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Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number

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Abstract

Key message

GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number.

Abstract

Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa. The panel genotyped with the 90 K Illumina Infinitum SNP array resulted in 26,814 SNPs for genome-wide association study (GWAS). Statistical analysis of the multi-environmental data for GY, GN, and TGW observed repeatability estimates of 0.76, 0.62, and 0.95, respectively. GWAS on BLUPs of combined environment analysis identified 38 loci associated with the traits. Among them four loci—6A (85 cM), 5A (98 cM), 3B (99 cM), and 2B (96 cM)—were associated with multiple traits. The study identified two loci that showed positive association between GY and TGW, with allelic substitution effects of 4% (GY) and 1.7% (TGW) for 6A locus and 0.2% (GY) and 7.2% (TGW) for 2B locus. The locus in chromosome 6A (79–85 cM) harbored a gene TaGW2-6A. We also identified that a combination of markers associated with GY, TGW, and GN together explained higher variation for GY (32%), than the markers associated with GY alone (27%). The marker-trait associations from the present study can be used for marker-assisted selection (MAS) and to discover the underlying genes for these traits in spring wheat.

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  • 16 February 2018

    Unfortunately, the Fig. 1 of this original article was incorrectly published. The corrected Fig. 1 is given below.

Abbreviations

WAMI:

The wheat association Mapping Initiative

BLUPs:

Best linear unbiased predictions

MLM:

Mixed linear models

GLM:

Generalized linear models

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Acknowledgements

This work was implemented by CIMMYT as part of the MasAgro in collaboration with CIMMYT, made possible by the generous support of SAGARPA, IWYP, and ARCADIA Any opinions, findings, conclusion, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of SAGARPA, IWYP, and ARCADIA.

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Authors and Affiliations

Authors

Contributions

SS, MR, ML conceived the study. SS, MR, SD genotyped the panel. SS did the genetic analysis and wrote the manuscript. All authors read, made constructive comments, and approved the manuscript.

Corresponding author

Correspondence to Sivakumar Sukumaran.

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The authors declare no conflict of interest.

Additional information

Communicated by Mark E. Sorrells.

A correction to this article is available online at https://doi.org/10.1007/s00122-018-3066-x.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2017_3037_MOESM1_ESM.tif

Supplementary material 1 (TIFF 1449 kb) Supplementary Fig. 1. Linkage disequilibrium (LD) plot of the chromosome 3B region showing high LD of the markers associated with the traits. Markers used were RAC875_c1997_2590 (85 cM), RAC875_c5427_447 (91 cM), BobWhite_c35398_181 (95 cM), and wsnp_CAP12_c2297_1121142 (119 cM)

122_2017_3037_MOESM2_ESM.tif

Supplementary material 2 (TIFF 1770 kb) Supplementary Fig. 2. Linkage disequilibrium (LD) plot of the chromosome 6A showing the high LD region (77–85 cM). Markers in chromosome 6A were wsnp_Ra_c61979_62215037 (77 cM), wsnp_Ku_rep_c72681_72356010 (78 cM), wsnp_Ra_rep_c100410_86374467 (79 cM), wsnp_Ku_rep_c112734_95776957 (80 cM), wsnp_Ex_c34545_42832894 (81 cM), wsnp_RFL_Contig4424_5193532 (82 cM), wsnp_Ex_c341_667884 (83 cM), wsnp_Ku_c4296_7807837 (84 cM), wsnp_Ra_c11269_18309313 (85 cM) and Excalibur_rep_c111263_307 (86 cM)

122_2017_3037_MOESM3_ESM.tif

Supplementary material 3 (TIFF 1756 kb) Supplementary Fig. 3. Linkage disequilibrium plot (LD) of the 5A region 90–98 cM showing the SNP at 98 cM is not in high LD with the SNPs from 89–98 cM. Markers in chromosome 5A were wsnp_Ra_c12183_19587379 (89 cM), wsnp_Ex_c5998_10513766 (90 cM), wsnp_Ex_rep_c66689_65010988 (91 cM), wsnp_RFL_Contig2265_1693968 (92 cM), wsnp_Ex_rep_c109532_92292121 (93 cM), wsnp_Ra_c3966_7286546 (94 cM), IAAV108 (95 cM), wsnp_BF484028B_Td_2_1 (96 cM), wsnp_Ex_c790_1554988 (97 cM), and wsnp_Ku_c42416_50159250 (98 cM)

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Sukumaran, S., Lopes, M., Dreisigacker, S. et al. Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number. Theor Appl Genet 131, 985–998 (2018). https://doi.org/10.1007/s00122-017-3037-7

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