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Large-scale phenotyping and genotyping of global maize germplasm and integrated linkage-linkage disequilibrium mapping for drought tolerance in maize

By: Yunbi Xu.
Contributor(s): Araus, J.L | Crouch, J.H [coaut.] | Gao, S.B [coaut.] | Guimaraes, C.T [coaut.] | Hao, Zhuanfang [coaut.] | Jianbing Yan | Li, J.S [coaut.] | Lu, Y.L [coaut.] | Rong, T.Z [coaut.] | Taba, S [coaut.] | Zhang, S.H [coaut.] | Vivek, B [coaut.] | Mugo, S.N [coaut.] | Magorokosho, C [coaut.] | Makumbi, D.
Material type: materialTypeLabelBookAnalytics: Show analyticsPublisher: 2009Description: p. 60.Summary: Characterization of genetic variation and identification of genes for drought tolerance is critical for improvement of maize adaptability. A total of 550 lines representing both temperate and tropical maize germplasm were evaluated for over 60 traits at vegetative and reproductive stages under both well-watered and water-stressed conditions. These lines include 220 recombinant inbred lines (RILs) from three populations and 106 backcrossed introgression lines (ILs) from 38 IL sets. Multiple drought tolerance criteria were screened for drought tolerance, including biomass before and after the drought stress as measured using the normalized difference vegetation index (NDVI), anthesis-silking interval, leaf senescence, chlorophyll content, root capacitance, final grain yield and drought tolerance index (DTI). Heritability estimates and genetic correlation among selection criteria indicate great potentiality of using NDVI for drought tolerance screening. The 45 lines with the best level of drought tolerance produced an average of more than 700 kernels per plot (Xu et al, this conference). All the tested lines have been genotyped using two SNP chips containing 3072 single nucleotide polymorphisms (SNPs), with 2139 informative and high-quality markers selected for genetic mapping. One of the SNP chips was developed from candidate genes related to drought tolerance. By linkage mapping using the three RIL populations, 179 quantitative trait loci were identified by composite interval mapping, explaining an average of 20.1% of the phenotypic variance. By linkage disequilibrium (LD)-based association mapping using 106 ILs, 46 marker-trait associations were identified. Two candidate genes for drought tolerance inferred from two SNPs were shared by both mapping methods (Hao et al, this conference). Preliminary results from LD mapping using all 535 lines (after excluding open-pollinated varieties) identified 39 marker-trait associations involving 18 markers and 17 traits (P-marker value <10-8). Twelve of the 18 SNPs can be traced back to genes with known function, which may relate to maize drought tolerance. 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 will be presented at the conference. 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.Collection: CIMMYT Staff Publications Collection
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Conference proceedings CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection CIS-5775 (Browse shelf) Available
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Abstract only

Characterization of genetic variation and identification of genes for drought tolerance is critical for improvement of maize adaptability. A total of 550 lines representing both temperate and tropical maize germplasm were evaluated for over 60 traits at vegetative and reproductive stages under both well-watered and water-stressed conditions. These lines include 220 recombinant inbred lines (RILs) from three populations and 106 backcrossed introgression lines (ILs) from 38 IL sets. Multiple drought tolerance criteria were screened for drought tolerance, including biomass before and after the drought stress as measured using the normalized difference vegetation index (NDVI), anthesis-silking interval, leaf senescence, chlorophyll content, root capacitance, final grain yield and drought tolerance index (DTI). Heritability estimates and genetic correlation among selection criteria indicate great potentiality of using NDVI for drought tolerance screening. The 45 lines with the best level of drought tolerance produced an average of more than 700 kernels per plot (Xu et al, this conference). All the tested lines have been genotyped using two SNP chips containing 3072 single nucleotide polymorphisms (SNPs), with 2139 informative and high-quality markers selected for genetic mapping. One of the SNP chips was developed from candidate genes related to drought tolerance. By linkage mapping using the three RIL populations, 179 quantitative trait loci were identified by composite interval mapping, explaining an average of 20.1% of the phenotypic variance. By linkage disequilibrium (LD)-based association mapping using 106 ILs, 46 marker-trait associations were identified. Two candidate genes for drought tolerance inferred from two SNPs were shared by both mapping methods (Hao et al, this conference). Preliminary results from LD mapping using all 535 lines (after excluding open-pollinated varieties) identified 39 marker-trait associations involving 18 markers and 17 traits (P-marker value <10-8). Twelve of the 18 SNPs can be traced back to genes with known function, which may relate to maize drought tolerance. 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 will be presented at the conference. 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

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