Abstract
Seed nutrients in legumes are important for human health, particularly in developing countries with heavy reliance on plant-based diets, and among vegetarians in developed nations. Here, we report on our efforts to uncover the genetic basis underlying the phenotypic variation for protein, zinc, calcium concentrations, and iron bioavailability present in 206 accessions of dry bean (Phaseolus vulgaris L.) from the Andean Diversity Panel (ADP). We used 8111 single nucleotide polymorphisms (SNPs) generated with genotyping-by-sequencing (GBS) to examine the allelic variants’ associations with seed protein, zinc, and calcium concentrations, and iron bioavailability in the 206 ADP accessions grown over 2 years in Michigan. These efforts identified phenotypic variation among the ADP genotypes for each of the traits, with the highest variation (5.4-fold) found for cooked seed iron bioavailability. In addition, significant SNP-trait associations were found and explained from 6.3 to 13.2% of the phenotypic variation. These results expand the current understanding of the genetic architecture underlying these complex nutritional quality traits and iron bioavailability in dry beans. Furthermore, they have utility for future nutritional quality breeding efforts to better biofortify dry bean through genomics-assisted breeding.
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Abbreviations
- ADP:
-
Andean diversity panel
- BLASTN:
-
Basic local alignment search tool for nucleotides
- FeBIO:
-
Iron bioavailability
- GBS:
-
Genotyping-by-sequencing
- GLM:
-
General linear model
- GWAS:
-
Genome-wide association study
- LD:
-
Linkage disequilibrium
- MLM:
-
Mixed linear model
- PCA:
-
Principal component analysis
- Pv:
-
Phaseolus vulgaris chromosome
- QTL:
-
Quantitative trait loci
- RILs:
-
Recombinant inbred lines
- SNP:
-
Single nucleotide polymorphism
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Acknowledgements
We thank the Feed the Future Norman Borlaug Commemorative Research Initiative (NBCRI) Grain Legumes Project, a research partnership between US Agency for International Development (USAID) and the USDA-ARS, and the Feed the Future Innovation Lab for Collaborative Research on Grain Legumes by USAID as part of Feed the Future US Government’s global hunger and food security initiative, under the terms of Cooperative Agreement No. EDH-A-00-07-00005-00, for financial support. The contents of this publication do not necessarily reflect the views or policies of the US Department of Agriculture, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government.
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DNK designed the experiments, collected and analyzed data, and wrote the manuscript. JPH conducted genotyping and SNP calling and wrote manuscript. TGP conducted genotyping and reviewed the manuscript. MAG conducted mineral analysis and reviewed the manuscript. RPG conducted iron bioavailability analysis and reviewed the manuscript. KAC designed the experiments, collected data, and wrote and edited the manuscript.
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Supplemental Table S1
List of all Andean Diversity Panel dry bean genotypes and genotype by sequencing key (XLS 329 kb)
Supplemental Figure S1
Histogram showing the distribution of seed protein, zinc, iron, and iron bioavailability in the cooked dry bean seed samples of 206 ADP genotypes that were grown in Michigan, USA for two field seasons (PNG 233 kb)
Supplemental Figure S2
Histogram showing the distribution of seed potassium, calcium, phosphorus, and phytic acid concentration in the cooked dry bean seed samples of 206 ADP genotypes that were grown in Michigan, USA for two field seasons (PNG 224 kb)
Supplemental Figure S3
GLM-based Manhattan plots depicting genome-wide marker-trait association in cooked dry bean seeds protein concentration (A), zinc concentration (C), calcium concentration (E), and iron bioavailability (G) The cutoff (red horizontal line) is based on the qFDR ≤ 0.1 used to declare genome-wide significance. The Quantile-Quantile plots testing for model goodness of fit and SNP marker inflation of the GLM model of cooked dry bean seed samples for protein concentration (B), zinc concentration (D), calcium concentration (F), and iron bioavailability (H) are also provided. (PNG 1437 kb)
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Katuuramu, D.N., Hart, J.P., Porch, T.G. et al. Genome-wide association analysis of nutritional composition-related traits and iron bioavailability in cooked dry beans (Phaseolus vulgaris L.). Mol Breeding 38, 44 (2018). https://doi.org/10.1007/s11032-018-0798-x
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DOI: https://doi.org/10.1007/s11032-018-0798-x