Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Analysis of TOC in Five RIL Subpopulations
2.2. Phylogenetic Tree, PCA, and Population Structure Analysis
2.3. LD Decay Analysis
2.4. Genome-Wide Association Analysis for TOC in Maize
2.5. Genetic Map Construction and QTL Mapping of TOC in the Five RIL Subpopulations
2.6. Identification of Candidate Genes Related to TOC and Haplotype Analysis
3. Discussion
3.1. Comparison of Loci Significantly Associated with TOC with Previously Reported QTLs
3.2. Functional Annotation of Candidate Genes
3.3. Mechanism of Synthesis of TOC in Maize
3.4. Genetic Effects of Oil Content in Tropical Maize
4. Materials and Methods
4.1. Plant Materials and Population Development
4.2. Experimental Design and Oil Content Estimation
4.3. Statistical Analysis of TOC and Estimation of Heritability
4.4. DNA Extraction and Genotyping-by-Sequencing (GBS)
4.5. Phylogenetic Tree, PCA, and Linkage Disequilibrium Analysis
4.6. Genome-Wide Association Analysis
4.7. Construction of Genetic Map and QTL Mapping
4.8. Identification and Functional Annotation of Candidate Genes
4.9. Haplotype Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Population | Environment | Mean | Standard Deviation | Skewness | Kurtosis | Coefficient of Variation (%) | Heritability (h2) (%) | Correlation Coefficient |
---|---|---|---|---|---|---|---|---|
(r) | ||||||||
pop1 | 22YS | 5.273 | 0.662 | −0.158 | −0.481 | 12.60% | 88.1 | 22YS/23JH = 0.77 ** |
23JH | 5.189 | 0.623 | 0.375 | −0.226 | 12% | 23JH/21YS = 0.73 ** | ||
21YS | 5.199 | 0.711 | 0.070 | −0.080 | 13.70% | 21YS/22YS = 0.68 ** | ||
total | 5.220 | 0.665 | 0.079 | −0.286 | 12.74% | |||
pop2 | 22YS | 5.164 | 0.590 | 0.146 | −0.010 | 11.40% | 93.1 | 22YS/23JH = 0.89 ** |
23JH | 5.050 | 0.550 | 0.314 | −0.334 | 10.90% | 23JH/21YS = 0.91 ** | ||
21YS | 4.910 | 0.610 | 0.203 | −0.217 | 12.40% | 21YS/22YS = 0.72 ** | ||
total | 5.041 | 0.591 | 0.185 | −0.192 | 11.72% | |||
pop3 | 22YS | 5.501 | 0.809 | −0.243 | −0.071 | 14.70% | 83.9 | 22YS/23JH = 0.87 ** |
23JH | 5.320 | 0.623 | 0.052 | −0.441 | 11.70% | 23JH/21YS = 0.79 ** | ||
21YS | 5.120 | 0.620 | 0.019 | −0.387 | 12.10% | 21YS/22YS = 0.47 ** | ||
total | 5.313 | 0.704 | 0.041 | −0.160 | 13.25% | |||
pop4 | 22YS | 4.884 | 0.432 | 0.533 | −0.045 | 8.80% | 79.4 | 22YS/23JH = 0.78 ** |
23JH | 4.888 | 0.371 | 0.163 | −0.925 | 7.60% | 23JH/21YS = 0.76 ** | ||
21YS | 4.912 | 0.439 | 0.353 | −0.087 | 8.90% | 21YS/22YS = 0.40 ** | ||
total | 4.895 | 0.413 | 0.378 | −0.233 | 8.44% | |||
pop5 | 22YS | 5.276 | 0.592 | 0.241 | −0.402 | 11.20% | 91.6 | 22YS/23JH = 0.91 ** |
23JH | 5.214 | 0.542 | 0.242 | −0.644 | 10.40% | 23JH/21YS = 0.88 ** | ||
21YS | 5.167 | 0.504 | 0.222 | −0.274 | 9.80% | 21YS/22YS = 0.70 ** | ||
total | 5.216 | 0.547 | 0.263 | −0.412 | 10.49% |
Env. | Chr. | SNP | ref | alt | −log(P) | Additive Effect | Dominance Effect | PVE |
---|---|---|---|---|---|---|---|---|
22YS | 1 | 75,791,466 | G | T | 5.23 | −0.26 | 0.35 | 0.035 |
22YS | 3 | 2,108,126 | G | A | 4.80 | 0.20 | 0.20 | 0.075 |
22YS | 3 | 7,453,745 | G | A | 5.46 | 0.30 | 0.04 | 0.053 |
22YS | 3 | 8,646,933 | C | A | 6.15 | 0.33 | −0.11 | 0.046 |
22YS | 3 | 9,226,566 | G | T | 4.54 | −0.28 | −0.21 | 0.036 |
22YS | 3 | 9,371,935 | C | T | 5.14 | −0.29 | −0.20 | 0.038 |
22YS | 3 | 230,340,051 | C | T | 4.68 | −0.24 | 0.14 | 0.062 |
22YS | 3 | 230,499,437 | G | A | 4.57 | 0.25 | 0.04 | 0.028 |
22YS | 4 | 52,876,804 | A | G | 4.77 | −0.19 | −0.48 | 0.035 |
22YS | 4 | 203,717,068 | A | G | 6.45 | −0.41 | −0.01 | 0.073 |
22YS | 5 | 216,419,106 | A | T | 5.30 | −0.26 | −0.05 | 0.049 |
22YS | 6 | 19,088,018 | C | T | 4.63 | NaN | NaN | 0.029 |
22YS | 7 | 140,826,856 | C | T | 4.94 | 0.31 | 0.06 | 0.042 |
22YS | 8 | 1,952,449 | C | T | 5.22 | 0.15 | −0.13 | 0.038 |
22YS | 8 | 172,972,407 | T | C | 4.99 | −0.27 | 0.13 | 0.055 |
22YS, BLUP | 8 | 173,247,098 | A | T | 6.86 | −0.37 | −0.18 | 0.070 |
22YS, 23JH, BLUP | 8 | 174,055,891 | T | C | 6.32 | −0.27 | −0.48 | 0.098 |
22YS | 8 | 177,414,430 | C | T | 4.71 | −0.22 | −0.01 | 0.077 |
22YS | 9 | 13,835,261 | C | T | 4.72 | −0.25 | 0.00 | 0.092 |
22YS, 23JH, BLUP | 9 | 14,820,336 | C | A | 5.25 | 0.24 | −0.14 | 0.055 |
22YS, 23JH, BLUP | 9 | 92,493,718 | T | C | 5.24 | −0.57 | −0.16 | 0.053 |
22YS | 10 | 115,482,753 | G | A | 4.67 | 0.23 | 0.27 | 0.110 |
22YS | 10 | 138,012,512 | T | G | 5.23 | 0.35 | −0.61 | 0.117 |
23JH | 1 | 89,810,991 | G | T | 4.61 | −0.36 | −0.11 | 0.053 |
23JH | 2 | 172,364,269 | T | C | 5.02 | NaN | NaN | 0.083 |
23JH, BLUP | 4 | 80,064,051 | C | A | 4.84 | 0.26 | 0.12 | 0.034 |
23JH, BLUP | 9 | 110,672,521 | T | C | 4.83 | −0.25 | 0.21 | 0.071 |
23JH, 21YS | 10 | 17,500,491 | C | G | 4.85 | NaN | NaN | 0.057 |
21YS | 2 | 5,102,776 | G | T | 5.08 | −0.27 | −0.58 | 0.064 |
21YS | 2 | 62,659,851 | G | A | 5.21 | NaN | NaN | 0.088 |
21YS | 4 | 131,018,543 | C | A | 5.40 | NaN | NaN | 0.072 |
21YS | 4 | 132,312,280 | C | T | 4.76 | NaN | NaN | 0.055 |
21YS | 5 | 221,373,665 | G | A | 6.13 | 0.22 | −0.01 | 0.059 |
21YS | 5 | 222,162,464 | T | C | 4.70 | 0.17 | −0.01 | 0.044 |
21YS | 7 | 21,816,794 | C | G | 5.00 | 0.24 | −0.13 | 0.073 |
21YS | 7 | 165,218,537 | A | G | 5.96 | 0.26 | −0.17 | 0.084 |
21YS | 9 | 40,627,693 | G | A | 5.45 | NaN | NaN | 0.075 |
21YS | 9 | 54,914,157 | T | C | 4.64 | NaN | NaN | 0.057 |
21YS | 9 | 108,901,209 | A | G | 4.89 | 0.20 | 0.34 | 0.053 |
21YS, BLUP | 9 | 108,933,426 | A | G | 7.44 | 0.29 | −0.09 | 0.108 |
21YS | 9 | 109,017,561 | A | G | 5.50 | 0.21 | −0.15 | 0.075 |
21YS | 9 | 109,122,650 | G | A | 4.58 | −0.20 | 0.14 | 0.080 |
21YS | 9 | 109,283,271 | G | A | 4.94 | −0.16 | −0.34 | 0.086 |
21YS | 9 | 109,407,646 | C | T | 5.07 | 0.22 | 0.16 | 0.063 |
21YS | 9 | 109,451,171 | G | C | 4.94 | −0.20 | 0.09 | 0.057 |
21YS | 9 | 110,611,574 | G | T | 5.70 | 0.29 | −0.32 | 0.132 |
21YS | 9 | 110,672,521 | T | C | 5.71 | −0.25 | −0.19 | 0.110 |
21YS | 10 | 17,500,491 | C | G | 4.60 | NaN | NaN | 0.074 |
BLUP | 7 | 142,297,954 | A | G | 4.83 | 0.19 | −0.09 | 0.076 |
BLUP | 9 | 108,933,426 | A | G | 4.51 | 0.21 | −0.03 | 0.081 |
BLUP | 9 | 152,304,134 | T | A | 4.94 | 0.17 | −0.11 | 0.056 |
Mapping Population | QTL | Chromosome | Position (cM) | Mapping Interval (bp) | LOD | Additive Effect | R2 |
---|---|---|---|---|---|---|---|
pop1 | qTOC2-1 | 2 | 115 | 29,801,036–37,206,712 | 2.90 | 0.163 | 0.090 |
qTOC2-2 | 2 | 106.98 | 14,177,571–47,384,437 | 4.63 | 0.130 | 0.060 | |
qTOC2-3 | 2 | 117.03 | 14,177,571–37,206,712 | 3.75 | 0.130 | 0.050 | |
qTOC3-1 | 3 | 33.25 | 193,353,260–227,027,669 | 3.82 | −0.098 | 0.030 | |
qTOC9-1 | 9 | 75.92 | 110,367,967–125,469,868 | 3.39 | −0.106 | 0.030 | |
pop3 | qTOC1-1 | 1 | 27.11 | 273,307,800–273,997,185 | 3.81 | 0.400 | 0.131 |
qTOC1-2 | 1 | 198.72 | 61,742,795–76,153,784 | 3.82 | 0.250 | 0.014 | |
qTOC4-1 | 4 | 232.73 | 161,621,304–164,227,248 | 5.65 | 0.650 | 0.199 | |
qTOC4-2 | 4 | 599.88 | 172,418,126–175,502,163 | 3.46 | 0.320 | 0.143 | |
qTOC7-1 | 7 | 199.1 | 50,416,681–50,735,457 | 4.33 | −0.560 | 0.151 | |
pop4 | qTOC5-1 | 5 | 34.22 | 79,346,283–81,012,543 | 3.31 | 0.038 | 0.005 |
qTOC7-1 | 7 | 29.17 | 132,794,775–153,544,218 | 3.01 | −0.146 | 0.110 | |
qTOC8-1 | 8 | 89.73 | 10,663,910–30,775,820 | 4.61 | −0.166 | 0.124 | |
pop5 | qTOC2-1 | 2 | 1.57 | 222,088,040–232,416,169 | 3.75 | −0.290 | 0.144 |
qTOC2-2 | 2 | 15.67 | 159,679,997–163,407,700 | 5.73 | 0.360 | 0.231 | |
qTOC3-1 | 3 | 33.53 | 114,248,818–166,417,378 | 4.27 | −0.240 | 0.177 | |
qTOC5-1 | 5 | 22.99 | 135,409,128–153,772,976 | 3.92 | 0.280 | 0.146 | |
qTOC5-2 | 5 | 55.99 | 31,369,431–38,866,833 | 2.80 | −0.230 | 0.103 |
SNP/QTL | Chromosome | Position | Mapping Interval (bp) | Candidate Gene | Candidate Gene Range (bp) | Gene Annotation |
---|---|---|---|---|---|---|
SNP-75791466 | 1 | 75,791,466 bp | [75,771,466–75,811,466] | Zm00001d029550 | 75,797,114–75,806,603 | Diacylglycerol Kinase 1 |
qTOC1-2 | 1 | 198.72 cM | 61,742,795–76,153,784 | |||
SNP-75791466 | 1 | 75,791,466 bp | [75,771,466–75,811,466] | Zm00001d029551 | 75,803,417–75,804,837 | NaN |
qTOC1-2 | 1 | 198.72 cM | 61,742,795–76,153,784 |
Gene ID | SNP Position | Haplotype | Hap_Sample_Num 1 |
---|---|---|---|
Zm00001d029550 | Chr1: 75,791,466 bp | GTTCTACG(Hap1) | 192 |
ATCTGGTA(Hap2) | 74 | ||
ACCTGGTA(Hap3) | 32 | ||
Zm00001d029551 | Chr1: 75,791,466 bp | GTTCT(Hap1) | 129 |
ATCTG(Hap2) | 126 | ||
ACCTG(Hap3) | 40 |
Materials | Population Type | Trait | QTL | Marker/Physical Interval | LOD | PVE (%) | Reference |
---|---|---|---|---|---|---|---|
B73, By804 | RIL | KO | qKO1-1 | umc1598–umc1884 | - | 14.3 | [25] |
Ku13, Sc55 | RIL | OIL | qOLE1-1 | 66.4–71.0 Mb | 4.84 | 11.06 | [8] |
B73, By804 | RIL | OIL | OIL1-1 | umc2217–bnlg2086 | - | - | [11] |
B73, By804 | RIL | EER | qEEWR1-1 | 73,374,836–73,376,998 bp | - | - | [26] |
Parent | Pedigree | Heterotic Group | Ecological Type | Total Oil Content (%) |
---|---|---|---|---|
Ye107 | Derived from US hybrid DeKalb XL80 | Reid | Temperate | 3.51 |
CML312 | S89500-F2-2-2-1-1-B*5-2-1-6-1(DH) | nonReid | Subtropical | 6.8 |
CML384 | P502c1#-771-2-2-1-3-B-1-1-3-1(DH) | Reid | Subtropical | 7.03 |
CML395 | 90323B-1-B-1-B*4-1-1-2-1(DH) | nonReid | Tropical | 7.1 |
YML46 | SW1-1-1-2-1-2-1 | Suwan | Tropical | 5.9 |
YML32 | Suwan 1(S)C9-S8-346-2 (Kei 8902)-3-4-4-6 | Suwan | Tropical | 7.3 |
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Shi, M.; Sun, J.; Jiang, F.; Shaw, R.K.; Ijaz, B.; Fan, X. Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm. Int. J. Mol. Sci. 2024, 25, 10813. https://doi.org/10.3390/ijms251910813
Shi M, Sun J, Jiang F, Shaw RK, Ijaz B, Fan X. Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm. International Journal of Molecular Sciences. 2024; 25(19):10813. https://doi.org/10.3390/ijms251910813
Chicago/Turabian StyleShi, Mengfei, Jiachen Sun, Fuyan Jiang, Ranjan K. Shaw, Babar Ijaz, and Xingming Fan. 2024. "Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm" International Journal of Molecular Sciences 25, no. 19: 10813. https://doi.org/10.3390/ijms251910813