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Open AccessArticle

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean

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Department of Field Crops, Faculty of Agricultural and Natural Science, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey
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Department of Horticulture, Faculty of Agriculture and Natural Sciences, Bolu Abant Izzet Baysal University, Bolu 14000, Turkey
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Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey
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Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas 58140, Turkey
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Department of Horticulture, Faculty of Agricultural, Tokat Gaziosmanpasa University, Tokat 60010, Turkey
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CREA Research Center for Cereal and Industrial Crops, 40128 Bologna, Italy
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School of life Sciences, The Chinese university of Hong Kong, Shatin, 999077, N.T., Hong Kong, China
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Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana 1000, Turkey
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Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok 690950, Russian
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Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Division of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea
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Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea
*
Authors to whom correspondence should be addressed.
Genes 2020, 11(1), 36; https://doi.org/10.3390/genes11010036
Received: 11 November 2019 / Revised: 20 December 2019 / Accepted: 24 December 2019 / Published: 28 December 2019
(This article belongs to the Special Issue Genetic Improvement of Cereals and Grain Legumes)
Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity. View Full-Text
Keywords: Phaseolus vulgaris; germplasm characterization; GWAS; genetic basis; genotype by environment interaction; mixed linear model Phaseolus vulgaris; germplasm characterization; GWAS; genetic basis; genotype by environment interaction; mixed linear model
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    Description: Table S1. Passport data of Turkish common bean germplasm used in this study Table S2. Antioxidant activity (µmol TE/g fw) in four environments for Turkish common bean germplasm Table S3. Comparison of mean, maximum and minimum for antioxidant activity (µmol TE/g fw) between Turkish common bean landraces and commercial cultivars under four environments
MDPI and ACS Style

Nadeem, M.A.; Gündoğdu, M.; Ercişli, S.; Karaköy, T.; Saracoğlu, O.; Habyarimana, E.; Lin, X.; Hatipoğlu, R.; Nawaz, M.A.; Sameeullah, M.; Ahmad, F.; Jung, B.-M.; Chung, G.; Baloch, F.S. Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean. Genes 2020, 11, 36.

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