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Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize

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Abstract

Drought often delays developmental events so that plant height and above-ground biomass are reduced, resulting in yield loss due to inadequate photosynthate. In this study, plant height and biomass measured by the Normalized Difference Vegetation Index (NDVI) were used as criteria for drought tolerance. A total of 305 lines representing temperate, tropical and subtropical maize germplasm were genotyped using two single nucleotide polymorphism (SNP) chips each containing 1536 markers, from which 2052 informative SNPs and 386 haplotypes each constructed with two or more SNPs were used for linkage disequilibrium (LD) or association mapping. Single SNP- and haplotype-based LD mapping identified two significant SNPs and three haplotype loci [a total of four quantitative trait loci (QTL)] for plant height under well-watered and water-stressed conditions. For biomass, 32 SNPs and 12 haplotype loci (30 QTL) were identified using NDVIs measured at seven stages under the two water regimes. Some significant SNP and haplotype loci for NDVI were shared by different stages. Comparing significant loci identified by single SNP- and haplotype-based LD mapping, we found that six out of the 14 chromosomal regions defined by haplotype loci each included at least one significant SNP for the same trait. Significant SNP haplotype loci explained much higher phenotypic variation than individual SNPs. Moreover, we found that two significant SNPs (two QTL) and one haplotype locus were shared by plant height and NDVI. The results indicate the power of comparative LD mapping using single SNPs and SNP haplotypes with QTL shared by plant height and biomass as secondary traits for drought tolerance in maize.

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Abbreviations

abph1:

Aberrant phyllotaxy1

ALDH:

Aldehyde dehydrogenase

ASI:

Anthesis–silking interval

CAAS:

Chinese Academy of Agricultural Sciences

CIMMYT:

International Maize and Wheat Improvement Center

DAP:

Days after planting

DT chip:

Drought tolerance candidate gene based chip

GWAS:

Genome-wide association study

HP:

Haplotype

IL:

Introgression line

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

MLM:

Mixed linear model

NDVI:

Normalized Difference Vegetation Index

NIR:

Near infrared region

OPA:

Oligo pool assay

PC:

Principal component

PCA:

Principal component analysis

PH:

Plant height

PIC:

Polymorphism information content

RA chip:

Random candidate gene based chip

SNP:

Single nucleotide polymorphism

VIS:

Visible region

WS:

Water-stressed

WW:

Well-watered

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Acknowledgments

The SNP chips used in this study were developed through a collaborative project between Cornell University (Ed Buckler and Tim Setter) and CIMMYT (Marilyn Warburton and Jianbing Yan). Maize drought tolerance work was funded by the Rockefeller Foundation, Bill and Melinda Gates Foundation, Generation Challenge Programme, European Community, National High Technology Research and Development Program of China (No. 2009AA10AA03-2) and National Basic Research Program of China (No.2007CB108900).

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Authors and Affiliations

  1. Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China

    Yanli Lu, Jie Xu, Zhimin Yuan, Hai Lan & Tingzhao Rong

  2. Institute of Crop Science/International Maize and Wheat Improvement Center (CIMMYT), National Key Facilities for Crop Genetic Resources and Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Yunbi Xu

  3. Institue of Crop Science, National Key Facilities for Crop Genetic Resources and Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Zhuanfang Hao, Chuanxiao Xie, Xinhai Li & Shihuang Zhang

  4. International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, 502324, Andhra Pradesh, India

    Trushar Shah

  5. CIMMYT, Km 45, Carretera, Mexico-Veracruz, El Batan, Texcoco, Mexico

    Yanli Lu & Yunbi Xu

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  1. Yanli Lu
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Corresponding authors

Correspondence to Tingzhao Rong or Yunbi Xu.

Electronic supplementary material

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11032_2011_9631_MOESM1_ESM.xls

List of 305 maize inbred lines used in the study. Information provided in this supplemental table includes ID, brief name, sample name, origin, adaptation, kernel color, and kernel texture (XLS 155 kb)

11032_2011_9631_MOESM2_ESM.xls

Putative candidate genes for significant loci identified by single SNP-based and haplotype-based linkage disequilibrium (LD) mapping. WW: well-watered; WS: water-stressed. *Significant loci identified by both single SNP- and haplotype-based LD mapping. Gene identification numbers, positions and functions were based on maize B73 genome (http://www.maizesequence.org) and NCBI website (http://www.ncbi.nlm.nih.gov/) (XLS 32 kb)

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Lu, Y., Xu, J., Yuan, Z. et al. Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize. Mol Breeding 30, 407–418 (2012). https://doi.org/10.1007/s11032-011-9631-5

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