecular marker L10 and application with the high bar QTL close linkage of rice |
| CN107142317A (en) * | 2017-06-02 | 2017-09-08 | 中国水稻研究所 | A kind of method excavated and verify the Plant Height of Rice allele with cumulative effect |
| CN108197435A (en) * | 2018-01-29 | 2018-06-22 | 绥化学院 | Localization method between a kind of multiple characters multi-region for containing error based on marker site genotype |
| CN108197435B (en) * | 2018-01-29 | 2022-02-25 | 绥化学院 | Marker locus genotype error-containing multi-character multi-interval positioning method |
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