Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (8): 173-184.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0386
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WU Yuan-ming1(), LIN Jia-yi1, LIU Yu-xi1, LI Dan-ting2, ZHANG Zong-qiong2, ZHENG Xiao-ming3,4,5, PANG Hong-bo1()
Received:
2023-04-22
Online:
2023-08-26
Published:
2023-09-05
Contact:
PANG Hong-bo
E-mail:19861602091@163.com;panghb@synu.edu.cn
WU Yuan-ming, LIN Jia-yi, LIU Yu-xi, LI Dan-ting, ZHANG Zong-qiong, ZHENG Xiao-ming, PANG Hong-bo. Identification of Rice Plant Height-associated QTL Using BSA-seq and RNA-seq[J]. Biotechnology Bulletin, 2023, 39(8): 173-184.
基因 Gene | 引物序列 Primer sequence(5'-3') | 产物大小 Product size/bp |
---|---|---|
LOC_Os07g02770 | F: GAGAGCATGGCAAGGAAGGT | 130 |
R: TAGTGCGGTGCATTTGTCCT | ||
LOC_Os07g02850 | F: GCGTCTGCAGGAAGAAGTCC | 125 |
R: CTGCACCAGCCACATGAATC | ||
LOC_Os07g04220 | F: CCCGCCATTAGTCCACAGAG | 128 |
R: TTGCTGGTGGGCCTGATATG | ||
LOC_Os07g05050 | F: CGAACTCCCAAACACCTCGG | 241 |
R: GGTTCTTGGGCTTCCAGCTAA | ||
LOC_Os07g05720 | F: TCTCCATGTCCTCGGGTCTT | 175 |
R: GGGCTGAAGAGGAACGGAAT | ||
OsActin | F: AGACCTTCAACACCCCTGCT | 110 |
R: GTGGCTGACACCATCACCAG |
Table 1 List of primers for RT-qPCR analysis
基因 Gene | 引物序列 Primer sequence(5'-3') | 产物大小 Product size/bp |
---|---|---|
LOC_Os07g02770 | F: GAGAGCATGGCAAGGAAGGT | 130 |
R: TAGTGCGGTGCATTTGTCCT | ||
LOC_Os07g02850 | F: GCGTCTGCAGGAAGAAGTCC | 125 |
R: CTGCACCAGCCACATGAATC | ||
LOC_Os07g04220 | F: CCCGCCATTAGTCCACAGAG | 128 |
R: TTGCTGGTGGGCCTGATATG | ||
LOC_Os07g05050 | F: CGAACTCCCAAACACCTCGG | 241 |
R: GGTTCTTGGGCTTCCAGCTAA | ||
LOC_Os07g05720 | F: TCTCCATGTCCTCGGGTCTT | 175 |
R: GGGCTGAAGAGGAACGGAAT | ||
OsActin | F: AGACCTTCAACACCCCTGCT | 110 |
R: GTGGCTGACACCATCACCAG |
Fig. 2 Plant height phenotype analysis of CSSL populations A: The tallest and shortest individuals in CSSL populations(Bar=25 cm).B: Distribution of average plant heights of CSSL populations
样品Sample | 原始数据 Raw base/bp | 过滤后的有效数据 Clean base/bp | 比对率Mapping rate/% | 平均测序深度Average depth(×) | 至少覆盖1个碱基的位点的比例Coverage at least 1×/% | 至少覆盖4个碱基的位点的比例Coverage at least 4×/% | Phred 数值大于20的碱基比例Q20/% | Phred 数值大于30的碱基比例Q30/% | 碱基G和C的含量GC/% |
---|---|---|---|---|---|---|---|---|---|
YZ8 | 11 134 196 100 | 11 134 054 800 | 99.00 | 23.81 | 82.46 | 79.06 | 97.57 | 93.31 | 44.60 |
GCWR | 14 338 273 200 | 14 338 088 700 | 98.65 | 28.82 | 85.26 | 82.67 | 97.78 | 93.79 | 44.23 |
H-pool | 5 067 688 200 | 5 067 637 200 | 99.04 | 11.36 | 82.27 | 74.08 | 97.11 | 92.15 | 43.59 |
L-pool | 4 969 848 300 | 4 969 806 000 | 99.02 | 11.43 | 81.81 | 74.14 | 97.14 | 92.13 | 43.61 |
Table 2 Summary of NGS data for BSA-seq analysis
样品Sample | 原始数据 Raw base/bp | 过滤后的有效数据 Clean base/bp | 比对率Mapping rate/% | 平均测序深度Average depth(×) | 至少覆盖1个碱基的位点的比例Coverage at least 1×/% | 至少覆盖4个碱基的位点的比例Coverage at least 4×/% | Phred 数值大于20的碱基比例Q20/% | Phred 数值大于30的碱基比例Q30/% | 碱基G和C的含量GC/% |
---|---|---|---|---|---|---|---|---|---|
YZ8 | 11 134 196 100 | 11 134 054 800 | 99.00 | 23.81 | 82.46 | 79.06 | 97.57 | 93.31 | 44.60 |
GCWR | 14 338 273 200 | 14 338 088 700 | 98.65 | 28.82 | 85.26 | 82.67 | 97.78 | 93.79 | 44.23 |
H-pool | 5 067 688 200 | 5 067 637 200 | 99.04 | 11.36 | 82.27 | 74.08 | 97.11 | 92.15 | 43.59 |
L-pool | 4 969 848 300 | 4 969 806 000 | 99.02 | 11.43 | 81.81 | 74.14 | 97.14 | 92.13 | 43.61 |
染色体 Chromosome | 起始位置 Start/bp | 终止位置 End/bp | 大小 Size/Mb | 基因数量 Gene number |
---|---|---|---|---|
7 | 1 | 2 848 000 | 2.848 | 141 |
10 | 3 796 001 | 5 088 000 | 1.292 | 135 |
总计Total | - | - | 4.140 | 276 |
Table 3 Candidate genome regions related to plant height mapping by Δ(SNP-index)and Δ(InDel-index)
染色体 Chromosome | 起始位置 Start/bp | 终止位置 End/bp | 大小 Size/Mb | 基因数量 Gene number |
---|---|---|---|---|
7 | 1 | 2 848 000 | 2.848 | 141 |
10 | 3 796 001 | 5 088 000 | 1.292 | 135 |
总计Total | - | - | 4.140 | 276 |
功能注释数据库 Annotated database | 注释基因数目 Number of annotated genes |
---|---|
eggNOG | 26 |
Uniprot | 41 |
GO | 48 |
KEGG | 20 |
总计Total | 78 |
Table 4 Statistics of functional annotation results for genes in candidate intervals
功能注释数据库 Annotated database | 注释基因数目 Number of annotated genes |
---|---|
eggNOG | 26 |
Uniprot | 41 |
GO | 48 |
KEGG | 20 |
总计Total | 78 |
基因 Gene ID | 基因注释 Gene annotation |
---|---|
LOC_Os07g02770 | 含F-box和亮氨酸富集重复序列的蛋白 Protein containing F-box and leucine-enriched repeats |
LOC_Os07g02850 | 含DUF538结构域的蛋白 Protein containing DUF538 domain |
LOC_Os07g04220 | 光敏色素信号与损伤相关的受体类激酶 Wound and phytochrome signaling involved receptor like kinase |
LOC_Os07g05050 | 含DEAD-box的ATP依赖的RNA解旋酶 ATP-dependent RNA helicase containing DEAD-box |
LOC_Os07g05720 | TCP转录因子 TCP family transcription factor |
Table 5 Results of functional annotation of candidate genes
基因 Gene ID | 基因注释 Gene annotation |
---|---|
LOC_Os07g02770 | 含F-box和亮氨酸富集重复序列的蛋白 Protein containing F-box and leucine-enriched repeats |
LOC_Os07g02850 | 含DUF538结构域的蛋白 Protein containing DUF538 domain |
LOC_Os07g04220 | 光敏色素信号与损伤相关的受体类激酶 Wound and phytochrome signaling involved receptor like kinase |
LOC_Os07g05050 | 含DEAD-box的ATP依赖的RNA解旋酶 ATP-dependent RNA helicase containing DEAD-box |
LOC_Os07g05720 | TCP转录因子 TCP family transcription factor |
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