Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat

Abstract

Key message

GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated.

Abstract

Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding.

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Abbreviations

BLUE:

Best linear unbiased estimation

FarmCPU:

Fixed and random model circulating probability unification

GWAS:

Genome-wide association study

GY:

Grain yield

H 2 :

Broad-sense heritability

KASP:

Kompetitive allele-specific PCR

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

MAS:

Marker-assisted selection

MTA:

Marker-trait association

NIRS:

Near-infrared spectroscopy

PIC:

Polymorphism information content

QTL:

Quantitative trait locus/loci

SWSCC:

Stem water-soluble carbohydrate content

TKW:

Thousand-kernel weight

WSC:

Water-soluble carbohydrate

WSC10:

Stem WSC content at 10 days post-anthesis

WSC20:

Stem WSC content at 20 days post-anthesis

WSC30:

Stem WSC content at 30 days post-anthesis

YHVWWZ:

Yellow and Huai Valleys Winter Wheat Zone

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Acknowledgements

The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for review of this manuscript. This work was funded by the National Key Research and Development Programs of China (2016YFD0101804, 2016YFD0101802), National Natural Science Foundation of China (31461143021, 31671691), and CAAS Science and Technology Innovation Program.

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LF performed the experiments, analyzed data, and wrote the manuscript; SY, YJ, MY and YZ participated in field trials; RJ and JW provided assistance for stem WSC content assays; JW assisted in marker development; JL and JW assisted in data analysis; YX, XX and ZH designed the experiment. YX, XX, AR and ZH assisted in writing the manuscript.

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Correspondence to Zhonghu He or Yonggui Xiao.

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Fu, L., Wu, J., Yang, S. et al. Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat. Theor Appl Genet (2020). https://doi.org/10.1007/s00122-020-03640-x

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