Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (6): 141-148.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1386
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CUI Xue-qiang(), HUANG Chang-yan, DENG Jie-ling, LI Xian-min, LI Xiu-ling, ZHANG Zi-bin()
Received:
2022-11-09
Online:
2023-06-26
Published:
2023-07-07
Contact:
ZHANG Zi-bin
E-mail:yncuixueqiang@126.com;candou154@126.com
CUI Xue-qiang, HUANG Chang-yan, DENG Jie-ling, LI Xian-min, LI Xiu-ling, ZHANG Zi-bin. SNP Markers Development and Genetic Relationship Analysis of Dendrobium Germplasms Using SLAF-seq Technology[J]. Biotechnology Bulletin, 2023, 39(6): 141-148.
种质编号 Germplasm No. | 总读数 Total reads | GC含量 GC content/% | Q30含量 Q30 content/% | 种质编号 Germplasm No. | 总读数 Total reads | GC含量 GC content/% | Q30含量 Q30 content/% | |
---|---|---|---|---|---|---|---|---|
1 | 2 206 424 | 40.80 | 94.43 | 32 | 5 359 710 | 39.13 | 92.60 | |
2 | 3 392 758 | 39.52 | 94.06 | 33 | 1 927 034 | 39.04 | 91.41 | |
3 | 1 685 725 | 40.68 | 94.30 | 34 | 1 001 860 | 40.88 | 89.71 | |
4 | 2 397 802 | 41.36 | 93.61 | 35 | 1 738 186 | 38.96 | 91.29 | |
5 | 2 407 877 | 40.88 | 94.25 | 36 | 1 570 013 | 38.62 | 90.59 | |
6 | 3 816 221 | 37.99 | 93.65 | 37 | 2 817 541 | 42.10 | 94.61 | |
7 | 1 236 847 | 45.65 | 92.95 | 38 | 2 262 024 | 41.10 | 94.49 | |
8 | 2 603 097 | 40.01 | 94.46 | 39 | 1 506 192 | 40.21 | 94.35 | |
9 | 2 266 706 | 40.64 | 94.09 | 40 | 1 658 896 | 39.49 | 94.57 | |
10 | 2 741 663 | 39.42 | 93.77 | 41 | 2 398 814 | 41.12 | 94.63 | |
11 | 2 888 849 | 39.57 | 94.72 | 42 | 2 010 374 | 39.09 | 94.46 | |
12 | 5 033 204 | 39.52 | 94.34 | 43 | 2 253 253 | 38.95 | 94.61 | |
13 | 1 177 834 | 39.60 | 93.56 | 44 | 2 443 737 | 39.60 | 94.03 | |
14 | 1 558 521 | 39.04 | 93.06 | 45 | 3 295 369 | 39.07 | 94.86 | |
15 | 3 350 246 | 42.91 | 94.67 | 46 | 1 067 643 | 38.75 | 94.67 | |
16 | 2 508 628 | 39.29 | 93.40 | 47 | 2 170 007 | 39.61 | 94.40 | |
17 | 3 008 190 | 39.45 | 93.23 | 48 | 1 954 914 | 39.23 | 94.37 | |
18 | 2 892 775 | 42.48 | 94.54 | 49 | 2 394 534 | 39.06 | 94.48 | |
19 | 3 799 474 | 41.30 | 94.54 | 50 | 2 899 967 | 39.27 | 94.52 | |
20 | 3 265 332 | 41.98 | 94.56 | 51 | 2 199 124 | 46.38 | 94.72 | |
21 | 2 223 263 | 38.82 | 93.44 | 52 | 3 270 085 | 40.08 | 94.66 | |
22 | 2 536 748 | 40.32 | 94.25 | 53 | 1 303 118 | 39.41 | 94.51 | |
23 | 3 663 842 | 40.96 | 94.71 | 54 | 3 465 111 | 38.97 | 94.13 | |
24 | 576 195 | 42.98 | 93.34 | 55 | 2 955 467 | 39.29 | 94.76 | |
25 | 5 218 665 | 39.01 | 93.00 | 56 | 4 757 901 | 39.73 | 94.79 | |
26 | 2 318 866 | 39.08 | 93.03 | 57 | 4 802 384 | 40.06 | 94.62 | |
27 | 2 752 538 | 41.06 | 94.50 | 58 | 2 339 558 | 40.16 | 94.63 | |
28 | 1 709 658 | 38.85 | 90.70 | 59 | 2 787 875 | 38.80 | 94.67 | |
29 | 3 965 547 | 38.44 | 94.48 | 60 | 1 857 241 | 42.29 | 93.80 | |
30 | 1 831 691 | 38.73 | 91.14 | SD | 7 293 431 | 42.86 | 94.33 | |
31 | 3 836 959 | 40.67 | 94.49 |
Table 1 Data statistics of genomic sequences generated by SLAF-seq
种质编号 Germplasm No. | 总读数 Total reads | GC含量 GC content/% | Q30含量 Q30 content/% | 种质编号 Germplasm No. | 总读数 Total reads | GC含量 GC content/% | Q30含量 Q30 content/% | |
---|---|---|---|---|---|---|---|---|
1 | 2 206 424 | 40.80 | 94.43 | 32 | 5 359 710 | 39.13 | 92.60 | |
2 | 3 392 758 | 39.52 | 94.06 | 33 | 1 927 034 | 39.04 | 91.41 | |
3 | 1 685 725 | 40.68 | 94.30 | 34 | 1 001 860 | 40.88 | 89.71 | |
4 | 2 397 802 | 41.36 | 93.61 | 35 | 1 738 186 | 38.96 | 91.29 | |
5 | 2 407 877 | 40.88 | 94.25 | 36 | 1 570 013 | 38.62 | 90.59 | |
6 | 3 816 221 | 37.99 | 93.65 | 37 | 2 817 541 | 42.10 | 94.61 | |
7 | 1 236 847 | 45.65 | 92.95 | 38 | 2 262 024 | 41.10 | 94.49 | |
8 | 2 603 097 | 40.01 | 94.46 | 39 | 1 506 192 | 40.21 | 94.35 | |
9 | 2 266 706 | 40.64 | 94.09 | 40 | 1 658 896 | 39.49 | 94.57 | |
10 | 2 741 663 | 39.42 | 93.77 | 41 | 2 398 814 | 41.12 | 94.63 | |
11 | 2 888 849 | 39.57 | 94.72 | 42 | 2 010 374 | 39.09 | 94.46 | |
12 | 5 033 204 | 39.52 | 94.34 | 43 | 2 253 253 | 38.95 | 94.61 | |
13 | 1 177 834 | 39.60 | 93.56 | 44 | 2 443 737 | 39.60 | 94.03 | |
14 | 1 558 521 | 39.04 | 93.06 | 45 | 3 295 369 | 39.07 | 94.86 | |
15 | 3 350 246 | 42.91 | 94.67 | 46 | 1 067 643 | 38.75 | 94.67 | |
16 | 2 508 628 | 39.29 | 93.40 | 47 | 2 170 007 | 39.61 | 94.40 | |
17 | 3 008 190 | 39.45 | 93.23 | 48 | 1 954 914 | 39.23 | 94.37 | |
18 | 2 892 775 | 42.48 | 94.54 | 49 | 2 394 534 | 39.06 | 94.48 | |
19 | 3 799 474 | 41.30 | 94.54 | 50 | 2 899 967 | 39.27 | 94.52 | |
20 | 3 265 332 | 41.98 | 94.56 | 51 | 2 199 124 | 46.38 | 94.72 | |
21 | 2 223 263 | 38.82 | 93.44 | 52 | 3 270 085 | 40.08 | 94.66 | |
22 | 2 536 748 | 40.32 | 94.25 | 53 | 1 303 118 | 39.41 | 94.51 | |
23 | 3 663 842 | 40.96 | 94.71 | 54 | 3 465 111 | 38.97 | 94.13 | |
24 | 576 195 | 42.98 | 93.34 | 55 | 2 955 467 | 39.29 | 94.76 | |
25 | 5 218 665 | 39.01 | 93.00 | 56 | 4 757 901 | 39.73 | 94.79 | |
26 | 2 318 866 | 39.08 | 93.03 | 57 | 4 802 384 | 40.06 | 94.62 | |
27 | 2 752 538 | 41.06 | 94.50 | 58 | 2 339 558 | 40.16 | 94.63 | |
28 | 1 709 658 | 38.85 | 90.70 | 59 | 2 787 875 | 38.80 | 94.67 | |
29 | 3 965 547 | 38.44 | 94.48 | 60 | 1 857 241 | 42.29 | 93.80 | |
30 | 1 831 691 | 38.73 | 91.14 | SD | 7 293 431 | 42.86 | 94.33 | |
31 | 3 836 959 | 40.67 | 94.49 |
SLAF标签总数 Total of SLAF tags | 多态性SLAF标签数 Number of polymorphic SLAF tags | 非多态性SLAF标签数 Number of non-polymorphic SLAF tags | SNP总数 Total of SNP | 完整度 Integrity ratio/% | 杂合率 Hetloci ratio/% |
---|---|---|---|---|---|
1 337 217 | 1 049 638 | 287 579 | 11 248 186 | 2.71-24.89 | 1.13-5.74 |
Table 2 Information statistics of SLAF tags and identified SNP
SLAF标签总数 Total of SLAF tags | 多态性SLAF标签数 Number of polymorphic SLAF tags | 非多态性SLAF标签数 Number of non-polymorphic SLAF tags | SNP总数 Total of SNP | 完整度 Integrity ratio/% | 杂合率 Hetloci ratio/% |
---|---|---|---|---|---|
1 337 217 | 1 049 638 | 287 579 | 11 248 186 | 2.71-24.89 | 1.13-5.74 |
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