Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau
Abstract
:1. Introduction
2. Materials and Methods
2.1. Transcriptome Sequencing and EST-SSR Design
2.2. Plant Materials and DNA Extraction
2.3. Genetic Diversity Analysis
2.4. Phenotypic Variation and Association Analysis
2.5. Genetic and Phenotypic Differentiation Analysis
3. Results
3.1. De Novo Assembly and Distribution of SSR Repeats
3.2. Genetic Relationship Analysis
3.3. Inflorescence Phenotypic Characteristics, Shattering, and Tassel Analysis
3.4. Associations between Genetic, Phylogenetic, Geographical, and Climatic Distance
4. Discussion
4.1. Characterization of E. nutans Transcriptome and EST-SSR Distribution
4.2. SSR Validation and Genetic Analysis
4.3. Phenotypic Variation and Association Analysis
4.4. How Genotypic and Phenotypic Differentiation Is Affected by Geography and Environment
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Length Range (bp) | Transcripts | Unigene |
---|---|---|
200–500 | 205,785 | 88,679 |
500–1000 | 123,056 | 111,828 |
1000–2000 | 83,850 | 82,173 |
>2000 | 21,973 | 21,874 |
Total Number | 434,637 | 304,554 |
Total Length | 327,236,286 | 283,614,840 |
N50 Length | 1062 | 1194 |
N90 Length | 337 | 478 |
Mean Length | 753 | 931 |
Number of Repeat Units | Mono- | Di- | Tri- | Tetra- | Penta- | Hexa- | Total | Percentage (%) |
---|---|---|---|---|---|---|---|---|
5 | 0 | 0 | 12,830 | 860 | 198 | 79 | 13,967 | 28.82 |
6 | 0 | 3733 | 4731 | 272 | 11 | 23 | 8770 | 18.10 |
7 | 0 | 1784 | 2002 | 31 | 9 | 7 | 3833 | 7.91 |
8 | 0 | 1131 | 870 | 17 | 2 | 7 | 2027 | 4.18 |
9 | 0 | 742 | 158 | 6 | 0 | 1 | 907 | 1.87 |
10 | 6017 | 501 | 112 | 4 | 0 | 0 | 6634 | 13.69 |
11 | 2665 | 476 | 63 | 0 | 0 | 0 | 3204 | 6.61 |
12 | 1501 | 511 | 39 | 0 | 0 | 0 | 2051 | 4.23 |
13 | 821 | 219 | 19 | 1 | 0 | 0 | 1060 | 2.19 |
14 | 707 | 210 | 16 | 0 | 0 | 0 | 933 | 1.93 |
15 | 506 | 195 | 9 | 0 | 0 | 0 | 710 | 1.47 |
>15 | 3550 | 793 | 18 | 0 | 0 | 0 | 4361 | 9.00 |
Total | 15,767 | 10,295 | 20,867 | 1191 | 220 | 117 | 48,457 | 100.00 |
Percentage (%) | 32.54 | 21.25 | 43.06 | 2.46 | 0.45 | 0.24 | 100.00 |
Quantitative Traits | Mean | Max | Min | SD | Variation Coefficient (%) | Genetic Diversity Index |
---|---|---|---|---|---|---|
SKN | 42.99 | 68.80 | 27.70 | 7.20 | 16.74 | 1.94 |
SKL (mm) | 27.97 | 40.16 | 14.16 | 4.92 | 17.61 | 1.88 |
OGL (mm) | 4.62 | 7.37 | 3.04 | 0.74 | 16.03 | 1.77 |
OGW (mm) | 0.95 | 1.30 | 0.62 | 0.16 | 16.94 | 1.82 |
OGAL (mm) | 1.51 | 3.07 | 0.30 | 0.54 | 35.50 | 1.94 |
IGL (mm) | 3.66 | 5.90 | 1.53 | 0.69 | 19.01 | 1.92 |
IGW (mm) | 0.79 | 1.14 | 0.35 | 0.17 | 21.76 | 2.03 |
IGAL (mm) | 1.23 | 2.37 | 0.33 | 0.45 | 36.48 | 2.03 |
OLL (mm) | 9.42 | 11.46 | 7.67 | 0.69 | 7.34 | 1.94 |
OLW (mm) | 2.18 | 3.10 | 1.60 | 0.43 | 19.73 | 1.63 |
OLAL (mm) | 14.55 | 21.27 | 5.43 | 3.55 | 24.37 | 1.97 |
ILL (mm) | 8.75 | 10.16 | 6.77 | 0.71 | 8.17 | 1.96 |
ILW (mm) | 1.81 | 2.37 | 1.35 | 0.24 | 13.15 | 2.04 |
Trait | Marker | p | Marker_R2 | Trait | Marker | p | Marker_R2 |
---|---|---|---|---|---|---|---|
BTS | EN48-260 bp | 0.00305 | 0.28356 | OGL | EN57-183 bp | 0.00084 | 0.33773 |
IGAL | EN5-256 bp | 0.00019 | 0.40221 | OGL | EN99-150 bp | 0.00153 | 0.31079 |
IGAL | EN55-256 bp | 0.00368 | 0.26985 | OGW | EN5-256 bp | 0.00126 | 0.32361 |
IGL | EN57-183 bp | 0.00975 | 0.21398 | OGW | EN58-243 bp | 0.00898 | 0.22701 |
IGW | EN5-256 bp | 0.00018 | 0.40794 | OLAL | EN5-235 bp | 0.00079 | 0.32793 |
IGW | EN58-243 bp | 0.00967 | 0.22345 | OLL | EN5-235 bp | 0.00583 | 0.23654 |
ILL | EN35-207 bp | 0.00252 | 0.26241 | OLW | EN55-208 bp | 0.00888 | 0.22983 |
ILL | EN91-239 bp | 0.00746 | 0.21351 | SKL | EN5-235 bp | 0.00293 | 0.27998 |
OGAL | EN5-256 bp | 0.00063 | 0.35446 | SKN | EN90-228 bp | 0.00567 | 0.19378 |
OGAL | EN55-208 bp | 0.00594 | 0.24807 | SKN | EN99-164 bp | 0.00611 | 0.19025 |
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Li, J.; Tian, H.; Ji, W.; Zhang, C.; Chen, S. Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau. Agronomy 2023, 13, 1004. https://doi.org/10.3390/agronomy13041004
Li J, Tian H, Ji W, Zhang C, Chen S. Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau. Agronomy. 2023; 13(4):1004. https://doi.org/10.3390/agronomy13041004
Chicago/Turabian StyleLi, Jin, Haoqi Tian, Wenqin Ji, Changbing Zhang, and Shiyong Chen. 2023. "Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau" Agronomy 13, no. 4: 1004. https://doi.org/10.3390/agronomy13041004