日本落叶松×兴安落叶松RAPD、SSR遗传图谱构建与QTL定位
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摘要
落叶松是我国北方主要造林及用材树种,在建筑材、纸浆材等方面发挥重要作用。本研究选用黑龙江省牡丹江市林口县青山林场的日本落叶松(Larix kaempefri)×兴安落叶松(L.gmelinii)及其145个F1个体为作图群体,同时运用RAPD (Random Amplified Polymorphic DNA)和SSR (Simple sequence repeat)构建日本落叶松(Larix kaempefri)×兴安落叶松(L.gmelinii)的遗传连锁图谱,并首次结合生长性状(树高、胸径、冠幅和材积)、材性性状(木材密度、管胞长度、管胞宽度和管胞长宽比)进行QTLs定位分析,为落叶松分子标记辅助育种提供理论依据。
1.通过文献检索获得适合落叶松的SSR、搜索EST序列设计EST-SSR引物。通过文献检索得到SSR引物118对；登陆NCBI的dbEST数据库搜索EST序列,共获EST序列40605条,应用SSRIT软件在线搜索EST-SSR位点,用Primer3设计,共设计EST-SSR引物796对。
2.通过正交设计优化了落叶松RAPD-PCR、SSR-PCR反应体系。确立适合于本研究群体的RAPD-PCR反应体系为：20μl的反应体系中,TaqDNA聚合酶为1U,Mg2+ 3.0 mmol·L-1, dNTP 0.25 mmol·L-1,引物0.5μmol·L-1,模板DNA 50 ng;确立SSR-PCR反应体系为：20μL的反应体系中,TaqDNA聚合酶为1U, Mg2+ 3.0 mmol·L-1, dNTP 0.25 mmol·L-1,上下游引物各0.45μmol·L-1,模板DNA50ng。
3.筛选RAPD引物210个、SSR引物17对,共获得603个多态性位点(581个RAPD、22个SSR)。平均每个RAPD引物获得2.8个标记位点,每对SSR引物获得1.3个标记位点,扩增产物的DNA片段长度多数在150-2000 bp之间。χ2检验(χ20.05(1)=3.84)检验结果显示,扩增位点中,444个位点符合1：1拟测交分离(日本落叶松220/兴安落叶松224),46个位点符合3：1分离(日本落叶松29/兴安落叶松17),113个位点属于偏分离位点。有308个位点来自日本落叶松,占51.08%,295个位点来自兴安落叶松,占48.92%。
4.利用JoinMap3.0设置最小LOD值≥3.0,重组率≤0.45进行遗传作图,通过对拟测交分离位点进行两点连锁分析,构建了日本落叶松×兴安落叶松遗传连锁图谱。日本落叶松中的48个连锁标记构成了5个不同的连锁群(4个以上标记),4个三连体和6个连锁对,168个为非连锁位点,平均图距11.9cM。而来自兴安落叶松的91个标记构成了9个连锁群(4个以上标记),2个三连体和5个连锁对,128个为非连锁位点,平均图距6.1cM。估算的日本落叶松遗传图谱框架图和连锁群总长度为290.1cM和546.5cM,估算的兴安落叶松遗传图谱框架图和连锁群总长度分别为147.7cM和262.0cM。
5.对构图群体生长性状进行测定,包括树高、胸径、冠幅、材积等生长性状,并同时进行木材密度(Wood Specific Gravity,WSG)、管胞长度(Tracheid Length, TL)、管胞宽度(TracheidWidth, TW)、和管胞长宽比的测定。变异分析结果表明,日×兴F1群体内个体间生长性状、材性性状均存在较大变异,并且生长性状与材性性状间存在相关。
6.通过标记位点与性状间的关联分析,获得生长性状和材性性状QTLs。采用WinQTLCart 2.5对群体的数量性状进行复合区间作图,以似然比LOD值≥1.5为阂值对QTL进行定位分析。通过标记位点与性状间的关联分析,获得与生长性状关联的QTL标记位点4个,获得与材性性状相关的QTLs 20个,其中,日本落叶松管胞长度和管胞长宽比QTLs各1个,兴安落叶松木材密度QTLs9个、管胞长度QTLs 4个和管胞宽度QTLs 5个。各QTLs的LOD值在1.5-11.9,贡献率在0.0105%-45.9986%。
Larch (Larix spp) is a main species of afforestation and timber, it plays an important role in buliding and paper pulp timber. Larix kaempefri, Larix gmelinii and their 145 full-sib F1 individuals in Qingshan forest farm Linkou county Mudanjiang city Heilongjiang province were used as the mapping population, and RAPD (Random Amplified Polymorphic DNA) and SSR(Simple sequence repeat) were used to construct the genetic linkage map of L. kaempefri and L.gmelinii. It was the first time to QTL mapping analysis combination with growth characters (height、diameter、average crown and volume)、wood characters(Wood Specific Gravity、Tracheid Length、Tracheid Width and TL/TW ratio) and it provided theoretical basis for molecular marker-assisted breeding of larch.
1. SSR primers that suitable for larch were obtained. We got 118 pairs SSR primers by searching in literatures; and searching 40605 ESTs by logging in dbEST database of NCBI, searching EST-SSR loci by using SSRIT software on internet,then it designed 796 pairs EST-SSR primers using Primer3.
2. Through the orthogonal design,the Larix RAPD-PCR and SSR-PCR reaction systems was optimized. RAPD-PCR reaction system:20μl total volume for RAPD reaction contained 1.0U Taq DNA polymerase,3.0 mmol·L-1 Mg2+,0.25 mmol·L-1 dNTP,0.5μmol·L-1 primer,50 ng DNA template; SSR-PCR reaction system:20μl total volume for SSR reaction contained 1.0U Taq DNA polymerase,3.0 mmol·L-1 Mg2+,0.25 mmol·L-1 dNTP,0.45μmol·L-1 each upstream and downstream primer,50 ng DNA template.
3.210 RAPD primers and 17 pairs SSR primers were obtained through the optimized reaction system of larch RAPD-PCR、SSR-PCR respectively, and total 603 polymorphism loci (581 loci of RAPD,22 loci of SSR) were identified. The average number of markers produced by per RAPD primer was 2.8, and one pairs SSR primers amplified 1.3 markers in average. The size of amplified DNA bands ranged from 150 to 2000 bp.χ2test (χ20.05(1) =3.84) showed that 444 loci belonged to 1:1 pseudo-testcross separation (220 belong to Larix Kaempferi while 224 belong to Larix gmelini),46 belonged to 3:1(29 belongs to Larix Kaempferi while 17 belong to Larix gmelini), while the other 113 loci belonged to segregation distortion among all. There were 51.8%(308 loci) from L. kaempferi while the other 48.92% (295) originated from L.gmelinii.
4.The pseudo-testcross separated loci were carried out by a two-point linkage analysis using JoinMap 3.0 with a LOD threshold of 3.0 and a recombination threshold 0.45, and then the genetic linkage map of Larix kaempefri and L.gmelinii have been constructed. The maternal Japanese larch map consisted of 48 linkage markers placed in 5 linkage groups(four or more sites per group),4 triplets,6 linkage pairs, and 168 non-linkage markers, the average map distance was 11.9 cM. The paternal Chinese larch map consisted of 91 linkage markers in 9 linkage groups (four or more sites per group),2 triplets,5 linkage pairs, and 128 non-linkage 'markers, the average map distance was 6.1 cM. The genetic map framework length and linkage group total length of Larix Kaempferi were 290.1cM and 546.5 cM respectively, while the ones of Larix gmelini were 147.7 cM and 262.0 cM respectively.
5. Measured the growth traits of composition population, which included tree height, diameter, crown width and volume, and also measured Wood Specific Gravity、Tracheid Length、Tracheid Length and Tracheid Length to Tracheid Width ratio. Variances result shown: the difference of growth traits and timber characteristics mainly existed between individuals in the F1 population of Japanese Larch X Chinese Larch, and the growth traits were related to timber characteristics.
6.With the association analysis between markers and characters, QTL loci that ralated to growth character and wood character were obtained. WinQTLCart2.5 were taken to composite interval mapping of population quantitative characters, it setted LOD≥1.5 to mapping analysis of QTL. With the association analysis between markers and characters,4 QTL loci that ralated to growth character were obtained;20 QTL loci that ralated to wood character were obtained,of which,each 1 QTL related to Tracheid Length and TL/TW ratio of L. Kaempferi; 9 QTL related to Wood Specific Gravity、4 QTL related to Tracheid Length、5 QTL related to Tracheid Width of L. gmelini were detected. The LOD values in the 1.5-11.9, the contribution rate of 0.0105%-45.9986% of each QTLs.
1.通过文献检索获得适合落叶松的SSR、搜索EST序列设计EST-SSR引物。通过文献检索得到SSR引物118对；登陆NCBI的dbEST数据库搜索EST序列,共获EST序列40605条,应用SSRIT软件在线搜索EST-SSR位点,用Primer3设计,共设计EST-SSR引物796对。
2.通过正交设计优化了落叶松RAPD-PCR、SSR-PCR反应体系。确立适合于本研究群体的RAPD-PCR反应体系为：20μl的反应体系中,TaqDNA聚合酶为1U,Mg2+ 3.0 mmol·L-1, dNTP 0.25 mmol·L-1,引物0.5μmol·L-1,模板DNA 50 ng;确立SSR-PCR反应体系为：20μL的反应体系中,TaqDNA聚合酶为1U, Mg2+ 3.0 mmol·L-1, dNTP 0.25 mmol·L-1,上下游引物各0.45μmol·L-1,模板DNA50ng。
3.筛选RAPD引物210个、SSR引物17对,共获得603个多态性位点(581个RAPD、22个SSR)。平均每个RAPD引物获得2.8个标记位点,每对SSR引物获得1.3个标记位点,扩增产物的DNA片段长度多数在150-2000 bp之间。χ2检验(χ20.05(1)=3.84)检验结果显示,扩增位点中,444个位点符合1：1拟测交分离(日本落叶松220/兴安落叶松224),46个位点符合3：1分离(日本落叶松29/兴安落叶松17),113个位点属于偏分离位点。有308个位点来自日本落叶松,占51.08%,295个位点来自兴安落叶松,占48.92%。
4.利用JoinMap3.0设置最小LOD值≥3.0,重组率≤0.45进行遗传作图,通过对拟测交分离位点进行两点连锁分析,构建了日本落叶松×兴安落叶松遗传连锁图谱。日本落叶松中的48个连锁标记构成了5个不同的连锁群(4个以上标记),4个三连体和6个连锁对,168个为非连锁位点,平均图距11.9cM。而来自兴安落叶松的91个标记构成了9个连锁群(4个以上标记),2个三连体和5个连锁对,128个为非连锁位点,平均图距6.1cM。估算的日本落叶松遗传图谱框架图和连锁群总长度为290.1cM和546.5cM,估算的兴安落叶松遗传图谱框架图和连锁群总长度分别为147.7cM和262.0cM。
5.对构图群体生长性状进行测定,包括树高、胸径、冠幅、材积等生长性状,并同时进行木材密度(Wood Specific Gravity,WSG)、管胞长度(Tracheid Length, TL)、管胞宽度(TracheidWidth, TW)、和管胞长宽比的测定。变异分析结果表明,日×兴F1群体内个体间生长性状、材性性状均存在较大变异,并且生长性状与材性性状间存在相关。
6.通过标记位点与性状间的关联分析,获得生长性状和材性性状QTLs。采用WinQTLCart 2.5对群体的数量性状进行复合区间作图,以似然比LOD值≥1.5为阂值对QTL进行定位分析。通过标记位点与性状间的关联分析,获得与生长性状关联的QTL标记位点4个,获得与材性性状相关的QTLs 20个,其中,日本落叶松管胞长度和管胞长宽比QTLs各1个,兴安落叶松木材密度QTLs9个、管胞长度QTLs 4个和管胞宽度QTLs 5个。各QTLs的LOD值在1.5-11.9,贡献率在0.0105%-45.9986%。
Larch (Larix spp) is a main species of afforestation and timber, it plays an important role in buliding and paper pulp timber. Larix kaempefri, Larix gmelinii and their 145 full-sib F1 individuals in Qingshan forest farm Linkou county Mudanjiang city Heilongjiang province were used as the mapping population, and RAPD (Random Amplified Polymorphic DNA) and SSR(Simple sequence repeat) were used to construct the genetic linkage map of L. kaempefri and L.gmelinii. It was the first time to QTL mapping analysis combination with growth characters (height、diameter、average crown and volume)、wood characters(Wood Specific Gravity、Tracheid Length、Tracheid Width and TL/TW ratio) and it provided theoretical basis for molecular marker-assisted breeding of larch.
1. SSR primers that suitable for larch were obtained. We got 118 pairs SSR primers by searching in literatures; and searching 40605 ESTs by logging in dbEST database of NCBI, searching EST-SSR loci by using SSRIT software on internet,then it designed 796 pairs EST-SSR primers using Primer3.
2. Through the orthogonal design,the Larix RAPD-PCR and SSR-PCR reaction systems was optimized. RAPD-PCR reaction system:20μl total volume for RAPD reaction contained 1.0U Taq DNA polymerase,3.0 mmol·L-1 Mg2+,0.25 mmol·L-1 dNTP,0.5μmol·L-1 primer,50 ng DNA template; SSR-PCR reaction system:20μl total volume for SSR reaction contained 1.0U Taq DNA polymerase,3.0 mmol·L-1 Mg2+,0.25 mmol·L-1 dNTP,0.45μmol·L-1 each upstream and downstream primer,50 ng DNA template.
3.210 RAPD primers and 17 pairs SSR primers were obtained through the optimized reaction system of larch RAPD-PCR、SSR-PCR respectively, and total 603 polymorphism loci (581 loci of RAPD,22 loci of SSR) were identified. The average number of markers produced by per RAPD primer was 2.8, and one pairs SSR primers amplified 1.3 markers in average. The size of amplified DNA bands ranged from 150 to 2000 bp.χ2test (χ20.05(1) =3.84) showed that 444 loci belonged to 1:1 pseudo-testcross separation (220 belong to Larix Kaempferi while 224 belong to Larix gmelini),46 belonged to 3:1(29 belongs to Larix Kaempferi while 17 belong to Larix gmelini), while the other 113 loci belonged to segregation distortion among all. There were 51.8%(308 loci) from L. kaempferi while the other 48.92% (295) originated from L.gmelinii.
4.The pseudo-testcross separated loci were carried out by a two-point linkage analysis using JoinMap 3.0 with a LOD threshold of 3.0 and a recombination threshold 0.45, and then the genetic linkage map of Larix kaempefri and L.gmelinii have been constructed. The maternal Japanese larch map consisted of 48 linkage markers placed in 5 linkage groups(four or more sites per group),4 triplets,6 linkage pairs, and 168 non-linkage markers, the average map distance was 11.9 cM. The paternal Chinese larch map consisted of 91 linkage markers in 9 linkage groups (four or more sites per group),2 triplets,5 linkage pairs, and 128 non-linkage 'markers, the average map distance was 6.1 cM. The genetic map framework length and linkage group total length of Larix Kaempferi were 290.1cM and 546.5 cM respectively, while the ones of Larix gmelini were 147.7 cM and 262.0 cM respectively.
5. Measured the growth traits of composition population, which included tree height, diameter, crown width and volume, and also measured Wood Specific Gravity、Tracheid Length、Tracheid Length and Tracheid Length to Tracheid Width ratio. Variances result shown: the difference of growth traits and timber characteristics mainly existed between individuals in the F1 population of Japanese Larch X Chinese Larch, and the growth traits were related to timber characteristics.
6.With the association analysis between markers and characters, QTL loci that ralated to growth character and wood character were obtained. WinQTLCart2.5 were taken to composite interval mapping of population quantitative characters, it setted LOD≥1.5 to mapping analysis of QTL. With the association analysis between markers and characters,4 QTL loci that ralated to growth character were obtained;20 QTL loci that ralated to wood character were obtained,of which,each 1 QTL related to Tracheid Length and TL/TW ratio of L. Kaempferi; 9 QTL related to Wood Specific Gravity、4 QTL related to Tracheid Length、5 QTL related to Tracheid Width of L. gmelini were detected. The LOD values in the 1.5-11.9, the contribution rate of 0.0105%-45.9986% of each QTLs.
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