WO2001049104A3 - Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations - Google Patents

Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations Download PDF

Info

Publication number
WO2001049104A3
WO2001049104A3 PCT/US2000/034971 US0034971W WO0149104A3 WO 2001049104 A3 WO2001049104 A3 WO 2001049104A3 US 0034971 W US0034971 W US 0034971W WO 0149104 A3 WO0149104 A3 WO 0149104A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
mapping
qtl
mqm
haplo
Prior art date
Application number
PCT/US2000/034971
Other languages
French (fr)
Other versions
WO2001049104A2 (en
Inventor
Ritsert C Jansen
William D Beavis
Original Assignee
Pioneer Hi Bred Int
Ritsert C Jansen
William D Beavis
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Pioneer Hi Bred Int, Ritsert C Jansen, William D Beavis filed Critical Pioneer Hi Bred Int
Priority to EP00989407A priority Critical patent/EP1265476A2/en
Priority to AU25915/01A priority patent/AU2591501A/en
Publication of WO2001049104A2 publication Critical patent/WO2001049104A2/en
Publication of WO2001049104A3 publication Critical patent/WO2001049104A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40—Population genetics; Linkage disequilibrium

Abstract

Methods for mapping a phenotypic trait to a corresponding chromosomal location are provided. Statistical methods which correlate pedigrees with multiple genetic markers, the haplotype, to determine identical-by-descent (IBD) data are employed to map phenotypic traits. The statistical models provided are a HAPLO-IM+ model, a HAPLO-MQM model, and a HAPLO-MQM+ model. These statistical methods are applied to map traits determined alternatively by single genes or by quantitative trait loci. Methods of marker assisted selection (MAS) using a variety of genetic markers are provided. Plants selected by MAS using the methods are provided. Additionally, methods for cloning nucleic acids corresponding to phenotypic traits that are in linkage disequilibrium with genetic markers are provided, and for transducing them into plant cells are provided. Transgenic plants transduced with the cloned nucleic acids corresponding to phenotypic traits, e.g. QTL, are provided.
PCT/US2000/034971 1999-12-30 2000-12-21 Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations WO2001049104A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP00989407A EP1265476A2 (en) 1999-12-30 2000-12-21 Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations
AU25915/01A AU2591501A (en) 1999-12-30 2000-12-21 Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mappingqtl's in plant breeding populations

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US17398599P 1999-12-30 1999-12-30
US60/173,985 1999-12-30
US17511700P 2000-01-06 2000-01-06
US60/175,117 2000-01-06
US18033000P 2000-02-04 2000-02-04
US60/180,330 2000-02-04

Publications (2)

Publication Number Publication Date
WO2001049104A2 WO2001049104A2 (en) 2001-07-12
WO2001049104A3 true WO2001049104A3 (en) 2002-08-15

Family

ID=27390364

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/034971 WO2001049104A2 (en) 1999-12-30 2000-12-21 Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations

Country Status (3)

Country Link
EP (1) EP1265476A2 (en)
AU (1) AU2591501A (en)
WO (1) WO2001049104A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105524993A (en) * 2016-01-12 2016-04-27 四川农业大学 Molecular marker HRM1 of barley grain length gene LkI1 and application of molecular marker

Families Citing this family (36)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
BR0209700A (en) 2001-06-07 2004-10-13 Pioneer Hi Bred Int Resistance to sclerotinia production by qtl control in soybean
CA2525956A1 (en) * 2003-05-28 2005-01-06 Pioneer Hi-Bred International, Inc. Plant breeding method
CA2531119A1 (en) * 2003-07-07 2005-02-17 Pioneer Hi-Bred International, Inc. Qtl "mapping as-you-go"
AR051673A1 (en) 2004-11-17 2007-01-31 Pioneer Hi Bred Int GENETIC LOCI ASSOCIATED WITH TOLERANCE TO SCLEROTINIA IN SOJA
AP2693A (en) 2005-05-27 2013-07-16 Monsanto Technology Llc Soybean event MON89788 and methods for detection thereof
AR063688A1 (en) 2006-08-15 2009-02-11 Monsanto Technology Llc COMPOSITIONS AND METHODS FOR PLANT PRODUCTION USING THE HIGH DENSITY MARKER INFORMATION
AU2008204740A1 (en) * 2007-01-12 2008-07-17 Monsanto Do Brasil Ltda. Microsatellite-based fingerprinting system for Saccharum complex
CL2008001682A1 (en) 2007-06-08 2008-12-12 Monsanto Technology Llc Methods for plant improvement through the use of direct nucleic acid sequence information.
BRPI0815841A2 (en) 2007-08-29 2015-09-01 Monsanto Technology Llc Methods and compositions for improving preferred traits.
US8900808B2 (en) 2008-07-15 2014-12-02 E.I. Du Pont De Nemours And Company Genetic loci associated with mechanical stalk strength in maize
US8321147B2 (en) 2008-10-02 2012-11-27 Pioneer Hi-Bred International, Inc Statistical approach for optimal use of genetic information collected on historical pedigrees, genotyped with dense marker maps, into routine pedigree analysis of active maize breeding populations
KR101674904B1 (en) 2009-02-26 2016-11-10 더 유니버시티 오브 노쓰 캐롤라이나 엣 채플 힐 Interventional drug delivery system and associated methods
US10555527B2 (en) 2009-05-18 2020-02-11 Monsanto Technology Llc Use of glyphosate for disease suppression and yield enhancement in soybean
CN103184277A (en) * 2011-12-30 2013-07-03 北京林业大学 Plum blossom genetic map construction method
AU2013235401A1 (en) 2012-03-20 2014-10-16 Dow Agrosciences Llc Molecular markers for low palmitic acid content in sunflower (Helianthus annus), and methods of using the same
CN102703586B (en) * 2012-05-18 2015-01-07 北京林业大学 Method for constructing Prunus mume Sieb.et Zucc SSR (simple sequence repeat) genetic map
CN102907312A (en) * 2012-11-02 2013-02-06 青岛农业大学 Breeding method for drought-resistant and high-yield wheat
EP2929070A4 (en) 2012-12-05 2016-06-01 Genepeeks Inc System and method for the computational prediction of expression of single-gene phenotypes
CN104004749B (en) * 2013-02-27 2016-05-04 中国农业科学院蔬菜花卉研究所 Chain SSR labeled primer and the application thereof of cucumber black fruit Ci Jiyin B
CN103882033B (en) * 2014-03-26 2016-04-20 湖南杂交水稻研究中心 Rice Panicle Traits regulatory gene PT2 and application thereof
CN104313149B (en) * 2014-10-22 2016-02-10 武汉市蔬菜科学研究所 A kind of being applicable to detects molecule marker and the application that Folium Raphani marginal slit carves proterties
CN105695478B (en) * 2014-12-09 2020-03-03 中国科学院上海生命科学研究院 Gene for regulating plant type and yield of plant and application thereof
CN105524994B (en) * 2016-01-12 2018-08-28 四川农业大学 The molecular labeling HRM7 of barley grain length gene Lkl2 a kind of and its application
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
CN107896972B (en) * 2017-11-09 2019-12-31 四川农业大学 Method for breeding perennial feeding coix seeds by distant hybridization
CN109468399A (en) * 2018-12-05 2019-03-15 中国科学院西北高原生物研究所 A kind of northwest spring wheat character is associated with label and the method for effect analysis
WO2021092251A1 (en) 2019-11-05 2021-05-14 Apeel Technology, Inc. Prediction of infection in plant products
CN110669865B (en) * 2019-11-06 2021-03-16 中国科学院武汉植物园 SSR molecular marker for identifying Thailand lotus germplasm and application
CN110698550B (en) * 2019-11-11 2021-07-06 北京林业大学 Molecular detection method for rapidly identifying real plum/apricot plum strain
CN111489790B (en) * 2020-04-02 2023-03-17 华中农业大学 RapMap method for rapidly and high-throughput positioning and cloning plant QTL gene
CN112593007B (en) * 2021-01-11 2022-07-01 四川农业大学 SNP molecular marker linked with wheat grain length QTL and application thereof
CN112941218B (en) * 2021-02-04 2022-10-04 湖北省农业科学院粮食作物研究所 Method for identifying authenticity of yam germplasm resources by virtue of cpPSSR molecular marker method
US20220254447A1 (en) * 2021-02-05 2022-08-11 Monsanto Technology Llc Intermediate recurrent parents, an accelerated and efficient multi-layer trait delivery system
ES2940627A1 (en) * 2021-08-12 2023-05-09 The State Of Israel Ministry Of Agriculture & Rural Development Agricultural Res Organization Aro Vo Methods to increase the yield of prunus dulcis and plants produced by the same. (Machine-translation by Google Translate, not legally binding)
CN113699268B (en) * 2021-09-02 2022-09-30 河北师范大学 Wheat thousand grain weight character related SNP site and application thereof
CN114752683B (en) * 2022-04-18 2023-08-08 广东海洋大学 Construction method of QTL locus related to sex characteristics of Sillago sihama

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999032661A1 (en) * 1997-12-22 1999-07-01 Pioneer-Hi-Bred International, Inc. Qtl mapping in plant breeding populations

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999032661A1 (en) * 1997-12-22 1999-07-01 Pioneer-Hi-Bred International, Inc. Qtl mapping in plant breeding populations

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
ALMASY L & BLANGERO J: "Multipoint quantitative-trait linkage analysis in general pedigrees", AMERICAN JOURNAL OF HUMAN GENETICS, vol. 62, no. 5, May 1998 (1998-05-01), pages 1198 - 1211, XP002201087 *
BUTRUILLE DAVID V ET AL: "Linkage analysis of molecular markers and quantitative trait loci in populations of inbred backcross lines of Brassica napus L.", GENETICS, vol. 153, no. 2, October 1999 (1999-10-01), pages 949 - 964, XP002201082, ISSN: 0016-6731 *
JANSEN RITSERT C ET AL: "A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families.", GENETICS, vol. 148, no. 1, January 1998 (1998-01-01), pages 391 - 399, XP002201085, ISSN: 0016-6731 *
JANSEN RITSERT C: "Complex plant traits: time for polygenic analysis", TRENDS IN PLANT SCIENCE, vol. 1, no. 3, March 1996 (1996-03-01), pages 89 - 94, XP002201088 *
RIQUET JULIETTE ET AL: "Fine-mapping of quantitative trait loci by identity by descent in outbred populations: Application to milk production in dairy cattle.", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES, vol. 96, no. 16, 3 August 1999 (1999-08-03), Aug. 3, 1999, pages 9252 - 9257, XP002201086, ISSN: 0027-8424 *
XIE C ET AL: "SIB MATING DESIGNS FOR MAPPING QUANTITATIVE TRAIT LOCI", GENETICA, KLUWER ACADEMIC PRESS, DORDRECHT, NL, vol. 1, no. 104, 1998, pages 9 - 19, XP001070508, ISSN: 0016-6707 *
XIE CHONGQING ET AL: "Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method.", GENETICS, vol. 149, no. 2, June 1998 (1998-06-01), pages 1139 - 1146, XP002201084, ISSN: 0016-6731 *
XU SHIZHONG: "Mapping quantitative trait loci using multiple families of line crosses.", GENETICS, vol. 148, no. 1, January 1998 (1998-01-01), pages 517 - 524, XP002201083, ISSN: 0016-6731 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105524993A (en) * 2016-01-12 2016-04-27 四川农业大学 Molecular marker HRM1 of barley grain length gene LkI1 and application of molecular marker

Also Published As

Publication number Publication date
EP1265476A2 (en) 2002-12-18
WO2001049104A2 (en) 2001-07-12
AU2591501A (en) 2001-07-16

Similar Documents

Publication Publication Date Title
WO2001049104A3 (en) Mqm mapping using haplotyped putative qtl-alleles: a simple approach for mapping qtl's in plant breeding populations
Ferris et al. Leaf stomatal and epidermal cell development: identification of putative quantitative trait loci in relation to elevated carbon dioxide concentration in poplar
Cheliak et al. Temporal variation of the mating system in a natural population of jack pine
Mestries et al. Analyses of quantitative trait loci associated with resistance to shape Sclerotinia sclerotiorum in sunflowers (shape Helianthus annuus L.) using molecular markers
Van Treuren et al. Relationships between plant density, outcrossing rates and seed set in natural and experimental populations of Scabiosa columbaria
Huether Jr Exposure of natural genetic variability underlying the pentamerous corolla constancy in Linanthus androsaceus ssp. androsaceus
See et al. Mapping genes controlling variation in barley grain protein concentration
Stebbins Variation and evolution in plants: progress during the past twenty years
Stojałowski et al. DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.)
Touzet et al. Combined genetic and physiological analysis of a locus contributing to quantitative variation
Nemoto et al. Inheritance of early elongation ability in floating rice revealed by diallel and QTL analyses
Surles et al. Mating systems in open-pollinated families of black locust (Robinia pseudoacacia)
Morgante et al. Selection against inbreds in early life-cycle phases in Pinus leucodermis Ant.
Klekowski Mutation rates in mangroves and other plants
Krauss Restricted gene flow within the morphologically complex species Persoonia mollis (Proteaceae): contrasting evidence from the mating system and pollen dispersal
CN101760541A (en) Principle of quantitative trait locus (QTL) positioning
Burczyk Mating system variation in a Scots pine clonal seed orchard
Mohammadi et al. QTL analysis for phenologic traits in doubled haploid population of barley
EL-KAssAY et al. Temporal Variation in the Outcrossing Rate in a Natural
Vickery Jr et al. Comparison of six approaches to the classification of Mimulus sect. Erythranthe (Scrophulariaceae)
Benson et al. Molecular identification of Malus hupehensis (Tea crabapple) accessions using simple sequence repeats
Tigerstedt Genetic adaptation of plants in the subarctic environment
Ng et al. Mating system and seed variation of Acacia hybrid (A. mangium× A. auriculiformis)
CN105624154A (en) Molecular marker of corn northern leaf blight resistant QTL and application thereof
Oxford et al. Variation in characters affecting fitness between radiate and non-radiate morphs in natural populations of groundsel (Senecio vulgaris L.)

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2000989407

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 2000989407

Country of ref document: EP

NENP Non-entry into the national phase

Ref country code: JP

WWW Wipo information: withdrawn in national office

Ref document number: 2000989407

Country of ref document: EP