Transcriptome maps of Populus tomentosa: Characteristics and its applications
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1 Transcriptome maps of Populus tomentosa: Characteristics and its applications PhD. Li bo & Pro.Zhang Zhiyi
2 Discrete traits and quantitative traits Discrete trait: color, gender, et al Quantitative trait: size, production, height, et al. Most economic traits
3 Quantitative traits: big trouble Simpson, Tell me why ones are small and the others are so big? Controlled by many genes Genes with minor effects Complicated to decipher Ho,you d better ask God!
4 QTL mapping can answer???? fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size Frary,et al. Science, 2000,289 (7), P85-87
5 Development of Linkage Map in Populus Summary: >12 projects >9 species or hybrids most under pseudo testcross strategy Most based on genomic DNA markers, RAPD, AFLP, SSR, ISSR et al. Yin et al, (2004) TAG, 109:
6 Protocol: Transcriptome map RNA dscdna AFLP Genotyping Examples: Potato (Brugmans,2002) Arabidopsis (Brugmans,2002) Cotton (Pan,2007) Potato (Ritter,2008)
7 Differences between genetic map and transcriptome map Nature of the markers Reflection of specific tissue and development stage Novel markers: differential expression (rare) cleavage site mutation
8 Cleavage site mutation within exons DNA level No Polymorphism RNA level Polymorphism marker detectable
9 Work flow Specific tissues cdna-aflp assay Cloning specificexpression genes Transcriptome maps Phenotyping Marker sequencing QTL analysis Gene maps Comparative genomics
10 Mapping pedigree and materials Mapping pedigree: (P.tomentosa P.bolleana) X P.tomentosa 7 years old,132 genotypes Materials: total RNA from developing xylem
11 Marker systems cdna-aflp analysis: RNA cdna dscdna AFLP Genotyping SSR analysis: DNA PCR PAGE gel testing Genotyping
12 RNA from different tissues Mature xylem Phloem Cambium Developing Mature Bark xylem xylem
13 Preparation (1): Primer selection Pre-amplification: E+0/M+0, E+0/M+1, E+1/M+0, E+1/M+1, NO obvious difference E02/M02 E02/M03E03M02 E03M03 Sel-amplification: E+2/M+2,E+2/M+3,E+3/M+2, E+3/M+3 E+2/M+3 or E+3/M+2 is ideal for mapping
14 Preparation (2): Polymorphism estimation E11M33 E13M40 E15M56 E16M56 Polymorphism Analysis with 21 random chosen primers
15 Polymorphism analysis of (P. tomentosa P. bolleana) and P. tomentosa
16 RNA isolation Ds cdna syntheses cdna-aflp analysis DNA isolation SSR analysis
17 Transcriptome map construction 47 primer had been selected from 3 hundreds And analyzed within BC1 population.
18 Display of marker polymorphism 1:1 segregation markers Quantitative expression markers
19 Polymorphism analysis of cdna-aflp markers
20
21 Transcriptome map of P.Tomentosa E11M31_380 E63M15_160 E63M12_240 E33M E44M23_140r E63M19_360r E44M15_220 ORPM-203 E63M11_155 E44M15_165 E34M18_155 E54M E54M17_350r E54M17_235 E17M68_200r E51M16_145 E44M20_330 E33M11_410 E34M22_340 E44M21_135 E72M19_ LG1 E34M18_355 E34M22_275 E31M11_380r E44M21_330 E33M E54M17_270 E72M E44M20_390 E17M68_310 E44M15_390 E63M14_330 E11M31_200 E63M20_85 E34M12_ LG2 E44M E15M68_90 E34M14_420r E33M14_310r E20M88_310r E34M18_105 E31M11_180 E33M19_350 E31M12_145 PMGC-575 E13M56_510 E63M19_305 E44M23_120 PMGC-93 E31M20_255 E11M31_85 E63M12_220 E44M24_245 E44M22_255 E34M18_275 E33M E13M56_ LG3 E34M14_90 E63M18_235r E44M21_375 E44M15_90 E20M88_75 E11M31_295r E19M88_135 E31M20_140 E31M12_380 E63M19_220 E33M26_395 E33M26_345 E31M20_230 E51M LG4 E51M E44M22_220 E11M33_195 E51M16_75 E44M13_515 E13M56_370 E17M68_375 E44M22_340 E34M21_155 E63M15_480 E63M16_550r E44M15_120 E33M13_ LG5 E44M E13M40_235 E34M14_155 E44M20_220 E33M14_415 E15M68_280r E33M LG6 E63M11_215 E33M11_65 E31M12_285 E63M18_145 E11M33_120 E33M24_280 E33M19_200 E31M24_95 E31M11_550 E72M19_215 E44M15_355r E44M13_160 E15M56_465r E44M LG7 E44M13_220 ORPM-206 E34M22_200 E34M14_255 E33M13_95 E19M88_95 E34M21_ LG8 E51M15_325 E51M15_290 E13M56_95 E51M16_300 E72M19_465 E33M13_195 E54M17_290 E33M19_145 E13M40_110r E33M14_240 E34M14_275r E44M LG9 E34M18_225 E34M22_175r E31M12_240r E33M26_145 E44M13_270 E54M17_145 E15M68_260 E44M23-98 E31M14_ LG10 E44M E31M24_200 E13M56_210 E51M16_290 E34M14_125 E34M13_135 E34M LG11 E33M19_255 E11M33_330 E34M18_70 E63M18_95 E34M12_340 E34M13_150 E33M26_ LG12 E33M13_145 E63M12_145 E34M11_385 E34M22_360 E31M14_135 E72M19_135 E34M22_385 E51M16_350r E13M40_200r LG13 E44M11_255 E15M56_175 E44M13_390 E44M22_360 E63M23_ LG14 E44M22_175 E31M12_315 E63M E34M11_235 E51M15_ LG15 E63M16_135 E33M24_320 E63M11_85r E20M88_215r LG16 E11M31_135 E31M11_460 E31M20_315r E15M56_220r E44M13_300 E34M21_350 E33M24_220r E63M16_250 E34M11_140 E34M E63M LG17 E11M31_350 E54M17_310 E63M14_235 E19M88_ LG18
22 Transcriptome map of P.tomentosa P.bolleana E31M20_75 E44M13_450 E33M13_130 E15M68_160 E15M56_310 E31M12_195 E15M68_410 E31M11_490 E19M88_230 E33M11_385 E63M18_190r E19M88_260r E11M33_215r E33M19_375 E33M24_135 E34M13_ LG1 E34M22_295 E63M12_340 E44M11_365r E31M12_460 E19M88_210 E11M31_110r E31M14_350 E44M13_205 E44M20_145 E34M21_130 ORPM_202 E31M14_ LG2 E34M18_315r E44M23_205 E63M16_100 E44M24_375 E31M20_190 E33M14_150 E31M14_210 E34M21_250 E44M13_350r E13M56_ LG3 E31M24_370r E20M88_185r E44M15_455 E31M14_400 E63M19_330 E13M56_330 E63M15_295 E44M15_135 E63M15_235 ORPM_21 E44M21_285 E44M13_135r LG4 E44M24_190 E44M11_155 E63M12_180 E34M13_315 E63M16_ LG5 E63M11_105 E51M15_480 E63M20_315 E44M11_195 E34M13_350 E34M13_360 E63M19_255r E63M14_280r LG6 E44M24_315 E34M12_260 E63M20_235 E63M14_415 E31M14_560r E33M14_345 E34M11_500 E51M16_515 E13M40_ LG7 E34M14_465 E34M21_235 E34M14_260 E44M15_190 E44M11_330 E34M22_250 E20M88_ LG8 E33M14_205 E63M23_190r E34M13_185r E15M56_355r E33M24_340 E11M31_275 E15M68_ LG9 E31M11_235 E15M56_405 E20M88_130 E31M12_335 E44M21_ LG10 E34M18_170 E34M18_140r E51M16_420 E17M68_520 E63M20_150 E44M23_260 E34M12_360 E51M15_245r E11M33_350r LG11 E33M11_275 E20M88_260 E15M56_130 E51M15_ LG12 E44M15_285 E31M24_285 E11M33_295 E44M15_245r LG13 2
23 Characteristics of transcriptome map of P. tomentosa
24 Characteristics of transcriptome map of (P. tomentosa P. bolleana) P. tomentosa
25 Characterization of transcriptome map Genome estimation of P.tomentosa P. bolleana and P. tomentosa
26 Marker distribution analysis across LGs Linkage length Length Number of Number of Poission Value Group of LG of Expected LG observed marker expected marker LG LG ** LG LG LG LG LG * LG LG LG LG LG LG LG LG LG LG *** LG * P 0.05; **P 0.01;*** P 0.001
27 Marker distribution analysis across LGs Linkage length Length Number of Number of Poission Value Group of LG of Expected LG observed marker expected marker LG LG LG LG LG LG LG LG LG LG LG * LG LG * P 0.05
28 Heterozygosity estimation within transcribed regions
29
30 Comparison between whole genome and transcribed regions
31 Other work Transcriptome map from root-born seedlings QTL analysis sequencing the markers
32
33 Acknowledgement Pro. Zhang zhiyi, Pro. Zhang Deqiang, Pro. An xinmin, Dr. Wang zeliang, Ms. Jiang xibing, and other colleagues. This study was Supported by National Natural Sciences Foundation of China (No ) and eleventh five-year plan (2006BAD01A15-2).
34 Thanks very much!
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