Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. DNA Extraction and SNP Genotyping
2.3. Data Management and Analysis
3. Results
3.1. Genetic Variability of 365 Rice Accessions Based on SNP Markers
3.2. Population Structure of Thai Landraces
3.3. Genetic Distance and Phylogeny of the 365 Accessions
3.4. Genetic Differentiation, AMOVA, and Isolation-by-Distance Analyses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Marker | Chr. | Position | REF | ALT | MAF | Na | Ho | He | PIC |
---|---|---|---|---|---|---|---|---|---|
R01002684973 | 1 | 2684973 | C | A | 0.65 | 2 | 0 | 0.46 | 0.35 |
R01008961781 | 1 | 8961781 | C | A | 0.89 | 2 | 0.01 | 0.19 | 0.17 |
R01023762056 | 1 | 23762056 | G | A | 0.7 | 2 | 0 | 0.42 | 0.33 |
R01033064986 | 1 | 33064986 | T | C | 0.91 | 2 | 0 | 0.16 | 0.15 |
R01033454937 | 1 | 33454937 | A | T | 0.64 | 2 | 0 | 0.46 | 0.36 |
R01034609753 | 1 | 34609753 | C | G | 0.93 | 2 | 0 | 0.13 | 0.12 |
R01036673058 | 1 | 36673058 | C | T | 0.91 | 2 | 0 | 0.17 | 0.15 |
R02008303326 | 2 | 8303326 | G | A | 0.89 | 2 | 0.01 | 0.20 | 0.18 |
R02008313120 | 2 | 8313120 | G | T | 0.69 | 2 | 0.01 | 0.43 | 0.34 |
R02008315835 | 2 | 8315835 | T | A | 0.94 | 2 | 0 | 0.12 | 0.11 |
R02010864977 | 2 | 10864977 | G | T | 0.82 | 2 | 0 | 0.30 | 0.25 |
R02019361361 | 2 | 19361361 | A | C | 0.9 | 2 | 0 | 0.18 | 0.17 |
R02019361451 | 2 | 19361451 | G | T | 0.9 | 2 | 0 | 0.18 | 0.17 |
R03016733359 | 3 | 16733359 | A | C | 0.72 | 2 | 0.02 | 0.40 | 0.32 |
R03017286744 | 3 | 17286744 | G | T | 0.81 | 2 | 0 | 0.31 | 0.26 |
R03017571575 | 3 | 17571575 | G | A | 0.84 | 2 | 0.01 | 0.27 | 0.23 |
R03031335170 | 3 | 31335170 | C | T | 0.84 | 2 | 0.01 | 0.27 | 0.23 |
R03031437173 | 3 | 31437173 | C | A | 0.91 | 2 | 0 | 0.16 | 0.15 |
R04001019335 | 4 | 1019335 | A | G | 0.79 | 2 | 0 | 0.33 | 0.28 |
R04005867320 | 4 | 5867320 | T | G | 0.66 | 2 | 0 | 0.45 | 0.35 |
R04006451939 | 4 | 6451939 | C | T | 0.86 | 2 | 0 | 0.24 | 0.21 |
R04006968050 | 4 | 6968050 | A | G | 0.93 | 2 | 0 | 0.13 | 0.12 |
R04011087541 | 4 | 11087541 | G | T | 0.69 | 2 | 0.02 | 0.43 | 0.34 |
R04011803874 | 4 | 11803874 | T | A | 0.58 | 2 | 0 | 0.49 | 0.37 |
R04016214692 | 4 | 16214692 | CA | TG | 0.57 | 2 | 0 | 0.49 | 0.37 |
R04016218749 | 4 | 16218749 | T | G | 0.57 | 2 | 0.01 | 0.49 | 0.37 |
R04022184296 | 4 | 22184296 | A | G | 0.64 | 2 | 0.02 | 0.46 | 0.35 |
R04023172729 | 4 | 23172729 | T | G | 0.74 | 2 | 0 | 0.38 | 0.31 |
R04023175725 | 4 | 23175725 | T | C | 0.75 | 2 | 0 | 0.37 | 0.3 |
R05003673333 | 5 | 3673333 | T | C | 0.68 | 2 | 0.01 | 0.44 | 0.34 |
R05019155333 | 5 | 19155333 | A | G | 0.59 | 2 | 0.01 | 0.48 | 0.37 |
R05019155705 | 5 | 19155705 | G | T | 0.5 | 2 | 0.01 | 0.50 | 0.37 |
R05023218617 | 5 | 23218617 | A | C | 0.7 | 2 | 0 | 0.42 | 0.33 |
R05026487913 | 5 | 26487913 | A | G | 0.91 | 2 | 0 | 0.17 | 0.15 |
R05028876504 | 5 | 28876504 | A | T | 0.91 | 2 | 0.01 | 0.16 | 0.15 |
R05028876779 | 5 | 28876779 | A | C | 0.91 | 2 | 0.01 | 0.16 | 0.15 |
R06001693194 | 6 | 1693194 | G | A | 0.54 | 2 | 0.01 | 0.50 | 0.37 |
R06001693411 | 6 | 1693411 | A | C | 0.56 | 2 | 0.01 | 0.49 | 0.37 |
R06001765760 | 6 | 1765760 | G | T | 0.54 | 2 | 0 | 0.50 | 0.37 |
R06001768006 | 6 | 1768006 | A | C | 0.79 | 2 | 0 | 0.33 | 0.27 |
R06001768724 | 6 | 1768724 | T | C | 0.82 | 2 | 0 | 0.29 | 0.25 |
R06001768997 | 6 | 1768997 | C | T | 0.69 | 2 | 0.01 | 0.43 | 0.34 |
R06006752886 | 6 | 6752886 | G | T | 0.55 | 2 | 0.01 | 0.49 | 0.37 |
R07005873563 | 7 | 5873563 | G | A | 0.79 | 2 | 0 | 0.33 | 0.28 |
R07020013105 | 7 | 20013105 | G | T | 0.55 | 2 | 0 | 0.49 | 0.37 |
R07020826100 | 7 | 20826100 | G | T | 0.82 | 2 | 0.01 | 0.30 | 0.26 |
R07024350575 | 7 | 24350575 | C | T | 0.91 | 2 | 0 | 0.17 | 0.15 |
R07025982551 | 7 | 25982551 | A | G | 0.91 | 2 | 0 | 0.16 | 0.15 |
R07027746661 | 7 | 27746661 | C | G | 0.53 | 2 | 0.01 | 0.50 | 0.37 |
R08002269285 | 8 | 2269285 | G | C | 0.56 | 2 | 0 | 0.49 | 0.37 |
R08002890407 | 8 | 2890407 | G | A | 0.63 | 2 | 0 | 0.46 | 0.36 |
R08003007900 | 8 | 3007900 | C | G | 0.54 | 2 | 0 | 0.50 | 0.37 |
R08020382861 | 8 | 20382861 | ATTATGGC | -:- | 0.87 | 2 | 0 | 0.23 | 0.2 |
R08027057202 | 8 | 27057202 | G | A | 0.83 | 2 | 0 | 0.28 | 0.24 |
R08027176617 | 8 | 27176617 | C | A | 0.72 | 2 | 0 | 0.40 | 0.32 |
R08027943348 | 8 | 27943348 | G | A | 0.86 | 2 | 0 | 0.24 | 0.21 |
R09004198183 | 9 | 4198183 | C | A | 0.77 | 2 | 0.01 | 0.35 | 0.29 |
R09007245205 | 9 | 7245205 | A | T | 0.9 | 2 | 0.01 | 0.18 | 0.16 |
R09007245448 | 9 | 7245448 | C | T | 0.9 | 2 | 0.01 | 0.18 | 0.16 |
R09007245650 | 9 | 7245650 | A | G | 0.9 | 2 | 0 | 0.17 | 0.16 |
R09007245739 | 9 | 7245739 | C | G | 0.9 | 2 | 0.01 | 0.17 | 0.16 |
R09007246222 | 9 | 7246223 | T | G | 0.9 | 2 | 0.01 | 0.18 | 0.16 |
R09007246804 | 9 | 7246804 | T | G | 0.85 | 2 | 0.01 | 0.26 | 0.23 |
R10015680316 | 10 | 15680316 | C | A | 0.92 | 2 | 0 | 0.15 | 0.14 |
R10021955049 | 10 | 21955049 | A | G | 0.9 | 2 | 0 | 0.18 | 0.16 |
R11013840467 | 11 | 13840467 | A | G | 0.81 | 2 | 0 | 0.30 | 0.26 |
R11014118135 | 11 | 14118135 | A | G | 0.6 | 2 | 0.01 | 0.48 | 0.36 |
R11014169508 | 11 | 14169508 | C | A | 0.75 | 2 | 0.01 | 0.37 | 0.3 |
R11021481048 | 11 | 21481048 | ATT | -:- | 0.52 | 2 | 0 | 0.50 | 0.37 |
R11028209211 | 11 | 28209211 | A | T | 0.7 | 2 | 0 | 0.42 | 0.33 |
R12009613648 | 12 | 9613648 | A | C | 0.9 | 2 | 0.01 | 0.18 | 0.17 |
R12018759236 | 12 | 18759236 | T | G | 0.85 | 2 | 0 | 0.25 | 0.22 |
R12018856177 | 12 | 18856177 | G | A | 0.83 | 2 | 0 | 0.29 | 0.24 |
R12022373643 | 12 | 22373643 | A | G | 0.69 | 2 | 0.01 | 0.43 | 0.34 |
R12023173265 | 12 | 23173265 | T | A | 0.77 | 2 | 0 | 0.36 | 0.29 |
Population | Sample Size | Major Allele Frequency/Locus | Mean Gene Diversity | Mean PIC Value |
---|---|---|---|---|
All subpopulations | 365 | 0.76 | 0.33 | 0.26 |
Central (C) | 89 | 0.77 | 0.32 | 0.25 |
Northern (N) | 96 | 0.80 | 0.29 | 0.24 |
Northeastern (NE) | 86 | 0.81 | 0.28 | 0.23 |
Southern (S) | 94 | 0.77 | 0.31 | 0.25 |
Population | Sample Size | Major Allele Frequency /Locus | Mean Gene Diversity | Mean PIC Value |
---|---|---|---|---|
All subpopulations | 365 | 0.76 | 0.32 | 0.26 |
Group I (indica) | 167 | 0.80 | 0.27 | 0.21 |
Group II (indica) | 166 | 0.82 | 0.24 | 0.19 |
Group III (japonica) | 32 | 0.93 | 0.09 | 0.07 |
Subpopulations | Central | North | Northeast | South |
---|---|---|---|---|
Central (C) | 0.000 | |||
Northern (N) | 0.039 | 0.000 | ||
Northeast (NE) | 0.023 | 0.016 | 0.000 | |
South (S) | 0.052 | 0.069 | 0.078 | 0.000 |
Source | df | SS | MS | Estimated Variance | Percentage of Total Variance | Probability (p) |
---|---|---|---|---|---|---|
Among Pops | 3 | 1463.724 | 487.908 | 4.835 | 9% | <0.001 |
Within Pops | 361 | 16970.874 | 47.011 | 47.011 | 91% | |
Total | 364 | 18434.597 | 51.846 | 100% |
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Aesomnuk, W.; Ruengphayak, S.; Ruanjaichon, V.; Sreewongchai, T.; Malumpong, C.; Vanavichit, A.; Toojinda, T.; Wanchana, S.; Arikit, S. Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers. Agronomy 2021, 11, 995. https://doi.org/10.3390/agronomy11050995
Aesomnuk W, Ruengphayak S, Ruanjaichon V, Sreewongchai T, Malumpong C, Vanavichit A, Toojinda T, Wanchana S, Arikit S. Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers. Agronomy. 2021; 11(5):995. https://doi.org/10.3390/agronomy11050995
Chicago/Turabian StyleAesomnuk, Wanchana, Siriphat Ruengphayak, Vinitchan Ruanjaichon, Tanee Sreewongchai, Chanate Malumpong, Apichart Vanavichit, Theerayut Toojinda, Samart Wanchana, and Siwaret Arikit. 2021. "Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers" Agronomy 11, no. 5: 995. https://doi.org/10.3390/agronomy11050995