Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (7): 185-194.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1510
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XU Jian-xia1(), DING Yan-qing1, FENG Zhou1,2, CAO Ning1, CHENG Bin1, GAO Xu1, ZOU Gui-hua3, ZHANG Li-yi1()
Received:
2022-12-10
Online:
2023-07-26
Published:
2023-08-17
Contact:
ZHANG Li-yi
E-mail:529438648 @qq.com;lyzhang1997@hotmail.com
XU Jian-xia, DING Yan-qing, FENG Zhou, CAO Ning, CHENG Bin, GAO Xu, ZOU Gui-hua, ZHANG Li-yi. QTL Mapping of Sorghum Plant Height and Internode Numbers Based on Super-GBS Technique[J]. Biotechnology Bulletin, 2023, 39(7): 185-194.
性状 Trait | 环境 Environment | 亲本Parents | RIL群体RIL population | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
BTx623 | 红缨子 Hongyingzi | 最小值 Minimum | 最大值 Maximum | 平均值 Mean | 标准差 SD | 变异系数 CV/% | 偏度 Skewness | 峰度 Kurtosis | ||||
株高 PH/cm | 2020GY | 120.33 | 266.33 | 101.00 | 360.67 | 207.37 | 56.94 | 27.46 | 0.176 | -0.769 | ||
2020AS | 132.67 | 284.00 | 106.67 | 320.33 | 197.99 | 47.66 | 24.07 | 0.192 | -0.773 | |||
2020LD | 122.00 | 196.33 | 81.67 | 254.00 | 178.02 | 31.65 | 17.78 | -0.213 | -0.453 | |||
2021GY | 124.33 | 215.00 | 105.00 | 316.67 | 201.16 | 43.32 | 21.53 | 0.070 | -0.513 | |||
2021AS | 147.00 | 238.67 | 107.33 | 321.67 | 196.15 | 42.99 | 21.92 | 0.188 | -0.671 | |||
节间数 IN | 2020GY | 8.67 | 10.67 | 5.67 | 13.33 | 9.73 | 1.19 | 12.22 | 0.144 | 0.404 | ||
2020AS | 7.67 | 10.33 | 6.00 | 12.67 | 8.75 | 1.27 | 14.52 | 0.509 | -0.248 | |||
2020LD | 7.00 | 9.33 | 4.67 | 11.00 | 7.48 | 0.98 | 13.07 | 0.402 | 1.609 | |||
2021GY | 7.00 | 8.67 | 5.33 | 11.00 | 8.19 | 0.98 | 12.02 | 0.016 | 0.673 | |||
2021AS | 7.00 | 9.67 | 5.33 | 12.67 | 8.49 | 1.41 | 16.64 | 0.377 | -0.087 |
Table 1 Phenotypic statistics of plant height and internode numbers in the RIL population in five environments
性状 Trait | 环境 Environment | 亲本Parents | RIL群体RIL population | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
BTx623 | 红缨子 Hongyingzi | 最小值 Minimum | 最大值 Maximum | 平均值 Mean | 标准差 SD | 变异系数 CV/% | 偏度 Skewness | 峰度 Kurtosis | ||||
株高 PH/cm | 2020GY | 120.33 | 266.33 | 101.00 | 360.67 | 207.37 | 56.94 | 27.46 | 0.176 | -0.769 | ||
2020AS | 132.67 | 284.00 | 106.67 | 320.33 | 197.99 | 47.66 | 24.07 | 0.192 | -0.773 | |||
2020LD | 122.00 | 196.33 | 81.67 | 254.00 | 178.02 | 31.65 | 17.78 | -0.213 | -0.453 | |||
2021GY | 124.33 | 215.00 | 105.00 | 316.67 | 201.16 | 43.32 | 21.53 | 0.070 | -0.513 | |||
2021AS | 147.00 | 238.67 | 107.33 | 321.67 | 196.15 | 42.99 | 21.92 | 0.188 | -0.671 | |||
节间数 IN | 2020GY | 8.67 | 10.67 | 5.67 | 13.33 | 9.73 | 1.19 | 12.22 | 0.144 | 0.404 | ||
2020AS | 7.67 | 10.33 | 6.00 | 12.67 | 8.75 | 1.27 | 14.52 | 0.509 | -0.248 | |||
2020LD | 7.00 | 9.33 | 4.67 | 11.00 | 7.48 | 0.98 | 13.07 | 0.402 | 1.609 | |||
2021GY | 7.00 | 8.67 | 5.33 | 11.00 | 8.19 | 0.98 | 12.02 | 0.016 | 0.673 | |||
2021AS | 7.00 | 9.67 | 5.33 | 12.67 | 8.49 | 1.41 | 16.64 | 0.377 | -0.087 |
Fig. 1 Frequency distribution of plant heights(A)and internode numbers(B) in RIL population in five environments of Guiyang(2020GY),Anshun(2020AS)and Ledong(2020LD)in 2020, as well as Guiyang(2021GY)and Anshun(2021AS)in 2021
性状Trait | 2020GY-PH | 2020AS-PH | 2020SY-PH | 2021GY-PH | 2021AS-PH | 2020GY-IN | 2020AS-IN | 2020SY-IN | 2021GY-IN | 2021AS-IN |
---|---|---|---|---|---|---|---|---|---|---|
2020GY-PH | 1.000 | |||||||||
2020AS-PH | 0.832** | 1.000 | ||||||||
2020SY-PH | 0.884** | 0.783** | 1.000 | |||||||
2021GY-PH | 0.860** | 0.826** | 0.856** | 1.000 | ||||||
2021AS-PH | 0.844** | 0.760** | 0.814** | 0.861** | 1.000 | |||||
2020GY-IN | 0.474** | 0.457** | 0.387** | 0.418** | 0.381** | 1.000 | ||||
2020AS-IN | 0.399** | 0.584** | 0.317** | 0.383** | 0.380** | 0.651** | 1.000 | |||
2020SY-IN | 0.431** | 0.422** | 0.491** | 0.428** | 0.367** | 0.671** | 0.500** | 1.000 | ||
2021GY-IN | 0.380** | 0.472** | 0.302** | 0.472** | 0.390** | 0.684** | 0.665** | 0.575** | 1.000 | |
2021AS-IN | 0.475** | 0.512** | 0.432** | 0.515** | 0.618** | 0.567** | 0.633** | 0.508** | 0.599** | 1.000 |
Table 2 Correlation analysis of plant heighst and internode numbers in the RIL population
性状Trait | 2020GY-PH | 2020AS-PH | 2020SY-PH | 2021GY-PH | 2021AS-PH | 2020GY-IN | 2020AS-IN | 2020SY-IN | 2021GY-IN | 2021AS-IN |
---|---|---|---|---|---|---|---|---|---|---|
2020GY-PH | 1.000 | |||||||||
2020AS-PH | 0.832** | 1.000 | ||||||||
2020SY-PH | 0.884** | 0.783** | 1.000 | |||||||
2021GY-PH | 0.860** | 0.826** | 0.856** | 1.000 | ||||||
2021AS-PH | 0.844** | 0.760** | 0.814** | 0.861** | 1.000 | |||||
2020GY-IN | 0.474** | 0.457** | 0.387** | 0.418** | 0.381** | 1.000 | ||||
2020AS-IN | 0.399** | 0.584** | 0.317** | 0.383** | 0.380** | 0.651** | 1.000 | |||
2020SY-IN | 0.431** | 0.422** | 0.491** | 0.428** | 0.367** | 0.671** | 0.500** | 1.000 | ||
2021GY-IN | 0.380** | 0.472** | 0.302** | 0.472** | 0.390** | 0.684** | 0.665** | 0.575** | 1.000 | |
2021AS-IN | 0.475** | 0.512** | 0.432** | 0.515** | 0.618** | 0.567** | 0.633** | 0.508** | 0.599** | 1.000 |
性状 Trait | 均方 Mean square | F值F value | 广义遗传率 h2B/% | |||||
---|---|---|---|---|---|---|---|---|
基因型Genotype | 环境Environment | 基因型iro G×E | 基因型Genotype | 环境Environment | 基因型iro G×E | |||
株高PH | 26 001.18 | 75 159.27 | 1 238.43 | 224.52** | 649.01** | 10.69** | 95.23 | |
节间数IN | 14.05 | 419.71 | 1.70 | 43.24** | 1 291.97** | 5.23** | 85.78 |
Table 3 Variance analysis and broad heritability of plant height and internode numbers
性状 Trait | 均方 Mean square | F值F value | 广义遗传率 h2B/% | |||||
---|---|---|---|---|---|---|---|---|
基因型Genotype | 环境Environment | 基因型iro G×E | 基因型Genotype | 环境Environment | 基因型iro G×E | |||
株高PH | 26 001.18 | 75 159.27 | 1 238.43 | 224.52** | 649.01** | 10.69** | 95.23 | |
节间数IN | 14.05 | 419.71 | 1.70 | 43.24** | 1 291.97** | 5.23** | 85.78 |
性状 Trait | 染色体 Chr. | 位点 QTL | 环境 Env. | 位置 Pos./cM | 标记区间 Marker interval | 物理距离 Phy./Mb | 阈值 LOD | 贡献率 PVE/% | 加性效应 Add |
---|---|---|---|---|---|---|---|---|---|
株高 PH | 1 | qPH1.1 | 2021AS | 19.50 | Sb01819-Sb01824 | 19.72-20.13 | 5.12 | 5.12 | -10.43 |
qPH1.2 | 2021AS | 29.40 | Sb01925-Sb01957 | 25.81-27.00 | 10.14 | 15.19 | 15.19 | ||
2020GY | 30.90 | Sb01939-Sb01941 | 26.58-26.58 | 2.68 | 2.82 | 9.10 | |||
3 | qPH3.1 | 2020GY | 63.50 | Sb035554-Sb035557 | 56.08-56.14 | 8.58 | 9.13 | -13.99 | |
2020AS | 63.50 | Sb035554-Sb035557 | 56.08-56.14 | 4.39 | 4.39 | -10.23 | |||
qPH3.2 | 2021GY | 65.30 | Sb035584-Sb035595 | 56.41-56.90 | 9.19 | 10.72 | -15.19 | ||
2021AS | 65.30 | Sb035584-Sb035595 | 56.41-56.90 | 4.15 | 4.46 | -11.39 | |||
4 | qPH4.1 | 2020AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 5.83 | 6.66 | -12.04 | |
2021AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 4.00 | 4.01 | -9.30 | |||
2021GY | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 3.70 | 3.55 | -9.25 | |||
qPH4.2 | 2020GY | 3.50 | Sb046608-Sb046614 | 2.01-2.27 | 5.15 | 5.58 | -12.81 | ||
9 | qPH9.1 | 2020AS | 85.90 | Sb0915270-Sb0915408 | 54.55-58.47 | 6.98 | 11.36 | -15.74 | |
2021AS | 85.50 | Sb0915270-Sb0915408 | 54.55-58.47 | 4.35 | 5.98 | -11.39 | |||
2020GY | 86.20 | Sb0915270-Sb0915408 | 54.55-58.47 | 7.07 | 11.30 | -18.27 | |||
2020GY | 93.60 | Sb0915373-Sb0915384 | 57.67-57.85 | 24.84 | 34.34 | -31.69 | |||
2020AS | 93.60 | Sb0915373-Sb0915384 | 57.67-57.85 | 20.75 | 27.82 | -24.51 | |||
2021AS | 93.70 | Sb0915373-Sb0915384 | 57.67-57.85 | 15.95 | 18.25 | -19.78 | |||
节间数 IN | 1 | qIN1.1 | 2020LD | 53.60 | Sb011709-Sb011710 | 62.62-62.71 | 3.03 | 4.19 | 0.22 |
3 | qIN3.1 | 2020AS | 59.30 | Sb035466-Sb035520 | 53.57-55.06 | 19.22 | 23.92 | -0.72 | |
2021AS | 60.00 | Sb035466-Sb035520 | 53.57-55.06 | 10.89 | 18.64 | -0.62 | |||
qIN3.2 | 2020GY | 65.10 | Sb035598-Sb035611 | 56.91-57.32 | 5.29 | 7.98 | -0.33 | ||
2021GY | 65.40 | Sb035560-Sb035597 | 56.23-56.91 | 6.84 | 11.90 | -1.33 | |||
4 | qIN4.1 | 2020AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 6.05 | 6.37 | -0.37 | |
qIN4.2 | 2020LD | 60.90 | Sb047891-Sb047937 | 55.91-57.11 | 3.24 | 4.99 | -0.24 | ||
qIN4.3 | 2020AS | 70.20 | Sb048094-Sb048097 | 60.95-61.09 | 2.55 | 2.56 | -0.23 | ||
8 | qIN8.1 | 2020GY | 76.50 | Sb0813812-Sb0813988 | 58.25-60.76 | 4.30 | 8.77 | 0.35 | |
2020LD | 76.20 | Sb0813812-Sb0813988 | 58.25-60.76 | 7.90 | 14.84 | 0.41 | |||
qIN8.2 | 2020AS | 85.30 | Sb0814059-Sb0814062 | 62.02-62.05 | 2.96 | 2.96 | 0.25 | ||
9 | qIN9.1 | 2021GY | 77.50 | Sb0915233-Sb0915254 | 52.93-53.94 | 3.84 | 6.99 | -0.39 | |
2021AS | 79.60 | Sb0915254-Sb0915270 | 53.94-54.55 | 4.20 | 6.73 | -0.37 | |||
2020GY | 81.50 | Sb0915254-Sb0915270 | 53.94-54.55 | 4.45 | 6.60 | -0.31 | |||
qIN9.2 | 2020LD | 93.50 | Sb0915373-Sb0915384 | 57.67-57.85 | 9.15 | 13.47 | -0.39 | ||
qIN9.3 | 2020GY | 98.30 | Sb0915437-Sb0915441 | 58.96-58.99 | 6.75 | 10.05 | -0.37 | ||
2020AS | 97.70 | Sb0915434-Sb0915435 | 58.82-58.88 | 7.92 | 8.57 | -0.43 | |||
2021AS | 97.90 | Sb0915435-Sb0915437 | 58.88-58.96 | 4.62 | 7.18 | -0.38 |
Table 4 QTL mapping results of plant height and internode numbers
性状 Trait | 染色体 Chr. | 位点 QTL | 环境 Env. | 位置 Pos./cM | 标记区间 Marker interval | 物理距离 Phy./Mb | 阈值 LOD | 贡献率 PVE/% | 加性效应 Add |
---|---|---|---|---|---|---|---|---|---|
株高 PH | 1 | qPH1.1 | 2021AS | 19.50 | Sb01819-Sb01824 | 19.72-20.13 | 5.12 | 5.12 | -10.43 |
qPH1.2 | 2021AS | 29.40 | Sb01925-Sb01957 | 25.81-27.00 | 10.14 | 15.19 | 15.19 | ||
2020GY | 30.90 | Sb01939-Sb01941 | 26.58-26.58 | 2.68 | 2.82 | 9.10 | |||
3 | qPH3.1 | 2020GY | 63.50 | Sb035554-Sb035557 | 56.08-56.14 | 8.58 | 9.13 | -13.99 | |
2020AS | 63.50 | Sb035554-Sb035557 | 56.08-56.14 | 4.39 | 4.39 | -10.23 | |||
qPH3.2 | 2021GY | 65.30 | Sb035584-Sb035595 | 56.41-56.90 | 9.19 | 10.72 | -15.19 | ||
2021AS | 65.30 | Sb035584-Sb035595 | 56.41-56.90 | 4.15 | 4.46 | -11.39 | |||
4 | qPH4.1 | 2020AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 5.83 | 6.66 | -12.04 | |
2021AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 4.00 | 4.01 | -9.30 | |||
2021GY | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 3.70 | 3.55 | -9.25 | |||
qPH4.2 | 2020GY | 3.50 | Sb046608-Sb046614 | 2.01-2.27 | 5.15 | 5.58 | -12.81 | ||
9 | qPH9.1 | 2020AS | 85.90 | Sb0915270-Sb0915408 | 54.55-58.47 | 6.98 | 11.36 | -15.74 | |
2021AS | 85.50 | Sb0915270-Sb0915408 | 54.55-58.47 | 4.35 | 5.98 | -11.39 | |||
2020GY | 86.20 | Sb0915270-Sb0915408 | 54.55-58.47 | 7.07 | 11.30 | -18.27 | |||
2020GY | 93.60 | Sb0915373-Sb0915384 | 57.67-57.85 | 24.84 | 34.34 | -31.69 | |||
2020AS | 93.60 | Sb0915373-Sb0915384 | 57.67-57.85 | 20.75 | 27.82 | -24.51 | |||
2021AS | 93.70 | Sb0915373-Sb0915384 | 57.67-57.85 | 15.95 | 18.25 | -19.78 | |||
节间数 IN | 1 | qIN1.1 | 2020LD | 53.60 | Sb011709-Sb011710 | 62.62-62.71 | 3.03 | 4.19 | 0.22 |
3 | qIN3.1 | 2020AS | 59.30 | Sb035466-Sb035520 | 53.57-55.06 | 19.22 | 23.92 | -0.72 | |
2021AS | 60.00 | Sb035466-Sb035520 | 53.57-55.06 | 10.89 | 18.64 | -0.62 | |||
qIN3.2 | 2020GY | 65.10 | Sb035598-Sb035611 | 56.91-57.32 | 5.29 | 7.98 | -0.33 | ||
2021GY | 65.40 | Sb035560-Sb035597 | 56.23-56.91 | 6.84 | 11.90 | -1.33 | |||
4 | qIN4.1 | 2020AS | 0.50 | Sb046572-Sb046576 | 1.48-1.53 | 6.05 | 6.37 | -0.37 | |
qIN4.2 | 2020LD | 60.90 | Sb047891-Sb047937 | 55.91-57.11 | 3.24 | 4.99 | -0.24 | ||
qIN4.3 | 2020AS | 70.20 | Sb048094-Sb048097 | 60.95-61.09 | 2.55 | 2.56 | -0.23 | ||
8 | qIN8.1 | 2020GY | 76.50 | Sb0813812-Sb0813988 | 58.25-60.76 | 4.30 | 8.77 | 0.35 | |
2020LD | 76.20 | Sb0813812-Sb0813988 | 58.25-60.76 | 7.90 | 14.84 | 0.41 | |||
qIN8.2 | 2020AS | 85.30 | Sb0814059-Sb0814062 | 62.02-62.05 | 2.96 | 2.96 | 0.25 | ||
9 | qIN9.1 | 2021GY | 77.50 | Sb0915233-Sb0915254 | 52.93-53.94 | 3.84 | 6.99 | -0.39 | |
2021AS | 79.60 | Sb0915254-Sb0915270 | 53.94-54.55 | 4.20 | 6.73 | -0.37 | |||
2020GY | 81.50 | Sb0915254-Sb0915270 | 53.94-54.55 | 4.45 | 6.60 | -0.31 | |||
qIN9.2 | 2020LD | 93.50 | Sb0915373-Sb0915384 | 57.67-57.85 | 9.15 | 13.47 | -0.39 | ||
qIN9.3 | 2020GY | 98.30 | Sb0915437-Sb0915441 | 58.96-58.99 | 6.75 | 10.05 | -0.37 | ||
2020AS | 97.70 | Sb0915434-Sb0915435 | 58.82-58.88 | 7.92 | 8.57 | -0.43 | |||
2021AS | 97.90 | Sb0915435-Sb0915437 | 58.88-58.96 | 4.62 | 7.18 | -0.38 |
Fig. 2 Schematic diagram of high-density genetic map and chromosomes with important QTL regions QTLs identified in one environment and in two or more environments are shown in black and red, respectively
QTL | 候选基因 Candidate gene | 基因组位置 Genomic location | 同源基因 Orthologous gene | 蛋白注释 Proteins annotation | 相似性 Similarity/% |
---|---|---|---|---|---|
qPH1.2 | Sobic001G248600 | Chr01:26782638-26792923 | OsCPS1(LOC_Os02g17780) | 对映型柯巴基焦磷酸合酶 Ent-copalyl diphosphate synthase | 82.30 |
qPH3.2/qIN3.2 | Sobic003G227000 | Chr03:56425156-56426899 | OsOFP2(LOC_Os01g43610) | 卵形家族蛋白 Ovate family protein | 68.20 |
qPH3.2 | Sobic003G227300 | Chr03:56472263-56479136 | Dlf1(LOC_Os01g43650) | WRKY转录因子 WRKY transcription factor | 76.40 |
qPH9.1/qIN9.2 | Sobic.009G230800/DW1 | Chr09:57093313-57095643 | OsGA2ox(LOC_Os05g48700) | 赤霉素2氧化酶 Gibberellin 2-oxidase gene | 87.00 |
qIN8.1 | Sobic008G173300 | Chr08:60694532-60695140 | DEC1(LOC_Os12g42250) | 节间伸长抑制因子;C2H2锌指转录因子 Decelerator of internode elongation; Cys2His2(C2H2)zinc-finger transcription factor | 56.00 |
Table 5 Functional annotation of candidate genes in important QTL intervals
QTL | 候选基因 Candidate gene | 基因组位置 Genomic location | 同源基因 Orthologous gene | 蛋白注释 Proteins annotation | 相似性 Similarity/% |
---|---|---|---|---|---|
qPH1.2 | Sobic001G248600 | Chr01:26782638-26792923 | OsCPS1(LOC_Os02g17780) | 对映型柯巴基焦磷酸合酶 Ent-copalyl diphosphate synthase | 82.30 |
qPH3.2/qIN3.2 | Sobic003G227000 | Chr03:56425156-56426899 | OsOFP2(LOC_Os01g43610) | 卵形家族蛋白 Ovate family protein | 68.20 |
qPH3.2 | Sobic003G227300 | Chr03:56472263-56479136 | Dlf1(LOC_Os01g43650) | WRKY转录因子 WRKY transcription factor | 76.40 |
qPH9.1/qIN9.2 | Sobic.009G230800/DW1 | Chr09:57093313-57095643 | OsGA2ox(LOC_Os05g48700) | 赤霉素2氧化酶 Gibberellin 2-oxidase gene | 87.00 |
qIN8.1 | Sobic008G173300 | Chr08:60694532-60695140 | DEC1(LOC_Os12g42250) | 节间伸长抑制因子;C2H2锌指转录因子 Decelerator of internode elongation; Cys2His2(C2H2)zinc-finger transcription factor | 56.00 |
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