Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Trait Measurements
2.3. Genotyping
3. Statistical Analysis
3.1. Phenotypic Analysis
3.2. Quality Control and Genotypic Analysis
3.3. Joint Analysis of Agronomic-Based and Molecular Data
4. Results
4.1. Diversity Based on Agronomic Traits
4.2. Genetic Diversity and Population Structure Based on SNP Markers
4.3. Combined Analysis of Phenotypic and Genotypic Data
5. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ANOVA | Analysis of variance |
BIC | Bayesian information criterion |
CTAB | Cetyltrimethylammonium bromide |
DAPC | Discriminant analysis of principal components |
DNA | Deoxyribonucleic acid |
GBS | Genotyping-by-sequencing |
IBS | Identity by State |
LD | Linkage disequilibrium |
SNP | Single nucleotide polymorphism |
SSA | sub-Saharan Africa |
PIC | Polymorphic information content |
TASSEL | Trait Analysis by aSSociation, Evolution and Linkage |
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Source Population | Genetic Background of Source Population | Lines Evaluated |
---|---|---|
ZDIP | Lines derived from a backcross (BC4) containing a Z. diploperennis accession as a donor parent plus lines derived from bi-parental crosses involving one parent derived from the same Z. diploperennis backcross | 39 |
TZLC | A late-maturing composite formed by crossing TZB-SR with seven inbred lines developed for field resistance to S. hermonthica plus lines derived from bi-parental crosses involving one parent derived from the same source populations | 44 |
TZEC | An early maturing composite formed by crossing TZESR-W C3 with eight inbred lines developed for field resistance to S. hermonthica plus lines derived from bi-parental crosses involving one parent derived from the same composite | 13 |
IWDS | A synthetic formed from medium maturing white inbred lines and improved for resistance to Striga and drought plus lines derived from bi-parental crosses involving one parent derived from these synthetic | 30 |
MIXED | Lines derived from diverse source populations plus the tolerant lines expensively used as donors of field resistance to form populations | 24 |
Variables | PC1 | PC2 | PC3 |
---|---|---|---|
Days to silking | −0.441 | 0.855 | −0.068 |
Ear aspect | 0.884 | 0.070 | −0.303 |
Ear per plant | −0.824 | −0.064 | 0.324 |
Plant height | −0.388 | 0.212 | −0.221 |
Striga count at 8 WAP | 0.651 | 0.148 | 0.712 |
Striga count at 10 WAP | 0.633 | 0.182 | 0.719 |
Striga damage at 8 WAP | 0.878 | 0.107 | −0.092 |
Striga damage at 10 WAP | 0.881 | 0.201 | −0.085 |
Yield | −0.786 | −0.173 | 0.434 |
Anthesis silking interval | −0.302 | 0.908 | 0.014 |
Eigenvalue | 4.886 | 1.745 | 1.478 |
Variance (%) | 48.863 | 17.459 | 14.784 |
Cumulative variance (%) | 48.863 | 66.321 | 81.105 |
MAF | Ho | He | PIC | |
---|---|---|---|---|
Minimum | 0.05 | 0.00 | 0.10 | 0.1 |
Maximum | 0.50 | 0.98 | 0.50 | 0.47 |
Mean | 0.24 | 0.10 | 0.32 | 0.26 |
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Share and Cite
Stanley, A.; Menkir, A.; Paterne, A.; Ifie, B.; Tongoona, P.; Unachukwu, N.; Meseka, S.; Mengesha, W.; Gedil, M. Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers. Plants 2020, 9, 1223. https://doi.org/10.3390/plants9091223
Stanley A, Menkir A, Paterne A, Ifie B, Tongoona P, Unachukwu N, Meseka S, Mengesha W, Gedil M. Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers. Plants. 2020; 9(9):1223. https://doi.org/10.3390/plants9091223
Chicago/Turabian StyleStanley, Adekemi, Abebe Menkir, Agre Paterne, Beatrice Ifie, Pangirayi Tongoona, Nnanna Unachukwu, Silvestro Meseka, Wende Mengesha, and Melaku Gedil. 2020. "Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers" Plants 9, no. 9: 1223. https://doi.org/10.3390/plants9091223