Characterization of Okra (Abelmoschus esculentus L.) Accessions with Variable Drought Tolerance through Simple Sequence Repeat Markers and Phenotypic Traits
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. DNA Extraction, Purification, and Quantification
2.3. Polymerase Chain Reaction (PCR) and SSR Analysis
2.4. Marker Data Analysis
2.4.1. Computation of Principal Coordinate Analysis (PCoA) and Genetic Parameters
2.4.2. Cluster Analysis
2.5. Phenotyping Okra Accessions
2.5.1. Experimental Design and Crop Establishment
2.5.2. Phenotypic Data Collection
2.5.3. Phenotypic Data Analysis
3. Results and Discussion
3.1. Marker Characterization
3.2. Principal Coordinate Analysis (PCoA) of 26 Okra Accessions Genotyped Using 9 SSR Markers
3.3. Heatmap Cluster
3.4. Cluster Analysis
3.5. Accession and Environmental Effects on Phenotypic Traits
3.5.1. Performance of Okra Accessions for Phenotypic Traits under Drought-Stressed and Non-Stressed Conditions
3.5.2. Associations among Phenotypic Traits under Drought-Stressed and Non-Stressed Conditions
3.5.3. Principal Component Analysis (PCA)
3.5.4. Phenotypic Hierarchical Clustering
3.6. Comparison of Phenotypic and Genotypic Hierarchical Clusters
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accession Code | Accession Number | Geographical Origin |
---|---|---|
LS01 | VI033775 | Malaysia |
LS02 | VI033797 | Malaysia |
LS03 | VI056457 | Yugoslavia |
LS04 | VI039651 | Bangladesh |
LS05 | VI046561 | Thailand |
LS06 | VI047672 | Bangladesh |
LS07 | VI050150 | Taiwan |
LS08 | VI050957 | Zambia |
LS09 | VI050960 | Zambia |
LS10 | VI055110 | Malaysia |
LS11 | VI055119 | Myanmar |
LS12 | VI055219 | Malaysia |
LS13 | VI055220 | Malaysia |
LS14 | VI055421 | Viet Nam |
LS15 | VI056069 | Cambodia |
LS16 | VI056079 | Cambodia |
LS17 | VI056081 | Cambodia |
LS18 | VI056449 | United States of America |
LS19 | VI060131 | Mali |
LS20 | VI060313 | Tanzania |
LS21 | VI060679 | India |
LS22 | VI060803 | Turkey |
LS23 | VI060817 | Brazil |
LS24 | VI060822 | Nigeria |
LS25 | VI060823 | Nigeria |
LS26 | Clemson Spineless | South Africa |
Marker Name | Forward Primer Sequence | Reverse Primer Sequence | PIC |
---|---|---|---|
Okra 111 | GATGGAATTGAGAAACCAGA | TGTGTTCTTCACTCTCGTCA | 0.89 |
Okra 152 | GCTCTATTGATGGCGAGTAA | AAAGTCATCCAAGGTGACAA | 0.81 |
Okra 166 | TTCCAGTTGGAGAGGTAAGA | CTTCCATTTCATCGACTTTC | 0.82 |
AVRDC-Okra17 | ACGAGAGTGAAGTGGAACTG | CTCCTCTTTCCTTTTTCCAT | 0.81 |
AVRDC-Okra70 | GTAGCTGAACCCTTTGCTTA | CTATCATGGCGGATTCTTTA | 0.98 |
AVRDC-Okra39 | TGAGGTGATGATGTGAGAGA | TTGTAGATGAGGTTTGAACG | 0.99 |
AVRDC-Okra64 | AAGGAGGAGAAAGAGAAGGA | ATTTACTTGAGCAGCAGCAG | 0.87 |
AVRDC-Okra9 | ACCTTGAACACCAGGTACAG | TTGCTCTTATGAAGCAGTGA | 0.85 |
AVRDC-Okra57 | CGAGGAGACCATGGAAGAAG | ATGAGGAGGACGAGCAAGAA | 0.78 |
Okra137 | GAGAGAGATTGCTTCGACTG | TAAACTTTAAACTCAGCGGC | 0.80 |
Marker | Genetic Parameters | ||||||
---|---|---|---|---|---|---|---|
Na | Ne | I | Ho | He | FIS | PIC | |
AVRDC-Okra70 | 3 | 2.47 | 0.97 | 1.00 | 0.60 | −0.68 | 0.60 |
AVRDC-Okra64 | 2 | 2.00 | 0.69 | 1.00 | 0.50 | −1.00 | 0.50 |
Okra 152 | 2 | 2.00 | 0.69 | 1.00 | 0.50 | −1.00 | 0.50 |
Okra 166 | 2 | 2.00 | 0.69 | 1.00 | 0.50 | −1.00 | 0.50 |
AVRDC-Okra9 | 5 | 2.76 | 1.16 | 1.00 | 0.64 | −0.57 | 0.64 |
AVRDC-Okra39 | 3 | 2.31 | 0.91 | 1.00 | 0.57 | −0.76 | 0.57 |
Okra 111 | 2 | 2.00 | 0.69 | 1.00 | 0.50 | −1.00 | 0.50 |
Okra137 | 3 | 2.58 | 1.01 | 1.00 | 0.61 | −0.63 | 0.61 |
AVRDC-Okra57 | 2 | 2.00 | 0.69 | 1.00 | 0.50 | −1.00 | 0.50 |
Average | 2.70 | 2.24 | 0.83 | 1.00 | 0.54 | −0.85 | 0.55 |
Standard deviation | 1.00 | 0.30 | 0.18 | 0.00 | 0.06 | 0.19 | 0.06 |
Standard error | 0.34 | 0.15 | 0.10 | 0.10 | 0.06 | 0.06 | 0.02 |
S.O.V. | df | PH | DTM | FPL | DPL | DPW | NPPP | PYPP | AGB | HI | RW | RSR |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Replications | 1 | 23.80 ns | 11.44 ns | 21.61 * | 35.41 ns | 81.39 * | 0.01 ns | 55.20 * | 1423.50 ** | 1153 ns | 1.50 ns | 1.09 ** |
Incomplete blocks | 1 | 2063.50 ** | 0.08 ns | 9.99 ns | 11.22 ns | 13.89 ns | 3.47 ns | 1.11 ns | 104.56 ns | 790.10 ns | 85.87 * | 0.09 ns |
Genotype (G) | 26 | 336.40 * | 225.57 * | 15.15 ** | 13.76 ns | 7.54 ns | 7.92 * | 15.97 * | 136.00 * | 664.10 ns | 17.97 * | 0.14 ns |
Water regime (WC) | 1 | 2231.00 ** | 75.84 ns | 77.13 ** | 13.18 ns | 10.93 ns | 16.56 * | 229.47 ** | 578.52 ns | 4736.10 * | 82.41 * | 0.04 ns |
G × WC | 25 | 234.60 ns | 89.58 * | 6.82 * | 10.15 ns | 6.99 ns | 4.43 ns | 12.01 * | 55.27 ns | 714.90 ns | 8.91 ns | 0.07 ns |
Residual | 49 | 139.80 | 48.05 | 3.96 | 11.88 | 8.26 | 3.98 | 6.96 | 75.76 | 429.40 | 10.19 | 0.09 |
Accession Code | PH (cm) | DTM | FPL (cm) | DPL (cm) | DPW (g Per Plant) | NPPP | PYPP (g Per Plant) | AGB (g Per Plant) | HI (%) | RW (g Per Plant) | RSR | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | DS | NS | |
LS01 | 71.50 | 64.25 | 80.25 | 95.17 | 3.92 | 7.96 | 11.59 | 7.78 | 6.50 | 2.00 | 3.50 | 8.00 | 3.92 | 7.02 | 13.92 | 13.02 | 17.15 | 54.91 | 5.25 | 7.75 | 0.58 | 0.59 |
LS02 | 65.37 | 61.62 | 101.00 | 95.67 | 5.19 | 7.13 | 9.13 | 1.75 | 4.00 | 0.00 | 3.50 | 3.50 | 2.58 | 7.83 | 7.08 | 17.83 | 36.67 | 44.47 | 6.00 | 5.25 | 0.83 | 0.30 |
LS03 | 60.50 | 68.38 | 83.00 | 83.50 | 3.03 | 5.96 | 5.15 | 6.83 | 3.50 | 3.50 | 8.00 | 7.00 | 2.50 | 8.79 | 17.50 | 17.29 | 13.96 | 51.86 | 5.25 | 6.25 | 0.33 | 0.37 |
LS04 | 49.87 | 52.12 | 86.25 | 86.75 | 6.21 | 7.50 | 8.29 | 8.54 | 1.00 | 2.50 | 6.00 | 5.50 | 4.19 | 6.09 | 9.19 | 12.09 | 47.52 | 56.69 | 0.75 | 3.00 | 0.09 | 0.29 |
LS05 | 54.50 | 72.50 | 89.00 | 80.25 | 5.73 | 7.25 | 6.50 | 7.08 | 2.00 | 8.00 | 4.00 | 5.50 | 6.17 | 7.33 | 16.17 | 18.33 | 38.30 | 44.78 | 5.25 | 3.75 | 0.32 | 0.27 |
LS06 | 61.50 | 82.88 | 77.00 | 77.00 | 8.23 | 9.06 | 4.50 | 8.85 | 2.50 | 5.50 | 4.00 | 5.00 | 5.05 | 8.00 | 16.55 | 29.50 | 62.42 | 30.64 | 4.00 | 7.50 | 0.50 | 0.25 |
LS07 | 58.38 | 70.38 | 86.25 | 89.00 | 8.58 | 4.96 | 7.60 | 9.00 | 3.00 | 6.50 | 4.00 | 3.50 | 7.92 | 2.92 | 16.92 | 14.92 | 65.16 | 29.01 | 5.00 | 4.50 | 0.34 | 0.37 |
LS08 | 73.50 | 64.00 | 77.00 | 95.00 | 6.00 | 1.50 | 3.50 | 4.67 | 1.50 | 1.00 | 4.50 | 2.50 | 6.58 | 2.63 | 21.58 | 17.12 | 41.57 | 8.97 | 8.75 | 12.25 | 0.49 | 0.96 |
LS09 | 82.25 | 69.75 | 89.67 | 83.50 | 3.80 | 7.83 | 7.50 | 4.21 | 1.00 | 1.00 | 3.00 | 3.00 | 4.60 | 7.17 | 17.10 | 16.67 | 21.83 | 48.07 | 10.50 | 7.75 | 0.85 | 0.50 |
LS10 | 68.75 | 88.25 | 95.17 | 90.00 | 10.17 | 11.50 | 0.00 | 8.38 | 0.00 | 1.50 | 3.00 | 3.50 | 14.00 | 13.25 | 32.00 | 37.75 | 43.75 | 35.80 | 4.00 | 7.25 | 0.13 | 0.20 |
LS11 | 79.00 | 66.50 | 95.50 | 86.00 | 6.51 | 9.75 | 8.33 | 3.63 | 3.00 | 0.00 | 6.00 | 4.00 | 6.76 | 9.23 | 16.76 | 19.23 | 40.34 | 47.33 | 7.75 | 9.00 | 0.46 | 0.47 |
LS12 | 65.25 | 82.38 | 101.00 | 83.17 | 3.99 | 5.51 | 3.75 | 5.08 | 2.50 | 4.00 | 6.50 | 6.50 | 2.85 | 7.68 | 19.85 | 21.68 | 19.12 | 46.84 | 5.00 | 7.25 | 0.33 | 0.40 |
LS13 | 74.25 | 49.75 | 80.25 | 98.25 | 2.50 | 7.46 | 5.71 | 6.19 | 2.50 | 0.50 | 1.00 | 5.50 | 2.00 | 6.13 | 17.00 | 9.13 | 10.98 | 79.55 | 6.50 | 4.00 | 0.40 | 0.48 |
LS14 | 65.50 | 87.25 | 86.42 | 83.17 | 5.93 | 8.09 | 6.44 | 7.38 | 0.50 | 3.00 | 4.50 | 6.00 | 4.48 | 8.56 | 18.97 | 23.06 | 23.56 | 60.68 | 8.00 | 8.25 | 0.42 | 0.49 |
LS15 | 52.50 | 57.88 | 89.00 | 92.42 | 6.71 | 5.47 | 6.40 | 6.40 | 1.50 | 1.50 | 5.00 | 6.00 | 4.71 | 4.82 | 10.71 | 8.32 | 47.71 | 57.66 | 3.50 | 3.75 | 0.40 | 0.45 |
LS16 | 53.50 | 78.12 | 95.17 | 92.25 | 3.95 | 7.75 | 7.40 | 6.92 | 3.50 | 3.00 | 2.50 | 4.50 | 2.63 | 11.55 | 13.62 | 24.55 | 18.99 | 47.05 | 4.25 | 8.75 | 0.29 | 0.36 |
LS17 | 67.00 | 79.00 | 98.00 | 83.50 | 4.23 | 3.88 | 4.75 | 8.08 | 1.00 | 5.00 | 5.50 | 3.50 | 3.69 | 6.00 | 21.19 | 20.00 | 23.54 | 30.08 | 7.00 | 9.25 | 0.49 | 0.46 |
LS18 | 83.62 | 75.00 | 98.25 | 86.75 | 7.21 | 7.33 | 7.75 | 10.38 | 1.50 | 1.50 | 6.00 | 3.50 | 5.42 | 6.10 | 16.42 | 25.10 | 33.94 | 24.68 | 10.75 | 6.25 | 0.74 | 0.25 |
LS19 | 54.12 | 72.00 | 95.50 | 83.50 | 1.00 | 0.00 | 4.00 | 5.25 | 0.50 | 0.00 | 1.00 | 1.00 | 0.50 | 0.00 | 6.50 | 12.50 | 16.67 | 0.00 | 5.50 | 9.25 | 1.43 | 0.73 |
LS20 | 60.25 | 67.12 | 95.16 | 89.67 | 1.81 | 8.46 | 1.88 | 7.63 | 0.00 | 2.50 | 2.50 | 4.00 | 0.75 | 8.08 | 11.25 | 18.08 | 7.89 | 48.95 | 4.50 | 6.25 | 0.45 | 0.42 |
LS21 | 54.12 | 66.25 | 92.17 | 92.25 | 8.50 | 10.08 | 7.58 | 7.58 | 4.00 | 1.50 | 6.00 | 6.00 | 4.17 | 9.58 | 10.17 | 12.08 | 41.96 | 84.21 | 2.00 | 2.75 | 0.27 | 0.24 |
LS22 | 63.50 | 119.25 | 89.67 | 92.75 | 5.52 | 8.04 | 5.83 | 7.63 | 0.00 | 6.00 | 3.00 | 6.00 | 1.75 | 11.44 | 10.75 | 37.94 | 12.96 | 30.57 | 6.25 | 11.75 | 0.62 | 0.31 |
LS23 | 69.75 | 86.75 | 92.17 | 89.50 | 4.94 | 7.29 | 6.13 | 8.79 | 2.50 | 5.00 | 2.50 | 7.00 | 5.88 | 8.00 | 20.87 | 34.50 | 30.75 | 23.72 | 6.50 | 10.00 | 0.35 | 0.28 |
LS24 | 59.12 | 86.25 | 95.17 | 77.00 | 4.83 | 5.31 | 1.50 | 3.38 | 0.00 | 0.50 | 3.00 | 2.50 | 4.17 | 6.88 | 17.17 | 25.87 | 27.86 | 19.23 | 1.00 | 9.50 | 0.11 | 0.42 |
LS25 | 59.62 | 83.62 | 101.00 | 90.00 | 0.00 | 6.92 | 0.00 | 3.50 | 0.00 | 0.00 | 1.00 | 3.50 | 0.00 | 7.04 | 12.50 | 26.54 | 0.00 | 35.18 | 1.50 | 10.75 | 0.04 | 0.41 |
LS26 | 46.12 | 52.62 | 86.75 | 83.50 | 4.67 | 5.63 | 5.45 | 3.05 | 2.00 | 1.50 | 2.00 | 6.00 | 4.00 | 5.24 | 6.00 | 7.24 | 33.33 | 82.28 | 1.75 | 2.50 | 0.15 | 0.22 |
Mean | 63.59 | 73.23 | 90.61 | 87.67 | 5.12 | 6.83 | 5.64 | 6.46 | 1.92 | 2.58 | 3.90 | 4.71 | 4.28 | 7.21 | 15.30 | 20.01 | 29.92 | 43.20 | 5.25 | 7.10 | 0.44 | 0.40 |
p-value | ns | ** | * | ns | * | * | ns | ns | * | * | * | ns | * | ns | * | * | ns | * | ns | ns | * | ns |
SED | 11.73 | 12.84 | 6.29 | 7.49 | 1.73 | 2.13 | 3.19 | 3.77 | 2.41 | 3.25 | 1.85 | 2.17 | 2.29 | 2.95 | 7.63 | 9.81 | 21.16 | 20.58 | 3.10 | 3.29 | 0.37 | 0.17 |
LSD (5%) | 34.24 | 26.44 | 12.96 | 15.97 | 5.05 | 4.39 | 9.32 | 7.77 | 7.05 | 6.69 | 5.41 | 4.48 | 6.68 | 6.08 | 22.26 | 20.21 | 43.67 | 42.38 | 9.04 | 6.77 | 1.09 | 0.35 |
CV (%) | 18.48 | 17.53 | 6.94 | 8.54 | 34.77 | 31.22 | 55.83 | 58.42 | 65.12 | 56.10 | 47.68 | 46.12 | 56.79 | 40.93 | 50.20 | 49.02 | 69.23 | 47.63 | 58.87 | 46.35 | 63.74 | 42.66 |
Traits | PH | DTM | FPL | DPL | DPW | NPPP | PYPP | AGB | HI | RW | RSR |
---|---|---|---|---|---|---|---|---|---|---|---|
PH | 0.01 ns | 0.06 ns | 0.14 ns | 0.07 ns | 0.10 ns | 0.24 ns | 0.52 ** | −0.19 ns | 0.81 ** | 0.32 ns | |
DTM | −0.22 ns | −0.20 ns | −0.24 ns | −0.27 ns | −0.05 ns | 0.52 ** | −0.06 ns | −0.29 ns | −0.05 ns | 0.07 ns | |
FPL | 0.16 ns | 0.12 ns | 0.21 ns | 0.12 ns | 0.43 * | 0.81 ** | 0.36 ns | 0.85 ** | 0.03 ns | −0.23 ns | |
DPL | 0.24 ns | 0.03 ns | 0.26 ns | 0.71 ** | 0.30 ns | −0.03 ns | −0.35 ns | 0.25 ns | 0.29 ns | 0.28 ns | |
DPW | 0.41 * | −0.29 ns | 0.06 ns | 0.58 ** | 0.27 ns | 0.04 ns | −0.14 ns | 0.17 ns | 0.03 ns | 0.05 ns | |
NPPP | −0.03 ns | 0.15 ns | 0.39 ** | 0.24 ns | 0.38 ns | 0.26 ns | 0.19 ns | 0.34 ns | 0.14 ns | −0.15 ns | |
PYPP | 0.46 ** | 0.08 ns | 0.83 ** | 0.16 ns | 0.15 ns | 0.37 ns | 0.69 ** | 0.67 ** | 0.13 ns | −0.27 ns | |
AGB | 0.88 ** | −0.14 ns | 0.36 ns | 0.27 ns | 0.30 ns | −0.06 ns | 0.60 ** | 0.13 ns | 0.34 ns | 0.27 ns | |
HI | −0.47 * | 0.22 ns | 0.50 ** | −0.07 ns | −0.11 ns | 0.61 ** | 0.31 ns | −0.48 * | −0.09 ns | −0.13 ns | |
RW | 0.70 ** | −0.02 ns | −0.24 ns | −0.12 ns | −0.05 ns | −0.32 ns | −0.08 ns | 0.62 ** | −0.69 ** | 0.58 ** | |
RSR | −0.18 ns | 0.20 ns | −0.65 ** | −0.29 ns | −0.33 ns | −0.35 ns | −0.57 ** | −0.31 ns | −0.37 ns | 0.49 * |
Traits | Drought-Stressed | Non-Stressed | |||||
---|---|---|---|---|---|---|---|
PC1 | PC2 | PC3 | PC1 | PC2 | PC3 | PC4 | |
PH | 0.32 | 0.74 | 0.46 | 0.55 | 0.76 | 0.05 | 0.01 |
DTM | −0.33 | −0.03 | 0.32 | −0.09 | −0.27 | 0.48 | 0.74 |
FPL | 0.89 | −0.23 | −0.07 | 0.79 | −0.31 | 0.37 | −0.09 |
DPL | 0.29 | 0.50 | −0.73 | 0.51 | 0.05 | −0.53 | 0.41 |
DPW | 0.28 | 0.30 | −0.69 | 0.53 | 0.17 | −0.71 | 0.17 |
NPPP | 0.53 | 0.07 | −0.22 | 0.53 | −0.49 | −0.15 | 0.37 |
PYPP | 0.87 | −0.20 | 0.30 | 0.85 | −0.01 | 0.46 | −0.05 |
AGB | 0.58 | 0.01 | 0.70 | 0.64 | 0.71 | 0.19 | −0.02 |
HI | 0.78 | −0.29 | −0.27 | 0.24 | −0.90 | 0.16 | −0.01 |
RW | 0.26 | 0.87 | 0.30 | −0.06 | 0.88 | 0.31 | 0.21 |
RSR | −0.20 | 0.74 | −0.07 | −0.76 | 0.30 | 0.10 | 0.39 |
Explained variance (eigenvalue) | 3.27 | 2.38 | 2.13 | 3.55 | 3.19 | 1.56 | 1.09 |
Proportion of total variance (%) | 29.69 | 21.64 | 19.37 | 32.24 | 28.99 | 14.22 | 9.89 |
Cumulative variance (%) | 29.69 | 51.33 | 70.70 | 32.24 | 61.23 | 75.45 | 85.34 |
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Mkhabela, S.S.; Shimelis, H.; Gerrano, A.S.; Mashilo, J.; Shayanowako, A. Characterization of Okra (Abelmoschus esculentus L.) Accessions with Variable Drought Tolerance through Simple Sequence Repeat Markers and Phenotypic Traits. Diversity 2022, 14, 747. https://doi.org/10.3390/d14090747
Mkhabela SS, Shimelis H, Gerrano AS, Mashilo J, Shayanowako A. Characterization of Okra (Abelmoschus esculentus L.) Accessions with Variable Drought Tolerance through Simple Sequence Repeat Markers and Phenotypic Traits. Diversity. 2022; 14(9):747. https://doi.org/10.3390/d14090747
Chicago/Turabian StyleMkhabela, Sonto Silindile, Hussein Shimelis, Abe Shegro Gerrano, Jacob Mashilo, and Admire Shayanowako. 2022. "Characterization of Okra (Abelmoschus esculentus L.) Accessions with Variable Drought Tolerance through Simple Sequence Repeat Markers and Phenotypic Traits" Diversity 14, no. 9: 747. https://doi.org/10.3390/d14090747