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Association mapping identifies loci for canopy temperature under drought in diverse soybean genotypes

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Abstract

Drought stress is a global constraint for crop production, and improving crop tolerance to drought is of critical importance. Because transpiration cools a crop canopy, a cool canopy under drought indicates a genotype still has access to soil moisture. Because measurements of canopy temperature may be increased in scale in field environments, it is particularly attractive for large-scale, phenotypic evaluations. Our objectives were to identify genomic regions associated with canopy temperature (CT) and to identify extreme genotypes for CT. A diverse panel consisting of 345 maturity group IV soybean accessions was evaluated in three environments for CT. Within each environment CT was normalized (nCT) on a scale from 0 to 1. A set of 31,260 polymorphic single nucleotide polymorphisms (SNPs) with a minor allele frequency ≥ 5% was used for association mapping of nCT. Association mapping identified 52 SNPs significantly associated with nCT, and these SNPs likely tagged 34 different genomic regions. Averaged across all environments, eight genomic regions showed significant associations with nCT. Several genes in the identified genomic regions had reported functions related to transpiration or water acquisition including root development, response to abscisic acid, water deprivation, stomatal complex morphogenesis, and signal transduction. Fifteen of the SNPs associated with nCT were coincident with SNPs for canopy wilting. Favorable alleles from significant SNPs may be an important resource for pyramiding genes, and several genotypes were identified as sources of drought-tolerant alleles that could be used in breeding programs for improving drought tolerance.

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Abbreviations

AAE:

Across all environments

BLUP:

Best unbiased linear prediction

CT:

Canopy temperature

GEBV:

Genomic estimated breeding value

GWAM:

Genome-wide association mapping

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

nCT:

Normalized canopy temperature

QTLs:

Quantitative trait loci

SNPs:

Single nucleotide polymorphisms

TAGV:

True additive genetic value

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Acknowledgements

The authors gratefully acknowledge partial funding of this research from the United Soybean Board. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. The USDA is an equal opportunity provider and employer. Appreciation is also extended to Marilynn Davies and Jody Hedge for excellent technical assistance (Grant No. 1820-172-0118-A).

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Authors and Affiliations

  1. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA

    Avjinder S. Kaler, C. Andy King & Larry C. Purcell

  2. Crop Genetics Research Unit, USDA-ARS, 141 Experimental Station Road, Stoneville, MS, 38776, USA

    Jeffery D. Ray

  3. Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA

    William T. Schapaugh & Antonio R. Asebedo

  4. Agriculture Statistics Lab, University of Arkansas, Fayetteville, AR, 72701, USA

    E. E. Gbur

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  1. Avjinder S. Kaler
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Correspondence to Larry C. Purcell.

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Kaler, A.S., Ray, J.D., Schapaugh, W.T. et al. Association mapping identifies loci for canopy temperature under drought in diverse soybean genotypes. Euphytica 214, 135 (2018). https://doi.org/10.1007/s10681-018-2215-2

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