Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Evaluation under Alkaline Stress
2.2. Correlation Analysis
2.3. Principal Component Analysis (PCA)
2.4. Phenotypic Clustering
2.5. Population Structure
2.6. Linkage Disequilibrium (LD)
2.7. GWAS Analysis
2.8. Candidate Genes/QTLs for Alkalinity Tolerance
2.9. Expression Profiling of Selected Candidate Genes under Alkalinity Stress
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Plant Materials
5.2. Statistical Analysis
5.3. SNP Genotyping and Quality Control
5.4. Structure Analysis and Linkage Disequilibrium
5.5. Association Mapping
5.6. Candidate Gene Analysis
5.7. Expression Profiling of Selected Genes by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR)
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait a | Min | Max | Mean | Standard Deviation | RIL Pr > Fc b | Heritability |
---|---|---|---|---|---|---|
AKT | 1.0 | 9.0 | 4.75 | 2.05 | 0.002 ** | 0.87 |
SHL | 21.3 | 63.0 | 37.7 | 6.6 | 0.047 * | 0.64 |
RTL | 7.0 | 22.7 | 16.4 | 3.2 | 0.029 * | 0.52 |
RSR | 0.16 | 0.76 | 0.46 | 0.21 | 0.029 * | 0.69 |
Inv_FW | 0.01 | 0.30 | 0.16 | 0.07 | 0.0003 ** | 0.61 |
log_DW | −2.84 | −0.60 | −1.50 | 0.43 | 0.029 * | 0.53 |
SNC | 661.6 | 3508.1 | 1730.1 | 440.3 | 0.032 * | 0.77 |
SKC | 326.3 | 1077.9 | 657.7 | 138.3 | 0.048 * | 0.84 |
SNK | 0.88 | 5.95 | 2.79 | 1.11 | 0.041 * | 0.81 |
Trait a | AKT | SHL | RTL | RSR | Inv_FW | log_DW | SNC | SKC | SNK |
---|---|---|---|---|---|---|---|---|---|
AKT | 1.000 | ||||||||
SHL | −0.123 * | 1.000 | |||||||
RTL | −0.147 * | 0.02 | 1.000 | ||||||
RSR | −0.154 * | −0.757 ** | −0.533 ** | 1.000 | |||||
Inv_FW | −0.909 ** | 0.127 * | 0.174 * | −0.173 * | 1.000 | ||||
log_DW | −0.954 ** | 0.139 * | 0.170 * | −0.181 * | 0.961 ** | 1.000 | |||
SNC | 0.467 ** | −0.028 | −0.074 | −0.027 | −0.36 ** | −0.423 ** | 1.000 | ||
SKC | −0.053 * | 0.004 | 0.009 | 0.002 | 0.155 * | 0.094 | −0.87 ** | 1.000 | |
SNK | 0.321 ** | −0.028 | −0.002 | −0.015 | −0.18 ** | −0.258 ** | 0.742 ** | −0.674 ** | 1.000 |
Clusters | Genotypes |
---|---|
Cluster 1 (Highly Susceptible) | Hasawi, Roy J, Djogolan, Dular, Cypress, Vegold, ChN1264, Toro-2, Belle Patna, N22, Magnolia, Glutinous Zenith, Jazzman-2, Toro, Chengri, Azucena, Chambal, Bluebonnet, Orion, Adair, Pratao Tipo Guedes, Dholamon 560, Hill medium, KN-1-B-361-1-8-67 |
Cluster 2 (Tolerant) | PSBRC-50, CL111, Caloro, Cheriviruppu, CL131, Trenasse, Pirogue, LA0802140, Jupiter, LA0702085, Rexona, FL478, Geumgangbyeo, Neptune, CL261, FL318, Caffey, Lacassine, CLPK873, Cocodrie, Lacrosse, Sunbonnet, Lafitte, Dellmati, Carolina Gold, Bengal, Century Patna, CL152, Nato, MS-1996-9, Glutinous Selection, Saturn Rogue, Langmanbi, Milagrosa, Zhenshan 97, R-50, Mars, Kasalath, Sarioo50, IR 8, M202, Zenith, IR 64, Arkansas Fortuna, Texmont, Kranti, TP 49, Millie, Kirak, Chung yuen, IRGC1244, Newrex, RD, IRGC32567, Kitaake, Brazos, M-204, Delitus, Italica Livorno, CT-329 |
Cluster 3 (Highly Tolerant) | Saturn, Della, JN100, Moroberekan, JN349, Nipponbare, Mercury, BHA1115, IR 29, Dellrose, Lotus, Agami, Neches, Epagri, Cheniere, CSR11, Vandana, Gu Ze, IR 50, Panidhan II, Koshihikari, Teqing, Taichung 65, Daido, Lemont, Quilloa 66304, Dellmont, Kanchan, Swarna, W149, Perum karuppan, Taipe 309, Hayamasari |
Cluster 4 (Moderately Tolerant) | LA110, CL142, Century Rogue, Pokkali, Pecos, Nona Bokra, Wells, Gold Zenith, Skybonnet, Tebonnet, Nira, Vista, TCCP, Templeton, Nova 66, IRRI147, Taggert, Bluebelle, Arang, Ecrevisse, Smooth Zenith, Damodar, Kalia, MS-1995-15, SLO16, Rexark, V20B, Ning Yang Keng, Stormproof, Starbonnet, B573-A4-20-6, R-27, Gold Nato, Naylamp, Azaurel, Melrose, Jinheung, Arkrose, Dixiebelle, Nerretto, PSRR-1, Bala, Co39, San Tou Thou, IR4432-52-6-4, Hill LongGrain, Bharathy, H4, IARI 5823, Early Prolific, Fatehpur 3, Prelude, WC10380 |
Cluster 5 (Susceptible) | Pinkaeo, LAH10, Mermentau, Evangeline, CR5272, R609, Jes, Della-2, CL162, R-54, Radin Ebos 33, Kokubelle, LaGrue, Jackson |
Source of Variation | DF a | Sum of Squares | Mean Sum of Squares | Variance (%) | p-Value b |
---|---|---|---|---|---|
Among population | 4 | 495.8 | 123.9 | 61 | <0.0001 |
Within population | 163 | 1129.8 | 6.9 | 39 | <0.001 |
Total | 167 | 1625.6 | 100 |
Chr. | No. of SNPs | Chr. Size (bp) † | SNP Density (bp/SNP) | LD $ Distance (bp) | |
---|---|---|---|---|---|
1 | 93 | 43,270,923 | 465,279 | 15,193,454 | |
2 | 81 | 35,937,250 | 443,670 | 13,604,743 | |
3 | 78 | 36,413,819 | 466,844 | 12,513,847 | |
4 | 66 | 35,502,694 | 537,920 | 11,534,383 | |
5 | 64 | 29,958,434 | 468,101 | 10,451,492 | |
6 | 85 | 31,248,787 | 367,633 | 11,193,100 | |
7 | 59 | 29,697,621 | 503,350 | 11,473,349 | |
8 | 72 | 28,443,022 | 395,042 | 9,654,739 | |
9 | 58 | 23,012,720 | 396,772 | 7,434,300 | |
10 | 54 | 23,207,287 | 429,765 | 7,334,850 | |
11 | 59 | 29,021,106 | 491,884 | 9,261,105 | |
12 | 62 | 27,531,856 | 444,063 | 8,644,012 | |
Total | 830 | 373,245,519 | Mean | 450,861 | 10,691,115 |
Trait a | SNP | Locus | Annotation | QTLs/Genes in Previous Studies |
---|---|---|---|---|
AKT | S04_29881066 | Os04g50090 | Helix–loop–helix DNA-binding protein | qSNK4-2 [12] |
S08_14184612 | Os08g23440 | amino acid permease family protein | LOC_Os08g23440 [16] | |
SHL | S04_22808095 | Os04g38340 | ER-Golgi intermediate-compartment protein 3 | qDLR4 [26] |
S12_23066809 | Os12g37570 | protein kinase family protein | ||
S12_23108164 | Os12g37640 | xaa-Pro aminopeptidase | ||
RTL | S02_35216781 | Os02g58139 | OsSigP1-Type I Signal Peptidase homolog | |
S04_29715617 | Os04g49850 | Expressed protein | qSNK4-2 [12] | |
S04_34925111 | Os04g58730 | AT-hook-motif-domain-containing protein | qSNK4-2 [12] | |
S05_1487229 | Os05g03510 | Expressed protein | ||
S07_28409912 | Os07g47500 | Histone-arginine methyltransferase CARM1 | qRGR7 [25] | |
RSR | S01_23656773 | Os01g41790 | Expressed protein | |
S01_37680628 | Os01g64910 | Anthocyanidin 5,3-O-glucosyltransferase | ||
S05_24090514 | Os05g41130 | OsFBX168-F-box-domain-containing protein | qRRN5 [25] | |
S10_18098744 | Os10g35570 | Expressed protein | qSKC10.18 [2,7] | |
S12_3544726 | Os12g07210 | Expressed protein | ||
log_DW | S01_36150523 | Os01g62450 | Expressed protein | |
S05_7195992 | Os05g12510 | Expressed protein | qDLRa5-3 [24] | |
inv_FW | S01_3236648 | Os01g06820 | hcr2-0B, putative | |
SKC | S09_19322095 | Os09g32350 | Expressed protein | qSNC9.19 [2] |
S09_19683788 | Os09g32972 | MYB protein | qSNC9.19 [2] | |
S10_18834021 | Os10g35230 | Rf1, mitochondrial precursor | qSKC10.18 [2,7] | |
SNC | S02_3477202 | Os02g06890 | OTU-like cysteine protease family protein | |
S03_14554651 | Os03g25480 | Cytochrome P450 | Os03g25480 [16] | |
S06_15335573 | Os06g39580 | Hypothetical protein | qARL6 [38] | |
S07_29627590 | Os07g49470 | Protein kinase APK1B, chloroplast precursor | ||
S08_15439243 | Os08g25390 | Bifunctional homoserine dehydrogenase | Os08g25390 [16] | |
S09_22076185 | Os09g38340 | ZOS9-17-C2H2 zinc finger protein | ||
SNK | S04_34643455 | Os04g58160 | Fiber protein Fb34, putative | qSNK4-2 [12] |
Trait a | QTLs | Lead SNP | Position | p-Value | R2 (%) | QTLs in a Previous Study |
---|---|---|---|---|---|---|
SHL | qSHL12 | S12_23108164 | 23,108,164 | 0.00058 | 11 | - |
log_DW | qlog_DW1 | S01_36150523 | 36,150,523 | 0.00008 | 14 | qSHL1.38 [2,7] |
SNC | qSNC7 | S07_29627590 | 29,627,590 | 0.00027 | 11 | - |
SKC | qSKC9 | S09_19322095 | 19,322,095 | 0.00037 | 22 | qSNC9.19 [2] |
SKC | qSKC10 | S10_18834021 | 18,834,021 | 0.00021 | 18 | qSKC10.18 [2,7] |
SNK | qSNK4 | S04_34643455 | 34,643,455 | 0.00002 | 16 | qSNK4-2 [12] |
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Singh, L.; Pruthi, R.; Chapagain, S.; Subudhi, P.K. Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice. Plants 2023, 12, 2206. https://doi.org/10.3390/plants12112206
Singh L, Pruthi R, Chapagain S, Subudhi PK. Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice. Plants. 2023; 12(11):2206. https://doi.org/10.3390/plants12112206
Chicago/Turabian StyleSingh, Lovepreet, Rajat Pruthi, Sandeep Chapagain, and Prasanta K. Subudhi. 2023. "Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice" Plants 12, no. 11: 2206. https://doi.org/10.3390/plants12112206