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基于单片段代换系的水稻苗高QTL定位和上位性效应分析

张龙廷, 吴静, 熊喜娟, 董景芳, 张少红, 赵均良, 刘自强, 杨梯丰

张龙廷, 吴静, 熊喜娟, 等. 基于单片段代换系的水稻苗高QTL定位和上位性效应分析[J]. 华南农业大学学报, 2023, 44(6): 881-888. DOI: 10.7671/j.issn.1001-411X.202306067
引用本文: 张龙廷, 吴静, 熊喜娟, 等. 基于单片段代换系的水稻苗高QTL定位和上位性效应分析[J]. 华南农业大学学报, 2023, 44(6): 881-888. DOI: 10.7671/j.issn.1001-411X.202306067
ZHANG Longting, WU Jing, XIONG Xijuan, et al. QTL mapping and epistatic effect analysis of seedling height based on single segment substitution lines in rice[J]. Journal of South China Agricultural University, 2023, 44(6): 881-888. DOI: 10.7671/j.issn.1001-411X.202306067
Citation: ZHANG Longting, WU Jing, XIONG Xijuan, et al. QTL mapping and epistatic effect analysis of seedling height based on single segment substitution lines in rice[J]. Journal of South China Agricultural University, 2023, 44(6): 881-888. DOI: 10.7671/j.issn.1001-411X.202306067

基于单片段代换系的水稻苗高QTL定位和上位性效应分析

基金项目: 广东省重点领域研发计划(2022B0202060002);广东省科技特派员项目(KTP20210269);广东省水稻育种新技术重点实验室课题(2020B1212060047);广州市科技计划重点项目(201804020078)
详细信息
    作者简介:

    张龙廷,硕士研究生,主要从事水稻分子育种研究,E-mail: 2955134545@qq.com

    吴 静,硕士研究生,主要从事水稻分子育种研究,E-mail: 1154966358@qq.com

    熊喜娟,硕士研究生,主要从事水稻分子育种研究,Email:3511692659@qq.com;†表示同等贡献

    通讯作者:

    杨梯丰,研究员,博士,主要从事水稻分子育种研究,E-mail: yangtifeng@gdaas.cn

  • 中图分类号: S511;Q311.1

QTL mapping and epistatic effect analysis of seedling height based on single segment substitution lines in rice

  • 摘要:
    目的 

    挖掘控制水稻苗高的稳定QTL,并分析其上位性效应,为水稻苗高的分子育种提供QTL和理论参考。

    方法 

    以IR65598-112-2为供体、优良品种‘华粳籼74’为受体的单片段代换系(Single segment substitution line,SSSL)为材料,通过测定SSSL与‘华粳籼74’的苗高差异,对苗高QTL进行定位;通过代换作图缩小QTL的区间,并分析2个苗高QTL的上位性效应。

    结果 

    在第3号染色体长臂端定位到2个相邻的苗高QTLs (qSH3-1qSH3-2),分别位于第3号染色体的32.59—33.08 Mb和33.16—34.81 Mb区间,长度分别为0.49和1.65 Mb;加性效应分别为−0.86和−1.09 cm;加性效应表型贡献值分别为−4.14%和−5.15%;包含这2个QTL的SSSL的苗高与‘华粳籼74’无显著差异。

    结论 

    本研究定位到2个苗高QTL,这2个QTL之间可能存在显著的上位性。

    Abstract:
    Objective 

    To find out the stable QTLs controlling rice seedling height, analyze their epistatic effects, and provide QTL and theoretical references for molecular breeding of rice seedling height.

    Method 

    The single segment substitution lines (SSSLs) with IR65598-112-2 as donor and ‘Huajingxian 74’ as receptor were used as materials. The difference of seedling height between SSSL and ‘Huajingxian 74’ was measured, and the QTLs of seedling height were mapped. The QTL interval was narrowed by substitution mapping, and the epistatic effects of two seedling height QTLs were also analyzed.

    Result 

    Two adjacent QTLs (qSH3-1 and qSH3-2) for seedling height were mapped on the long arm of chromosome 3, which were located in the intervals of 32.59−33.08 and 33.16−34.81 Mb, with the lengths of 0.49 and 1.65 Mb, respectively. The additive effects were −0.86 and −1.09 cm, respectively. The phenotypic contribution rate of additive effects were −4.14% and −5.15%, respectively. However, there was no significant difference of seedling height between SSSL harboring these two QTLs and ‘Huajingxian 74’.

    Conclusion 

    Two QTLs for seedling height were identified, and there may be significant epistasis effects between the two QTLs.

  • 图  1   K1、K11与‘华粳籼74’的苗高差异

    “*”“**”分别表示在P < 0.05和P < 0.01水平差异显著和极显著(t检验)

    Figure  1.   Differences in seedling height between K1, K11 and ‘Huajingxian 74’

    “*” and “**” indicate significant and very significant differences at P < 0.05 and P < 0.01 levels respectively (t test)

    图  2   qSH3-1qSH3-2位置示意图

    Figure  2.   Position schematic diagram of qSH3-1 and qSH3-2

    图  3   K1、K6和‘华粳籼74’的苗高差异

    柱子上方的不同小写字母表示在P<0.05水平差异显著(Duncan’s法)

    Figure  3.   Differences in seedling height of K1, K6 and ‘Huajingxian 74’

    Different lowercase letters on the columns indicate significant differences at P < 0.05 level (Duncan’s method)

    图  4   qSH3-1的代换作图

    Figure  4.   Substitution mapping of qSH3-1

    图  5   K1、K11、K13和‘华粳籼74’的苗高差异

    柱子上方的不同小写字母表示在P<0.05水平差异显著(Duncan’s法)

    Figure  5.   Differences in seedling height of K1, K11, K13 and ‘Huajingxian 74’

    Different lowercase letters on the columns indicate significant differences at P<0.05 level (Duncan’s method)

    图  6   qSH3-1qSH3-2上位性效应

    Figure  6.   Epistatic effects between qSH3-1 and qSH3-2

    表  1   试验SSSLs的信息

    Table  1   Information of testing SSSLs

    SSSL供体
    Donor
    染色体
    Chromosome
    代换片段
    Substitution segment
    片段位置/Mb
    Segment position
    K1 IR65598-112-233C52-5—3C33.1331.76—33.08
    K6 IR65598-112-233C52-5—3C32.7031.69—32.59
    K11IR65598-112-233C52-7—3C34.9033.16—34.81
    K13IR65598-112-233C52-5—3C34.9031.69—34.81
    下载: 导出CSV

    表  2   用于检测代换片段的分子标记

    Table  2   Molecular markers for screening of substitution segments

    引物
    Primer
    染色体
    Chromosome
    位置/Mb
    Position
    正向序列(5′→3′)
    Forward sequence
    反向序列(5′→3′)
    Reverse sequence
    3C52-5331.69ATTCTATGCCGCCAACCAAGAATTGTCAACTTCAGCATCCC
    3C31.83331.83GATGTCAGGGAAAGAAGAAACGCATTCTGGGTCAACATACAC
    3C31.93331.93AGAAGGCAAACGGCTGACAAAGCGTGCTGAACTGGAGATACAAA
    3C32.10332.10CCTTTGAACCTCGTGGGCTGGTGCGGGAACCCTATC
    3C52-3332.24TACAGCCTCCTAATAGCATTGACCTCGAAGCTGCCGGTGTTG
    3C32.48332.48CGCAGGAACAAACAACGAGAGGGAGTAATGGATACGAAGA
    3C32.70332.70CCATCTCATTTATCAAGTCAAAGCCGTCTCGGGAGTGTA
    3C52-6332.91GAGCATAAAGGCATTGGTTGTACCGTTTGTTCGGATAGATG
    3C33.03333.03GCACTCGCCATCCTGACACATTAGCTCGCTTCGTTT
    3C33.13333.13GGAAACTTTGGTTGTCCCTGCTTGGAGCGTCGTTTGTGC
    3C52-7333.19AGAACACCCGCTCCATCGAGCAGCACGCAGCCGCCTT
    RM130333.39TGTTGCTTGCCCTCACGAAGGGTCGCGTGCTTGGTTTTGGTTC
    3C34.25334.25GAACTGATACGGTAGGATGGATGGACACGGACTCTTT
    3C52-8334.61GACGAGGAGGAGGAAGAGGAAGCAATCGGAGCAGCAAGAG
    3C34.72334.72TGGAGGAATCAAGGAGACATTGAGAAAGAGGCGTAA
    3C34.90334.90TCAGCAAACAATCTACTACCGCACAGGACGCACTCAACAT
    3C35.15335.15TTGCTGCGGTGGACCTCTTTCGGCACCAGTGGGGACAT
    3C35.39335.39TGCTCGGGAACCAGACGTTGAATCCTGCTGCTTTGA
    3C52-4335.74TGAACCAATGGAAACCTTGAGTCCCTGTATGCGGATGAT
    下载: 导出CSV

    表  3   苗高QTL的加性效应与加性效应表型贡献率1)

    Table  3   Additive effect and additive effect phenotypic contribution rate of QTL in seedling height

    SSSLQTL染色体
    Chromosome
    位置/Mb
    Position
    3次试验的加性效应/cm
    Additive effects of three tests
    整体加性效应/cm
    Average additive
    effect
    表型贡献率/%
    Phenotypic
    contribution rate
    123
    K1qSH3-1331.76—33.08−1.57−0.27−0.86**−4.14
    K11qSH3-2333.16—34.81−0.75−0.62−1.33−1.09**−5.15
     1) “**”表示K1、K11与‘华粳籼74’的苗高在P < 0.01水平差异极显著(t检验);“—”表示未检测到QTL;负效应“−”表示受体表型值减小
     1) “**” indicates that the seedling heights of K1 and K11 are highly significantly different from that of ‘Huajingxian 74’ at P < 0.01 (t test); “—” indicates that no QTL is detected; Negative effect “−” indicates a decrease in receptor phenotype value
    下载: 导出CSV

    表  4   qSH3-1qSH3-2区间内CDS和启动子区域都发生变异的基因

    Table  4   Variation genes in both CDS and promoter regions in qSH3-1 and qSH3-2 intervals

    QTL变异类型
    Variation type
    基因名称
    Gene name
    qSH3-1 密码子改变和删除
    Codon change and deletion
    Os03g0793300Os03g0786600
    密码子删除 Codon deletion Os03g0785200
    密码子插入 Codon insertion Os03g0785800Os03g0787000Os03g0791432Os03g0792300
    移码 Frame shift Os03g0788000Os03g0790000Os03g0793100Os03g0793700
    qSH3-2 密码子改变和删除
    Codon change and deletion
    Os03g0800200Os03g0800500Os03g0809400Os03g0812800Os03g0816000Os03g0820700
    密码子删除 Codon deletion Os03g0796900Os03g0797500Os03g0798400Os03g0802900Os03g0810800Os03g0811400Os03g0812400Os03g0816500Os03g0816700Os03g0821200Os03g0825900
    密码子插入 Codon insertion Os03g0800900Os03g0801800Os03g0802700Os03g0817200Os03g0823400Os03g0824650Os03g0828300
    密码子插入/剪接位点区域
    Codon insertion/splice site region
    Os03g0828500
    移码 Frame shift Os03g0814500Os03g0824300Os03g0824400Os03g0826600
    起始密码子缺失 Start codon lost Os03g0815100
      终止密码子缺失 Stop codon lost Os03g0821250
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-07-10
  • 网络出版日期:  2023-11-12
  • 发布日期:  2023-09-13
  • 刊出日期:  2023-11-09

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