Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize
Abstract
:1. Introduction
2. Materials and Methods
2.1. Germplasm Materials and Experimental Design
2.2. Phenotypic Data Collection
2.3. Statistical Analyses for Phenotypic Data
2.4. Genome-Wide Association Study
2.5. Total RNA Extraction and Sequencing
2.6. KASP Marker Development and Validation
3. Results
3.1. Phenotypic Data Analysis for Aphid Resistance
3.2. GWAS
3.3. RNA-Seq
3.4. Functional Verification of the Gene Cluster on Chromosome 4S
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Aphid Resistant Score | Symptom |
---|---|
0 | No aphid |
1 | Aphid cover area is less than 5% of the tassel or leaf. |
2 | Aphid cover area is more than 5% and less than 30%, and there are very few aphids in the lower leaves. |
3 | Aphid cover area is more than 30% and less than 50%, and there are very few aphids in the lower leaves. |
4 | The aphid covers the tassel more than 50%, and there are some aphids in the lower leaves. |
5 | The tassels and lower leaves are covered with dense aphids. |
Environments | Mean ± SD | Range | σg2 | σge2 | σe2 | H2 |
---|---|---|---|---|---|---|
ARS_E1 | 2.83 ± 1.76 | 0.00–5.00 | 2.74 | 0.32 | 0.94 | |
ARS_E2 | 2.98 ± 1.37 | 0.00–5.00 | 1.44 | 0.29 | 0.91 | |
ARS_E3 | 2.92 ± 1.58 | 0.00–5.00 | 1.61 | 0.85 | 0.78 | |
Combine | 2.91 ± 1.58 | 0.00–5.00 | 1.17 | 0.78 | 0.47 | 0.77 |
Chr | Position | Gene | Function Annotation |
---|---|---|---|
1 | 219548351 | GRMZM2G127361 | Oxidoreductase zinc-binding dehydrogenase family protein |
1 | 82154848 | GRMZM2G132690 | Heavy metal transport/detoxification superfamily protein |
2 | 196411877 | GRMZM2G114107 | winged-helix DNA-binding transcription factor family protein |
2 | 3387748 | GRMZM2G047448 | (PGA6, WUS, WUS1) Homeodomain-like superfamily protein |
3 | 196434589 | GRMZM2G352234 | Pentatricopeptide repeat (PPR) superfamily protein |
4 | 3261014 | GRMZM2G085661 | (CYP71B37) cytochrome P450 family 71 subfamily B polypeptide 37, benzoxazinone synthesis 2 |
4 | 240329225 | GRMZM2G054162 | (IBM1) Transcription factor jumonji (jmjC) domain-containing protein |
5 | 15323527 | GRMZM2G161411 | (ATWRKY23, WRKY23) WRKY DNA-binding protein 23 |
5 | 201461600 | GRMZM2G147430 | Phosphoribulokinase/Uridine kinase family |
5 | 147624523 | GRMZM2G026490 | NHL domain-containing protein |
6 | 145107284 | GRMZM2G479523 | (GL22) germin-like protein subfamily 2 member 2 precursor |
6 | 158441896 | GRMZM2G176133 | Ribosomal protein L33 family protein |
6 | 161283910 | GRMZM2G034225 | expressed protein |
7 | 8677546 | GRMZM2G107408 | expressed protein |
7 | 167601337 | GRMZM2G056407 | (ATMYB94, ATMYBCP70, MYB94) myb domain protein 94 |
7 | 156116120 | GRMZM2G465999 | S-locus lectin protein kinase family protein |
8 | 151270345 | GRMZM2G017305 | P-loop containing nucleoside triphosphate hydrolases superfamily protein |
8 | 163281806 | GRMZM2G065893 | (RGLG2) RING domain ligase2 |
9 | 100282128 | GRMZM2G423693 | Nucleotide-diphospho-sugar transferase family protein |
10 | 133276617 | GRMZM2G123719 | (ATSCO1, ATSCO1/CPEF-G, SCO1) Translation elongation factor EFG/EF2 protein |
10 | 133332879 | GRMZM2G054418 | ATP binding microtubule motor family protein |
10 | 137656350 | GRMZM2G155762 | basic helix–loop–helix (bHLH) DNA-binding superfamily protein |
Pathway ID | KEGG Pathway | Gene Number | p_adj |
---|---|---|---|
ko00402 | Benzoxazinoid biosynthesis | 5 | 5.9 × 10−3 |
ko00500 | Starch and sucrose metabolism | 17 | 1.6 × 10−2 |
ko00052 | Galactose metabolism | 9 | 3.1 × 10−2 |
ko00480 | Glutathione metabolism | 12 | 4.0 × 10−2 |
ko01200 | Carbon metabolism | 23 | 4.2 × 10−2 |
Allele | Number | Average Disease Grade | Increased Resistance | p-Value |
---|---|---|---|---|
Favorite allele | 145 | 4.75 | 18.50% | 1.29 × 10−5 |
Normal allele | 313 | 5.83 |
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Sun, D.; Wei, Y.; Han, C.; Li, X.; Zhang, Z.; Wang, S.; Zhou, Z.; Gao, J.; Chen, J.; Wu, J. Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize. Plants 2025, 14, 1614. https://doi.org/10.3390/plants14111614
Sun D, Wei Y, Han C, Li X, Zhang Z, Wang S, Zhou Z, Gao J, Chen J, Wu J. Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize. Plants. 2025; 14(11):1614. https://doi.org/10.3390/plants14111614
Chicago/Turabian StyleSun, Doudou, Yijun Wei, Chunyan Han, Xiaopeng Li, Zhen Zhang, Shiwei Wang, Zijian Zhou, Jingyang Gao, Jiafa Chen, and Jianyu Wu. 2025. "Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize" Plants 14, no. 11: 1614. https://doi.org/10.3390/plants14111614
APA StyleSun, D., Wei, Y., Han, C., Li, X., Zhang, Z., Wang, S., Zhou, Z., Gao, J., Chen, J., & Wu, J. (2025). Genome-Wide Association Study and RNA-Seq Elucidate the Genetic Mechanisms Behind Aphid (Rhopalosiphum maidis F.) Resistance in Maize. Plants, 14(11), 1614. https://doi.org/10.3390/plants14111614