Inter Simple Sequence Repeat-Based Genetic Divergence and Varietal Identification of Banana in Pakistan
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and DNA Markers
2.2. Genomic DNA Isolation and Quantification
2.3. Polymerase Chain Reaction (PCR)
2.4. Gel Electrophoresis
2.5. Scoring and Data Analysis
3. Results
3.1. Gene Diversity and Polymorphic Information Content (PIC)
3.2. Cluster Analysis
3.3. Principal Component Analysis (PCA) of Three Genomic Groups of 14 Banana Varieties
3.4. Genetic Distance within Conserved DNA-Derived Polymorphism Used in Assessing the Genetic Diversity of Three Genomic Groups of 14 Banana Varieties
3.5. Varietal Identification Using ISSR Markers
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Primer | Scorable Bands | Product Size bp | Polymorphic Bands | Ratio of Polymorphism | PIC |
---|---|---|---|---|---|
UBC-815 | 6 | 300–1000 | 4 | 66.66 | 0.72 |
UBC-811 | 10 | 150–650 | 5 | 50 | 0.83 |
UBC-864 | 7 | 250–650 | 5 | 71.42 | 0.75 |
UBC-840 | 8 | 300–1500 | 4 | 50 | 0.85 |
ISSR-2 | 9 | 200–650 | 4 | 44.44 | 0.85 |
UBC-862 | 5 | 200–500 | 4 | 80 | 0.75 |
ISSR-4 | 9 | 200–850 | 4 | 44.44 | 0.83 |
IG-03 | 9 | 180–700 | 3 | 33.33 | 0.84 |
IG-23 | 5 | 200–600 | 5 | 100 | 0.74 |
UBC-834 | 12 | 200–1400 | 3 | 25 | 0.88 |
UBC-835 | 9 | 200–1300 | 3 | 33.33 | 0.86 |
UBC-807 | 10 | 200–600 | 3 | 30 | 0.84 |
UBC-818 | 8 | 300–900 | 3 | 37.5 | 0.84 |
UBC-826 | 7 | 400–630 | 3 | 42.85 | 0.77 |
UBC-880 | 6 | 300–650 | 4 | 66.66 | 0.78 |
ISSR-3 | 5 | 300–1000 | 3 | 60 | 0.63 |
UBC-827 | 8 | 200–1000 | 4 | 50 | 0.74 |
IG-02 | 7 | 400–1000 | 3 | 42.85 | 0.84 |
UBC-868 | 4 | 250–400 | 2 | 50 | 0.67 |
IG-19 | 5 | 250–900 | 2 | 40 | 0.74 |
UBC-808 | 6 | 100–850 | 3 | 50 | 0.81 |
UBC-844 | 6 | 400–850 | 2 | 33.33 | 0.80 |
UBC-822 | 5 | 300–850 | 3 | 60 | 0.65 |
IG-05 | 3 | 200–400 | 2 | 66.66 | 0.65 |
UBC-823 | 6 | 400–850 | 2 | 33.32 | 0.81 |
UBC-861 | 5 | 380–600 | 2 | 40 | 0.76 |
UBC-847 | 3 | 250–350 | 1 | 33.33 | 0.53 |
UBC-817 | 5 | 200–600 | 2 | 40 | 0.68 |
UBC-813 | 5 | 300–800 | 2 | 40 | 0.68 |
DBD | 2 | 450–480 | 1 | 50 | 0.58 |
UBC-857 | 2 | 500–1100 | 1 | 50 | 0.46 |
ISSR-1 | 10 | 130–600 | 5 | 50 | 0.81 |
UBC-812 | 6 | 200–600 | 3 | 50 | 0.82 |
UBC-809 | 6 | 100–450 | 2 | 33.33 | 0.78 |
UBC-810 | 6 | 300–650 | 3 | 50 | 0.80 |
UBC-854 | 3 | 150–400 | 1 | 33.33 | 0.56 |
UBC-842 | 10 | 150–650 | 5 | 50 | 0.83 |
UBC-836 | 6 | 200–500 | 3 | 50 | 0.74 |
UBC-841 | 6 | 150–480 | 2 | 33.33 | 0.82 |
UBC-848 | 10 | 200–850 | 5 | 50 | 0.85 |
Total | 260 | 121 | 1915.11 | ||
46.53 | 47.87 |
PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC 10 | PC 11 | PC 12 | PC 13 | PC 14 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Standard deviation | 3.0212 | 2.3728 | 2.0913 | 1.98585 | 1.87144 | 1.8365 | 1.6333 | 1.43221 | 1.29681 | 1.2319 | 1.08501 | 1.057 | 1.02461 | 2.2 × 10−15 |
Proportion of Variance | 0.2214 | 0.1366 | 0.1061 | 0.09565 | 0.08494 | 0.0818 | 0.0647 | 0.04975 | 0.04079 | 0.03724 | 0.02855 | 0.0271 | 0.02546 | 0 |
Cumulative proportion | 0.2214 | 0.3579 | 0.464 | 0.55966 | 0.64461 | 0.7264 | 0.7911 | 0.84086 | 0.88164 | 0.91889 | 0.94744 | 0.9745 | 1 | 1 |
Variety Name | Markers Uniquely Identifying Varieties |
---|---|
NIGAB-1 | UBC-835670 *, UBC-827210, UBC-827310, UBC- 808850 |
NIGAB-2 | UBC-827500 |
NIGAB-3 | UBC-835220 |
GRAND-NAINE | UBC-835690, UBC-815600, UBC-815700, UBC-815850, IG-191050, ISSR-3850, UBC-808450, UBC-822700 |
ADI ** | Did not produce a unique allele |
GAYL ** | Did not produce a unique allele |
JAFA ** | Did not produce a unique allele |
DHAKA | UBC-811680, UBC-815600, UBC-815700, UBC-815850, IG-191050, ISSR-3850, UBC-808450, UBC-822700, |
RED BANANA | UBC-811600, UBC-864450, UBC-835170, ISSR-4350, UBC-827600 |
DAJIAO | UBC-811250, UBC-864220, UB-864660, IG-19530, UBC-8351150, ISSR-3550, ISSR-3630, UBC-822600, UBC-826600, UBC-817250 |
FENJIAO | UBC-811500, UBC-864300, UBC-864840, UBC-864850, UBC-864950, IG-19850, UBC-8351000, ISSR-4400, ISSR-3320, ISSR-3600, UBC-822310, UBC-826580 |
BASRAI | UBC-827550, UBC-826650 |
SPROUT-1 | UBC-811290, UBC-815690, ISSR-4900 |
SPROUT-2 | UBC-808170, UBC-817500 |
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Noor, S.; Muhammad, A.; Shahzad, A.; Hussain, I.; Zeshan, M.; Ali, K.; Begum, S.; Aqeel, M.; Numan, M.; Muazzam Naz, R.M.; et al. Inter Simple Sequence Repeat-Based Genetic Divergence and Varietal Identification of Banana in Pakistan. Agronomy 2022, 12, 2932. https://doi.org/10.3390/agronomy12122932
Noor S, Muhammad A, Shahzad A, Hussain I, Zeshan M, Ali K, Begum S, Aqeel M, Numan M, Muazzam Naz RM, et al. Inter Simple Sequence Repeat-Based Genetic Divergence and Varietal Identification of Banana in Pakistan. Agronomy. 2022; 12(12):2932. https://doi.org/10.3390/agronomy12122932
Chicago/Turabian StyleNoor, Saima, Aish Muhammad, Armghan Shahzad, Iqbal Hussain, Muhammad Zeshan, Kazim Ali, Sania Begum, Muhammad Aqeel, Mian Numan, Raja Mohib Muazzam Naz, and et al. 2022. "Inter Simple Sequence Repeat-Based Genetic Divergence and Varietal Identification of Banana in Pakistan" Agronomy 12, no. 12: 2932. https://doi.org/10.3390/agronomy12122932