Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits
Abstract
:1. Introduction
2. Results
2.1. Variability in Agronomic Traits of Assessed Genotypes
2.2. Genotype and Genotype × Year Interaction Effects on Agronomic Traits of D. alata Accessions
2.3. Population Structure Analysis and Genetic Diversity Pattern in 188 Accessions of D. alata Using Molecular-Based SNP Markers
2.4. Discriminant Analysis of Principal Components (DAPC)
2.5. Genetic Diversity within Groups and Population Using Molecular-Based SNP Data
3. Discussion
3.1. Genetic Diversity of D. alata Accessions from CNRA Genebank Using Molecular Data
3.2. Agronomic Trait Variations over Years for D. alata Accessions
3.3. Agronomic Performance of D. alata Genotypes within and among Defined Clusters
3.4. Broad-Sense Heritability for Agronomic Traits
4. Materials and Methods
4.1. Experimental Site
4.2. Plant Material and Experimental Design
4.3. Phenotypic Data Collection
4.4. Collection and Preparation of Leaf Samples of D. alata Accessions for Genotyping
4.5. Genotyping and SNP Marker Quality Control
4.6. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Agronomic Traits | Year of Assessment | Statistical Test | ||
---|---|---|---|---|
2018 | 2019 | F | p-Value | |
Yield (t ha−1) | 8.71 ± 5.19 a | 7.43 ± 3.46 b | 8.11 | 0.004 |
ADSS | 2.43 ± 0.49 b | 3.08 ± 0.61 a | 118.22 | <0.001 |
Tuber length (cm) | 15.63 ± 3.71 b | 16.94 ± 4.22 a | 10.39 | 0.001 |
Tuber width (cm) | 8.91 ± 1.65 b | 11.58 ± 2.58 a | 143.48 | <0.001 |
Tuber circumference (cm) | 21.80 ± 4.16 b | 23.58 ± 5.17 a | 14.27 | <0.001 |
Dry matter content (%) | 27.83 ± 3.27 b | 30.91 ± 4.82 a | 51.16 | <0.001 |
VPR (%) | 40.12 ± 26.78 a | 25.65 ± 26.75 b | 26.71 | <0.001 |
MVPR (%) | 51.64 ± 25.05 a | 37.76 ± 21.99 b | 29.74 | <0.001 |
WVPR (%) | 8.37 ± 15.58 b | 36.01 ± 27.40 a | 140.46 | <0.001 |
Wilks’ lambda | - | - | 0.175 | <0.001 |
Agronomic Trait | Genotype | Year | Genotype × Year | H2 |
---|---|---|---|---|
Yield (t ha−1) | 6243.00 *** | 573.00 *** | 1042.00 ns | 0.72 |
ADSS | 166.25 *** | 70.42 *** | 61.74 *** | 0.74 |
Length (cm) | 8696.00 *** | 379.00 *** | 2122.00 *** | 0.56 |
Width (cm) | 2368.60 *** | 1389.70 *** | 860.80 *** | 0.79 |
Circumference (cm) | 11,225.00 *** | 728.00 *** | 3484.00 *** | 0.62 |
Dry matter content (%) | 6945.00 *** | 501.00 *** | 1399.00 ns | 0.72 |
VPR (%) | 296,970.00 ** | 28,334.00 *** | 182,861.00 ns | 0.80 |
MVPR (%) | 214,054.00 ns | 29,728.00 *** | 164,661.00 ns | 0.71 |
WYPR (%) | 214,404.00 *** | 113,915.00 *** | 106,119.00 * | 0.74 |
Agronomic Traits | Cluster 1 (n = 41) | Cluster 2 (n = 69) | Cluster 3 (n = 42) | Cluster 4 (n = 36) | CV (%) | Statistical Tests | |
---|---|---|---|---|---|---|---|
F | p | ||||||
Yield (t ha−1) | 7.17 ± 4.53 a | 6.47 ± 3.72 ab | 5.98 ± 3.71 b | 6.26 ± 3.65 b | 60.21 | 2.80 | 0.039 |
ADSS | 2.77 ± 0.70 ab | 2.71 ± 0.72 b | 2.91 ± 0.73 a | 2.65 ± 0.62 b | 25.53 | 3.95 | 0.008 |
Length (cm) | 17.88 ± 4.87 a | 15.82 ± 3.97 b | 15.47 ± 4.42 b | 16.06 ± 4.27 b | 26.74 | 9.54 | <0.001 |
Width (cm) | 10.47 ± 2.78 a | 10.60 ± 2.86 a | 9.77 ± 3.01 b | 10.05 ± 2.66 ab | 27.69 | 3.27 | 0.021 |
Circumference (cm) | 23.25 ± 5.04 a | 23.32 ± 5.32 a | 21.38 ± 5.32 b | 22.47 ± 5.39 ab | 23.26 | 5.15 | 0.001 |
DMC (%) | 28.65 ± 3.88 a | 28.89 ± 3.84 a | 27.49 ± 4.11 b | 29.25 ± 3.74 a | 13.61 | 6.18 | <0.001 |
VPR (%) | 36.48 ± 36.92 | 32.28 ± 35.66 | 28.22 ± 34.14 | 32.84 ± 36.48 | 110.44 | 1.40 | 0.239 |
MVPR (%) | 45.40 ± 34.22 | 48.92 ± 33.67 | 43.65 ± 34.10 | 45.29 ± 34.88 | 73.72 | 0.90 | 0.438 |
WYPR (%) | 18.11 ± 26.23 b | 19.06 ± 27.01 b | 28.02 ± 33.20 a | 21.86 ± 29.12 ab | 134.28 | 4.09 | 0.007 |
Wilks’ lambda | 2.93 | <0.001 |
Grouping Pattern | Na | AP | I | MVF | Ho | He | Fis | PIC | MAF |
---|---|---|---|---|---|---|---|---|---|
Population (n = 188) | 23,444 | 0.00 | 0.34 | 1.63 × 10−5 | 0.294 | 0.158 | −0.398 | 0.276 | 0.209 |
Cluster 4 (n = 38) | 21,669 | 0.00 | 0.25 | 0.004 | 0.185 | 0.096 | −0.927 | 0.154 | 0.093 |
Cluster 3 (n = 43) | 21,798 | 0.00 | 0.28 | 0.007 | 0.211 | 0.138 | −0.529 | 0.183 | 0.115 |
Cluster 1 (n = 26) | 21,153 | 0.00 | 0.29 | 0.008 | 0.227 | 0.121 | −0.876 | 0.184 | 0.116 |
Cluster 2 (n = 81) | 23,442 | 175.00 | 0.54 | 0.022 | 0.259 | 0.278 | 0.068 | 0.270 | 0.202 |
Hardy–Weinberg Equilibrium Test | Mann–Whitney U Test | |||||
---|---|---|---|---|---|---|
Clusters | Proportion (%) of SNP Markers | Mean Rank | Statistical Tests | |||
Significant | No Significant | Ho | He | U × 105 | p | |
Cluster 4 | 62.81 | 37.19 | 3346.40 | 3249.24 | 52.08 | <0.037 |
Cluster 3 | 70.54 | 29.46 | 3543.78 | 2792.65 | 35.16 | <0.001 |
Cluster 1 | 66.67 | 33.33 | 3442.60 | 2724.33 | 34.58 | <0.001 |
Cluster 2 | 48.71 | 51.29 | 3857.80 | 4617.80 | 73.75 | <0.001 |
Population | 62.18 | 37.82 | 5013.12 | 3517.88 | 59.065 | <0.001 |
Nei’s Genetic Distance and Fixation Index (FST) | Analysis of Molecular Variance (AMOVA) | ||||||||
---|---|---|---|---|---|---|---|---|---|
Clusters | Nei’s Distance | FST | Sources | df | SS | MS | Variance | Variance % | |
3-4 | 0.61 | 0.42 | Among clusters | 3 | 239,269.83 | 79,756.61 | 1825.43 | 61.29 | |
1-4 | 0.37 | 0.29 | Within clusters | 184 | 212,132.69 | 1152.90 | 1152.90 | 38.71 | |
2-4 | 0.31 | 0.24 | Statistical tests | phiPT | 0.61 | ||||
1-3 | 0.45 | 0.34 | P | 0.001 | |||||
2-3 | 0.24 | 0.20 | |||||||
2-1 | 0.30 | 0.23 |
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Bakayoko, L.; Pokou, D.N.; Kouassi, A.B.; Agre, P.A.; Kouakou, A.M.; Dibi, K.E.B.; Nzue, B.; Mondo, J.M.; Adebola, P.; Akintayo, O.T.; et al. Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits. Plants 2021, 10, 2562. https://doi.org/10.3390/plants10122562
Bakayoko L, Pokou DN, Kouassi AB, Agre PA, Kouakou AM, Dibi KEB, Nzue B, Mondo JM, Adebola P, Akintayo OT, et al. Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits. Plants. 2021; 10(12):2562. https://doi.org/10.3390/plants10122562
Chicago/Turabian StyleBakayoko, Lassana, Désiré N’Da Pokou, Abou Bakari Kouassi, Paterne A. Agre, Amani Michel Kouakou, Konan Evrard Brice Dibi, Boni Nzue, Jean M. Mondo, Patrick Adebola, Oluyemi T. Akintayo, and et al. 2021. "Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits" Plants 10, no. 12: 2562. https://doi.org/10.3390/plants10122562