Abstract
Genetic diversity in plant breeding is key to dissecting the genetic architecture of complex economical traits. Genome-wide association studies (GWAS) and genomic selection (GS) have emerged as promising tools to accelerate agronomic trait improvement efficiency, defining current breeding strategies. The key objective of this study was to investigate the genetic architecture and perform genomic prediction of yield, specific gravity (SG), and dry matter (DM) traits, using a diversity panel of 568 Solanum tuberosum Andigenum accessions. Analyses were carried out using a total of 4271 Single Nucleotide Polymorphisms (SNPs) obtained using the SolCAP SNP array 8 K version. Yield data were collected from field evaluations during three consecutive years, while tuber quality traits (SG and DM) were evaluated in 1 year. To this end, population structure was first examined and revealed two main subpopulations. GWAS analysis identified candidate loci for yield in chromosomes 1, 3, 4 and 11, with minor effects on phenotypic variation (< 1–10%). Important genomic regions were detected for SG in chromosomes 5, 6, and 8, and in DM in chromosome 7, though they explained only a small fraction of the phenotypic variation (< 1–2% for SG and 3% for DM). Functional annotation of candidate genes showed promising genomic regions related to tuber growth, quality and development that could further be verified by other tools (i.e., gene editing). Furthermore, the predicted capacity of the cross-validation process between subpopulations was low for yield and specific gravity. However, when the prediction process was conducted across the entire population, the predictive power increase, as a greater diversity in the data enables better prediction. Instead, dry matter genomic prediction accuracies were higher in accordance with its higher narrow sense heritability value. These findings enriched GWAS analyses in an Andigenum potato collection and reinforce the potential of applying GS in Colombian breeding programs using diverse populations.
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The datasets generated during and/or analysed during the current study are available from the first author on reasonable request.
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Acknowledgements
The authors gratefully acknowledge Raul Iván Valbuena-Benavides as the CCC collection leader and curator; he designed and developed the field trials. Furthermore, the authors want to acknowledge Arturo Díaz and Hugo Gómez for their collaboration in the field trials and Shane Teachworth for copy editing.
Funding
This research was supported by the Ministerio de Agricultura y Desarrollo Rural of Colombia under the project “BGA Conservación en Campo BG Vegetal” with 1002443 code, managed by Agrosavia.
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FEE-R, LFF, JB-C and GAG-M conceived the study. ZLL-P and BCO collected, generated, and organized yield and quality data. GAG-M and FEE-R organized and analysed the phenotypic data. JB-C organized and generated the SNP data. CFA performed the GWAS and Genomic selection analysis. The first draft of the manuscript was written by GAG-M, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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10681_2024_3337_MOESM2_ESM.tiff
(A) Delta K value estimated using the Evanno method (Evanno et al. 2005) and (B) Optimal number of clusters determined by the Silhouette method. (TIFF 217 KB)
10681_2024_3337_MOESM3_ESM.tiff
Boxplots showing the effect of the significant markers associated with (A) Yield, (B) Specific gravity and (C) Dry matter. The letters on the X axis represent allele variants and p represents the variation across variants, 0: AAAA, 1: AAAB, 2: AABB, 3: ABBB or 4: BBBB. (TIFF 111220 KB)
10681_2024_3337_MOESM4_ESM.tiff
Partitioning of the genetic variance for three traits; yield, specific gravity and dry matter. Vg represents additive variance; Vge represents the interaction between year and genotype, and Ve represents residual genetic variance. (TIFF 4903 KB)
10681_2024_3337_MOESM5_ESM.xlsx
List of accessions of the diversity panel from the Colombian Central Collection of S. tuberosum group Andigenum used in this study. (XLSX 40 KB)
10681_2024_3337_MOESM6_ESM.xlsx
List of all QTLs identified by year for the diversity panel from the Colombian Central Collection of S. tuberosum group Andigenum. AD: additive, DOM: 1-dominant, DD: 2-dominant, DGEN: diplo-General, GEN: General. (XLSX 16 KB)
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Garzón-Martínez, G.A., Azevedo, C.F., Berdugo-Cely, J.A. et al. Genetic dissection of yield and quality-related traits in a Colombian Andigenum potato collection, revealed by genome-wide association and genomic prediction analyses. Euphytica 220, 79 (2024). https://doi.org/10.1007/s10681-024-03337-y
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DOI: https://doi.org/10.1007/s10681-024-03337-y