Xinjiang Agricultural Sciences ›› 2023, Vol. 60 ›› Issue (10): 2341-2351.DOI: 10.6048/j.issn.1001-4330.2023.10.001
• Crop Genetics and Breeding·Germplasm Resources·Molecular Genetics • Previous Articles Next Articles
SUN Fenglei1(), REN Jiaojiao1, LEI Bin2, GAO Wenwei1, QU Yanying1()
Received:
2023-01-21
Online:
2023-10-20
Published:
2023-11-01
Correspondence author:
QU Yanying(1962-),Yantai, Shandong Province,professor,doctor,mainly engaged in cotton genetics and breeding,(E-mail)Supported by:
孙丰磊1(), 任姣姣1, 雷斌2, 高文伟1, 曲延英1()
通讯作者:
曲延英(1962-),女,山东烟台人,教授,博士,硕士生/博士生导师,研究方向为棉花遗传育种,(E-mail)作者简介:
孙丰磊(1992-),男,新疆阿图什人,博士,研究方向为棉花遗传育种,(E-mail)1271297139@qq.com
基金资助:
CLC Number:
SUN Fenglei, REN Jiaojiao, LEI Bin, GAO Wenwei, QU Yanying. QTL mapping and genomic selection of maize leaf width[J]. Xinjiang Agricultural Sciences, 2023, 60(10): 2341-2351.
孙丰磊, 任姣姣, 雷斌, 高文伟, 曲延英. 基于BSA分析技术对陆地棉抗旱基因的鉴定[J]. 新疆农业科学, 2023, 60(10): 2341-2351.
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样品 编号 ID | 过滤后的 reads数 Clean Reads | 过滤后的 碱基数 Clean Base | Q30含量 Q30 (%) | 样品 GC 含量 GC (%) |
---|---|---|---|---|
奎 85-174 Kui 85-174 | 119 060 015 | 35 718 004 500 | 93.61 | 35.64 |
石远321 Shiyuan 321 | 121 194 054 | 36 358 216 200 | 93.03 | 35.73 |
抗性强池 Strong resistance pool | 223 420 448 | 67 026 134 400 | 93.38 | 35.43 |
抗性弱池 Weak resistance pool | 190 811 397 | 57 243 419 100 | 93.37 | 35.59 |
Tab.1 Sample sequencing data quality statistics
样品 编号 ID | 过滤后的 reads数 Clean Reads | 过滤后的 碱基数 Clean Base | Q30含量 Q30 (%) | 样品 GC 含量 GC (%) |
---|---|---|---|---|
奎 85-174 Kui 85-174 | 119 060 015 | 35 718 004 500 | 93.61 | 35.64 |
石远321 Shiyuan 321 | 121 194 054 | 36 358 216 200 | 93.03 | 35.73 |
抗性强池 Strong resistance pool | 223 420 448 | 67 026 134 400 | 93.38 | 35.43 |
抗性弱池 Weak resistance pool | 190 811 397 | 57 243 419 100 | 93.37 | 35.59 |
样品编号 ID | 总reads数 Total reads | 比对率 Mapped (%) | 测序 深度 Depth | 覆盖率Cov ratio | ||
---|---|---|---|---|---|---|
1X (%) | 5X (%) | 10X (%) | ||||
奎 85-174 Kui 85-174 | 238 120 030 | 99.10 | 13 | 98.61 | 93.02 | 72.61 |
石远321 Shiyuan 321 | 242 388 108 | 99.07 | 14 | 98.58 | 93.08 | 73.17 |
抗性强池 Strong resistance pool | 382 622 794 | 98.93 | 22 | 99.41 | 97.61 | 92.93 |
抗性弱池 Weak resistance pool | 446 840 896 | 99.08 | 26 | 99.50 | 98.21 | 95.73 |
Tab.2 Statistical results after comparison with reference genes
样品编号 ID | 总reads数 Total reads | 比对率 Mapped (%) | 测序 深度 Depth | 覆盖率Cov ratio | ||
---|---|---|---|---|---|---|
1X (%) | 5X (%) | 10X (%) | ||||
奎 85-174 Kui 85-174 | 238 120 030 | 99.10 | 13 | 98.61 | 93.02 | 72.61 |
石远321 Shiyuan 321 | 242 388 108 | 99.07 | 14 | 98.58 | 93.08 | 73.17 |
抗性强池 Strong resistance pool | 382 622 794 | 98.93 | 22 | 99.41 | 97.61 | 92.93 |
抗性弱池 Weak resistance pool | 446 840 896 | 99.08 | 26 | 99.50 | 98.21 | 95.73 |
Fig.2 ED correlation value distribution on chromosomes Note:The horizontal asis represents the chromosome name,colored dots represent the ED value of each SNP,the black line represents the fitted ED value,the red dashed line represents the significance correlation threshold,the same as below
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A02 | 98 457 690 | 100 146 685 | 1.69 | 52 |
2 | A07 | 3 977 843 | 8 487 185 | 4.51 | 331 |
3 | A10 | 103 006 562 | 103 092 019 | 0.09 | 1 |
4 | A10 | 77 360 750 | 100 680 043 | 23.32 | 439 |
5 | D07 | 35 719 935 | 40 976 937 | 5.26 | 75 |
6 | D07 | 43 116 892 | 47 471 182 | 4.35 | 81 |
Total | - | - | 39.22 | 979 |
Tab.3 ED algorithm correlation candidate area
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A02 | 98 457 690 | 100 146 685 | 1.69 | 52 |
2 | A07 | 3 977 843 | 8 487 185 | 4.51 | 331 |
3 | A10 | 103 006 562 | 103 092 019 | 0.09 | 1 |
4 | A10 | 77 360 750 | 100 680 043 | 23.32 | 439 |
5 | D07 | 35 719 935 | 40 976 937 | 5.26 | 75 |
6 | D07 | 43 116 892 | 47 471 182 | 4.35 | 81 |
Total | - | - | 39.22 | 979 |
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A07 | 8 173 206 | 8 374 137 | 0.20 | 20 |
2 | A10 | 81 963 832 | 85 854 861 | 3.89 | 38 |
3 | D07 | 43 758 098 | 45 777 408 | 2.02 | 28 |
Total | - | - | 6.12 | 86 |
Tab.4 SNP-index algorithm correlation candidate area
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A07 | 8 173 206 | 8 374 137 | 0.20 | 20 |
2 | A10 | 81 963 832 | 85 854 861 | 3.89 | 38 |
3 | D07 | 43 758 098 | 45 777 408 | 2.02 | 28 |
Total | - | - | 6.12 | 86 |
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A07 | 8 173 206 | 8 374 137 | 0.20 | 20 |
2 | A10 | 81 963 832 | 85 854 861 | 3.89 | 38 |
3 | D07 | 43 758 098 | 45 777 408 | 2.02 | 28 |
Total | - | - | 6.12 | 86 |
Tab.5 ED and SNP-index two algorithms associate candidate regions
序号 No. | 染色体 编号 Chromo some ID | 关联区域 起始位置 Start | 关联区域 结束位置 End | 关联 大小 Size (Mb) | 基因 数目 Gene Number |
---|---|---|---|---|---|
1 | A07 | 8 173 206 | 8 374 137 | 0.20 | 20 |
2 | A10 | 81 963 832 | 85 854 861 | 3.89 | 38 |
3 | D07 | 43 758 098 | 45 777 408 | 2.02 | 28 |
Total | - | - | 6.12 | 86 |
GO分类 Categories of GO | GO编号 GO ID | GO分组 GO Term | 富集节 点的显 著性 统计 KS |
---|---|---|---|
细胞组分 Cellular compo nent | GO:0044435 | 质体部分0.045 | |
GO:0044434 | 叶绿体部分 | 0.053 | |
GO:0031967 | 细胞器膜 | 0.143 | |
GO:1990234 | 转移酶复合体 | 0.154 | |
GO:0009507 | 叶绿体 | 0.157 | |
GO:0003964 | rna导向的DNA 聚合酶活性 | 0.000 001 9 | |
分子功能 Molecular Function | GO:0016984 | 核糖二磷酸羧化酶活性 | 0.028 |
GO:0019904 | 蛋白质结构域特异性结合 | 0.034 1 | |
GO: 0051213 | 双加氧酶活性 | 0.056 9 | |
GO:0019203 | 碳水化合物磷酸酶活性 | 0.061 3 | |
GO:0015074 | DNA整合 | 9.60 E-12 | |
GO:0006278 | 依赖RNA的DNA复制 | 1.40 E-06 | |
生物过程 Biological process | GO:0019400 | 糖醇代谢过程 | 0.021 |
GO:0071554 | 细胞壁组织或生物合成 | 0.051 | |
GO:1901615 | 有机羟基化合物代谢过程 | 0.065 |
Tab.6 GO annotation of genes in candidate regions
GO分类 Categories of GO | GO编号 GO ID | GO分组 GO Term | 富集节 点的显 著性 统计 KS |
---|---|---|---|
细胞组分 Cellular compo nent | GO:0044435 | 质体部分0.045 | |
GO:0044434 | 叶绿体部分 | 0.053 | |
GO:0031967 | 细胞器膜 | 0.143 | |
GO:1990234 | 转移酶复合体 | 0.154 | |
GO:0009507 | 叶绿体 | 0.157 | |
GO:0003964 | rna导向的DNA 聚合酶活性 | 0.000 001 9 | |
分子功能 Molecular Function | GO:0016984 | 核糖二磷酸羧化酶活性 | 0.028 |
GO:0019904 | 蛋白质结构域特异性结合 | 0.034 1 | |
GO: 0051213 | 双加氧酶活性 | 0.056 9 | |
GO:0019203 | 碳水化合物磷酸酶活性 | 0.061 3 | |
GO:0015074 | DNA整合 | 9.60 E-12 | |
GO:0006278 | 依赖RNA的DNA复制 | 1.40 E-06 | |
生物过程 Biological process | GO:0019400 | 糖醇代谢过程 | 0.021 |
GO:0071554 | 细胞壁组织或生物合成 | 0.051 | |
GO:1901615 | 有机羟基化合物代谢过程 | 0.065 |
序号 No. | 基因 Gene | 类型 Type |
---|---|---|
1 | GH_A07G0703 | 分子功能、细胞组分、生物过程 |
2 | GH_A07G0709 | 分子功能、细胞组分、生物过程 |
3 | GH_A07G0699 | 分子功能、细胞组分、生物过程 |
4 | GH_D07G1935 | 分子功能、细胞组分、生物过程 |
5 | GH_A10G1607 | 分子功能、细胞组分、生物过程 |
6 | GH_A07G0705 | 分子功能、细胞组分、生物过程 |
7 | GH_A07G0714 | 分子功能、生物过程 |
8 | GH_A10G1610 | 分子功能、细胞组分 |
9 | GH_A10G1596 | 分子功能、生物过程 |
10 | GH_A10G1602 | 分子功能、生物过程 |
11 | GH_A10G1608 | 分子功能、生物过程 |
12 | GH_A10G1623 | 分子功能、生物过程 |
Tab.7 Candidate gene statistics (partial)
序号 No. | 基因 Gene | 类型 Type |
---|---|---|
1 | GH_A07G0703 | 分子功能、细胞组分、生物过程 |
2 | GH_A07G0709 | 分子功能、细胞组分、生物过程 |
3 | GH_A07G0699 | 分子功能、细胞组分、生物过程 |
4 | GH_D07G1935 | 分子功能、细胞组分、生物过程 |
5 | GH_A10G1607 | 分子功能、细胞组分、生物过程 |
6 | GH_A07G0705 | 分子功能、细胞组分、生物过程 |
7 | GH_A07G0714 | 分子功能、生物过程 |
8 | GH_A10G1610 | 分子功能、细胞组分 |
9 | GH_A10G1596 | 分子功能、生物过程 |
10 | GH_A10G1602 | 分子功能、生物过程 |
11 | GH_A10G1608 | 分子功能、生物过程 |
12 | GH_A10G1623 | 分子功能、生物过程 |
序号 No. | 基因 Gene | 候选基因 Candidate gene | 基因注释 Gene annotation |
---|---|---|---|
1 | GH_A07G0703 | RFS | hydrolase activity, hydrolyzing O-glycosyl compounds, sucrose biosynthetic |
2 | GH_A07G0709 | PPT1 | Phosphoenolpyruvate/phosphate translocator 1, chloroplastic -like protein |
3 | GH_A07G0699 | murG | serine-type endopeptidase activity, regulation of transcription, DNA-templated |
4 | GH_A07G0705 | gmppA | ADP-glucose pyrophosphorylase family protein isoform 1 |
5 | GH_A07G0714 | PMT2 | S-adenosyl-L-methionine-dependent methyltransferases superfamily protein |
6 | GH_D07G1935 | RBCS | ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit |
7 | GH_D07G1925 | TFT4 | protein domain specific binding |
8 | GH_D07G1939 | CRS2B | Chloroplastic group IIB intron splicing facilitator CRS2-B |
9 | GH_A10G1607 | PNC1 | class Ⅲ peroxidase |
10 | GH_A10G1610 | ASP1 | Aspartate aminotransferase isoform 1 |
11 | GH_A10G1596 | HST | Hydroxycinnamoyl-Coenzyme A shikimate/quinate hydroxycinnamoyltransferase -like protein |
12 | GH_A10G1602 | alkB | Alpha-ketoglutarate-dependent dioxygenase AlkB |
13 | GH_A10G1608 | PNC1 | Cationic peroxidase 1 (Precursor) |
14 | GH_A10G1623 | TY3B-I | RNA-directed DNA polymerase activity, Transposon Ty3-I Gag-Pol polyprotein |
15 | GH_A07G0703 | RFS | Galactinol-sucrose galactosyltransferase |
Tab.8 Drought resistance candidate genes and annotations
序号 No. | 基因 Gene | 候选基因 Candidate gene | 基因注释 Gene annotation |
---|---|---|---|
1 | GH_A07G0703 | RFS | hydrolase activity, hydrolyzing O-glycosyl compounds, sucrose biosynthetic |
2 | GH_A07G0709 | PPT1 | Phosphoenolpyruvate/phosphate translocator 1, chloroplastic -like protein |
3 | GH_A07G0699 | murG | serine-type endopeptidase activity, regulation of transcription, DNA-templated |
4 | GH_A07G0705 | gmppA | ADP-glucose pyrophosphorylase family protein isoform 1 |
5 | GH_A07G0714 | PMT2 | S-adenosyl-L-methionine-dependent methyltransferases superfamily protein |
6 | GH_D07G1935 | RBCS | ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit |
7 | GH_D07G1925 | TFT4 | protein domain specific binding |
8 | GH_D07G1939 | CRS2B | Chloroplastic group IIB intron splicing facilitator CRS2-B |
9 | GH_A10G1607 | PNC1 | class Ⅲ peroxidase |
10 | GH_A10G1610 | ASP1 | Aspartate aminotransferase isoform 1 |
11 | GH_A10G1596 | HST | Hydroxycinnamoyl-Coenzyme A shikimate/quinate hydroxycinnamoyltransferase -like protein |
12 | GH_A10G1602 | alkB | Alpha-ketoglutarate-dependent dioxygenase AlkB |
13 | GH_A10G1608 | PNC1 | Cationic peroxidase 1 (Precursor) |
14 | GH_A10G1623 | TY3B-I | RNA-directed DNA polymerase activity, Transposon Ty3-I Gag-Pol polyprotein |
15 | GH_A07G0703 | RFS | Galactinol-sucrose galactosyltransferase |
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