Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Diversity of G. arboretum Population
2.2. Association Mapping of Salt Tolerance Related Traits Using SNP Markers
2.3. SNP Rich Regions Associated with RFW and RSL
2.4. SNP Rich Regions Associated with RChlC
2.5. SNP Rich Region Associated with RWC
2.6. SNP Rich Regions Associated with CIST
3. Discussion
3.1. Genetic Variation in Salt Tolerance Related Traits of G. arboretum Accessions
3.2. Association Mapping of Salt Tolerance Traits Using SNP Markers
4. Materials and Methods
4.1. Plant Materials and Sample Preparation
4.2. Trait Evaluation
4.3. DNA Extraction
4.4. Phenotypic Diversity
4.5. Genome-Wide Association Analysis
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
RGR | Relative germination rate |
RFW | Relative fresh weight |
RSL | Relative stem length |
RWC | Relative water content |
RChlC | Relative chlorophyll content; |
REC | Relative electric conduct; |
RMDA | Relative methylene dioxyamphetamine |
CIST | Comprehensive index of salt tolerance |
MMLM | Multi-Locus Mixed Model |
QTL | Quantitative trait loci; |
SSR | Simple sequence repeats |
SNP | Single-nucleotide polymorphism |
TW | Turgid weights; |
ANOVA | Analysis of variance; |
Quantile–quantile plots | |
LD | Linkage disequilibrium; |
GWAS | Genome-wide association study; |
HR | Homologous recombination |
ABA | Abscisic acid; |
GHs | Glycosyl hydrolases |
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Traits 1 | Mean | SD | Min | Max | CV | Mean Square | F | P > F |
---|---|---|---|---|---|---|---|---|
GR | 19.936 | 10.77 | 0 | 40 | 54.02 | 338.55 | 8.16 | <0.0001 |
FW | 0.371 | 0.089 | 0.02 | 0.77 | 24.2 | 0.128 | 34.16 | <0.0001 |
SL | 4.969 | 1.481 | 0.40 | 10.2 | 29.84 | 40.77 | 49.76 | <0.0001 |
WC | 1.112 | 3.481 | 0.36 | 96.97 | 312.9 | 31.83 | 4.01 | <0.0001 |
ChlC | 39.47 | 9.96 | 3.50 | 50.2 | 25.53 | 6763.5 | 8.31 | <0.0001 |
EC | 31.47 | 42.54 | 0.116 | 844.4 | 135.19 | 541.2 | 6.49 | <0.0001 |
MDA | 0.007 | 0.0046 | 0 | 0.04 | 59.8 | 0.000095 | 14.36 | <0.0001 |
Trait 1 | GR | FW | SL | WC | ChlC | EC | MDA |
---|---|---|---|---|---|---|---|
GR | 1 | 0.22 *** | 0.295 *** | −0.0178 | 0.112 ** | 0.0841 | 0.012 |
FW | 1 | 0.575 *** | −0.043 | 0.070 *** | 0.0613 | 0.135 *** | |
SL | 1 | −0.017 | 0.115 *** | −0.051 | 0.030 | ||
WC | 1 | 0.048 | 0.002 | 0.059 * | |||
ChlC | 1 | 0.1 ** | −0.073 * | ||||
EC | 1 | 0.079 * | |||||
MDA | 1 |
Chromosome | Total | RGR | RFW | RSL | RWC | RChlC | REC | RMDA | CIST |
---|---|---|---|---|---|---|---|---|---|
Chr-1 | 163 | 1 | 26 | 22 | 12 | 15 | 14 | 70 | 3 |
Chr-2 | 152 | 5 | 10 | 10 | 39 | 3 | 12 | 49 | 24 |
Chr-3 | 332 | 1 | 3 | 8 | 7 | 11 | 278 | 24 | 0 |
Chr-4 | 201 | 3 | 12 | 26 | 27 | 51 | 59 | 19 | 4 |
Chr-5 | 155 | 2 | 7 | 17 | 21 | 4 | 94 | 8 | 2 |
Chr-6 | 112 | 10 | 16 | 11 | 22 | 2 | 21 | 23 | 7 |
Chr-7 | 295 | 2 | 67 | 108 | 67 | 6 | 24 | 14 | 7 |
Chr-8 | 99 | 15 | 10 | 8 | 27 | 4 | 9 | 24 | 2 |
Chr-9 | 104 | 4 | 2 | 8 | 9 | 47 | 7 | 24 | 3 |
Chr-10 | 80 | 1 | 7 | 10 | 34 | 4 | 11 | 7 | 6 |
Chr-11 | 112 | 5 | 5 | 8 | 17 | 20 | 24 | 18 | 15 |
Chr-12 | 57 | 8 | 4 | 2 | 31 | 3 | 5 | 3 | 1 |
Chr-13 | 100 | 1 | 4 | 10 | 29 | 16 | 6 | 32 | 2 |
Chr-UN | 100 | 3 | 14 | 7 | 28 | 4 | 19 | 20 | 5 |
Total | 2062 | 61 | 187 | 255 | 370 | 190 | 583 | 335 | 81 |
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Dilnur, T.; Peng, Z.; Pan, Z.; Palanga, K.K.; Jia, Y.; Gong, W.; Du, X. Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers. Int. J. Mol. Sci. 2019, 20, 2168. https://doi.org/10.3390/ijms20092168
Dilnur T, Peng Z, Pan Z, Palanga KK, Jia Y, Gong W, Du X. Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers. International Journal of Molecular Sciences. 2019; 20(9):2168. https://doi.org/10.3390/ijms20092168
Chicago/Turabian StyleDilnur, Tussipkan, Zhen Peng, Zhaoe Pan, Koffi Kibalou Palanga, Yinhua Jia, Wenfang Gong, and Xiongming Du. 2019. "Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers" International Journal of Molecular Sciences 20, no. 9: 2168. https://doi.org/10.3390/ijms20092168