WO2018201754A1 - 黄瓜雄性不育基因、分子标记、筛选方法及其用途 - Google Patents

黄瓜雄性不育基因、分子标记、筛选方法及其用途 Download PDF

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WO2018201754A1
WO2018201754A1 PCT/CN2018/072412 CN2018072412W WO2018201754A1 WO 2018201754 A1 WO2018201754 A1 WO 2018201754A1 CN 2018072412 W CN2018072412 W CN 2018072412W WO 2018201754 A1 WO2018201754 A1 WO 2018201754A1
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seq
snp
cucumber
plant
pool
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韩毅科
杜胜利
赵峰月
魏爱民
刘楠
陈正武
付薪蒙
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天津科润农业科技股份有限公司黄瓜研究所
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Priority to US16/610,853 priority Critical patent/US11319600B2/en
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  • the present invention relates to the field of molecular genetic breeding techniques, in particular to SNP or InDel markers associated with cucumber male sterility genes, and their screening, as well as the obtained male sterility genes and their use in identifying male sterile plants.
  • the present application relates to a method of obtaining a plant male sterility molecular marker SNP or InDel marker and locating a male sterility gene.
  • the method includes the following steps:
  • Disposition group The male sterile line of the plant is crossed with the fertile distant breed as the male parent, and the hybrid F1 is obtained.
  • the hybrid F1 is selfed to obtain the F2 segregating population, and the F2 segregating population is male.
  • BSA Separation population group analysis
  • KASP Competitive allele-specific PCR
  • the genetic map was constructed to locate the male sterility gene.
  • This study introduced a sequencing depth-related parameter SNP-index of a SNP locus, which is the ratio of the number of reads containing a SNP at a site to the total number of reads detected at that site, ranging from 0-1. . If the parameter is 0, it means that all the detected reads are from the genome of the parent used as the reference genome; this parameter is 1, indicating that all reads are from another parent; if the parameter is 0.5, it represents this mix. The SNPs in the pool are consistent in frequency from the genomes of the two parents.
  • the plant is a cucumber.
  • the molecular marker is a SNP marker.
  • the molecular marker is an InDel marker.
  • the molecular markers are SNP markers and InDel markers.
  • the male sterility gene is located in a genomic fragment between SNP marker G729940C and SNP marker C974274G.
  • the male sterility gene is located on chromosome 3 of cucumber.
  • the male sterility gene is located on chromosome 3 of chromosomes 805, 509-807, 682.
  • the gene for controlling male sterility of cucumber is the Csa3M006660.1 gene represented by SEIQ NO: 1, which encodes a protein of an amino acid sequence as shown by SEIQ NO: 2.
  • a point mutation occurs at position 1258 of the Csa3M006660.1 gene of the cucumber sterile line.
  • the nucleic acid sequence of the Csa3M006660.1 gene of the cucumber sterile line is set forth in SEQ ID NO:3. It encodes a protein such as the amino acid sequence shown by SEIQ NO:4.
  • the SNP typing primers for the primers used in competitive allele-specific PCR are shown below.
  • the primers labeled for C304430G are:
  • AATTACATGAATAAGTGTTCGTAATTTCG (SEQ ID NO: 5) and AATTACATGAATAAGTGTTCGTAATTTCC (SEQ ID NO: 6);
  • the primers labeled for G564531C are:
  • GGTTTGGAATCTTGCTTGGCATTG SEQ ID NO: 7
  • GGTTTGGAATCTTGCTTGGCATTC SEQ ID NO: 8
  • the primers labeled for A701466G are:
  • ATCTAGAAACCAAATAAAAACTATAGCCAA SEQ ID NO: 9
  • CTAGAAACCAAATAAAAACTATAGCCAG SEQ ID NO: 10
  • the primers for the G729940C label are:
  • GGAACCCCTTCTGAAGCTGTG SEQ ID NO: 11
  • GGAACCCCTTTCTGAAGCTGTC SEQ ID NO: 12
  • the primers labeled for T785141C are:
  • the primers labeled for C974274G are:
  • the primers labeled for T1031386G are:
  • the primers labeled for T1101289C are:
  • AAGACTAATATGCCCTTCCTCTTCTA (SEQ ID NO: 19) and GACTAATATGCCCTTCCTCTTCTG (SEQ ID NO: 20)
  • the primers labeled for T1508343G are:
  • the primers labeled for A2179014C are:
  • One embodiment of the present invention relates to a method for identifying a cucumber sterile plant and a fertile strain, characterized in that if the base 1258 of the Csa3M006660.1 gene is G, the plant is a sterile strain.
  • the present invention identified 10 SNP markers which are more closely linked to the cucumber male sterility gene, and 6 of the SNP markers are more closely linked to the cucumber male sterility gene.
  • the present invention identifies for the first time that the cucumber male sterility gene is the Csa3M006660.1 gene located on chromosome 3 of cucumber.
  • the sterile gene identified by the present invention can recognize cucumber male sterile plants more directly and quickly, and can be used for efficient production of cucumber hybrids.
  • Figure 1 shows the distribution of the fertile pool and sterile pool ⁇ SNP-index on 7 chromosomes of cucumbers by separation population group analysis (BSA).
  • BSA separation population group analysis
  • Figure 2 shows candidate SNP markers for KASP genotyping and their corresponding primers.
  • FIG. 3 shows the KASP genotyping results for the C974274G marker.
  • (a) is the KASP genotyping result for the fertile individual;
  • (b) is the KASP genotyping result for the sterile individual.
  • Figure 4 is a genetic map constructed by SNP markers and fine mapping of mutant genes.
  • Figure 5 is the nucleic acid sequence of the obtained Csa3M006660.1 gene.
  • the acquisition of SNP molecular markers and sterility genes associated with male sterility traits in cucumbers includes the following steps:
  • Disposition group the "YL-5" male sterile line was crossed with the distant variety "D37-1" as the male parent to obtain the hybrid F1, and the hybrid F1 was selfed to obtain the F2 generation separated group, F2 There are two phenotypes of male fertility and male sterility in the generational segregation population.
  • BSA Separation population group analysis
  • the 99% confidence interval of the ⁇ (SNP-index) value was used to determine the locus of the target gene.
  • KASP Competitive allele-specific PCR
  • the strain is the typing on MF1 to MF-96.
  • Figure 3.b shows the typing of C974274G on 96 sterile plants, MS-1 to MS-96. Each point in the figure corresponds to this one.
  • Single plant red indicates that the gene of this single plant only carries the EXC tag sequence, ie the genotype of the locus is G/G, and the blue color indicates that the gene band of the single plant has only the FAM tag sequence, ie the genotype of the locus is C/ C, green represents the gene of the single plant with the EXC tag sequence and the FAM tag sequence, ie the genotype of the site is heterozygous G/C, black represents unrecognized; in addition, only the genotypes of the three genotypes The typing results of the clustered primers of each strain are available.
  • a genetic map was constructed based on the results of the typing (Fig. 4), and the sterile genes were finely mapped, and SNPs or InDel sites closely linked to the sterility traits were obtained.
  • the final located gene was Csa3M006660.1 ( Figure 5), six SNPs or InDel sites closely linked to the sterile trait.
  • Csa3M006660.1 has a typical PHD structure (Cys4HisCys3), which is an evolutionarily conserved zinc finger domain in eukaryotes, which can specifically recognize histone methylation. password.
  • Csa3M006660.1 has 49.8% homology with the Arabidopsis MMD1 amino acid sequence, has the same amino acid type at position 420, and has a PHD domain.
  • a number of reports have reported that Arabidopsis MMD1 mutations lead to male sterility and may regulate the meiosis of pollen mother cells.

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Abstract

一种与黄瓜雄性不育基因相关的SNP和InDel标记及其筛选方法,并根据这些标记筛选获得了黄瓜雄性不育基因。具体地,筛选方法包括如下步骤。(1)配置群体;(2)建库测序;(3)分离群体分组分析(BSA)和(4)竞争性等位基因特异性PCR(KASP),精细定位不育基因,并得到与不育性状紧密连锁的SNP或InDel位点。该雄性不育基因的获得为快速鉴定黄瓜雄性不育性植株和黄瓜杂交种的高效生产提供了有效的工具。

Description

黄瓜雄性不育基因、分子标记、筛选方法及其用途 技术领域
本发明涉及分子遗传育种技术领域,具体地说,涉及与黄瓜雄性不育基因相关的SNP或InDel的标记,及其筛选,以及获得的雄性不育基因及它们在鉴定雄性不育植株的用途。
背景技术
目前在其他作物上定位了很多雄性不育基因,并开发了很多与雄性不育基因紧密连锁的标记,但在在黄瓜上雄性不育基因的报道很少,更谈不上应用。此外,目前利用最多的是核质互作不育系、光敏不育系及温敏不育系等,对核不育基因的利用很少,主要是因为难以找到保持系。传统上基因定位的方法是利用已有的分子标记,分离群体中大量的筛选差异条带,定位基因太过耗时耗力。
虽然专利申请CN105420408A对黄瓜不育基因的分子标记进行了探索,但是其只获得了一个SNP标记,并且该SNP标记过于单一,不能定位黄瓜不育基因。
发明内容
在本申请的一个实施方案中,本申请涉及一种获得植物雄性不育分子标记SNP或InDel标记和定位雄性不育基因的方法。所述方法包括以下步骤:
(1)配置群体:将植物雄性不育系作为母本与可育远缘品种为父本进行杂交,得到杂种F1,由杂种F1自交得到F2代分离群体,F2代分离群体中存在雄性可育和雄性不育两种表型;
(2)建库测序:提取母本、父本、F2代中可育单株和不育单株的基因组DNA并分别混合形成4个混池即母本池、父本池、可育池及不育池,对各混池的基因组DNA进行双末端测序,对测序得到的读段用BWA软件与正常黄瓜基因组比对,基于比对的结果,使用GATK软件进行SNP的检测和注释;
(3)分离群体分组分析(BSA):根据测序获得的SNP的检测结果,计算可育池与不育池的Δ(SNP-index)值,采用Δ(SNP-index)值的99%的置信区间,来确定目标基因所在区域。其中SNP-index指某个染色体位点含有SNP的读段数与测到的该位点的总读段数的比值,Δ(SNP-index)指可育池与不育池的SNP-index值之差(Takagi等人,2013);
(4)竞争性等位基因特异性PCR(KASP):针对候选区间内选取的候选SNP位点设计SNP分型引物在938株F2群体中进行KASP分型,得到与不育性状紧密连锁的SNP或InDel位点;
(5)根据KSAP分型结果构建遗传图谱,定位雄性不育基因。
本研究引入了一个SNP位点的测序深度相关的参数SNP-index,该参数是指某个位点含有SNP的读段数与测到该位点的总读段数的比值,大小范围为0-1。若该参数为0,代表所有测到的读段都来自被用作参考基因组的那个亲本的基因组;该参数为1,代表所有读段都来自另一个亲本;该参数为0.5,则代表此混池中SNP来自两个亲本的基因组的频率一致。将两个池观测到的SNP都计算出SNP-index,然后将两个池的SNP-index值相减后得到Δ(SNP-index),将Δ(SNP-index)对应该SNP所在染色体位置作图,采用Δ(SNP-index)值的99%的置信区间筛选雄性不育基因候选区域。针对Δ(SNP-index)再做零假设,得出相应的p值,用于检验该数值的可信度,一般p<0.05才认为有统计学意义。
在本发明的一个实施方案中,所述植株是黄瓜。
在本发明的一个实施方案中,所述分子标记是SNP标记。
在本发明的一个实施方案中,所述分子标记是InDel标记。
在本发明的一个实施方案中,所述分子标记是SNP标记和InDel标记。
在本发明的一个实施方案中,雄性不育基因位于SNP标记G729940C和SNP标记C974274G之间的基因组片段。
在本发明的一个实施方案中,雄性不育基因位于黄瓜3号染色体上。
在本发明的一个实施方案中,雄性不育基因位于黄瓜3号染色体上805,509-807,682。
在本发明的一个实施方案中,控制黄瓜雄性不育的基因为SEIQ NO:1所示的Csa3M006660.1基因,其编码如SEIQ NO:2所示的氨基酸序列的蛋白质。
在本发明的一个实施方案中,黄瓜不育系的Csa3M006660.1基因第1258位发生点突变。
在本发明的一个实施方案中,黄瓜不育系的Csa3M006660.1基因的核酸序列如SEQ ID NO:3所示。其编码如SEIQ NO:4所示的氨基酸序列的蛋白质。
在本发明的一个实施方案中,竞争性等位基因特异性PCR(KASP)使用的引物的SNP分型引物如下所示所示。
针对C304430G标记的引物为:
AATTACATGAATAAGTGTTCGTAATTTCG(SEQ ID NO:5)和AATTACATGAATAAGTGTTCGTAATTTCC(SEQ ID NO:6);
针对G564531C标记的引物为:
GGTTTGGAATCTTGCTTGGCATTG(SEQ ID NO:7)和GGTTTGGAATCTTGCTTGGCATTC(SEQ ID NO:8)
针对A701466G标记的引物为:
ATCTAGAAACCAAATAAAAACTATAGCCAA(SEQ ID NO:9)和CTAGAAACCAAATAAAAACTATAGCCAG(SEQ ID NO:10)
针对G729940C标记的引物为:
GGAACCCCTTCTGAAGCTGTG(SEQ ID NO:11)和GGAACCCCTTCTGAAGCTGTC(SEQ ID NO:12)
针对T785141C标记的引物为:
GGGTCACGCAGATGGGTATTGA(SEQ ID NO:13)和GGTCACGCAGATGGGTATTGG(SEQ ID NO:14)
针对C974274G标记的引物为:
ATTTGGTTTCTTGATACTATCAATTATACC(SEQ ID NO:15)和ATTTGGTTTCTTGATACTATCAATTATACG(SEQ ID NO:16)
针对T1031386G标记的引物为:
TACGTGAATATTTTCTTTTTCTTTATACGTAT(SEQ ID NO:17)和CGTGAATATTTTCTTTTTCTTTATACGTAG(SEQ ID NO:18)
针对T1101289C标记的引物为:
AAGACTAATATGCCCTTCCTCTTCTA(SEQ ID NO:19)和GACTAATATGCCCTTCCTCTTCTG(SEQ ID NO:20)
针对T1508343G标记的引物为:
TATGTACAGCATCAACAAGTGTGCA(SEQ ID NO:21)和TGTACAGCATCAACAAGTGTGCC(SEQ ID NO:22)
针对A2179014C标记的引物为:
TTCGAACATATACAAAAGTAGATATATCAAAA(SEQ ID NO:23)和CGAACATATACAAAAGTAGATATATCAAAC(SEQ ID NO:24)。
本发明的一个实施方案涉及鉴定黄瓜不育株与可育株的方法,其特征在于,如果Csa3M006660.1基因第1258位碱基为G,那么该植株为不育株。
本发明鉴定了与黄瓜雄性不育基因更加紧密连锁的10个SNP标记,其中有6个SNP标记更加与黄瓜雄性不育基因紧密连锁。本发明首次鉴定出黄瓜雄性不育基因为位于黄瓜3号染色体的Csa3M006660.1基因。通过本发明鉴定的不育基因,能够更直接、快速识别黄瓜雄性不育株,而且能够用于黄瓜杂交种的高效生产。
附图说明
图1为通过分离群体分组分析(BSA)所示出的可育池和不育池ΔSNP-index在黄瓜7条染色体上的分布情况。
图2为KASP基因分型所用候选SNP标记及其对应的引物。
图3为C974274G标记的KASP基因分型结果。(a)为对可育单株的KASP基因分型结果;(b)为对不育单株的KASP基因分型结果。
图4为通过SNP标记构建的遗传图谱以及突变基因的精细定位。
图5为得到的Csa3M006660.1基因的核酸序列。
具体实施方式
通过结合说明书附图和以下实施例来具体说明本发明的具体实施方式。
实施例1
黄瓜雄性不育性状相关的SNP分子标记的及不育基因的获得,包括以下步骤:
(1)配置群体:将“YL-5”雄性不育系为母本与远缘品种“D37-1”为父本进行杂交,得到杂种F1,由杂种F1自交得到F2代分离群体,F2代分离群体中存在雄性可育和雄性不育两种表型。
(2)建库测序:鉴定表型后,通过CTAB法提取母本“YL-5”基因组DNA、父本“D37-1”基因组DNA、F2代中可育单株基因组DNA、F2代中不育单株基因组DNA,共形成4个混池即母本池、父本池、可育池及不育池。将检验合格的DNA样品用Illumina HiSeq 2500平台进行双末端测序,对测序得到的原始读段进行质量评估并过滤得到干净无杂质的读段,用BWA软件将干净无杂质的读段比对到黄瓜参考基因组,基于比对的结果,使用GATK软件进行SNP的检测和注释。
(3)分离群体分组分析(BSA):根据SNP的检测结果,计算可育池与不育池的SNP-index值,方法为覆盖该位点的突变基因型的读段占覆盖该位点的总读段数的比值,如覆盖某一位点的读段数为20,而突变基因型基因型的读段为15,则该位点SNP-index值为0.75。若SNP-index=0,则该读段来源于父本“D37-1”,若SNP-index=1,则该读段来源于母本“YL-5”。然后计算可育池与不育池的Δ(SNP-index)值,得到Δ(SNP-index)图(图1)。假设位点A为目标基因所在位点,则可育池该位点SNP-index=0(因可育池中有杂合基因型,所以实际值一般大于0,小于1),而不育 池该位点SNP-index=1,所以Δ(SNP-index)=1,所以Δ(SNP-index)越大,与接近目标基因。则本研究采用Δ(SNP-index)值的99%的置信区间,来确定目标基因所在位点,结果表明可育池与不育池仅在3号染色体末端813Kb(区域1:166710-564531,大小397Kb;区域2:1954776-2371279,大小416Kb)范围内出现明显的分离趋势。
(4)竞争性等位基因特异性PCR(KASP)分型:选取10个SNP位点,采用Leal-Bertioli等(2015)的方法进行引物设计,该项技术是基于引物末端碱基的特异匹配来对SNP分型以及检测插入和缺失(InDels)。针对10个SNP位点共设计了10套SNP分型引物(图2),并在948株F2群体中进行KASP分型。在948株F2分离群体中检测相应位点的基因型进行分型,部分结果见图3:该图为C974274G标记的KASP基因分型图,其中图3.a为C974274G标记在96份可育单株即MF1至MF-96上的分型情况,图3.b为C974274G标记在96份不育单株即MS-1至MS-96上的分型情况,图中每一个点都对应这一个单株,红色代表该单株的基因仅带有EXC标签序列即该位点基因型为G/G,蓝色代表该单株的基因带仅有FAM标签序列即该位点基因型为C/C,绿色代表该单株的基因即带有EXC标签序列也带有FAM标签序列即该位点基因型为杂合G/C,黑色代表未能识别;另外,只有使三种基因型的单株各自成簇的引物的分型结果才可用。从图3.a中可以看出96份可育单株中除一株未鉴定成功外,均成功分型,从图3.b中可以看出96份不育单株中均分型成功;另外,在两次的分型结果中,3种基因型的单株分簇情况良好,结果可用。
根据分型结果构建遗传图谱(图4),精细定位不育基因,并得到与不育性状紧密连锁的SNP或InDel位点。最终定位到的该基因为Csa3M006660.1(图5),与不育性状紧密连锁的6个SNP或InDel位点。
(5)序列与表达分析:通过氨基酸序列分析发现Csa3M006660.1具有典型的PHD结构(Cys4HisCys3),是真核生物中一种进化保守的锌指结构域,能特异性识别组蛋白的甲基化密码。
通过不同物种氨基酸序列同源对比以及28个不同品系黄瓜的序列分析发现Csa3M006660.1的第420位氨基酸高度保守,在可育植株中为酪氨酸Y,在不育植株中突变为天冬氨酸D。换言之,黄瓜不育系的Csa3M006660.1基因第1258位发生点突变,从T突变为G。
BLAST分析发现,Csa3M006660.1与拟南芥MMD1氨基酸序列的同源性为49.8%,在420位具有相同的氨基酸类型,并具有PHD结构域。有多篇文献报道拟南芥MMD1突变会导致雄性不育,可能调控花粉母细胞的减数分裂过程。
Csa3M006660.1表达模式分析发现该基因只在幼小花蕾中表达。
实施例2
不育基因的验证
申请人随机挑选了100株黄瓜正常可育珠和100株黄瓜不育株。针对SEQ ID NO:1设计引物。分别对这些植株的基因组进行PCR扩增并测序。结果显示,从所有的可育珠扩增获得的核酸序列其1258位碱基为T,而所有的不育株的基因扩增产物第1258位碱基为G。

Claims (7)

  1. 一种定位黄瓜雄性不育基因的方法,所述方法包括以下步骤:
    (1)配置群体:将植物雄性不育系作为母本与可育远缘品种为父本进行杂交,得到杂种F1,由杂种F1自交得到F2代分离群体,F2代分离群体中存在雄性可育和雄性不育两种表型;
    (2)建库测序:提取母本、父本、F2代中可育单株和不育单株的基因组DNA并分别混合形成4个混池即母本池、父本池、可育池及不育池,对各混池的基因组DNA进行双末端测序,对测序得到的读段用BWA软件与正常黄瓜基因组比对,基于比对的结果,使用GATK软件进行SNP的检测和注释;
    (3)分离群体分组分析(BSA):根据测序获得的SNP的检测结果,计算可育池与不育池的Δ(SNP-index)值,采用Δ(SNP-index)值的99%的置信区间,来确定目标基因所在区域,其中SNP-index指某个染色体位点含有SNP的读段数与测到的该位点的总读段数的比值,Δ(SNP-index)指可育池与不育池的SNP-index值之差;
    (4)竞争性等位基因特异性PCR(KASP):针对候选区间内选取的候选SNP位点设计SNP分型引物在F2群体中进行KASP分型,得到与不育性状紧密连锁的SNP或InDel位点;
    (5)根据KASP分型结果构建遗传图谱,定位雄性不育基因。
  2. 根据权利要求1所述的方法,其特征在于步骤(4)中F2群体中的植株至少为500株。
  3. 根据权利要求1所述的方法,其特征在于步骤(4)中F2群体中的植株为938株。
  4. 根据权利要求1的方法,其特征在于步骤(4)中所用的分型引物为:
    (1)AATTACATGAATAAGTGTTCGTAATTTCG(SEQ ID NO:5)和AATTACATGAATAAGTGTTCGTAATTTCC(SEQ ID NO:6);
    (2)GGTTTGGAATCTTGCTTGGCATTG(SEQ ID NO:7)和GGTTTGGAATCTTGCTTGGCATTC(SEQ ID NO:8);
    (3)ATCTAGAAACCAAATAAAAACTATAGCCAA(SEQ ID NO:9)和CTAGAAACCAAATAAAAACTATAGCCAG(SEQ ID NO:10);
    (4)GGAACCCCTTCTGAAGCTGTG(SEQ ID NO:11)和GGAACCCCTTCTGAAGCTGTC(SEQ ID NO:12);
    (5)GGGTCACGCAGATGGGTATTGA(SEQ ID NO:13)和GGTCACGCAGATGGGTATTGG(SEQ ID NO:14);
    (6)ATTTGGTTTCTTGATACTATCAATTATACC(SEQ ID NO:15)和ATTTGGTTTCTTGATACTATCAATTATACG(SEQ ID NO:16);
    (7)TACGTGAATATTTTCTTTTTCTTTATACGTAT(SEQ ID NO:17)和CGTGAATATTTTCTTTTTCTTTATACGTAG(SEQ ID NO:18);
    (8)AAGACTAATATGCCCTTCCTCTTCTA(SEQ ID NO:19)和GACTAATATGCCCTTCCTCTTCTG(SEQ ID NO:20);
    (9)TATGTACAGCATCAACAAGTGTGCA(SEQ ID NO:21)和TGTACAGCATCAACAAGTGTGCC(SEQ ID NO:22);
    (10)TTCGAACATATACAAAAGTAGATATATCAAAA(SEQ ID NO:23)和CGAACATATACAAAAGTAGATATATCAAAC(SEQ ID NO:24)。
  5. 一个决定黄瓜雄性不育的基因,其核酸序列如SEQ ID NO:1所示。
  6. 一种鉴定黄瓜雄性不育株的方法,其特征在于,如果黄瓜植株的SEQ ID NO:1所示的核酸序列第1258位碱基发生突变,那么该植株为不育株。
  7. 一种鉴定黄瓜雄性不育株的方法,其特征在于,如果黄瓜植株的SEQ ID NO:1所示的核酸序列第1258位碱基突变为G,那么该植株为不育株。
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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111485032A (zh) * 2020-06-12 2020-08-04 北京市农林科学院 一种鉴定黄瓜雌性系的方法及其使用的snp引物组合
CN114107535A (zh) * 2020-08-31 2022-03-01 北京市农林科学院 鉴定中国南瓜砧木去除嫁接黄瓜果实蜡粉性状的分子标记及其应用
CN116904638A (zh) * 2023-09-08 2023-10-20 山西稼祺农业科技有限公司 与藜麦早雌性状连锁的kasp标记及应用

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107058552B (zh) 2017-05-05 2020-08-14 天津科润农业科技股份有限公司黄瓜研究所 黄瓜雄性不育基因、分子标记、筛选方法及其用途
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CN109371157A (zh) * 2018-12-07 2019-02-22 天津科润农业科技股份有限公司 一种黄瓜不育基因相关caps的标记方法及应用
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CN112680461B (zh) * 2021-03-12 2021-06-22 北京首佳利华科技有限公司 雄性不育基因ZmPHD11及其在创制玉米雄性不育系中的应用
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CN113462803A (zh) * 2021-08-02 2021-10-01 青岛农业大学 基于多重pcr测序的黄瓜全基因组背景选择snp标记系统及其应用
CN116751890B (zh) * 2023-07-12 2024-02-13 北京市农林科学院 一种鉴定黄瓜品种线粒体dna指纹和杂交种纯度的方法及其引物组合
CN117106968A (zh) * 2023-10-19 2023-11-24 北京市农林科学院 一种鉴定黄瓜雌性强弱的引物组、试剂盒及其应用

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102260338A (zh) * 2010-05-25 2011-11-30 北京大学 植物雄性育性相关蛋白及其编码基因和应用
CN105420408A (zh) * 2016-01-27 2016-03-23 天津科润农业科技股份有限公司黄瓜研究所 黄瓜雄性不育基因相关snp标记及应用
CN105525000A (zh) * 2016-01-20 2016-04-27 江西师范大学 一种基于QTL-seq发掘东乡野生稻耐冷基因的方法
CN107058552A (zh) * 2017-05-05 2017-08-18 天津科润农业科技股份有限公司黄瓜研究所 黄瓜雄性不育基因、分子标记、筛选方法及其用途

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103525917B (zh) * 2013-09-24 2014-12-31 北京百迈客生物科技有限公司 基于高通量分型的高密度遗传图谱的构建和评价
CN104120126B (zh) * 2014-08-12 2016-10-26 新疆农业科学院园艺作物研究所 与番茄雄性不育基因紧密连锁的srap分子标记及其获得方法
BR112017011850A2 (pt) * 2014-12-05 2018-02-27 Univ Saskatchewan métodos e reagentes para detectar neisseria gonorrhoeae e seus determinantes de resistência antimicrobiana

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102260338A (zh) * 2010-05-25 2011-11-30 北京大学 植物雄性育性相关蛋白及其编码基因和应用
CN105525000A (zh) * 2016-01-20 2016-04-27 江西师范大学 一种基于QTL-seq发掘东乡野生稻耐冷基因的方法
CN105420408A (zh) * 2016-01-27 2016-03-23 天津科润农业科技股份有限公司黄瓜研究所 黄瓜雄性不育基因相关snp标记及应用
CN107058552A (zh) * 2017-05-05 2017-08-18 天津科润农业科技股份有限公司黄瓜研究所 黄瓜雄性不育基因、分子标记、筛选方法及其用途

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DATABASE Nucleotide [O] 23 March 2015 (2015-03-23), "PREDICTED: Cucumis sativus PHD Finger Protein Male Meiocyte Death 1 (LOC101209218), mRNA", XP055557284, Database accession no. XM_011654407.1 *
HAN, Y.K. ET AL.: "Fine Mapping of a Male Sterility Gene ms-3 in a Novel Cucumber (Cucumis sativus L.) Mutan t", THEORETICAL AND APPLIED GENETICS, vol. 131, 13 November 2017 (2017-11-13), pages 449 - 460, XP036394515 *
LIANG, J.L. ET AL.: "Map-based Cloning of the Dominant Genie Male Sterile Ms-cdl Gene in Cabbage (Brassica oleracea", THEOR APPL GENET., vol. 130, 4 October 2016 (2016-10-04), pages 71 - 79, XP036125976 *

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111485032A (zh) * 2020-06-12 2020-08-04 北京市农林科学院 一种鉴定黄瓜雌性系的方法及其使用的snp引物组合
CN111485032B (zh) * 2020-06-12 2021-06-22 北京市农林科学院 一种鉴定黄瓜雌性系的方法及其使用的snp引物组合
CN114107535A (zh) * 2020-08-31 2022-03-01 北京市农林科学院 鉴定中国南瓜砧木去除嫁接黄瓜果实蜡粉性状的分子标记及其应用
CN114107535B (zh) * 2020-08-31 2023-08-18 北京市农林科学院 鉴定中国南瓜砧木去除嫁接黄瓜果实蜡粉性状的分子标记及其应用
CN116904638A (zh) * 2023-09-08 2023-10-20 山西稼祺农业科技有限公司 与藜麦早雌性状连锁的kasp标记及应用
CN116904638B (zh) * 2023-09-08 2024-05-07 山西稼祺农业科技有限公司 与藜麦早雌性状连锁的kasp标记及应用

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