CN106929574B - SNP molecular marker of upland cotton No. 4 chromosome related to fiber strength - Google Patents
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Abstract
The invention belongs to the technical field of cotton molecular breeding, and discloses an SNP molecular marker related to the strength of upland cotton fibers, and detection and application thereof. The SNP molecular marker is obtained by taking a stable RIL population of cotton as a material through a genome re-sequencing method. The SNP markers disclosed by the invention are utilized to carry out molecular marker-assisted breeding selection, so that the breeding period can be greatly shortened, and the breeding efficiency of the cotton fiber strength can be improved.
Description
Technical Field
The invention belongs to the technical field of cotton molecular breeding, and particularly relates to an SNP molecular marker related to the strength of upland cotton fibers, and detection and application thereof.
Background
Cotton plays an important role in the world's economy as a major fiber crop. Among the four cotton species widely cultivated worldwide, upland cotton occupies the most important position, and the yield accounts for more than 90% of the total world cotton yield. With the increase of the demand of people on medium-high-grade textiles, the requirement on the quality of fibers is increasingly improved, but the traditional breeding means mainly selects through phenotypes, the breeding efficiency is low, and the requirement on quality breeding is difficult to meet. The development of molecular marker technology has made it possible to directly select quantitative trait genotypes. QTL positioning by constructing cotton genetic map can make breeder directly select genotype with quantitative characters such as fiber quality, etc. by using F2And RIL and other mapping groups carry out QTL positioning research on fiber quality, and great results are obtained. Especially, the development and application of the third generation marking technology SNP marker can lay a foundation for the later marker-assisted breeding. The SNP marker is the most potential molecular marker for development at present, and is suitable for large-scale automation and detection analysis with large quantity because of large quantity and wide distribution in the genome and no need of DNA banding according to the size of a fragment in the gene analysis process, and is widely applied to the fields of medicine, biology and the like at present. But has been less studied in cotton.
Kristen L and others use SNP markers as minimum units (recombination bins) for judging chromosome recombination events, judge the condition that each Bin of filial generation is from a parent and a female parent, and obtain a whole genome physical map of each filial generation, thereby constructing a Bin map for subsequent high-precision Genetic linkage map construction and QTL positioning (Kristen L Kump, Peter J Bradbury et al genome-side association map of quantitative resistance to southern leaf mapping [ J ] Nature genetics, 2011,43(2):163 168); yu et al applied whole genome re-sequencing to 241 rice RILs population for low depth re-sequencing, and constructed Bin map based on SNP, the Bin map has ultra-high density, can detect more QTL, and the detected QTL is more fine (Yu H, Xie W, Wang J, et al. Gains in QTL detection using an ultra-high density SNP map based on position sequencing
relative to traditional RFLP/SSR markers[J]PLoS ONE,2011,6(3): e 17595); xu et al constructed a high density Bin map by high depth re-sequencing rice parent 9311 and low depth re-sequencing 128 CSSLs, detecting 768 ten thousand SNP sites, these 128 CSSLs carrying 259 chromosome substitution fragments (Xu J, Zhao Q, Du P, et al]BMC Genomics,2010(11): 625); wuling et al, based on the limitation that SSR marker density is not enough in corn gene positioning, general SNP markers are only based on 2 genotype sequence differences and polymorphism is not enough when other genotype materials are detected, bioinformatics software is combined to develop high-polymorphism SNP markers based on EST sequences, 80363 SNP sites are finally discovered in the whole genome, 12388 SNP markers are developed, and the SNP markers have high polymorphism (Wuling et al, the bioinformatics method is utilized to develop corn single nucleotide polymorphism markers based on expressed sequence tags [ J]The journal of Nuclear agriculture, 2010,24(5): 968-; further developing a new generation of SNP markers for fine positioning of Julier and the like on the basis of preliminarily positioning the sensitive lethal gene of rice bentazon by utilizing SSR markers, positioning the gene in the range of 0.4 cM on the 3 rd chromosome as a result, co-separating 4 SNP markers from the gene, and finally finding out a coding cytochrome P on the chromosome450The deletion of a single base in the gene sequence of (a) leads to a frame shift mutation, so that the prediction is probably the cause of the rice bentazon sensitive death (Zhu Lei, the fine positioning of the rice bentazon sensitive death gene bel, Master graduate paper, Nanchang: Nanchang university, 2005); through SNP research on related genes of fiber development, the Chueagle separates seven tetraploid cotton seed materials with different fiber qualities and fiber development related gene fragments of two diploid ancestor cotton seeds by utilizing a PCR technology, obtains sequence information of five cotton fiber development related genes in nine cotton seed materials, and aims at high-strength cotton products of upland cottonStatistics is carried out on SNPs sites among lines, and nonsynonymous mutation is found in four cSNPs sites, so that the mutant cSNPs sites possibly have phenotypic effect (Chueagle, SNP research of fiber development related genes, cloning and expression analysis of cotton sucrose synthase gene fragments, Master graduation paper, Nanjing: Nanjing agriculture university, 2004); zhengweijia screening SSR and SNP molecular marker primers of New sea 21 and New land 36, and using the screened primers to screen two F2The colony is subjected to PCR amplification to construct a genetic linkage map, 864 pairs of SSR primers are selected in total to screen two parents, and 79 pairs of polymorphic primers are screened out in total, wherein the total amount of polymorphic primers accounts for 9.1%. 69 pairs of SSR primers and 11 sets of SNP primer pairs F screened from population2Carrying out genetic linkage analysis on the polymorphic markers amplified from the population to construct a genetic linkage map comprising 90 marker loci and 30 linkage groups, wherein the average distance between the markers is 55.9cM, the total length is 3135.84cM, and the genetic linkage map covers 62.71% of the cotton genome (Zhengweijia, development of SNP markers and construction of a sea-land genetic linkage map, a master paper, Wuluquinqi, Xinjiang agricultural university, 2013); zhu constructs genome-Wide SNP Linkage map through recombination Inbred line population, finds 2618 polymorphism SNP markers, wherein 16 stable QTLs exist in two environments, 12 QTLs relate to multiple Traits, and the QTLs are mainly distributed on chromosomes 5, 9, 10, 14, 19 and 20 (Li C, Zhu SJ et al genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the upper connected codon incorporated Linkage position, frontiers in Plant Science,2016,7: 218).
Yuan et al utilizes an abnormal cotton high-strength fiber introgression line 7235 and a upland cotton genetic standard line TM-1 as parents to construct F2、F2：3Separating the population, identifying a main effect QTL which can be detected in different cotton regions in China and in a plurality of environments such as the United states and the like and can explain more than 30 percent of phenotypic variation (molecular marker screening and positioning of high-quality fiber character QTLs of Yuan and the like, genetic report 2001,28(12): 1151-; shenxinlian uses 3 upland cotton high-strength fiber germplasm systems to construct 3F2An intra-linkage map is used to detect 38 QTLs associated with fiber quality by using a composite interval mapping method, wherein 15 stable QTLs can be simultaneously in F2And F2:3It was detected that at least 3 QTLs could be expressed in both populations (shenxinlian, screening, mapping and use of the QTL for cotton fiber quality on upland, doctrine, nanjing university of agriculture, 2004); the Shiyuzhen uses transgenic insect-resistant cotton varieties sGK321 and sGK9708 (Zhong41) widely planted in the yellow river basin as recurrent parents and respectively hybridizes with high-quality high-yield variety Tai121 and high-fiber quality introgression germplasm line 72351Generation material hybridization and backcross are carried out, two sets of hybridization backcross combinations are configured, 2 SSR markers which are closely linked with a located high-strength fiber QTL are applied, the 2 markers can be stably inherited and have stable QTL effect after multi-generation hybridization, backcross and selfing in different genetic backgrounds, the technology is combined with other means to carry out polymerization breeding research on genes with high quality, insect resistance and the like, the conventional upland cotton popularized varieties are quickly and effectively improved, high-yield, high-quality and insect-resistant cotton new materials or new strains (Shiyuzhen, Junwen, Yuqin and the like are created, and the main effect QTL linked with the strength of cotton fibers is applied to cotton molecular marker assisted breeding [ J Yuzhen, Junyun, Yuqin and the like]Molecular plant breeding, 2007,5(4): 521-527); giraffe utilizes 196 upland cotton recombinant inbred lines (F) which are constructed by taking SGK9708 as female parent and 0-153 as male parent6:8) A genetic linkage map which comprises 186 markers, has the total length of 827.84cM and the average distance between the markers of 4.45cM and covers 18.6 percent of a cotton genome is constructed, and QTL positioning and epistasis interaction analysis are carried out on the boll weight and the clothes character under 7 environments. 5 main effect QTLs (qBW-1-1, qBW-1-2, qLP-2-1, qLP-2-2 and qLP-4-2) which are stably expressed under multiple environments are positioned, QTL analysis of 4 pairs of QTLs for up-position interaction of the bell weight and 7 pairs of QTLs for up-position interaction of clothes (Jia Fei, Yuan Lu, and the like) and bell weight and clothes characters of a multi-environment land cotton (Gossypium hirsutum L.) recombination inbred line is detected [ J H1-1, qBW-1-2, qLP-2-1, qLP-2-2 and qLP-4-2 ]]Molecular plant breeding, 2011,9(8): 318-; wangtiankang and the like utilize 2 excellent fiber quality materials 0-153 and Xinluzao 24 and 2 large-area popularization varieties Lu cotton research 28 and Ji cotton 516 as parents to prepare double cross bred F1And in the population, 4 SSR markers linked with 3 fiber strength major QTLs are selected in an auxiliary manner, and the aggregation effect of different QTLs is researched. Results selection of 4 markers all showed significant genetic effects (Wangtiankang, jade, Yuan, etc., cotton fiber strengthMolecular marker assisted selection and aggregation effect research of major QTLs (J)]The cotton bulletin, 2014,26(5): 396-403); the Jamshed utilizes a Recombinant Inbred Line (RIL) population to construct a genetic map, the map coverage distance is 4110cM, the average distance between adjacent markers is 5.2cM, 47 QTLs are positioned to be stable in a multi-environment, the QTLs mostly exist in the form of aggregation groups and control two or more characters, and the QTLs are mainly concentrated in chromosomes 4, 7, 14 and 25 (Jamshed et al. identification of stable trait loci (QTLs) for fiber quality tradition and J sterile recombinant expressed line site [ J.]BMCGenomics,2016,17: 197); zhang constructs a high-density genetic map (Zhang et al. structural of a high-density genetic map by specific Loci amplified mapping (SLAF-seq.) and its mapping to Quantitative Trap Loci (QTL) analysis for a well-weighted in-plated cotta (Gossypium hirsutum.) [ J. in which the recombinant inbred line group constructed by two upland cotton varieties 0-153 and SGK9708 utilizes an SLAF sequence to construct 5521 single nucleotide polymorphism markers and covers the total distance of 3259.37cM].BMCPlant Biology,2016,16:79)。
In summary, SNP markers are the most promising molecular markers and are widely used, but the application in cotton is less, and most of the previous researches utilize segregation population such as F2、BC1The genetic background is complex, or the result is obtained by detecting under a single environment, so that the reliability and the stability are lacked, the QTL with multi-environment stability is few, and the initial aim of some researches is only to carry out the positioning of the target gene.
Disclosure of Invention
The technical problem to be solved by the invention is as follows: by screening the SNP molecular markers which are closely linked with the upland cotton fiber strength gene and stably express in a plurality of environments, the SNP molecular markers are applied to the auxiliary selection of cotton fiber quality, and the fiber quality level of cotton varieties in China can be improved as soon as possible.
The technical scheme provided by the invention is as follows: an SNP marker linked with the high-strength gene of upland cotton fiber is positioned inAmong 6 QTLs related to fiber strength, 4 of the 6 QTLs are stably detected in a multi-environment, the QTLs are positioned on the No. 4 chromosome of upland cotton, and 3 SNP markers with better typing can be obtained by screening; wherein is andqFS-chr04-2the linked SNP markers are CRI-SNP-198739, CRI-SNP-198740, CRI-SNP-198741 and CRI-SNP-198742; andqFS-chr04-3the linked SNP markers are CRI-SNP-198743, CRI-SNP-198744, CRI-SNP-198745, CRI-SNP-198746, CRI-SNP-198747, CRI-SNP-198748, CRI-SNP-198749, CRI-SNP-198750, CRI-SNP-198751, CRI-SNP-198752, CRI-SNP-198753, CRI-SNP-198754, CRI-SNP-198755, CRI-SNP-198756, CRI-SNP-198757, CRI-SNP-198758, CRI-SNP-198759, CRI-SNP-198760, CRI-SNP-198761, CRI-SNP-198762, CRI-SNP-198763, CRI-SNP-198764, CRI-SNP-198765, CRI-SNP-198766, CRI-SNP-198767, CRI-SNP-198768, CRI-SNP-198769, CRI-SNP-198770; andqFS-chr04-5the SNP markers of the linkage are CRI-SNP-198771 and CRI-SNP-198772, (wherein CRI: Cotton Research Institute stands for Cotton Institute of Chinese academy of agricultural sciences; SNP stands for marker type; number stands for marker development sequence), the positions of the SNP molecular markers on the chromosome, and the mutation bases are shown in the following table:
| name of label | SNP site | Mutant bases |
| CRI-SNP-198739 | 7700054 | T/C |
| CRI-SNP-198740 | 7720338 | T/C |
| CRI-SNP-198741 | 7721630 | G/T |
| CRI-SNP-198742 | 8177782 | A/G |
| CRI-SNP-198743 | 8254082 | T/G |
| CRI-SNP-198744 | 8254072 | T/C |
| CRI-SNP-198745 | 8260415 | C/T |
| CRI-SNP-198746 | 8297320 | C/T |
| CRI-SNP-198747 | 8356357 | G/A |
| CRI-SNP-198748 | 8442751 | A/T |
| CRI-SNP-198749 | 8817947 | C/T |
| CRI-SNP-198750 | 10632971 | G/T |
| CRI-SNP-198751 | 10678536 | T/C |
| CRI-SNP-198752 | 10678492 | T/G |
| CRI-SNP-198753 | 10707374 | G/A |
| CRI-SNP-198754 | 10697252 | C/T |
| CRI-SNP-198755 | 10730252 | A/T |
| CRI-SNP-198756 | 10794756 | T/A |
| CRI-SNP-198757 | 10733643 | T/C |
| CRI-SNP-198758 | 10745098 | G/A |
| CRI-SNP-198759 | 10745115 | A/G |
| CRI-SNP-198760 | 10761125 | A/G |
| CRI-SNP-198761 | 10750539 | T/C |
| CRI-SNP-198762 | 10750815 | C/T |
| CRI-SNP-198763 | 10758631 | A/G |
| CRI-SNP-198764 | 10842788 | G/A |
| CRI-SNP-198765 | 10890616 | G/A |
| CRI-SNP-198766 | 10890596 | C/T |
| CRI-SNP-198767 | 10890290 | A/G |
| CRI-SNP-198768 | 10863195 | G/T |
| CRI-SNP-198769 | 10843048 | G/A |
| CRI-SNP-198770 | 10874601 | G/A |
| CRI-SNP-198771 | 44993167 | T/C |
| CRI-SNP-198772 | 45071666 | T/C |
In the present invention, the QTL nomenclature is expressed in terms of the number of q + trait + linkage group + QTL (reference: McCouch SR, Cho YG, Yano M, et al. Report on QTL nomenclature, Rice Genet Newslett., 1997, 14: 11-13) with reference to the nomenclature rule of McCouch et al (1997) in RiceqFS-chr04-2Indicating a second QTL associated with fiber strength that maps to chromosome 4.
The SNP marker can effectively distinguish different SNP sites and different genotypes through an SNP genotyping experiment, so that different cotton samples can be screened, strains with high fiber strength can be screened, the breeding period is greatly shortened, and the breeding efficiency of the cotton fiber strength is improved.
Meanwhile, the invention also provides three QTLs for the strength of the upland cotton fibersqFS-chr04-2、qFS-chr04- 3、qFS-chr04-5Chain lockThe method for screening an SNP marker of (1), comprising the steps of:
(1) f is constructed by using a cotton 41 selected line SGK9708 in a field-promoted upland cotton cultivation variety and an upland cotton excellent line 0-153 with an Asian cotton high-strength fiber gene as parents2And F2:3A population;
（2）F2:3selfing each generation in the colony family, at F2:6The generation carries out single plant selection once, and plants the plants for two generations till F6:8Handle F6:8And later generations are used as a recombinant inbred line group to carry out multi-year and multi-point experiments;
(3) extracting DNA of the recombinant inbred line population and the parents;
(4) constructing a linkage map: performing enzyme digestion experiment on the genomic DNA of each detected sample, performing A treatment on the 3' end of the obtained enzyme digestion fragment (SLAF label), connecting a Dual-index sequencing joint, performing PCR amplification, purification, sample mixing and gel cutting to select a target fragment, sequencing, and constructing a genetic map of a sequencing result by using software (Zhang J, Guo W Z, Zhang T Z. molecular linking map of an al-localized cotton (Gossypium hirsutum L. Gossypium bar-base L.) with a cellular amplification. the application gene, 2002,105: 6-ion 1174);
(5) fiber strength QTL location: and screening the stable fiber strength main effect QTLs under a plurality of environments to obtain the 3 multi-environment stable fiber strength main effect QTLs and the linkage markers thereof.
The invention has the following beneficial effects:
the total number of loci related to the major genes of the multi-environment-stable high-strength fibers related to the invention is 3: (qFS- chr04-2、qFS-chr04-3、 qFS-chr04-5) By screening SNP markers which are closely linked with major genes of high-strength cotton fibers and stably express in a plurality of environments, the SNP markers are applied to auxiliary selection of cotton fiber quality, QTL positioning results are reliable, and the fiber quality level of cotton varieties in China can be improved as soon as possible.qFS-chr04-2Can be detected in 5 environments (specifically 2007-Anyang, 2008-Linqing, 2008-Quzhou and 2010-Anyang)4.88 to 8.83 percent, and the additive effect value is-0.91 to-0.63 cN/tex;qFS-chr04-3the method can be detected under 8 environments (specifically 2007 Anyang, 2008 Linqing, 2008 Quzhou, 2009 Quzhou, 2010 Gaoyi, 2010 Zhengzhou and 2013 Anyang), the interpretable phenotypic variation is 5.73-10.38%, and the additive effect value is-1.14 to-0.81 cN/tex;qFS-chr04-5the gene can be detected under 9 environments (specifically 2007 Anyang, 2008 Linqing, 2008 Quzhou, 2009 Anyang, 2010 Gaoyi, 2010 Zhengzhou and 2013 Anyang), the explained phenotypic variation is 4.69-12.6%, and the additive effect value is 0.78-1.33 cN/tex. The present invention utilizes a recombinant inbred line F6:8(RIL) screening stable fiber strength QTLs and molecular markers closely linked with the same, wherein the SNP molecular markers are obtained by taking stable RIL groups of cotton as materials through a genome re-sequencing method, strain lines with improved fiber strength are screened by using the molecular markers closely linked with the QTLs, and molecular marker-assisted breeding selection is carried out, so that the breeding period can be greatly shortened, and the breeding efficiency of the cotton fiber strength is improved.
Drawings
FIG. 1 is a genetic map obtained by genome re-sequencing with a total distance of 5197.17 cM.
FIG. 2 is a diagram showing the location of QTLs associated with intensity on chromosome 4, in which 3 of the SNP markers which are environmentally stable and which can be selected are individually shownqFS-chr04-2、qFS-chr04-3、qFS-chr04-5。
Detailed Description
The invention is further illustrated by the following detailed description of specific embodiments, which are not intended to be limiting but are merely exemplary.
(1) Recombinant inbred line F6:8Obtained by
For field planting and DNA extraction between 2007 and 2008, see patent application publication No.: CN 101613761a, inventive name: patent application document of SSR markers linked to major genes of cotton fiber strength. In 2009, respectively at the cotton institute test station of the Chinese academy of agricultural sciences of Anyang in Henan, China, the Quzhou test station of the Chinese university of agriculture and XinjiangKesudejia science and technology breeding limited laboratory station planting parents and F6:10And (4) a group. Adopting a one-line area in the circumference of Anyang and Quzhou, wherein the line length is 5 meters, the line spacing is 0.8m and (0.8+0.5) m respectively, and 20 plants are planted in each line; xinjiang adopts a 6-row area, 2 m rows long, and 15 plants in each row. Planting parents and F in the original seed field of the Hubei Gaoyao, the test station of the agricultural science institute of Anyang China in Henan province and Zhengzhou province in Henan province in 20106:11The group, Anyang and Zhengzhou, adopts a single-row area, the row length is 5m, and the row spacing is 0.8 m; the cognate adopts a single-row region with a row length of 4 m and a wide-narrow row (0.8+ 0.6) m. Each test point adopts an incomplete random block design, and the planting is repeated for two times. Taking field samples in the middle and last ten days of 9 months, collecting flowers according to families, and taking fiber samples of about 12g for fiber quality determination.
(2) The DNA of the recombinant inbred line population and the parents is extracted, and the specific method is a reference (Song national, improved CTAB method for quickly extracting cotton DNA, Cotton bulletin: 1998,10 (5) 273-.
(3) Selecting tetraploid Genome sequence of cotton provided by Cotton institute of Chinese agricultural sciences as reference Genome for electronic enzyme digestion prediction (Li FG, Fan GY, Lu CR, Xiao GH, Zou CS, Kohel RJ, Ma ZY, Shang HH, Ma XF, Wu JH, et al, Genome sequence of conserved uplink cotton (R))Gossypium hirsutumTM-1) videos information in genome evaluation, Nature Biotechnology, 2015, 33 (5)), and finally selecting HaeIII + SspI enzyme with the enzyme cutting rate of 98.61 percent to obtain 495.48Mreads, wherein the sequence with the enzyme section length of 364 and 414bp is defined as an SLAF label.
(4) According to the selected optimal enzyme digestion scheme, enzyme digestion experiments are carried out on the detected genome DNA of each sample, the obtained enzyme digestion fragments (SLAF labels) are processed by adding A at the 3' end, the obtained enzyme digestion fragments are connected with a Dual-index sequencing street, target fragments are selected through PCR amplification, purification, sample mixing and gel cutting, and IlluminaHiseqTM2500 is used for sequencing after the quality of the library is qualified.
(5) And identifying the original data obtained by sequencing by using the Dual-index to obtain the reads of each sample. And (4) developing the SLAF label in the parent and the offspring through a method of clustering among reads.
(6) By bioinformatic analysis, a total of 321797 SLAF tags were obtained, with 35300 polymorphic SLAF tags.
(7) And carrying out genotype coding on the polymorphic SLAF label, wherein the genotype coding rule is a 2-allele coding rule which is generally used in genetics, if the parental genotypes of a certain marker are aa (male parent) and bb (female parent), and the offspring genotype ab indicates that the sample is heterozygous in the coding type of the marker, wherein one genotype is from the male parent and one genotype is from the female parent.
(8) In order to ensure the quality of the genetic map, the SLAF tags are filtered according to the conditions that the sequencing depth of a parent is less than 10x, the integrity is less than 30 percent, the severe segregation (p-value <0.05) and the parents are heterozygous and two sets of genomes are aligned simultaneously, and 7958 SLAF tags are screened out in total.
(9) Dividing the SLAF labels into 26 linkage groups through positioning with a reference genome, calculating LOD values among high-quality molecular labels, performing linkage grouping through the LOD values, constructing a genetic map of each linkage group by adopting HighMap software, and obtaining the genetic map with the total map distance of 5197.17cM through correction (as shown in figure 1). The HighMap software was independently developed by Biotech, Inc. of Baimaike, Beijing.
(10) Based on the sequencing data of the SLAF, 44583 SNPs with polymorphism between parents are obtained by BWA and reference genome alignment of two diploid cottons, 10440 SNP markers are obtained by mapping after mass filtration.
(11) By adopting software QTL IciMapping V4.0 (http:// www. isbranding. net/software /) and software WinQTLCart 2.5, multi-environment QTL positioning analysis of fiber strength characters is carried out through phenotype data and genotype data of 11 environments (2007 Anyang, 2008 Linqing, 2008 Quzhou, 2009 Anyang, 2009 Quzhou, 2009 Anxusu, 2010 Anyang, 2010 Gaiyi, 2010 Zhengzhou, 2013 Anyang) so as to obtain 6 QTLs related to fiber strength, wherein the number of the QTLs is 4, and the obtained QTLs are correlated with the SNP markers, and finally, the SNP markers obvious to the fiber strength are screened (the QTLs are dyed on the QTLs)The position on the body is shown in fig. 2), wherein andqFS-chr04-2the linked SNP markers are CRI-SNP-198739, CRI-SNP-198740, CRI-SNP-198741 and CRI-SNP-198742; andqFS-chr04-3the linked SNP markers are CRI-SNP-198743, CRI-SNP-198744, CRI-SNP-198745, CRI-SNP-198746, CRI-SNP-198747, CRI-SNP-198748, CRI-SNP-198749, CRI-SNP-198750, CRI-SNP-198751, CRI-SNP-198752, CRI-SNP-198753, CRI-SNP-198754, CRI-SNP-198755, CRI-SNP-198756, CRI-SNP-198757, CRI-SNP-198758, CRI-SNP-198759, CRI-SNP-198760, CRI-SNP-198761, CRI-SNP-198762, CRI-SNP-198763, CRI-SNP-198764, CRI-SNP-198765, CRI-SNP-198766, CRI-SNP-198767, CRI-SNP-198768, CRI-SNP-198769, CRI-SNP-198770; andqFS-chr04-5the linked SNP markers are CRI-SNP-198771 and CRI-SNP-198772.
Claims (3)
1. The SNP markers linked with the high-strength gene of the upland cotton fiber are positioned in 6 QTLs related to the fiber strength, wherein 4 of the QTLs are stable to detect in multiple environments, the QTLs are positioned on the No. 4 chromosome of the upland cotton, and 3 SNP markers which can be screened to obtain better typing are positioned on the QTLs and are linked with the high-strength gene of the upland cotton fiberqFS-chr04-2The linked SNP markers are CRI-SNP-198739, CRI-SNP-198740, CRI-SNP-198741 and CRI-SNP-198742; andqFS-chr04-3the linked SNP markers are CRI-SNP-198743, CRI-SNP-198744, CRI-SNP-198745, CRI-SNP-198746, CRI-SNP-198747, CRI-SNP-198748, CRI-SNP-198749, CRI-SNP-198750, CRI-SNP-198751, CRI-SNP-198752, CRI-SNP-198753, CRI-SNP-198754, CRI-SNP-198755, CRI-SNP-198756, CRI-SNP-198757, CRI-SNP-198758, CRI-SNP-198759, CRI-SNP-198760, CRI-SNP-198761, CRI-SNP-198762, CRI-SNP-198763, CRI-SNP-198764, CRI-SNP-198765, CRI-SNP-198766, CRI-SNP-198767, CRI-SNP-198768, CRI-SNP-198769, CRI-SNP-198770; andqFS-chr04-5the linked SNP markers are CRI-SNP-198771, CRI-SNP-198772: the positions of the SNP molecular markers on the chromosome and the mutant bases are shown in the following table:
。
2. A method for screening the SNP molecular marker according to claim 1, comprising the steps of:
(1) f is constructed by using a cotton 41 selected line SGK9708 in a field-promoted upland cotton cultivation variety and an upland cotton excellent line 0-153 with an Asian cotton high-strength fiber gene as parents2And F2:3A population;
（2）F2:3selfing each generation in the colony family, at F2:6The generation carries out single plant selection once, and plants the plants for two generations till F6:8Handle F6:8And later generations are used as a recombinant inbred line group to carry out multi-year and multi-point experiments;
(3) extracting DNA of the recombinant inbred line population and the parents;
(4) constructing a linkage map: carrying out enzyme digestion experiment on the detected genome DNA of each sample, carrying out A addition treatment on the 3' end of the obtained enzyme digestion fragment SLAF label, connecting a Dual-index sequencing joint, carrying out PCR amplification, purification, sample mixing and gel cutting to select a target fragment, sequencing, and constructing a genetic map on the result;
(5) fiber strength QTL location: screening multiple environment stable fiber strength main effect QTLs, selecting SNP obvious to type of fiber strength to obtain 3 multiple environment stable fiber strength main effect QTLs from upland cotton as defined in claim 1qFS-chr04-2、qFS-chr04-3、qFS-chr04-5And linked SNP markers thereof.
3. The application of the SNP marker in molecular assisted breeding of the strength of upland cotton fibers, which is defined in claim 1, is characterized in that different SNP sites and different genotypes are effectively distinguished through a genotyping experiment of the SNP molecular marker, different cotton samples are screened, and strains with high fiber strength are screened out, so that the breeding period is greatly shortened, the breeding efficiency of the strength of the cotton fibers is improved, and the aim of molecular marker assisted breeding is fulfilled.
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Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2009143995A1 (en) * | 2008-05-26 | 2009-12-03 | Bayer Bioscience N.V. | Methods and means to modify fiber strength in fiber-producing plants |
| CN103497949A (en) * | 2013-10-15 | 2014-01-08 | 中国农业科学院棉花研究所 | Molecular markers from sea island cotton Hai 1 and related to cotton fiber strength and application of molecular markers |
| CN105524999A (en) * | 2016-01-19 | 2016-04-27 | 中国农业科学院棉花研究所 | Molecular marker linked with sea island cotton fiber length of cotton |
-
2017
- 2017-02-22 CN CN201710097731.6A patent/CN106929574B/en active Active
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2009143995A1 (en) * | 2008-05-26 | 2009-12-03 | Bayer Bioscience N.V. | Methods and means to modify fiber strength in fiber-producing plants |
| CN102076857A (en) * | 2008-05-26 | 2011-05-25 | 拜尔生物科学公司 | Methods and means to modify fiber strength in fiber-producing plants |
| CN103497949A (en) * | 2013-10-15 | 2014-01-08 | 中国农业科学院棉花研究所 | Molecular markers from sea island cotton Hai 1 and related to cotton fiber strength and application of molecular markers |
| CN105524999A (en) * | 2016-01-19 | 2016-04-27 | 中国农业科学院棉花研究所 | Molecular marker linked with sea island cotton fiber length of cotton |
Non-Patent Citations (4)
| Title |
|---|
| Genome-Wide SNP Linkage Mapping and QTL Analysis for Fiber Quality and Yield Traits in the Upland Cotton Recombinant Inbred Lines Population;Cong Li等;《Frontiers in Plant Science》;20160930;第7卷;第1-16页 * |
| Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population;Muhammad Jamshed等;《BMC Genomics》;20161231;第17卷(第197期);第10-11页Methods，第5页Fiber strength，补充文件3 * |
| Zhen Zhang等 High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength,Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.);Zhen Zhang等;《Plos one》;20150811;第1-17页 * |
| 陆地棉遗传图谱构建及产量和纤维品质性状QTL定位;陈利等;《作物学报》;20081231;第34卷(第7期);第1199-1205页 * |
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