CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2021, Vol. 43 ›› Issue (6): 1006-1015.doi: 10.19802/j.issn.1007-9084.2020358
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Wei-ming ZENG1(), Yan-zhu SU2(
), Zhen-guang LAI1, Shou-zhen YANG1, Huai-zhu CHEN1, Yu-rong TAN1, Zu-dong SUN1(
), Jun-yi GAI2(
)
Received:
2020-12-18
Online:
2021-12-22
Published:
2021-12-23
Contact:
Zu-dong SUN,Jun-yi GAI
E-mail:zengweiying_1981@163.com;2016201065@njau.edu.cn;sunzudong639@163.com;sri@njau.edu.cn;sunzudong639@163.com
CLC Number:
Wei-ming ZENG, Yan-zhu SU, Zhen-guang LAI, Shou-zhen YANG, Huai-zhu CHEN, Yu-rong TAN, Zu-dong SUN, Jun-yi GAI. Identification of candidate gene controlling shade-tolerant by BSA-Seq in soybean[J]. CHINESE JOURNAL OF OIL CROP SCIENCES, 2021, 43(6): 1006-1015.
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URL: http://www.jouroilcrops.cn/EN/10.19802/j.issn.1007-9084.2020358
Table 1
Quality statistics of raw data
样本 Sample | 原始序列数 Raw reads | 原始碱基数 Raw bases | 过滤后序列数 Clean reads | 过滤后碱基数 Clean bases | 有效率/% Clean_data/Raw_data | GC含量 Clean_GC_Rate/% | Q20/% | Q30 /% |
---|---|---|---|---|---|---|---|---|
齐佩华 Chippewa | 446 517 054 | 66 977 558 100 | 436 965 904 | 65 544 885 600 | 97.86 | 35.95 | 96.75 | 92.48 |
矮脚早 Aijiaozao | 481 894 166 | 72 284 124 900 | 470 835 464 | 70 625 319 600 | 97.71 | 35.99 | 96.78 | 92.58 |
不耐荫子代池 Shade-sensitive pool | 226 579 124 | 33 986 868 600 | 220 059 398 | 33 008 909 700 | 97.12 | 36.13 | 96.53 | 92.21 |
耐荫子代池 Shade-tolerant pool | 241 352 496 | 36 202 874 400 | 235 715 430 | 35 357 314 500 | 97.66 | 36.26 | 96.42 | 91.96 |
Table 2
Matching of quality control data with reference genome
样本 Sample | 过滤后序列数 Clean reads | 比对上数据 Mapping reads | 比对率 Mapping rate/% | 优质比对率 Properly paired ratio /% | 平均测序深度 Mean depth | 1×覆盖度Coverage≥1× /% | 5×覆盖度 Coverage≥5× /% | 10×覆盖度 Coverage≥10× /% | 20×覆盖度 Coverage≥20× /% |
---|---|---|---|---|---|---|---|---|---|
齐佩华 Chippewa | 438 671 653 | 437 443 549 | 99.72 | 99.67 | 66.43 | 96.66 | 96.15 | 95.70 | 94.57 |
矮脚早 Aijiaozao | 472 681 742 | 471 291 113 | 99.71 | 99.66 | 71.55 | 96.67 | 96.18 | 95.77 | 94.81 |
不耐荫子代池 Shade-sensitive pool | 220 976 673 | 220 417 324 | 99.75 | 99.70 | 33.44 | 95.84 | 94.77 | 93.64 | 86.78 |
耐荫子代池 Shade-tolerant pool | 236 607 701 | 234 782 375 | 99.23 | 99.17 | 35.64 | 96.05 | 95.12 | 94.13 | 89.01 |
Table 3
Annotation of variation sites
变异位点信息 Variation sites information | 齐佩华 Chippewa | 矮脚早 Aijiaozao | 不耐荫子代池 Shade-sensitive pool | 耐荫子代池 Shade-tolerant pool |
---|---|---|---|---|
内含子Intronic | 308 698 | 309 423 | 238 022 | 231 325 |
基因区间Intergenic | 2 418 189 | 2 427 587 | 1 903 252 | 1 732 717 |
可变剪切位点Splicing | 627 | 636 | 468 | 488 |
基因上游Upstream | 186 199 | 187 229 | 141 783 | 137 671 |
基因下游Downstream | 157 037 | 157 547 | 119 713 | 115 032 |
基因上游/基因下游Upstream/downstream | 12 062 | 12 169 | 8 996 | 9 087 |
5’非翻译区UTR5’ | 22 872 | 22 977 | 17 708 | 17 234 |
3’非翻译区UTR3’ | 28 787 | 28 986 | 22 314 | 22 196 |
终止子提前Stop gain | 1 586 | 1 588 | 1 222 | 1 143 |
终止子丢失Stop loss | 255 | 255 | 198 | 195 |
同义突变Synonymous | 46 852 | 46 917 | 36 819 | 35 892 |
非同义突变Non-synonymous | 64 674 | 64 807 | 50 059 | 49 900 |
SNP总数SNP numbers | 3 284 376 | 3 296 356 | 2 565 861 | 2 375 637 |
纯合突变SNP Hom SNP number | 3 277 649 | 3 289 593 | 2 559 560 | 2 369 398 |
杂合突变SNP Hete SNP number | 6 727 | 6 763 | 6 301 | 6 239 |
纯合突变SNP 比率Hom SNP rate(%) | 99.80 | 99.79 | 99.75 | 99.74 |
杂合突变SNP 比率Het SNP rate(%) | 0.20 | 0.21 | 0.25 | 0.26 |
转换Ts | 2 127 254 | 2 135 306 | 1 656 728 | 1 526 282 |
颠换Tv | 1 153 429 | 1 157 307 | 905 511 | 845 685 |
转换/颠换 Ts/Tv | 1.84 | 1.85 | 1.83 | 1.80 |
Table 4
Gene information in the candidate regions
编号 NO. | 基因编号 Gene ID | 基因注释 Gene description | 染色体 Chromosome | 功能预测 Functional analysis |
---|---|---|---|---|
1 | LOC778053 | MYB转录因子MYB128 MYB transcription factor MYB128 | Chr1 | RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation |
2 | LOC778160 | MYB转录因子MYBJ6 MYB transcription factor MYBJ6 | Chr1 | RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation |
3 | LOC100819082 | MYB/HD转录因子 MYB/HD-like transcription factor | Chr18 | RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation |
4 | LOC100805768 | 含NAC结构域的蛋白质 NAC domain-containing protein | Chr4 | RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation |
5 | LOC100805895 | WRKY转录因子WRKY70 Probable WRKY transcription factor 70-like | Chr9 | RNA生物合成-转录调控 RNA biosynthesis. transcriptional regulation |
6 | LOC547722 | DIM 1蛋白 DIM 1-like protein | Chr9 | RNA加工-前体mRNA剪接 RNA processing. pre-mRNA splicing |
7 | LOC100785211 | 含G补丁结构域蛋白质 G-patch domain-containing protein | Chr9 | RNA加工-前体mRNA剪接 RNA processing. pre-mRNA splicing |
8 | LOC100306084 | 蛋白酶体?亚基C1 Putative proteasome beta subunit C1 | Chr4 | 蛋白质内稳态-泛素蛋白酶体系统 Protein homeostasis. ubiquitin-proteasome system |
9 | LOC100306051 | 延长因子P Elongation factor P | Chr9 | 蛋白质生物合成-细胞组织 Protein biosynthesis. organelle machinery |
10 | LOC100805081 | 光敏色素相关丝氨酸/苏氨酸蛋白磷酸酶 Phytochrome-associated serine/threonine protein phosphatase-like | Chr9 | 蛋白质修饰-磷酸化 Protein modification. Phosphorylation |
11 | LOC100819620 | 丝氨酸/苏氨酸蛋白激酶NAK Probable serine/threonine-protein kinase NAK-like | Chr18 | 蛋白质修饰-磷酸化 Protein modification. Phosphorylation |
12 | LOC100804819 | S6激酶1 S6 Kinase 1 | Chr9 | 蛋白质修饰-磷酸化 Protein modification. Phosphorylation |
13 | LOC100272201 | 不含赖氨酸激酶10 With no lysine kinase 10 | Chr9 | 蛋白质修饰-磷酸化 Protein modification. Phosphorylation |
14 | LOC100794523 | inositol oxygenase 2-like 肌醇加氧酶2 | Chr1 | 碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis |
15 | LOC778158 | UDP糖焦磷酸化酶 UDP-sugar pyrophosphorylase | Chr4 | 碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis |
16 | LOC100776301 | GDP-L聚焦合酶2 Putative GDP-L-fucose synthase 2-lik | Chr9 | 碳水化合物代谢-核苷酸糖生物合成 Carbohydrate metabolism. nucleotide sugar biosynthesis |
17 | LOC100527431 | 磷脂酶A2 Phospholipase A2 | Chr1 | 脂类代谢-脂类降解 Lipid metabolism. lipid degradation |
18 | LOC100797904 | 磷脂酶A2同源物3 Phospholipase A2 homolog 3-like | Chr1 | 脂类代谢-脂类降解 Lipid metabolism. lipid degradation |
19 | LOC100775781 | 氧甾醇结合蛋白相关蛋白3B Oxysterol-binding protein-related protein 3B-like | Chr18 | 脂类代谢-脂类降解 Lipid metabolism. lipid trafficking |
20 | LOC100811114 | 生长素诱导蛋白5NG4 Auxin-induced protein 5NG4-like | Chr4 | 溶质运移-载体转运 Solute transport. carrier-mediated transport |
21 | LOC100170705 | 二硫化物异构酶蛋白 Protein disulfide isomerase-like protein | Chr4 | 酶分类- EC_5异构酶 Enzyme classification. EC_5 isomerases |
22 | LOC100818520 | 细胞色素P450 71D11 Cytochrome P450 71D11-like | Chr9 | 酶分类- EC_1氧化还原酶 Enzyme classification. EC_1 oxidoreductases |
23 | LOC100779492 | 异甘草素2-O-甲基转移酶 Isoliquiritigenin 2'-O-methyltransferase-like | Chr9 | 酶分类- EC_2转移酶 Enzyme classification. EC_2 transferases |
24 | LOC100796909 | 1-氨基环丙烷1-羧酸氧化酶5(ACC 氧化酶5) 1-aminocyclopropane-1-carboxylate oxidase 5-like | Chr4 | 植物激素作用-乙烯 Phytohormone action. Ethylene |
25 | LOC100499644 | FERONIA受体激酶 FERONIA receptor-like kinase | Chr9 | 植物激素作用-信号肽 Phytohormone action. signalling peptides |
26 | LOC548095 | 氨基酮戊酸盐,δ-脱水酶 Aminolevulinate, delta-, dehydratase | Chr4 | 辅酶代谢-四吡咯生物合成 Coenzyme metabolism. tetrapyrrol biosynthesis |
27 | LOC100500425 | 泛酸?-丙氨酸连接酶蛋白 Pantoate--beta-alanine ligase-like protein | Chr18 | 辅酶代谢-辅酶A生物合成 Coenzyme metabolism. coenzyme A biosynthesis |
28 | LOC100795951 | 蛋白质精氨酸N -甲基转移酶1 Probable protein arginine N-methyltransferase 1-like | Chr1 | 染色质组织-组蛋白修饰 Chromatin organisation. histone modifications |
29 | LOC547781 | 有丝分裂细胞周期蛋白a2类型 Mitotic cyclin a2-type | Chr4 | 细胞周期组织-细胞周期调控 Cell cycle organisation. cell cycle control |
30 | LOC 100500292 | 硫氧还蛋白 Thioredoxin-like protein | Chr4 | 氧化还原内稳态-叶绿体氧化还原内稳态 Redox homeostasis. chloroplast redox homeostasis |
31 | LOC 100804314 | 囊泡相关膜蛋白726 Putative vesicle-associated membrane protein 726-like | Chr18 | 囊泡运输- SNARE目标膜识别和融合复合物 Vesicle trafficking. SNARE target membrane recognition and fusion complexes |
32 | LOC 100499919 | 含ATPase激活剂结构域的蛋白质 ATPase activator domain-containing protein | Chr1 | - |
33 | LOC 100813615 | 含AP2结构域的转录因子6 AP2 domain-containing transcription factor 6 | Chr4 | - |
34 | LOC 100527117 | 钙结合蛋白 Putative calcium-binding protein | Chr4 | - |
35 | LOC 100526881 | 环/ U-盒超家族蛋白 RING/U-box superfamily protein | Chr4 | - |
36 | LOC 100806828 | 含TLC结构域蛋白质2 TLC domain-containing protein 2-like | Chr4 | - |
37 | LOC 100808386 | 四肽重复蛋白1 Tetratricopeptide repeat protein 1-like | Chr18 | - |
38 | LOC 100306706 | AAI_LTSS超家族蛋白 AAI_LTSS superfamily protein | Chr9 | - |
39 | LOC 100815671 | 阳离子过氧化物酶1 Cationic peroxidase 1-like | Chr9 | - |
40 | LOC 100798447 | 受体蛋白EIX2 Receptor-like protein EIX2-like | Chr9 | - |
41 | LOC 100527576 | 含Sel1重复序列蛋白 Sel1 repeat-containing protein | Chr9 | - |
42 | LOC 100819056 | 可溶性NSF附着蛋白SNAP09 Soluble NSF attachment protein SNAP09 | Chr9 | - |
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