Normal view MARC view ISBD view

Integrated linkage-linkage disequilibrium mapping for drought tolerance using global maize germplasm genotyped by two single nucleotide polymorphism chips

By: Lu, Y.L.
Contributor(s): Buckler, E.S | Crouch, J.H [coaut.] | Hao, Zhuanfang [coaut.] | Jianbing Yan | Li, J.S [coaut.] | Rong, T.Z [coaut.] | Shah, T [coaut.] | Taba, S [coaut.] | Zhang, S.H [coaut.] | Zhang, Z.W [coaut.] | Vivek, B [coaut.] | Mugo, S.N [coaut.] | Magorokosho, C [coaut.] | Yunbi Xu | Makumbi, D.
Material type: materialTypeLabelBookAnalytics: Show analyticsPublisher: 2009Description: p. 174.Summary: Drought is the most significant environment stress in agriculture worldwide and the first constraint to maize production. Improving yield under drought stress is a major goal in maize breeding. In this study, 535 temperate and tropical maize germplasm were phenotyped at vegetative and reproductive stages under well-watered and water-stressed regimes for 63 traits representing different selection criteria for drought tolerance, including biomass as measured as the normalized difference vegetation index (NDVI) with a portable spectroradiometer (GreenSeeker), anthesis-silking interval, leaf senescence, chlorophyll content, root capacitance, final grain yield and drought tolerance indix (DTI) (Xu et al, this conference). All tested lines were genotyped using two Illumina GoldenGate assay chips containing 3072 SNP makers that were designed from random sequences and the candidate genes related to drought tolerance. A total of 2139 informative SNPs were selected with high quality for population structure analysis and integrated linkage-linkage disequilibrium (LD) mapping. Seven major clusters identified by principal component (PC) analysis were consistent with geographic origins and pedigree information. Preliminary results from LD mapping using a general liner model combining PC-matrix identified 39 marker-trait associations involving 18 markers and 17 traits (P-marker value <10-8). Twelve of the 18 SNPs could be traced back to the genes that may relate to maize drought tolerance, such as those for starch synthase, sucrose synthase, terminal acidic SANT 1, phosphatidylserine decarboxylase, and phytochrome A2. Ten SNPs were co-associated with multiple traits that were phenotypically correlated, e.g, SNP PHM5716.60 on chromosome 3 associated with five correlated traits (ear number, ear weight, ear length, grain weight and flowing time). Nine traits were found each to be associated with more than two markers. For example, there were eight, five and two markers associated with ear weight, grain weight, and female flowering time, respectively. The average total variation explained by a marker is 7.0%, with the highest for SNP PZA03134.1 (18.1%) for DTI. Integrated linkage-LD mapping is underway and the results will be compared with those obtained by linkage-based mapping (Hao et al, this conference) and QTL reported in previous reports. The candidate gene-based SNP genotyping combined with the integrated linkage-LD mapping provides a powerful strategy for identifying genes associated with drought tolerance in maizeCollection: CIMMYT Staff Publications Collection
Tags from this library: No tags from this library for this title. Log in to add tags.
    average rating: 0.0 (0 votes)
Item type Current location Collection Call number Status Date due Barcode Item holds
Conference proceedings CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection CIS-5785 (Browse shelf) Available
Total holds: 0

Poster Abstract

Drought is the most significant environment stress in agriculture worldwide and the first constraint to maize production. Improving yield under drought stress is a major goal in maize breeding. In this study, 535 temperate and tropical maize germplasm were phenotyped at vegetative and reproductive stages under well-watered and water-stressed regimes for 63 traits representing different selection criteria for drought tolerance, including biomass as measured as the normalized difference vegetation index (NDVI) with a portable spectroradiometer (GreenSeeker), anthesis-silking interval, leaf senescence, chlorophyll content, root capacitance, final grain yield and drought tolerance indix (DTI) (Xu et al, this conference). All tested lines were genotyped using two Illumina GoldenGate assay chips containing 3072 SNP makers that were designed from random sequences and the candidate genes related to drought tolerance. A total of 2139 informative SNPs were selected with high quality for population structure analysis and integrated linkage-linkage disequilibrium (LD) mapping. Seven major clusters identified by principal component (PC) analysis were consistent with geographic origins and pedigree information. Preliminary results from LD mapping using a general liner model combining PC-matrix identified 39 marker-trait associations involving 18 markers and 17 traits (P-marker value <10-8). Twelve of the 18 SNPs could be traced back to the genes that may relate to maize drought tolerance, such as those for starch synthase, sucrose synthase, terminal acidic SANT 1, phosphatidylserine decarboxylase, and phytochrome A2. Ten SNPs were co-associated with multiple traits that were phenotypically correlated, e.g, SNP PHM5716.60 on chromosome 3 associated with five correlated traits (ear number, ear weight, ear length, grain weight and flowing time). Nine traits were found each to be associated with more than two markers. For example, there were eight, five and two markers associated with ear weight, grain weight, and female flowering time, respectively. The average total variation explained by a marker is 7.0%, with the highest for SNP PZA03134.1 (18.1%) for DTI. Integrated linkage-LD mapping is underway and the results will be compared with those obtained by linkage-based mapping (Hao et al, this conference) and QTL reported in previous reports. The candidate gene-based SNP genotyping combined with the integrated linkage-LD mapping provides a powerful strategy for identifying genes associated with drought tolerance in maize

Global Maize Program

English

Lucia Segura

INT2714|INT2735|INT2396|INT2460|INT2765

CIMMYT Staff Publications Collection

There are no comments for this item.

Log in to your account to post a comment.
baner

International Maize and Wheat Improvement Center (CIMMYT) © Copyright 2015. Carretera México-Veracruz. Km. 45, El Batán, Texcoco, México, C.P. 56237.
If you have any question, please contact us at CIMMYT-Knowledge-Center@cgiar.org

Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) © Copyright 2015. Carretera México-Veracruz. Km. 45, El Batán, Texcoco, México, C.P. 56237.
Si tiene cualquier pregunta, contáctenos a CIMMYT-Knowledge-Center@cgiar.org