Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Tiller Related Traits Phenotyping
2.2. EST-SSR Markers Development for P. juncea
2.3. Population Genotyping with EST-SSR Markers
2.4. Linkage Disequilibrium, Population Structure and Association Analysis
3. Results
3.1. Phenotypic Analysis of Tiller-Related Traits
3.2. The Polymorphism of SSR Markers, Genetic Diversity and Population Structure Analysis
3.3. Linkage Disequilibrium and Association Analysis of the P. juncea Population
4. Discussion
4.1. Phenotyping Analysis of the P. juncea Population
4.2. Genetic Diversity Analysis of P. juncea Material
4.3. Population Structure of P. juncea Germplasm Resources
4.4. Linkage Disequilibrium Analysis of P. juncea Population
4.5. Association Analysis of P. juncea
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait | Environment | Range | Mean | SD | Coefficient of Variation (%) |
---|---|---|---|---|---|
Plant height | Hohhot | 19.00~91.73 | 60.91 | 14.82 | 24.33 |
Baotou | 16.00~99.67 | 70.51 | 12.33 | 17.49 | |
BLUE | 14.44~95.13 | 65.21 | 11.74 | 18.01 | |
Reproductive tiller length | Hohhot | 23.17~107.43 | 72.19 | 14.77 | 20.46 |
Baotou | 25.00~111.08 | 82.90 | 13.56 | 16.36 | |
BLUE | 22.16~100.77 | 76.92 | 12.61 | 16.39 | |
Shoot height | Hohhot | 12.60~60.90 | 30.88 | 8.07 | 26.15 |
Baotou | 12.75~61.17 | 39.32 | 6.69 | 17.03 | |
BLUE | 12.52~53.10 | 34.84 | 5.50 | 15.79 | |
Clump basal diameter | Hohhot | 15.53~88.13 | 55.16 | 11.56 | 20.96 |
Baotou | 15.50~108.67 | 66.38 | 17.65 | 26.59 | |
BLUE | 11.09~97.06 | 60.23 | 12.80 | 21.25 | |
Leaf length | Hohhot | 15.56~50.05 | 33.56 | 5.50 | 16.39 |
Baotou | 20.33~52.73 | 40.46 | 5.55 | 13.72 | |
BLUE | 20.08~47.47 | 36.86 | 4.59 | 12.45 | |
Leaf width | Hohhot | 0.24~0.60 | 0.42 | 0.06 | 13.98 |
Baotou | 0.23~0.60 | 0.41 | 0.05 | 12.93 | |
BLUE | 0.26~0.56 | 0.42 | 0.05 | 11.04 | |
Canopy diameter | Hohhot | 25.53~102.75 | 66.79 | 12.55 | 18.78 |
Baotou | 31.50~105.83 | 74.29 | 12.36 | 16.64 | |
BLUE | 33.34~96.02 | 70.12 | 10.44 | 14.89 | |
Nutritional tiller number | Hohhot | 17.17~453.67 | 152.36 | 61.49 | 40.36 |
Baotou | 18.00~426.00 | 202.19 | 69.92 | 34.58 | |
BLUE | 15.36~397.67 | 174.90 | 53.51 | 30.60 | |
Nutritional tiller angle | Hohhot | 27.50~83.17 | 56.44 | 9.16 | 16.23 |
Baotou | 39.17~80.00 | 61.03 | 5.64 | 9.25 | |
BLUE | 41.07~79.16 | 58.73 | 4.75 | 8.09 | |
Reproductive tiller number | Hohhot | 4.00~182.00 | 45.46 | 31.20 | 68.64 |
Baotou | 8.00~325.00 | 89.25 | 45.23 | 50.68 | |
BLUE | 3.10~186.18 | 59.90 | 32.31 | 53.95 |
Traits | Indicator Eigenvector | |||
---|---|---|---|---|
I | II | III | IV | |
Plant height | 0.40 * | −0.16 | −0.10 | −0.29 |
Reproductive tiller length | 0.36 * | −0.06 | −0.07 | −0.16 |
Shoot height | 0.37 * | −0.27 | 0.28 | 0.34 |
Clump basal diameter | 0.31 * | 0.07 | −0.21 | −0.01 |
Leaf length | 0.28 | 0.30 * | 0.16 | 0.01 |
Leaf width | 0.13 | 0.72 * | −0.07 | −0.06 |
Canopy diameter | 0.30 | 0.23 * | 0.02 | −0.05 |
Nutritional tiller number | 0.25 | −0.09 | 0.34 | 0.79 * |
Nutritional tiller angle | 0.12 | −0.41 | 0.75 * | −0.24 |
Reproductive tiller number | 0.27 | −0.22 | 0.40 * | −0.29 |
Contribution (%) | 46.82 | 11.10 | 9.87 | 7.02 |
Cumulative Contribution (%) | 46.82 | 57.92 | 67.79 | 74.81 |
Sources of Variation | Degrees of Freedom | Sum of Squares | Mean Square | Variance of Components | Percentage Variation (%) | p Value | Fst |
---|---|---|---|---|---|---|---|
Among Pops | 20 | 18,235.035 | 911.752 | 18.957 | 34 | <0.001 | 0.341 |
Among Individuals | 459 | 21,331.484 | 46.474 | 9.826 | 18 | <0.001 | |
Within Individuals | 480 | 12,874.500 | 26.822 | 26.822 | 48 | <0.001 | |
Total | 959 | 52,441.020 | 55.605 | 100 | <0.001 |
Range of D′ Value | No. of Loci Pairs with Significant LD | Percentage of Loci Pairs with Significant LD (%) |
---|---|---|
0~0.2 | 2292 | 39.02 |
0.2~0.4 | 2072 | 35.27 |
0.4~0.6 | 886 | 15.08 |
0.6~0.8 | 342 | 5.82 |
0.8~1 | 282 | 4.80 |
Traits | Markers | p Value | R2/% | Traits | Markers | p Value | R2/% |
---|---|---|---|---|---|---|---|
Plant height | 028324 | 0.029 | 2.290 | Nutritional tiller number | 061356 | 0.033 | 2.230 |
139768A | 0.012 | 1.910 | 066842 | 0.017 | 2.530 | ||
OsIPT7 | 0.028 | 7.840 | 139768A | 0.026 | 1.520 | ||
Reproductive tiller length | 028324 | 0.033 | 2.190 | 185875 | 0.007 | 2.500 | |
139768A | 0.011 | 1.930 | OsIPT7 | 0.034 | 7.400 | ||
OsCKX1 | 0.033 | 1.490 | OsIPT8 | 0.014 | 1.960 | ||
OsIPT7 | 0.019 | 8.500 | Reproductive tiller number | 000516 | 0.023 | 1.060 | |
Shoot height | 139768A | 0.010 | 1.940 | 004435 | 0.013 | 1.880 | |
OsYUCCA6 | 0.039 | 1.430 | 019368C | 0.042 | 1.580 | ||
OsCKX1 | 0.042 | 1.360 | 026620 | 0.033 | 1.950 | ||
OsIPT7 | 0.014 | 9.150 | 028161A | 0.018 | 1.960 | ||
Clump basal diameter | 019368C | 0.036 | 1.680 | 028324 | 0.002 | 4.130 | |
028324 | 0.039 | 2.060 | 040957 | 0.008 | 4.190 | ||
070047 | 0.033 | 3.200 | 044262 | 0.029 | 3.350 | ||
139768A | 0.030 | 1.500 | 045589 | 0.021 | 1.100 | ||
Leaf length | 139768A | 0.012 | 1.870 | 070047 | 0.025 | 1.630 | |
OsYUCCA6 | 0.016 | 1.840 | 072525 | 0.001 | 2.100 | ||
OsCKX1 | 0.013 | 1.880 | 114416 | 0.029 | 1.550 | ||
OsIPT7 | 0.013 | 9.210 | 142612A | 0.021 | 1.600 | ||
Leaf width | 061356 | 0.031 | 2.390 | 167041 | 0.044 | 2.550 | |
065010 | 0.049 | 2.530 | 185875 | 0.006 | 2.670 | ||
139768A | 0.012 | 1.910 | 194938 | 0.007 | 2.620 | ||
OsYUCCA6 | 0.004 | 2.420 | OsD17 | 0.020 | 1.840 | ||
OsCKX1 | 0.010 | 2.030 | Canopy diameter | 139768A | 0.012 | 1.910 | |
OsIPT7 | 0.029 | 7.650 | OsYUCCA6 | 0.037 | 1.470 | ||
Nutritional tiller angle | 139768A | 0.011 | 1.890 | OsCKX1 | 0.009 | 2.030 | |
OsYUCCA6 | 0.011 | 1.990 | OsIPT7 | 0.014 | 9.100 | ||
OsIPT7 | 0.038 | 7.070 |
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Li, Z.; Wang, T.; Yun, L.; Ren, X.; Wang, Y.; Shi, F. Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea. Genes 2023, 14, 1970. https://doi.org/10.3390/genes14101970
Li Z, Wang T, Yun L, Ren X, Wang Y, Shi F. Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea. Genes. 2023; 14(10):1970. https://doi.org/10.3390/genes14101970
Chicago/Turabian StyleLi, Zhen, Tian Wang, Lan Yun, Xiaomin Ren, Yong Wang, and Fengling Shi. 2023. "Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea" Genes 14, no. 10: 1970. https://doi.org/10.3390/genes14101970