Journal of Agricultural Science and Technology ›› 2023, Vol. 25 ›› Issue (7): 29-42.DOI: 10.13304/j.nykjdb.2022.0089
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Yaqian SUN1(), Shiliang CHEN2, Jiahao CHU1, Xihuan LI1(
), Caiying ZHANG1(
)
Received:
2022-02-07
Accepted:
2022-04-12
Online:
2023-07-15
Published:
2023-08-25
Contact:
Xihuan LI,Caiying ZHANG
孙亚倩1(), 陈士亮2, 褚佳豪1, 李喜焕1(
), 张彩英1(
)
通讯作者:
李喜焕,张彩英
作者简介:
孙亚倩 E-mail: 1602032390@qq.com
基金资助:
CLC Number:
Yaqian SUN, Shiliang CHEN, Jiahao CHU, Xihuan LI, Caiying ZHANG. Mining of QTLs and Candidate Genes for Pod and Seed Traits via Combining BSA-seq and Linkage Mapping in Soybean[J]. Journal of Agricultural Science and Technology, 2023, 25(7): 29-42.
孙亚倩, 陈士亮, 褚佳豪, 李喜焕, 张彩英. 基于BSA-seq结合连锁分析发掘大豆荚粒性状QTLs及候选基因[J]. 中国农业科技导报, 2023, 25(7): 29-42.
项目 Item | 环境 Environment | 荚长 PL/cm | 荚宽 PW/cm | 荚重 PWT/g | 粒长 SL/cm | 粒宽 SW/cm | 粒重 SWT/g |
---|---|---|---|---|---|---|---|
LP | E1 | 4.68 | 1.21 | 1.81 | 1.41 | 0.86 | 0.51 |
E2 | 5.22 | 1.20 | 2.25 | 1.42 | 0.86 | 0.64 | |
E3 | 4.82 | 1.21 | 1.88 | 1.33 | 0.83 | 0.55 | |
E4 | 5.13 | 1.21 | 2.07 | 1.38 | 0.85 | 0.57 | |
均值Mean | 4.96 | 1.21 | 2.00 | 1.39 | 0.85 | 0.57 | |
SP | E1 | 4.06 | 1.10 | 1.49 | 1.30 | 0.79 | 0.45 |
E2 | 4.52 | 1.09 | 1.74 | 1.31 | 0.81 | 0.54 | |
E3 | 4.22 | 1.07 | 1.53 | 1.22 | 0.76 | 0.48 | |
E4 | 4.35 | 1.07 | 1.58 | 1.24 | 0.78 | 0.47 | |
均值Mean | 4.29 | 1.08 | 1.59 | 1.27 | 0.79 | 0.49 | |
显著性 Significance (P-value) | E1 | 4.3e-07 | 5.5e-07 | 4.2e-06 | 3.5e-05 | 6.0e-07 | 8.7e-04 |
E2 | 1.1e-12 | 1.3e-08 | 3.7e-09 | 6.4e-07 | 2.7e-07 | 2.1e-06 | |
E3 | 3.8e-10 | 7.1e-10 | 1.5e-05 | 2.6e-07 | 4.2e-07 | 1.3e-03 | |
E4 | 7.7e-11 | 9.5e-09 | 2.8e-08 | 2.2e-07 | 4.2e-06 | 5.1e-06 | |
多环境All environments | 5.6e-03 | 3.0e-06 | 1.0e-02 | 5.8e-03 | 2.6e-03 | 4.2e-02 |
Table 1 Genetic variation of extreme RIL lines on pod and seed traits for BSA-seq under different environments
项目 Item | 环境 Environment | 荚长 PL/cm | 荚宽 PW/cm | 荚重 PWT/g | 粒长 SL/cm | 粒宽 SW/cm | 粒重 SWT/g |
---|---|---|---|---|---|---|---|
LP | E1 | 4.68 | 1.21 | 1.81 | 1.41 | 0.86 | 0.51 |
E2 | 5.22 | 1.20 | 2.25 | 1.42 | 0.86 | 0.64 | |
E3 | 4.82 | 1.21 | 1.88 | 1.33 | 0.83 | 0.55 | |
E4 | 5.13 | 1.21 | 2.07 | 1.38 | 0.85 | 0.57 | |
均值Mean | 4.96 | 1.21 | 2.00 | 1.39 | 0.85 | 0.57 | |
SP | E1 | 4.06 | 1.10 | 1.49 | 1.30 | 0.79 | 0.45 |
E2 | 4.52 | 1.09 | 1.74 | 1.31 | 0.81 | 0.54 | |
E3 | 4.22 | 1.07 | 1.53 | 1.22 | 0.76 | 0.48 | |
E4 | 4.35 | 1.07 | 1.58 | 1.24 | 0.78 | 0.47 | |
均值Mean | 4.29 | 1.08 | 1.59 | 1.27 | 0.79 | 0.49 | |
显著性 Significance (P-value) | E1 | 4.3e-07 | 5.5e-07 | 4.2e-06 | 3.5e-05 | 6.0e-07 | 8.7e-04 |
E2 | 1.1e-12 | 1.3e-08 | 3.7e-09 | 6.4e-07 | 2.7e-07 | 2.1e-06 | |
E3 | 3.8e-10 | 7.1e-10 | 1.5e-05 | 2.6e-07 | 4.2e-07 | 1.3e-03 | |
E4 | 7.7e-11 | 9.5e-09 | 2.8e-08 | 2.2e-07 | 4.2e-06 | 5.1e-06 | |
多环境All environments | 5.6e-03 | 3.0e-06 | 1.0e-02 | 5.8e-03 | 2.6e-03 | 4.2e-02 |
样品Sample | 过滤后数据 Clean data/bp | Q20/% | Q30/% | GC/% | 总读段 Total reads | 读段比对率Mapped reads/% | 覆盖度 Coverage rate/% | |||
---|---|---|---|---|---|---|---|---|---|---|
1× | 4× | 10× | 20× | |||||||
KN7 | 30 185 672 700 | 97.29 | 92.63 | 36.42 | 200 007 218 | 98.08 | 98.20 | 97.28 | 94.97 | 79.68 |
C813 | 30 445 756 200 | 97.28 | 92.59 | 36.54 | 201 728 350 | 98.92 | 97.67 | 96.63 | 94.35 | 80.95 |
SP | 31 026 257 700 | 97.42 | 92.91 | 36.32 | 205 658 536 | 98.98 | 98.54 | 97.79 | 95.76 | 82.33 |
LP | 29 921 497 800 | 97.23 | 92.50 | 36.58 | 198 179 602 | 98.97 | 98.67 | 97.63 | 94.93 | 79.99 |
Table 2 Quality analysis of BSA-seq of two pools and soybean RIL parents
样品Sample | 过滤后数据 Clean data/bp | Q20/% | Q30/% | GC/% | 总读段 Total reads | 读段比对率Mapped reads/% | 覆盖度 Coverage rate/% | |||
---|---|---|---|---|---|---|---|---|---|---|
1× | 4× | 10× | 20× | |||||||
KN7 | 30 185 672 700 | 97.29 | 92.63 | 36.42 | 200 007 218 | 98.08 | 98.20 | 97.28 | 94.97 | 79.68 |
C813 | 30 445 756 200 | 97.28 | 92.59 | 36.54 | 201 728 350 | 98.92 | 97.67 | 96.63 | 94.35 | 80.95 |
SP | 31 026 257 700 | 97.42 | 92.91 | 36.32 | 205 658 536 | 98.98 | 98.54 | 97.79 | 95.76 | 82.33 |
LP | 29 921 497 800 | 97.23 | 92.50 | 36.58 | 198 179 602 | 98.97 | 98.67 | 97.63 | 94.93 | 79.99 |
项目 Item | C813 | KN7 | LP | SP | |
---|---|---|---|---|---|
SNP数量 SNP number | 1 619 731 | 1 953 331 | 2 412 499 | 2 397 371 | |
SNP所在基因组位置 SNP genome position | 下游 Downstream | 82 313 | 97 262 | 123 627 | 122 700 |
外显子区 Exonic | 61 800 | 72 657 | 91 369 | 89 863 | |
基因间Intergenic | 1 171 840 | 1 421 376 | 1 736 589 | 1 728 224 | |
内含子区Intronic | 163 852 | 195 463 | 249 905 | 246 732 | |
可变剪切位点 Splicing | 456 | 543 | 697 | 685 | |
上游Upstream | 96 035 | 114 708 | 143 985 | 144 040 | |
3’-UTR | 21 461 | 25 807 | 33 101 | 32 432 | |
5’-UTR | 14 584 | 16 642 | 21 941 | 21 530 | |
外显子&可变剪切Exonic & splicing | 25 | 23 | 36 | 35 | |
上游&下游Upstream & downstream | 7 342 | 8 811 | 11 195 | 11 072 | |
5’-UTR & 3’-UTR | 23 | 39 | 54 | 58 | |
SNP变异类型SNP mutation type | 非同义突变 Non-synonymous | 34 542 | 40 700 | 51 060 | 50 279 |
终止获得 Stop-gain | 726 | 894 | 1 089 | 1 077 | |
终止丢失 Stop-loss | 144 | 182 | 223 | 216 | |
同义突变Synonymous | 26 386 | 30 881 | 39 002 | 38 302 | |
未知 Unknown | 27 | 23 | 31 | 24 |
Table 3 SNP number and quality analysis of BSA-seq of two pools and soybean RIL parents
项目 Item | C813 | KN7 | LP | SP | |
---|---|---|---|---|---|
SNP数量 SNP number | 1 619 731 | 1 953 331 | 2 412 499 | 2 397 371 | |
SNP所在基因组位置 SNP genome position | 下游 Downstream | 82 313 | 97 262 | 123 627 | 122 700 |
外显子区 Exonic | 61 800 | 72 657 | 91 369 | 89 863 | |
基因间Intergenic | 1 171 840 | 1 421 376 | 1 736 589 | 1 728 224 | |
内含子区Intronic | 163 852 | 195 463 | 249 905 | 246 732 | |
可变剪切位点 Splicing | 456 | 543 | 697 | 685 | |
上游Upstream | 96 035 | 114 708 | 143 985 | 144 040 | |
3’-UTR | 21 461 | 25 807 | 33 101 | 32 432 | |
5’-UTR | 14 584 | 16 642 | 21 941 | 21 530 | |
外显子&可变剪切Exonic & splicing | 25 | 23 | 36 | 35 | |
上游&下游Upstream & downstream | 7 342 | 8 811 | 11 195 | 11 072 | |
5’-UTR & 3’-UTR | 23 | 39 | 54 | 58 | |
SNP变异类型SNP mutation type | 非同义突变 Non-synonymous | 34 542 | 40 700 | 51 060 | 50 279 |
终止获得 Stop-gain | 726 | 894 | 1 089 | 1 077 | |
终止丢失 Stop-loss | 144 | 182 | 223 | 216 | |
同义突变Synonymous | 26 386 | 30 881 | 39 002 | 38 302 | |
未知 Unknown | 27 | 23 | 31 | 24 |
项目Item | C813 | KN7 | LP | SP | |
---|---|---|---|---|---|
Indel数量 Indel number | 304 227 | 346 870 | 432 243 | 434 173 | |
Indel所在基因组位置 Indel genome position | 下游 Downstream | 23 599 | 26 795 | 34 163 | 34 277 |
外显子区 Exonic | 3 823 | 4 331 | 5 338 | 5 270 | |
基因间Intergenic | 191 138 | 218 488 | 268 913 | 270 622 | |
内含子区Intronic | 41 422 | 47 052 | 60 068 | 59 808 | |
可变剪切位点 Splicing | 182 | 207 | 244 | 246 | |
上游Upstream | 30 262 | 34 121 | 43 159 | 43 784 | |
3’-UTR | 6 081 | 7 174 | 9 062 | 8 946 | |
5’-UTR | 5 163 | 5 894 | 7 571 | 7 475 | |
外显子&可变剪切Exonic & splicing | 3 | 2 | 3 | 3 | |
上游&下游Upstream & downstream | 2 549 | 2 798 | 3 716 | 3 735 | |
5’-UTR & 3’-UTR | 5 | 8 | 6 | 7 | |
Indel变异类型 Indel mutation type | 移码缺失Frameshift deletion | 1 128 | 1 247 | 1 534 | 1 512 |
移码插入Frameshift insertion | 987 | 1 134 | 1 314 | 1 294 | |
非移码缺失Non-frameshift deletion | 878 | 1 007 | 1 299 | 1 282 | |
非移码插入Non-frameshift insertion | 749 | 851 | 1 082 | 1 067 | |
终止获得 Stop-gain | 69 | 72 | 92 | 95 | |
终止丢失 Stop-loss | 10 | 17 | 15 | 18 | |
未知Unknown | 5 | 5 | 5 | 5 |
Table 4 Indel number and quality analysis of BSA-seq of two pools and RIL parents
项目Item | C813 | KN7 | LP | SP | |
---|---|---|---|---|---|
Indel数量 Indel number | 304 227 | 346 870 | 432 243 | 434 173 | |
Indel所在基因组位置 Indel genome position | 下游 Downstream | 23 599 | 26 795 | 34 163 | 34 277 |
外显子区 Exonic | 3 823 | 4 331 | 5 338 | 5 270 | |
基因间Intergenic | 191 138 | 218 488 | 268 913 | 270 622 | |
内含子区Intronic | 41 422 | 47 052 | 60 068 | 59 808 | |
可变剪切位点 Splicing | 182 | 207 | 244 | 246 | |
上游Upstream | 30 262 | 34 121 | 43 159 | 43 784 | |
3’-UTR | 6 081 | 7 174 | 9 062 | 8 946 | |
5’-UTR | 5 163 | 5 894 | 7 571 | 7 475 | |
外显子&可变剪切Exonic & splicing | 3 | 2 | 3 | 3 | |
上游&下游Upstream & downstream | 2 549 | 2 798 | 3 716 | 3 735 | |
5’-UTR & 3’-UTR | 5 | 8 | 6 | 7 | |
Indel变异类型 Indel mutation type | 移码缺失Frameshift deletion | 1 128 | 1 247 | 1 534 | 1 512 |
移码插入Frameshift insertion | 987 | 1 134 | 1 314 | 1 294 | |
非移码缺失Non-frameshift deletion | 878 | 1 007 | 1 299 | 1 282 | |
非移码插入Non-frameshift insertion | 749 | 851 | 1 082 | 1 067 | |
终止获得 Stop-gain | 69 | 72 | 92 | 95 | |
终止丢失 Stop-loss | 10 | 17 | 15 | 18 | |
未知Unknown | 5 | 5 | 5 | 5 |
Fig. 1 Associated regions of soybean pod and seed traits via different methodsA: SNP-index method; B: ED method; C: G-statistic method; black lines indicate the fit curve; blue line indicate the confidence level 0.95 (P<0.05); red line indicate the confidence level 0.99 (P<0.01)
置信度Confidence level | 染色体 Chromosome | 起始位置 Start position /bp | 终止位置 End position /bp | 基因数量 Gene number |
---|---|---|---|---|
0.95 | Chr01 | 40 690 001 | 41 790 000 | 19 |
Chr02 | 41 180 001 | 44 100 000 | 246 | |
Chr02 | 45 540 001 | 47 550 000 | 236 | |
Chr03 | 39 550 001 | 41 670 000 | 228 | |
Chr04 | 35 390 001 | 36 590 000 | 17 | |
Chr04 | 41 290 001 | 42 390 000 | 30 | |
Chr06 | 9 260 001 | 10 280 000 | 98 | |
Chr07 | 8 310 001 | 11 590 000 | 173 | |
Chr07 | 12 960 001 | 16 950 000 | 202 | |
Chr07 | 19 560 001 | 20 870 000 | 20 | |
Chr07 | 22 020 001 | 23 400 000 | 1 | |
Chr07 | 25 340 001 | 27 930 000 | 12 | |
Chr07 | 28 330 001 | 29 520 000 | 13 | |
Chr07 | 29 640 001 | 32 490 000 | 25 | |
Chr09 | 7 890 001 | 9 230 000 | 38 | |
Chr12 | 37 500 001 | 38 500 000 | 82 | |
Chr13 | 20 600 001 | 22 520 000 | 189 | |
Chr14 | 44 180 001 | 46 170 000 | 136 | |
Chr15 | 14 470 001 | 16 910 000 | 88 | |
Chr16 | 15 650 001 | 16 710 000 | 7 | |
Chr16 | 18 160 001 | 19 450 000 | 22 | |
Chr16 | 34 770 001 | 35 850 000 | 49 | |
Chr17 | 8 300 001 | 9 500 000 | 121 | |
Chr19 | 46 210 001 | 50 580 000 | 495 | |
Chr20 | 4 100 001 | 5 720 000 | 28 | |
Chr20 | 10 380 001 | 11 500 000 | 6 | |
Chr20 | 34 990 001 | 38 100 000 | 295 | |
0.99 | Chr01 | 40 790 001 | 41 790 000 | 15 |
Chr07 | 9 770 001 | 11 210 000 | 57 | |
Chr12 | 37 500 001 | 38 500 000 | 82 | |
Chr19 | 46 970 001 | 48 610 000 | 182 |
Table 5 Genetic loci of soybean pod and seed traits via different methods
置信度Confidence level | 染色体 Chromosome | 起始位置 Start position /bp | 终止位置 End position /bp | 基因数量 Gene number |
---|---|---|---|---|
0.95 | Chr01 | 40 690 001 | 41 790 000 | 19 |
Chr02 | 41 180 001 | 44 100 000 | 246 | |
Chr02 | 45 540 001 | 47 550 000 | 236 | |
Chr03 | 39 550 001 | 41 670 000 | 228 | |
Chr04 | 35 390 001 | 36 590 000 | 17 | |
Chr04 | 41 290 001 | 42 390 000 | 30 | |
Chr06 | 9 260 001 | 10 280 000 | 98 | |
Chr07 | 8 310 001 | 11 590 000 | 173 | |
Chr07 | 12 960 001 | 16 950 000 | 202 | |
Chr07 | 19 560 001 | 20 870 000 | 20 | |
Chr07 | 22 020 001 | 23 400 000 | 1 | |
Chr07 | 25 340 001 | 27 930 000 | 12 | |
Chr07 | 28 330 001 | 29 520 000 | 13 | |
Chr07 | 29 640 001 | 32 490 000 | 25 | |
Chr09 | 7 890 001 | 9 230 000 | 38 | |
Chr12 | 37 500 001 | 38 500 000 | 82 | |
Chr13 | 20 600 001 | 22 520 000 | 189 | |
Chr14 | 44 180 001 | 46 170 000 | 136 | |
Chr15 | 14 470 001 | 16 910 000 | 88 | |
Chr16 | 15 650 001 | 16 710 000 | 7 | |
Chr16 | 18 160 001 | 19 450 000 | 22 | |
Chr16 | 34 770 001 | 35 850 000 | 49 | |
Chr17 | 8 300 001 | 9 500 000 | 121 | |
Chr19 | 46 210 001 | 50 580 000 | 495 | |
Chr20 | 4 100 001 | 5 720 000 | 28 | |
Chr20 | 10 380 001 | 11 500 000 | 6 | |
Chr20 | 34 990 001 | 38 100 000 | 295 | |
0.99 | Chr01 | 40 790 001 | 41 790 000 | 15 |
Chr07 | 9 770 001 | 11 210 000 | 57 | |
Chr12 | 37 500 001 | 38 500 000 | 82 | |
Chr19 | 46 970 001 | 48 610 000 | 182 |
染色体 Chromosome | 候选基因 Candidate gene | 非同义突变数量 Non-synonymous number | 基因注释 Gene annotation |
---|---|---|---|
Chr07 | Glyma.07G106700 | 2 | β-半乳糖苷酶β-galactosidase |
Chr07 | Glyma.07G108700 | 1 | CCR4-NOT转录复合物亚基CCR4-NOT transcription complex subunit |
Chr07 | Glyma.07G109500 | 1 | Squamosa启动子结合蛋白Squamosa promoter-binding-like protein |
Chr19 | Glyma.19G219500 | 1 | 硼转运体Boron transporter |
Chr19 | Glyma.19G219600 | 1 | NIM1-INTERACTING蛋白NIM1-INTERACTING protein |
Chr19 | Glyma.19G219700 | 1 | 多聚半乳糖醛酸酶Polygalacturonase |
Chr19 | Glyma.19G220000 | 4 | 锌指蛋白Zinc finger protein |
Chr19 | Glyma.19G220100 | 13 | 含WD重复蛋白WD repeat-containing protein |
Chr19 | Glyma.19G221700 | 5 | WRKY转录因子WRKY transcription factor |
Chr19 | Glyma.19G222200 | 2 | MYB转录因子MYB transcription factor |
Chr19 | Glyma.19G222300 | 2 | BnaC04g52040D |
Chr19 | Glyma.19G222400 | 1 | 果胶乙酰酯酶Pectin acetylesterase |
Chr19 | Glyma.19G222600 | 1 | 肽基脯氨酰顺反异构酶Peptidyl-prolyl cis-trans isomerase |
Chr19 | Glyma.19G223000 | 2 | 1,4-β-甘露糖苷酶1,4-β-mannosidase |
Chr19 | Glyma.19G223900 | 1 | BnaA06g39450D |
Chr19 | Glyma.19G224000 | 8 | 翻译起始因子IF-2类蛋白Translation initiation factor IF-2-like |
Chr19 | Glyma.19G224100 | 2 | 通用转录因子IIF亚基General transcription factor IIF subunit |
Chr19 | Glyma.19G224400 | 3 | NRT1/ PTR家族蛋白NRT1/ PTR family protein |
Chr19 | Glyma.19G224700 | 2 | 类PIF3转录因子Transcription factor PIF3-like |
Chr19 | Glyma.19G226000 | 1 | 丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase |
Chr19 | Glyma.19G227800 | 2 | 半乳醇合酶Galactinol synthase |
Chr19 | Glyma.19G228600 | 1 | 肽链释放因子Peptide chain release factor |
Chr19 | Glyma.19G229400 | 2 | 钙调素结合蛋白Calmodulin-binding protein |
Table 6 Candidate genes in the consistent regions with non-synonymous mutations in gene exons
染色体 Chromosome | 候选基因 Candidate gene | 非同义突变数量 Non-synonymous number | 基因注释 Gene annotation |
---|---|---|---|
Chr07 | Glyma.07G106700 | 2 | β-半乳糖苷酶β-galactosidase |
Chr07 | Glyma.07G108700 | 1 | CCR4-NOT转录复合物亚基CCR4-NOT transcription complex subunit |
Chr07 | Glyma.07G109500 | 1 | Squamosa启动子结合蛋白Squamosa promoter-binding-like protein |
Chr19 | Glyma.19G219500 | 1 | 硼转运体Boron transporter |
Chr19 | Glyma.19G219600 | 1 | NIM1-INTERACTING蛋白NIM1-INTERACTING protein |
Chr19 | Glyma.19G219700 | 1 | 多聚半乳糖醛酸酶Polygalacturonase |
Chr19 | Glyma.19G220000 | 4 | 锌指蛋白Zinc finger protein |
Chr19 | Glyma.19G220100 | 13 | 含WD重复蛋白WD repeat-containing protein |
Chr19 | Glyma.19G221700 | 5 | WRKY转录因子WRKY transcription factor |
Chr19 | Glyma.19G222200 | 2 | MYB转录因子MYB transcription factor |
Chr19 | Glyma.19G222300 | 2 | BnaC04g52040D |
Chr19 | Glyma.19G222400 | 1 | 果胶乙酰酯酶Pectin acetylesterase |
Chr19 | Glyma.19G222600 | 1 | 肽基脯氨酰顺反异构酶Peptidyl-prolyl cis-trans isomerase |
Chr19 | Glyma.19G223000 | 2 | 1,4-β-甘露糖苷酶1,4-β-mannosidase |
Chr19 | Glyma.19G223900 | 1 | BnaA06g39450D |
Chr19 | Glyma.19G224000 | 8 | 翻译起始因子IF-2类蛋白Translation initiation factor IF-2-like |
Chr19 | Glyma.19G224100 | 2 | 通用转录因子IIF亚基General transcription factor IIF subunit |
Chr19 | Glyma.19G224400 | 3 | NRT1/ PTR家族蛋白NRT1/ PTR family protein |
Chr19 | Glyma.19G224700 | 2 | 类PIF3转录因子Transcription factor PIF3-like |
Chr19 | Glyma.19G226000 | 1 | 丝氨酸/苏氨酸蛋白激酶Serine/threonine-protein kinase |
Chr19 | Glyma.19G227800 | 2 | 半乳醇合酶Galactinol synthase |
Chr19 | Glyma.19G228600 | 1 | 肽链释放因子Peptide chain release factor |
Chr19 | Glyma.19G229400 | 2 | 钙调素结合蛋白Calmodulin-binding protein |
Fig. 2 Expressions of candidate genes related to soybean pod and seed traits in C813Note:Pod-T1~Pod-T5 indicate 5 developmental stages of pod, Seed-T1~Seed-T3 indicate 3 developmental stages of seed.
Fig. 3 Expressions of candidate genes for soybean pod and seed traits in KN7Note:Pod-T1~Pod-T5 indicate 5 developmental stages of pod, Seed-T1~Seed-T3 indicate 3 developmental stages of seed.
染色体 Chromosome | 候选基因 Candidate gene | 非同义突变数量 Non-synonymous number | 基因注释 Gene annotation |
---|---|---|---|
Chr19 | Glyma.19G229500 | 2 | 类SAR DEFICIENT蛋白SAR DEFICIENT like |
Chr19 | Glyma.19G229800 | 1 | 类importin蛋白亚基Importin subunit alpha like |
Chr19 | Glyma.19G230100 | 1 | 驱动蛋白Kinesin |
Chr19 | Glyma.19G231000 | 3 | 类F-box蛋白F-box protein like |
Chr19 | Glyma.19G231200 | 5 | 类F-box/富LRR蛋白F-box/LRR-repeat protein like |
Chr19 | Glyma.19G231400 | 3 | 果胶酯酶Pectinesterase like |
Chr19 | Glyma.19G231500 | 1 | 果胶酯酶抑制因子Pectinesterase inhibitor |
Chr19 | Glyma.19G233900 | 1 | 呼吸氧化酶同源蛋白Respiratory burst oxidase homolog protein |
Chr19 | Glyma.19G234300 | 1 | Tudor/PWWP/MBT家族蛋白Tudor/PWWP/MBT superfamily protein |
Chr19 | Glyma.19G234400 | 3 | 酰基辅酶A结合域蛋白Acyl-CoA-binding domain-containing protein |
Chr19 | Glyma.19G235100 | 1 | Xaa-pro氨基肽酶Xaa-pro aminopeptidase |
Chr19 | Glyma.19G235300 | 1 | 微管结合蛋白Microtubule-binding protein |
Chr19 | Glyma.19G235400 | 2 | 驱动蛋白Kinesin |
Chr19 | Glyma.19G235500 | 1 | β-甘露糖苷酶β-mannosidase |
Chr19 | Glyma.19G235800 | 2 | 类RRP15蛋白RRP15-like protein |
Chr19 | Glyma.19G236700 | 1 | CAR1转录因子CAR1 transcription factor |
Chr19 | Glyma.19G236900 | 1 | bHLH转录因子bHLH transcription factor |
Table 6 Candidate genes in the consistent regions with non-synonymous mutations in gene exons
染色体 Chromosome | 候选基因 Candidate gene | 非同义突变数量 Non-synonymous number | 基因注释 Gene annotation |
---|---|---|---|
Chr19 | Glyma.19G229500 | 2 | 类SAR DEFICIENT蛋白SAR DEFICIENT like |
Chr19 | Glyma.19G229800 | 1 | 类importin蛋白亚基Importin subunit alpha like |
Chr19 | Glyma.19G230100 | 1 | 驱动蛋白Kinesin |
Chr19 | Glyma.19G231000 | 3 | 类F-box蛋白F-box protein like |
Chr19 | Glyma.19G231200 | 5 | 类F-box/富LRR蛋白F-box/LRR-repeat protein like |
Chr19 | Glyma.19G231400 | 3 | 果胶酯酶Pectinesterase like |
Chr19 | Glyma.19G231500 | 1 | 果胶酯酶抑制因子Pectinesterase inhibitor |
Chr19 | Glyma.19G233900 | 1 | 呼吸氧化酶同源蛋白Respiratory burst oxidase homolog protein |
Chr19 | Glyma.19G234300 | 1 | Tudor/PWWP/MBT家族蛋白Tudor/PWWP/MBT superfamily protein |
Chr19 | Glyma.19G234400 | 3 | 酰基辅酶A结合域蛋白Acyl-CoA-binding domain-containing protein |
Chr19 | Glyma.19G235100 | 1 | Xaa-pro氨基肽酶Xaa-pro aminopeptidase |
Chr19 | Glyma.19G235300 | 1 | 微管结合蛋白Microtubule-binding protein |
Chr19 | Glyma.19G235400 | 2 | 驱动蛋白Kinesin |
Chr19 | Glyma.19G235500 | 1 | β-甘露糖苷酶β-mannosidase |
Chr19 | Glyma.19G235800 | 2 | 类RRP15蛋白RRP15-like protein |
Chr19 | Glyma.19G236700 | 1 | CAR1转录因子CAR1 transcription factor |
Chr19 | Glyma.19G236900 | 1 | bHLH转录因子bHLH transcription factor |
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