梅花遗传连锁图谱构建和表型性状QTLs分析
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摘要
梅花(Prunus mume Sieb.et Zucc.,2n=2x=16)为蔷薇科(Rosaceae)李属(Prunus)植物。因其花期早、花型丰富、花色繁多和花香独特等特点被广泛应用于园林绿化。目前,梅花新品种的选育多采用杂交育种的方式,花费时间较长,而且在基因组水平上缺少对梅花与近缘种属间的比较基因组学分析,造成梅花起源问题仍未解决。本研究以梅花品种‘粉瓣’和‘扣子玉蝶’杂交得到的F1代作图群体为材料,利用简单重复序列(Simple Sequence Repeat, SSR)和单核苷酸多态性(Single Nucleotide Polymorphism, SNP)分子标记构建梅花高密度遗传图谱并锚定其基因组组装序列,在此基础上不仅与李属T×E参考图谱(基于扁桃'Texas'X桃'Earlygold'杂交得到Fz群体构建的遗传图谱)进行共线性分析,也进行主要表型性状的数量性状定位(Quantitative trait loci, QTLs)分析。主要结论如下：
1.在梅花全基因组序列的基础上,分析1～8bp核苷酸重复单元基序长度的SSR分布情况,其结果显示：在梅花基因组中,利用MISA (MIcroSAtellites identification tool)计算机程序,共鉴定188,149个SSRs标记,平均密度为793.9SSR/Mb。单核苷酸重复单元数量最多有67,183个SSRs标记。
2.在梅花、苹果和草莓基因组和基因组的不同区域分析SSR分布情况,结果显示：在蔷薇科三个物种中随着核苷酸重复单元基序长度的增加,SSR标记数量逐渐下降,富含AT核苷酸重复单元基序类型的SSR数量较多而富含GC核苷酸重复单元基序类型的SSR数量较少,且基因间区中分布的SSR数量显著地高于编码区中分布的SSR数量。
3.以梅花品种‘粉瓣’和‘扣子玉蝶’组合获得F1群体中的190棵子代为试验材料,从梅花基因组序列开发的SSR标记中随机选取670个,设计引物对其进行标记分离检测,结果显示：根据拟测交作图原理,利用144个多态性SSRs标记构建含有8条连锁群的梅花SSR框架遗传图谱,总遗传图距为668.7cM,共锚定71条梅花基因组组装序列,大小为66.5Mb,覆盖基因组28.1%。
4.按照与限制性内切位点相关DNA标签(Restriction-site Associated DNA-tag, RAD-tag)测序策略,通过生物信息学分析,在亲本与190棵杂交子代中共检测到2,166个多态性SNPs位点。根据拟测交作图原理,以P<0.05为阈值,经过卡方检验检测,有1,484个SNPs标记位点符合孟德尔分离比例(1：1或1：2：1),共产生3,229个多态性位点,平均每个SNP标记产生大约2个多态性位点。
5.利用1,484个SNPs标记对所构建的SSR框架遗传图谱进行加密,构建含有1,613个标记的梅花高密度遗传连锁图谱,共有8条连锁群,总遗传图距为780.9cM,标记间平均距离为0.5cM,锚定513条梅花基因组组装序列,大小为199.0Mb,覆盖基因组84.0%。
6.利用梅花遗传连锁图谱所锚定的199.0Mb基因组序列与李属参考图谱所锚定的613条蔷薇科保守同源序列(Rosaceae Conserved Ortholog Set, RosCOS)间进行共线性分析,结果显示：在梅花基因组进化过程中,仅有PM3和PM4染色体发生染色体重排事件,即PM3染色体来源于李属的PG1、PG6和PG7染色体,PM4染色体来源于李属的PG2和PG5染色体。
7.对梅花F1代作图群体的株高、地径、叶长、叶宽、叶面积和叶脉数目等6个表型性状的遗传变异进行统计和分析,并利用复合区间作图法检测与这些性状相关QTLs位点,其结果显示：共检测到控制这些表型性状的84个QTLs,其中控制叶面积和叶脉数目性状的QTLs最多均为35个,控制地径的QTL最少为1个。
总之,本研究结果为梅花基因组结构和功能研究、分子标记定向辅助育种和近缘物种间比较基因组学研究奠定重要的理论基础,对进一步开展梅花分子标记聚合育种提供重要借鉴和参考,为今后揭示梅花重要观赏性状的遗传机制和探索梅花起源具有重要意义。
Belonging to the Rosaceae, sub-family Prunoideae, mei(Prunus mume Sieb. et Zucc.,2n=2x=16) possesses early blossom, varying types of flowers, colorful corollas, and pleasant fragrance and is extensively grown as a garden ornamental plant. Up to now, new cultivars of mei are always bred using traditional hybridizations which spend a lot of time. Meanwhile, the origin of mei isn't still revealed as a result of the lack of the comparative genomic analyses between mei and related species. Here, a high density genetic linkage map using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers based on190F1segregating progeny generated from a cross between female P. mume 'Fenban' and male P. mume 'Kouzi Yudie' was constructed and was anchored genomic assembly sequences of mei, depanding on which not only the macro-colinearity between mei genome and Prunus T×E reference map [an interspecific almond 'Texas'×peach 'Earlygold'(T×E) F2mapping population] was identified, but also the quantitative trait loci (QTLs) for main phenotypic traits were detected in this study. The main results and conclusions are indicated as follows:
1. We performed the genome-wide characterization of SSRs ranging in length from1to8bp in the mei genome and the results were shown as follows:A total of188,149SSRs were identified at a frequency of793.9SSR/Mb using MIcroSAtellites identification tool (MISA) and mononucleotide repeats (67,183) were the most common type of SSRs.
2. We analysed the distribution of the repeat motifs of SSRs in the genomic and different genomic regions of mei, apple, and strawberry. The results were indicated as follows:The frequency of SSRs decreased with the increasing the repeat motif length, AT-rich repeat motifs were more common than GC-rich repeat motifs, and the frequency of SSRs was more common in intergenic regions than CDS regions in three genomes of Rosaceae.
3.670SSRs were chosen from the total SSRs identified in mei genome and were detected among parental lines and190Fi segregating progeny generated from a cross between P. mutne 'Fenban' and P. mume 'Kouzi Yudie'. The results were indicated as follows:A framework genetic linkage map of mei was constructed based on144polymorphic SSRs according to pseudo-test-cross strategy, containing eight linkage groups (LGs). The total genetic distance was668.7cM. Seventy one scaffolds covering about28.1%of mei assembled sequences were anchored to this genetic map, totaling to66.5Mb.
4. According to the restriction-site associated with DNA-tag (RAD-tag) strategy, about2,166polymorphic SNPs were detected among the parental lines and190F1segregating progeny using bioinformatics analysis. The polymorphic1,484SNPs exhibited standard Mendelian segregation (1:1or1:2:1) by χ2test at cutoff of P<0.05. About3,229SNPs polymorphic loci were found in this mapping population, occurring at an average two polymorphic loci of each SNPs.
5. We constructed a high density genetic linkage map including1,613markers based on the framework genetic linkage map added density using1,484polymorphic SNPs. This genetic map contained eight LGs, totaling to780.9cM. The average marker interval is0.5cM.513scaffolds covering about84.0%of mei assembled sequences were anchored to this high density genetic map, totaling to199.0Mb.
6. A high level of macro-collinearity was revealed by aligning the199.0Mb assembled sequences anchored to the mei genetic map and613sequences of Rosaceae Conserved Ortholog Set (RosCOS) anchored to the Prunus T×E reference map. The results were indicated as follows:Among the process of mei evolution, PM3and PM4underwent chromosome rearrangement and PM3was originated from PG1, PG6and PG7of Prunus, and PM4was originated from PG2and PG5of Prunus.
7. Hereditary variations of plant height, ground diameter, leafblade length, leafblade width, leafblade area and leafblade vein number were measured and analyzed based on F1mapping population of mei. These QTLs for these phenotypic traits using composit interval mapping. The results were shown as follows:There were84QTLs for these six phenotypic traits using composit interval mapping. Of these QTLs,35QTLs for leafblade area and for leafblade vein number were the most common, while only one QTL for ground diameter was the least.
In summary, this study may facilitate genomic structure and function, maker-assisted selection breeding, and comparative genomic analyses between mei and relative species, may further provide an important reference for molecular marker polymerization breeding of mei, and pave the way for the study of genetic mechanism of important ornamental traits and the origin of mei.
1.在梅花全基因组序列的基础上,分析1～8bp核苷酸重复单元基序长度的SSR分布情况,其结果显示：在梅花基因组中,利用MISA (MIcroSAtellites identification tool)计算机程序,共鉴定188,149个SSRs标记,平均密度为793.9SSR/Mb。单核苷酸重复单元数量最多有67,183个SSRs标记。
2.在梅花、苹果和草莓基因组和基因组的不同区域分析SSR分布情况,结果显示：在蔷薇科三个物种中随着核苷酸重复单元基序长度的增加,SSR标记数量逐渐下降,富含AT核苷酸重复单元基序类型的SSR数量较多而富含GC核苷酸重复单元基序类型的SSR数量较少,且基因间区中分布的SSR数量显著地高于编码区中分布的SSR数量。
3.以梅花品种‘粉瓣’和‘扣子玉蝶’组合获得F1群体中的190棵子代为试验材料,从梅花基因组序列开发的SSR标记中随机选取670个,设计引物对其进行标记分离检测,结果显示：根据拟测交作图原理,利用144个多态性SSRs标记构建含有8条连锁群的梅花SSR框架遗传图谱,总遗传图距为668.7cM,共锚定71条梅花基因组组装序列,大小为66.5Mb,覆盖基因组28.1%。
4.按照与限制性内切位点相关DNA标签(Restriction-site Associated DNA-tag, RAD-tag)测序策略,通过生物信息学分析,在亲本与190棵杂交子代中共检测到2,166个多态性SNPs位点。根据拟测交作图原理,以P<0.05为阈值,经过卡方检验检测,有1,484个SNPs标记位点符合孟德尔分离比例(1：1或1：2：1),共产生3,229个多态性位点,平均每个SNP标记产生大约2个多态性位点。
5.利用1,484个SNPs标记对所构建的SSR框架遗传图谱进行加密,构建含有1,613个标记的梅花高密度遗传连锁图谱,共有8条连锁群,总遗传图距为780.9cM,标记间平均距离为0.5cM,锚定513条梅花基因组组装序列,大小为199.0Mb,覆盖基因组84.0%。
6.利用梅花遗传连锁图谱所锚定的199.0Mb基因组序列与李属参考图谱所锚定的613条蔷薇科保守同源序列(Rosaceae Conserved Ortholog Set, RosCOS)间进行共线性分析,结果显示：在梅花基因组进化过程中,仅有PM3和PM4染色体发生染色体重排事件,即PM3染色体来源于李属的PG1、PG6和PG7染色体,PM4染色体来源于李属的PG2和PG5染色体。
7.对梅花F1代作图群体的株高、地径、叶长、叶宽、叶面积和叶脉数目等6个表型性状的遗传变异进行统计和分析,并利用复合区间作图法检测与这些性状相关QTLs位点,其结果显示：共检测到控制这些表型性状的84个QTLs,其中控制叶面积和叶脉数目性状的QTLs最多均为35个,控制地径的QTL最少为1个。
总之,本研究结果为梅花基因组结构和功能研究、分子标记定向辅助育种和近缘物种间比较基因组学研究奠定重要的理论基础,对进一步开展梅花分子标记聚合育种提供重要借鉴和参考,为今后揭示梅花重要观赏性状的遗传机制和探索梅花起源具有重要意义。
Belonging to the Rosaceae, sub-family Prunoideae, mei(Prunus mume Sieb. et Zucc.,2n=2x=16) possesses early blossom, varying types of flowers, colorful corollas, and pleasant fragrance and is extensively grown as a garden ornamental plant. Up to now, new cultivars of mei are always bred using traditional hybridizations which spend a lot of time. Meanwhile, the origin of mei isn't still revealed as a result of the lack of the comparative genomic analyses between mei and related species. Here, a high density genetic linkage map using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers based on190F1segregating progeny generated from a cross between female P. mume 'Fenban' and male P. mume 'Kouzi Yudie' was constructed and was anchored genomic assembly sequences of mei, depanding on which not only the macro-colinearity between mei genome and Prunus T×E reference map [an interspecific almond 'Texas'×peach 'Earlygold'(T×E) F2mapping population] was identified, but also the quantitative trait loci (QTLs) for main phenotypic traits were detected in this study. The main results and conclusions are indicated as follows:
1. We performed the genome-wide characterization of SSRs ranging in length from1to8bp in the mei genome and the results were shown as follows:A total of188,149SSRs were identified at a frequency of793.9SSR/Mb using MIcroSAtellites identification tool (MISA) and mononucleotide repeats (67,183) were the most common type of SSRs.
2. We analysed the distribution of the repeat motifs of SSRs in the genomic and different genomic regions of mei, apple, and strawberry. The results were indicated as follows:The frequency of SSRs decreased with the increasing the repeat motif length, AT-rich repeat motifs were more common than GC-rich repeat motifs, and the frequency of SSRs was more common in intergenic regions than CDS regions in three genomes of Rosaceae.
3.670SSRs were chosen from the total SSRs identified in mei genome and were detected among parental lines and190Fi segregating progeny generated from a cross between P. mutne 'Fenban' and P. mume 'Kouzi Yudie'. The results were indicated as follows:A framework genetic linkage map of mei was constructed based on144polymorphic SSRs according to pseudo-test-cross strategy, containing eight linkage groups (LGs). The total genetic distance was668.7cM. Seventy one scaffolds covering about28.1%of mei assembled sequences were anchored to this genetic map, totaling to66.5Mb.
4. According to the restriction-site associated with DNA-tag (RAD-tag) strategy, about2,166polymorphic SNPs were detected among the parental lines and190F1segregating progeny using bioinformatics analysis. The polymorphic1,484SNPs exhibited standard Mendelian segregation (1:1or1:2:1) by χ2test at cutoff of P<0.05. About3,229SNPs polymorphic loci were found in this mapping population, occurring at an average two polymorphic loci of each SNPs.
5. We constructed a high density genetic linkage map including1,613markers based on the framework genetic linkage map added density using1,484polymorphic SNPs. This genetic map contained eight LGs, totaling to780.9cM. The average marker interval is0.5cM.513scaffolds covering about84.0%of mei assembled sequences were anchored to this high density genetic map, totaling to199.0Mb.
6. A high level of macro-collinearity was revealed by aligning the199.0Mb assembled sequences anchored to the mei genetic map and613sequences of Rosaceae Conserved Ortholog Set (RosCOS) anchored to the Prunus T×E reference map. The results were indicated as follows:Among the process of mei evolution, PM3and PM4underwent chromosome rearrangement and PM3was originated from PG1, PG6and PG7of Prunus, and PM4was originated from PG2and PG5of Prunus.
7. Hereditary variations of plant height, ground diameter, leafblade length, leafblade width, leafblade area and leafblade vein number were measured and analyzed based on F1mapping population of mei. These QTLs for these phenotypic traits using composit interval mapping. The results were shown as follows:There were84QTLs for these six phenotypic traits using composit interval mapping. Of these QTLs,35QTLs for leafblade area and for leafblade vein number were the most common, while only one QTL for ground diameter was the least.
In summary, this study may facilitate genomic structure and function, maker-assisted selection breeding, and comparative genomic analyses between mei and relative species, may further provide an important reference for molecular marker polymerization breeding of mei, and pave the way for the study of genetic mechanism of important ornamental traits and the origin of mei.
引文
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