Abstract
Phenology is one of the most relevant traits for crop development since the duration and timing of plant developmental phases has direct consequences for yield potential. The relative timing of development is even more important in temperate conditions where cool season crops are planted under short days. Our objective was to identify the genomic regions associated with phenology in barley germplasm representative of breeding and production in the Southern Cone of South America. The germplasm was phenotyped for pre-anthesis and post-anthesis phase duration (and photoperiod sensitivity) in nine field experiments evaluated over four years in two locations. The population was genotyped with 1028 SNPs. A comprehensive GWAS was performed and QTL were detected for all traits. Genomic regions were associated with multiple phenology traits in multiple environments. Twenty-five QTL were identified, most of which were associated with more than one trait and/or to the same trait in a different environment. Some of the QTL could be associated with modifications of phase length (PL) or photoperiod sensitivity (PR) and others with both types of response. These findings provide an understanding of phenology in barley in temperate regions and can serve as a starting point for future research into specific genomic regions.
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Abbreviations
- SE:
-
Seedling emergence
- GDD:
-
Growing degree days
- PL:
-
Phase length
- PR:
-
Photoperiod sensitivity or response
- LD:
-
Linkage disequilibrium
- SEA:
-
Single-environment analysis
- MEMQ:
-
Multi-environment multi-QTL analysis
- ME:
-
Marker effect
- GE:
-
Global effect
- PRA:
-
Phase-reducing allele
- PIA:
-
Phase-increasing allele
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Acknowledgements
This research was funded by competitive grants awarded by the Instituto Nacional de Investigación Agropecuaria, Uruguay (FPTA 227), the Fondo Regional de Tecnología Agropecuaria (FONTAGRO, www.fontagro.org) (Project FTG-05617-06), and the Universidad de la República (Programa CSIC Grupos), Uruguay. The authors wish to thank Dr. Patrick M. Hayes (Oregon State University) and Dr. Kevin Smith (University of Minnesota) for their contributions to this research. We also want to express our appreciation for the comments of several anonymous reviewers, which helped to vastly improve our manuscript.
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10681_2022_2993_MOESM1_ESM.tif
Supplementary Figure 1 Phenotypic distribution of the traits evaluated in each experiment. Below each graph the corresponding statistics are displayed (TIF 6901 kb)
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Supplementary Figure 2 Intra-chromosomal LD (r2) decay of marker pairs over all chromosomes as a function of genetic distance (cM). The horizontal line (red dotted line) indicates the 95th percentile distribution of unliked r2). The fitting curve (green line) indicates the LD decay. The vertical line (blue dotted line) indicates the genetic distance value (2.54) when the fitting curve cross the critical r2 value (0.2) (TIF 1223 kb)
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Supplementary Figure 3 Circular-Manhattan plot of [−log 10 (P-values)] vs chromosomal position of SNP markers associated with each of the phenological traits evaluated, either as LP (a) or PR (b). Black-dashed line represents the association threshold p < 0.005; (−log10 (P-values) ? 2.3. The scale (−log10 (P-values) is shown from the center to the top of the figures. Each marker-trait association above the threshold is represented by red points. The most important markers detected by SEA and MEMQ are highlighted. The rings represent the seven phenological traits evaluated (TIF 16085 kb)
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Supplementary Figure 4. Correlations matrix among traits evaluated in each experiment. The distribution and H2 of each trait are shown on the diagonal. GDD for each phenological phase are displayed on the axes. Broad sense heritability estimates (displayed on the bottom of each histogram) were calculated following Piepho and Möhring 2007. On the bottom of the diagonal the bivariate scatter plot with a fitted line was presented. On the top of the diagonal the correlation value (Pearson method) plus the significance level as stars are shown. Each significance level is associated with a symbol: p-values (0.001, 0.01, 0.05, 0.1, 1) (“***”, “**”, “*”, “.”, “ ”) (TIF 16008 kb)
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Supplementary Figure 5 Pairwise Spearman correlation among experiments for Z20-Z30, Z30-Z49, SE-Z49 and Z49-Z90 generated with corrplot package (version 0.88) in R, using corrplot function. The colors represent the correlation sign (blue and red, positive and negative correlation, respectively) (* P <0.01; ** P <0.001; *** P <0.0001) (TIF 1467 kb)
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Supplementary Figure 6 Principal component analysis of the population using all informative SNPs, highlighting the genotypes involved in the LD among chromosomes. In the main LD complex, the genotypes with allele "0" for the markers; 11_20032 (2H), 11_20130 (3H), 11_10177 (5H), 11_20230 and 11_20103 (7H) were grouped together in the PCA analysis (red points). In the other LD complex, the genotypes with allele "0" for markers; 1120838 and 1120053 were also grouped together in the PCA analysis (blue points). The rest of the genotypes had other allelic combinations for the mentioned markers (grey points) (TIFF 894 kb)
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Locatelli, A., Bhatta, M., Gutiérrez, L. et al. Genetic control of barley phenology in South American environments. Euphytica 218, 53 (2022). https://doi.org/10.1007/s10681-022-02993-2
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DOI: https://doi.org/10.1007/s10681-022-02993-2