桃红色果肉性状的分子标记及序列分析
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摘要
由于桃世代周期长,利用传统的育种方法培育一个新品种需要10多年的时间，并且树体高大，进行杂交选种时需要占用大量的土地。近年来兴起的分子标记辅助育种技术可以有效缩短育种周期。在桃性状的分子标记方面前人已经做了大量的工作。在桃果实性状分子标记方面，已研究了果实果肉黄色和白色、有毛/无毛、果实非酸/酸性状、和果实成熟期等，对果实中不同部位花青素分布的分子标记还未见报道。SRAP标记技术是一种多态性和信息量丰富的新型分子标记技术，近年来在植物遗传多样性分析、种质鉴定、遗传连锁图的构建以及比较基因组学研究等方面得到广泛应用。我们利用梯度PCR技术，对SRAP-PCR过程中的两步退火温度进行了研究，以期获得较好的退火温度组合。我们利用桃品种的两个杂交群体重阳红×燕红和重阳红×大久保的后代，应用优化后的SRAP反应条件以及利用SSR标记等两种标记方法结合BSA方法对桃果肉不同部分的红色素进行了标记研究，并对获得的与桃果实近核色素紧密连锁的SRAP标记Me07Em02扩增得到的片段进行了回收、测序和分析，并登录桃基因组Peach v1.0进行了比对。研究结果如下：
1.SRAP-PCR退火温度的优化：根据已有文献设计了8条正向引物和11条反向引物，组合成88对引物，利用梯度PCR仪（型号：MJ200PCR），对SRAP-PCR过程中的两步退火温度进行了研究。通过对第一步前5轮循环的退火温度梯度(37.0℃,37.3℃,38.1℃,39.1℃、40.6℃,42.5℃,44.7℃,46.5℃,48.0℃,49.0℃,49.7℃,50.0℃)的实验，其退火温度可提高到41℃；对第二步后30轮循环的退火温度梯度(50.0℃,50.3℃,50.9℃,51.7℃,52.8℃,54.3℃,56.0℃,57.4℃,58.5℃,59.3℃,60.0℃)的实验，其退火温度可提高到52℃，同时发现不同的退火温度可扩增出不同的条带，并非随着退火温度的提高，可扩增条带减少，有些条带较高退火温度下出现。应用该程序，使用多个SRAP引物组合在桃品种进行扩增验证，均获得了良好的重复性结果。
2.以“重阳红”与“燕红”两个桃(Prunus persica(L.) Batsch)品种为亲本构建群体，通过对正交F1代果实果肉红色素多年的调查，分别对红色素在皮下、果肉和近核果肉的分布进行统计，在此基础上采用分离群体分组分析（bulked segregate analysis, BSA）法，将果肉红色素在果肉三个部位的分布分别记为“有”和“无”两个基因池，共3对6个基因池。应用优化后的相关序列扩增多态性（SRAP）和简单序列重复（SSR）分子标记技术法筛选与桃果肉红色素不同部位分布性状基因连锁的分子标记。通过对88对SRAP引物组合和分别来自桃属（Prunus persica）和苹果(Malus×domestica)的481对SSR引物组合同时在6个基因池间进行筛选，在各基因池间共筛选出4对SRAP引物组合（Me01Em08、Me05Em03、Me07Em04和Me07Em02）和5对SSR引物（UDP97-402、BPPCT023、UDP96-003、CH04g09、CPPCT028）。经138个单株的验证，该标记稳定出现。采用作图软件Mapmaker和回交群体模型进行标记分群和连锁分析，设定LOD值为3和最大重组值θ为0.50作为可信统计度与最大连锁标记数量之间的最佳组合，通过计算这些标记与桃果肉红色素性状基因的遗传距离。结果表明这些标记分别位于桃参考遗传连锁图谱的G2和G4两个连锁组，并分别与红色素在皮下和果肉的分布以及红色素在近核处果肉的分布相连锁。其中与红色素在近核处果肉的分布的标记为6个（UDP96-003、UDP97-402、Me01Em08、Me07Em02、CH04g09和Me07Em04），与红色素在皮下和果肉的分布的标记3个（BPPCT023、CPPCT028和Me05Em03），其中，SRAP标记Me07Em02与桃果实近核色素的遗传距离为0.0cM。
3.通过将SRAP引物组合在重阳红×大久保杂交群体中的扩增结果结合调查所得的近核色素数据，利用作图软件Mapmaker和回交群体模型进行计算该标记与桃果肉近核色素性状基因的遗传距离为2.1cM。
通过对与桃果实近核色素的紧密连锁的SRAP标记Me07Em02扩增片段的5个克隆的回收、T7/SP6双向测序，所测序的5个克隆序列完全一致，其全长110bp，其序列为:TGAGTCCAAACCGGTCCTGCTCAAGTGGAACCACATTGAGAACATGGCGCTCTAGCAGAGTGCAAAATAAGCAACTCTTTCAGTCTGCCATTGCAAATTCGTACGCAGTC（下划线部分序列为引物序列）。通过提交到桃基因组序列网站进行BLASTn比对，该序列在桃基因组序列上是单一拷贝，位于桃基因组序列Peach v1.0的scaffold_4上，应用DNAMAN序列分析软件分析该序列，表明该序列最大ORF框为108个bp，编码36个氨基酸，其氨基酸序列为：SPNRSCSSGTTLRTWRSSRQNKQLFQSAIANSYAV，该蛋白质序列在GenBank蛋白质序列库中没有比对出相似序列。
克隆了与桃果实果肉连锁的其它SRAP标记序列，其中一个是是桃反转录转座子的部分序列，另一个可能是putative calcium-transportingATPase13的部分序列。
4.根据获得的桃反转录转座子的部分序列，应用DANMAN和DNASTAR序列分析软件辅助，在桃基因组数据库和GenBank中进行BLASTn比对获得了桃反转录转座子的全基因组序列，位于Peach v1.0基因组的Scaffold-1的9939764bp-9944771bp位置，全长5008bp，其左右两边的LTR完全一致，长度为444bp，其最大ORF框位于该序列的487bp-4545bp，编码1535个氨基酸，将该氨基酸序列提交到GenBank中进行Protein BLAST比对，结果显示该序列也具有典型的copia-like反转录转座子的氨基酸序列特征。同时初步建立了桃反转录转座子标记方法，并对桃的遗传多样性进行了分析。
Peach is an important and a model species for the study on wood fruits in the Rosaceae family.Currently many research efforts have been focused on building saturated genetic linkage maps fromwhich gronomically important traits can be located. Several genetic linkage maps of intraspecific orinterspecific crosses in Prunus L. have been constructed and have been integrated in one T×E map withwith562markers. DNA markers and genome regions that are conserved among species are very usefulin map-based cloning of genes, marker-assisted selection (MAS) in breeding programs, and comparativemapping among related species.
Prunus persica (L.) Batsch has a long life cycle. It takes more than10years to cultivate a newvariety by using traditional breeding methods. In addition, P. persica (L.) Batsch trees are very tall, so itneeds to take up a lot of land for hybrid selection. In recent years, molecular marker-assisted breedingtechnology has attracted increasing attention, which can effectively shorten the breeding cycle of P.persica (L.) Batsch. A large number of researches were conducted on the molecular markers forcharacters of P. persica (L.) Batsch. In molecular markers for peach flesh characters, to be specific,yellow/white flesh, hairy/hairless, non-sour/sour tasteand fruit ripening characters had been studied.However, no research has been reported on molecular markers for the distribution of anthocyanins indifferent parts of fruit.
In this study, SRAP and SSR markers combining with the BSA method were used for selection ofmolecular markers linked with the distribution of anthocyanins in different parts of fruit.. The resultswere shown as follows:
1.SRAP is a new molecular marker which could provide high polymorphism and plentifulinformation. It is simple and has not the specie-specific character. It had been widely used for geneticdiversity, comparing genome analysis and map construction. The annealing temperature which affect theSRAP-PCR reactions was optimized in order to establish the SRAP molecular marker systemintemperatre fruits. The optimum system was as follows: the annealing temperature in the first5cycleswas41℃. the annealing temperature in the following30cycles was52℃. Amplications of this systemwere carriyed out with4primers on4varieties of peach. The results showed that the system was steadyand reliable.
2.The distribution of anthocyanin in the fruit flesh of peach is different and the genetic mechanismis complex. The distribution of anthocyanin in the different local of fruit flesh of peach such as fleshunder the skin, middle flesh and flesh around the stone was investigated from the cross Chongyanghong ×Yanhong for years. Based on the results, the sequence-related amplified polymorphism (SRAP) andSimple Sequence Repeats(SSR) by the way of bulked segregate analysis (BSA) were applied toconstruct a local genetic linkage map for the gene determined the distribution of anthocyanin in the fruitflesh of peach. This map, comprising four SRAP markers, five SSR markers and the anthocyanindensity loci. Four dominant SRAP markers (Me01Em08、Me05Em03、Me07Em02and Me07Em04) andfive dominant SSR markers (UDP97-402、BPPCT023、UDP96-003、CH04g09、CPPCT028) linked tothe locus of the gene determined the distribution of anthocyanin in the flesh. One dominant SRAPmarkers (Me07Em02) linked to the loci of the gene determined the color around the stone（Cs） atdistances of0.0cM,. These markers would provide an effective tool for marker assisted selection for thetrait of the anthocyanin intensity in the fresh of peach.
3. The molecular marker of Me07Em02linked to the Cs locus was tested in another progeniesfrom the cross of chongyanghong×Okubao, this marker linked to the Cs at a genetic distance of2.1cM.
Extraction of the fragment amplified with the SRAP primer of Me07Em02and sequencing5clones with T7/SP6, the result showed that the fragment length is110bp. The sequence as follows（primer sequences underlined）:TGAGTCCAAACCGGTCCTGCTCAAGTGGAACCACATTGAGAACATGGCGCTCTAGCAGAGTGCAAAATAAGCAACTCTTTCAGTCTGCCATTGCAAATTCGTACGCAGTC
The result of BLASTn with the sequence of Peach v1.0showed that this sequence is a single copysequence located on scaffold_4of Peach v1.0. The analysis result using the software of DNAMANindicated that the maximum ORF is108bp, coding36amino acid, the amino acid sequence isSPNRSCSSGTTLRTWRSSRQNKQLFQSAIANSYAV and no similar sequence was found in theprotein database of GenBank
The sequences of marker of Me01Em08, Me05Em03and Me07Em04were also obtained. Thesequence of Me01Em08is the copia-like retrotransposon of peach, the other, Me05Em03may bethe gene of putative calcium-transporting ATPase13.
4. The whole sequence of peach copia-like retratranposon was obtained located on the Peach v1.0genome of Scaffold-1. The whole sequence is5008bp and codes1535amino acid. The LTR length is444bp. The molecular marker based on the retrotransposon was obtained and application to the analysisof the diversity on peach.
1.SRAP-PCR退火温度的优化：根据已有文献设计了8条正向引物和11条反向引物，组合成88对引物，利用梯度PCR仪（型号：MJ200PCR），对SRAP-PCR过程中的两步退火温度进行了研究。通过对第一步前5轮循环的退火温度梯度(37.0℃,37.3℃,38.1℃,39.1℃、40.6℃,42.5℃,44.7℃,46.5℃,48.0℃,49.0℃,49.7℃,50.0℃)的实验，其退火温度可提高到41℃；对第二步后30轮循环的退火温度梯度(50.0℃,50.3℃,50.9℃,51.7℃,52.8℃,54.3℃,56.0℃,57.4℃,58.5℃,59.3℃,60.0℃)的实验，其退火温度可提高到52℃，同时发现不同的退火温度可扩增出不同的条带，并非随着退火温度的提高，可扩增条带减少，有些条带较高退火温度下出现。应用该程序，使用多个SRAP引物组合在桃品种进行扩增验证，均获得了良好的重复性结果。
2.以“重阳红”与“燕红”两个桃(Prunus persica(L.) Batsch)品种为亲本构建群体，通过对正交F1代果实果肉红色素多年的调查，分别对红色素在皮下、果肉和近核果肉的分布进行统计，在此基础上采用分离群体分组分析（bulked segregate analysis, BSA）法，将果肉红色素在果肉三个部位的分布分别记为“有”和“无”两个基因池，共3对6个基因池。应用优化后的相关序列扩增多态性（SRAP）和简单序列重复（SSR）分子标记技术法筛选与桃果肉红色素不同部位分布性状基因连锁的分子标记。通过对88对SRAP引物组合和分别来自桃属（Prunus persica）和苹果(Malus×domestica)的481对SSR引物组合同时在6个基因池间进行筛选，在各基因池间共筛选出4对SRAP引物组合（Me01Em08、Me05Em03、Me07Em04和Me07Em02）和5对SSR引物（UDP97-402、BPPCT023、UDP96-003、CH04g09、CPPCT028）。经138个单株的验证，该标记稳定出现。采用作图软件Mapmaker和回交群体模型进行标记分群和连锁分析，设定LOD值为3和最大重组值θ为0.50作为可信统计度与最大连锁标记数量之间的最佳组合，通过计算这些标记与桃果肉红色素性状基因的遗传距离。结果表明这些标记分别位于桃参考遗传连锁图谱的G2和G4两个连锁组，并分别与红色素在皮下和果肉的分布以及红色素在近核处果肉的分布相连锁。其中与红色素在近核处果肉的分布的标记为6个（UDP96-003、UDP97-402、Me01Em08、Me07Em02、CH04g09和Me07Em04），与红色素在皮下和果肉的分布的标记3个（BPPCT023、CPPCT028和Me05Em03），其中，SRAP标记Me07Em02与桃果实近核色素的遗传距离为0.0cM。
3.通过将SRAP引物组合在重阳红×大久保杂交群体中的扩增结果结合调查所得的近核色素数据，利用作图软件Mapmaker和回交群体模型进行计算该标记与桃果肉近核色素性状基因的遗传距离为2.1cM。
通过对与桃果实近核色素的紧密连锁的SRAP标记Me07Em02扩增片段的5个克隆的回收、T7/SP6双向测序，所测序的5个克隆序列完全一致，其全长110bp，其序列为:TGAGTCCAAACCGGTCCTGCTCAAGTGGAACCACATTGAGAACATGGCGCTCTAGCAGAGTGCAAAATAAGCAACTCTTTCAGTCTGCCATTGCAAATTCGTACGCAGTC（下划线部分序列为引物序列）。通过提交到桃基因组序列网站进行BLASTn比对，该序列在桃基因组序列上是单一拷贝，位于桃基因组序列Peach v1.0的scaffold_4上，应用DNAMAN序列分析软件分析该序列，表明该序列最大ORF框为108个bp，编码36个氨基酸，其氨基酸序列为：SPNRSCSSGTTLRTWRSSRQNKQLFQSAIANSYAV，该蛋白质序列在GenBank蛋白质序列库中没有比对出相似序列。
克隆了与桃果实果肉连锁的其它SRAP标记序列，其中一个是是桃反转录转座子的部分序列，另一个可能是putative calcium-transportingATPase13的部分序列。
4.根据获得的桃反转录转座子的部分序列，应用DANMAN和DNASTAR序列分析软件辅助，在桃基因组数据库和GenBank中进行BLASTn比对获得了桃反转录转座子的全基因组序列，位于Peach v1.0基因组的Scaffold-1的9939764bp-9944771bp位置，全长5008bp，其左右两边的LTR完全一致，长度为444bp，其最大ORF框位于该序列的487bp-4545bp，编码1535个氨基酸，将该氨基酸序列提交到GenBank中进行Protein BLAST比对，结果显示该序列也具有典型的copia-like反转录转座子的氨基酸序列特征。同时初步建立了桃反转录转座子标记方法，并对桃的遗传多样性进行了分析。
Peach is an important and a model species for the study on wood fruits in the Rosaceae family.Currently many research efforts have been focused on building saturated genetic linkage maps fromwhich gronomically important traits can be located. Several genetic linkage maps of intraspecific orinterspecific crosses in Prunus L. have been constructed and have been integrated in one T×E map withwith562markers. DNA markers and genome regions that are conserved among species are very usefulin map-based cloning of genes, marker-assisted selection (MAS) in breeding programs, and comparativemapping among related species.
Prunus persica (L.) Batsch has a long life cycle. It takes more than10years to cultivate a newvariety by using traditional breeding methods. In addition, P. persica (L.) Batsch trees are very tall, so itneeds to take up a lot of land for hybrid selection. In recent years, molecular marker-assisted breedingtechnology has attracted increasing attention, which can effectively shorten the breeding cycle of P.persica (L.) Batsch. A large number of researches were conducted on the molecular markers forcharacters of P. persica (L.) Batsch. In molecular markers for peach flesh characters, to be specific,yellow/white flesh, hairy/hairless, non-sour/sour tasteand fruit ripening characters had been studied.However, no research has been reported on molecular markers for the distribution of anthocyanins indifferent parts of fruit.
In this study, SRAP and SSR markers combining with the BSA method were used for selection ofmolecular markers linked with the distribution of anthocyanins in different parts of fruit.. The resultswere shown as follows:
1.SRAP is a new molecular marker which could provide high polymorphism and plentifulinformation. It is simple and has not the specie-specific character. It had been widely used for geneticdiversity, comparing genome analysis and map construction. The annealing temperature which affect theSRAP-PCR reactions was optimized in order to establish the SRAP molecular marker systemintemperatre fruits. The optimum system was as follows: the annealing temperature in the first5cycleswas41℃. the annealing temperature in the following30cycles was52℃. Amplications of this systemwere carriyed out with4primers on4varieties of peach. The results showed that the system was steadyand reliable.
2.The distribution of anthocyanin in the fruit flesh of peach is different and the genetic mechanismis complex. The distribution of anthocyanin in the different local of fruit flesh of peach such as fleshunder the skin, middle flesh and flesh around the stone was investigated from the cross Chongyanghong ×Yanhong for years. Based on the results, the sequence-related amplified polymorphism (SRAP) andSimple Sequence Repeats(SSR) by the way of bulked segregate analysis (BSA) were applied toconstruct a local genetic linkage map for the gene determined the distribution of anthocyanin in the fruitflesh of peach. This map, comprising four SRAP markers, five SSR markers and the anthocyanindensity loci. Four dominant SRAP markers (Me01Em08、Me05Em03、Me07Em02and Me07Em04) andfive dominant SSR markers (UDP97-402、BPPCT023、UDP96-003、CH04g09、CPPCT028) linked tothe locus of the gene determined the distribution of anthocyanin in the flesh. One dominant SRAPmarkers (Me07Em02) linked to the loci of the gene determined the color around the stone（Cs） atdistances of0.0cM,. These markers would provide an effective tool for marker assisted selection for thetrait of the anthocyanin intensity in the fresh of peach.
3. The molecular marker of Me07Em02linked to the Cs locus was tested in another progeniesfrom the cross of chongyanghong×Okubao, this marker linked to the Cs at a genetic distance of2.1cM.
Extraction of the fragment amplified with the SRAP primer of Me07Em02and sequencing5clones with T7/SP6, the result showed that the fragment length is110bp. The sequence as follows（primer sequences underlined）:TGAGTCCAAACCGGTCCTGCTCAAGTGGAACCACATTGAGAACATGGCGCTCTAGCAGAGTGCAAAATAAGCAACTCTTTCAGTCTGCCATTGCAAATTCGTACGCAGTC
The result of BLASTn with the sequence of Peach v1.0showed that this sequence is a single copysequence located on scaffold_4of Peach v1.0. The analysis result using the software of DNAMANindicated that the maximum ORF is108bp, coding36amino acid, the amino acid sequence isSPNRSCSSGTTLRTWRSSRQNKQLFQSAIANSYAV and no similar sequence was found in theprotein database of GenBank
The sequences of marker of Me01Em08, Me05Em03and Me07Em04were also obtained. Thesequence of Me01Em08is the copia-like retrotransposon of peach, the other, Me05Em03may bethe gene of putative calcium-transporting ATPase13.
4. The whole sequence of peach copia-like retratranposon was obtained located on the Peach v1.0genome of Scaffold-1. The whole sequence is5008bp and codes1535amino acid. The LTR length is444bp. The molecular marker based on the retrotransposon was obtained and application to the analysisof the diversity on peach.
引文
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