Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and DNA Isolation
2.2. Disease Screening
2.3. Genotyping Using SSR
2.4. Genetic Diversity and Population Structure Analysis
2.5. Linkage Disequilibrium and Marker-Trait Association Analysis
3. Results
3.1. Phenotypic Variability
3.2. Genetic Diversity and Population Structure Analysis
3.3. Marker Trait Association Analysis
4. Discussion
4.1. Genetic Diversity and Population Structure
4.2. Markers Trait Association Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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S. No. | SSR Locus | Bin Loc | PIC | MI | DI | Na | Ne | Obs_Hom |
---|---|---|---|---|---|---|---|---|
1 | phi 056 | 1.00 | 0.76 | 180.56 | 0.96 | 6 | 4.21 | 1.00 |
2 | bnlg 1884 | 1.05 | 0.67 | 133.08 | 0.93 | 5 | 3.42 | 1.00 |
3 | umc 1122 | 1.06 | 0.76 | 179.75 | 0.96 | 6 | 6.20 | 1.00 |
4 | bnlg615 | 1.07 | 0.61 | 97.17 | 0.90 | 4 | 2.62 | 0.92 |
5 | umc 2396 | 1.07 | 0.73 | 143.61 | 0.95 | 5 | 4.79 | 1.00 |
6 | umc 2047 | 1.09 | 0.72 | 113.31 | 0.93 | 4 | 3.55 | 1.00 |
7 | phi308707 | 1.10 | 0.67 | 105.53 | 0.92 | 4 | 3.01 | 1.00 |
8 | phi227562 | 1.11 | 0.64 | 125.79 | 0.93 | 5 | 2.77 | 1.00 |
9 | bnlg 1092 | 2.00 | 0.68 | 135.24 | 0.94 | 5 | 3.19 | 1.00 |
10 | phi 96100 | 2.01 | 0.63 | 124.03 | 0.93 | 5 | 2.73 | 0.97 |
11 | bnlg 2248 | 2.03 | 0.74 | 145.71 | 0.95 | 5 | 4.26 | 1.00 |
12 | umc1845 | 2.03 | 0.66 | 130.65 | 0.93 | 5 | 3.01 | 0.98 |
13 | phi 083 | 2.04 | 0.71 | 139.48 | 0.94 | 5 | 3.47 | 1.00 |
14 | nc 133 | 2.05 | 0.71 | 169.46 | 0.95 | 6 | 3.50 | 1.00 |
15 | bnlg1138 | 2.06 | 0.71 | 140.88 | 0.94 | 5 | 3.48 | 1.00 |
16 | nc 003 | 2.06 | 0.82 | 257.82 | 0.98 | 8 | 5.54 | 0.98 |
17 | umc1108 | 2.07 | 0.66 | 104.26 | 0.91 | 4 | 2.95 | 1.00 |
18 | phi090 | 2.08 | 0.72 | 198.65 | 0.96 | 7 | 3.55 | 1.00 |
19 | umc2077 | 2.09 | 0.61 | 121.11 | 0.92 | 5 | 2.58 | 1.00 |
20 | phi374118 | 3.02 | 0.78 | 185.54 | 0.96 | 6 | 4.93 | 1.00 |
21 | bnlg 1523 | 3.03 | 0.80 | 254.49 | 0.98 | 8 | 5.49 | 1.00 |
22 | umc 2259 | 3.03 | 0.78 | 185.41 | 0.96 | 6 | 4.61 | 1.00 |
23 | phi036 | 3.04 | 0.67 | 133.37 | 0.93 | 5 | 4.57 | 1.00 |
24 | phi 102228 | 3.06 | 0.70 | 110.11 | 0.92 | 4 | 3.32 | 1.00 |
25 | phi 046 | 3.08 | 0.61 | 145.47 | 0.94 | 6 | 2.59 | 1.00 |
26 | bnlg1108 | 3.08 | 0.75 | 147.45 | 0.95 | 5 | 3.98 | 1.00 |
27 | umc1594 | 3.09 | 0.68 | 133.52 | 0.94 | 5 | 3.09 | 1.00 |
28 | phi072 | 4.00 | 0.76 | 210.52 | 0.97 | 7 | 4.26 | 0.98 |
29 | phi096 | 4.04 | 0.78 | 153.20 | 0.96 | 5 | 4.80 | 1.00 |
30 | umc 1175 | 4.05 | 0.60 | 94.58 | 0.90 | 4 | 2.50 | 1.00 |
31 | umc 2284 | 4.06 | 0.86 | 304.31 | 0.98 | 9 | 7.13 | 0.96 |
32 | bnlg252 | 4.06 | 0.76 | 151.15 | 0.95 | 5 | 4.60 | 1.00 |
33 | phi093 | 4.08 | 0.70 | 137.42 | 0.94 | 5 | 3.14 | 0.78 |
34 | nc130 | 5.00 | 0.71 | 168.19 | 0.95 | 6 | 3.44 | 0.92 |
35 | phi024 | 5.01 | 0.80 | 189.34 | 0.97 | 6 | 5.72 | 1.00 |
36 | umc1332 | 5.04 | 0.78 | 216.81 | 0.97 | 7 | 4.72 | 0.93 |
37 | umc2303 | 5.05 | 0.85 | 334.58 | 0.98 | 9 | 7.73 | 0.97 |
38 | phi085 | 5.06 | 0.85 | 370.80 | 0.99 | 9 | 7.63 | 0.99 |
39 | dupssr14 | 8.09 | 0.68 | 134.47 | 0.94 | 5 | 3.43 | 0.73 |
40 | phi 015 | 8.08 | 0.64 | 126.12 | 0.93 | 5 | 2.62 | 0.90 |
41 | umc 1378 | 7.00 | 0.60 | 118.01 | 0.92 | 5 | 2.66 | 0.94 |
42 | bnlg1443 | 6.05 | 0.66 | 131.04 | 0.93 | 5 | 3.06 | 1.00 |
43 | duppsr 28 | 4.08 | 0.70 | 111.42 | 0.93 | 4 | 3.36 | 1.00 |
44 | phi076 | 4.11 | 0.62 | 98.64 | 0.91 | 4 | 2.66 | 1.00 |
45 | phi445613 | 6.05 | 0.69 | 108.49 | 0.92 | 4 | 2.68 | 1.00 |
46 | umc1520 | 6.06 | 0.71 | 168.34 | 0.95 | 6 | 3.62 | 1.00 |
47 | Zag249 | 6.01 | 0.66 | 131.12 | 0.93 | 5 | 2.94 | 1.00 |
Source | df | SS | MS | Est. Var. | % Var. | F-Stat. | Value | p |
---|---|---|---|---|---|---|---|---|
Between sub-populations | 4 | 931.79 | 232.95 | 2.13 | 7% | Fst | 0.07 | 0.001 |
Among individual (within a population) | 283 | 15,781.60 | 55.77 | 27.04 | 88% | Fis | 0.94 | 0.001 |
Within individual (across whole population) | 288 | 488.50 | 1.70 | 1.70 | 5% | Fit | 0.95 | 0.001 |
Total | 575 | 17,201.89 | 290.41 | 30.86 | 100% |
S. No. | Marker | Bin Location | Physical Position | Tandem Repeats | Marker R2 | FDR | PIC |
---|---|---|---|---|---|---|---|
1 | umc1122 # | 1.06 | 206027905–206027744 | (CGT)7 | 0.17 | 0.0097 | 0.76 |
2 | umc2396 # | 1.07 | NA * | (GTT)5 | 0.22 | 0.0003 | 0.73 |
3 | bnlg1092 | 2.00 | NA * | AG(30) | 0.16 | 0.0200 | 0.68 |
4 | phi083 # | 2.04 | 42235661–42235792 | AGCT | 0.13 | 0.0030 | 0.71 |
5 | bnlg1138 | 2.06 | NA * | AG(14) | 0.22 | 0.0110 | 0.71 |
6 | umc1108 | 2.07 | 191651695–191651816 | (ACGT)4 | 0.12 | 0.0012 | 0.66 |
7 | phi374118 | 3.02 | 17628581–17628810 | ACC | 0.16 | 0.0110 | 0.78 |
8 | phi076 | 4.11 | 248828113–248828277 | AGCGGG | 0.11 | 0.0020 | 0.62 |
9 | nc130 | 5.00 | 1231799–1231940 | AGC | 0.26 | 0.0001 | 0.71 |
10 | phi024 | 5.01 | 4540582–4540751 | CCT | 0.22 | 0.0200 | 0.80 |
11 | phi085 | 5.06 | 213469971–213469712 | AACGC | 0.26 | 0.0023 | 0.85 |
12 | phi075 | 6.00 | 6643571–6643381 | CT | 0.11 | 0.0020 | 0.49 |
13 | umc1520 | 6.06 | 169840623–169840474 | (GA)8 | 0.08 | 0.0164 | 0.71 |
14 | phi059 # | 10.02 | 8667388–8667241 | ACC | 0.12 | 0.0200 | 0.44 |
15 | umc1367 | 10.03 | 26019710–26019551 | (CGA)6 | 0.06 | 0.0400 | 0.23 |
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Kumar, B.; Choudhary, M.; Kumar, P.; Kumar, K.; Kumar, S.; Singh, B.K.; Lahkar, C.; Meenakshi; Kumar, P.; Dar, Z.A.; et al. Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes 2022, 13, 618. https://doi.org/10.3390/genes13040618
Kumar B, Choudhary M, Kumar P, Kumar K, Kumar S, Singh BK, Lahkar C, Meenakshi, Kumar P, Dar ZA, et al. Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes. 2022; 13(4):618. https://doi.org/10.3390/genes13040618
Chicago/Turabian StyleKumar, Bhupender, Mukesh Choudhary, Pardeep Kumar, Krishan Kumar, Sonu Kumar, Brijesh Kumar Singh, Chayanika Lahkar, Meenakshi, Pushpendra Kumar, Zahoor Ahmed Dar, and et al. 2022. "Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers" Genes 13, no. 4: 618. https://doi.org/10.3390/genes13040618
APA StyleKumar, B., Choudhary, M., Kumar, P., Kumar, K., Kumar, S., Singh, B. K., Lahkar, C., Meenakshi, Kumar, P., Dar, Z. A., Devlash, R., Hooda, K. S., Guleria, S. K., & Rakshit, S. (2022). Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes, 13(4), 618. https://doi.org/10.3390/genes13040618