Tseeb-Locus Fragment Fragment Sequencing (SLAF-SEQ)
Kev ua hauj lwm
Cov txheej txheem technical
Cov Nta
● Kev sib txuas rau ntawm novaseEQ nrog PE150.
● Kev npaj lub tsev qiv ntawv nrog ob chav barcoding, ua kom cov pas dej ntawm ntau dua 1000 khom nqi.
● Cov txheej txheem no tuaj yeem siv nrog lossis tsis muaj qhov siv genome, nrog sib txawv bioinformatic pipelines rau txhua kis:
Nrog siv genome: SNP thiab Indel nrhiav pom
Tsis muaj kev siv Genome: Qauv pawg thiab SnP nrhiav pom
● Nyob rau hauv lubHauv silicoUa ntej tsim theem kev txwv enzyme sib xyaw ua ke yog pom cov uas tsim cov kev faib tawm ntawm cov cim npe ntawm cov genome.
● Thaum sim ua ntej ua ntej, peb txoj kev sib xyaw ua ke kom tsim tau 9 daim ntaub ntawv Slaf, thiab cov ntaub ntawv no yog siv los xaiv cov kev sib txuam zoo tshaj plaws rau txoj haujlwm.
Kev Pabcuam Zoo
●Kev Saib Xyuas Cov Qauv Loj: Kev sib xyaw ua ke ntawm cov qib siab barcode tso cai rau cov kev sib txuas lus sib xws, thiab cov lej uas tag sib tham tau sib ntsib ntawm ntau yam kev tshawb fawb.
● Tsawg txoj kev vam khom rau ntawm cov genome: Nws tuaj yeem siv rau hom tsiaj nrog lossis tsis muaj kev siv genome.
●Saj siab kho qauv tsim: Ib leeg-enzyme, dual-enzyme zom, thiab ntau hom enzymes tuaj yeem xaiv rau cov hom phiaj tshawb fawb lossis hom. TusHauv silicoKev tsim qauv ua ntej yog nqa tawm kom ntseeg tau tias qhov kev tsim qauv enzyme zoo.
● High efficiency hauv enzymatic zom: Lub conduction ntawm ib tugHauv silicoPre-design thiab kev sim ua ntej kev ua ntej tsim qauv nrog txawm faib cov cim npe ntawm lub chromosome ntawm lub chromosome ntawm lub chromosome ntawm lub chromosome (1 slfit tag / 4kb) thiab txo qis rov ua se (<5%).
●Kev txawj ntse dav: Peb pab neeg coj kev muaj txiaj ntsig ntawm kev paub rau txhua txoj haujlwm, nrog cov phiaj xwm taug qab ntau dua 5000 hom, suav nrog cov nroj tsuag, tsiaj, kab, thiab dej yug me nyuam.
● Kev Tsim Nyog Tus Kheej Bioinformicatic Workflow: BMKGAE tsim kho cov khoom siv Bioinformatic ua haujlwm rau SLAF-SQEQ kom ntseeg tau tias kev ntseeg tau thiab qhov tseeb ntawm kev ntseeg tau.
Kev Pabcuam Tshwj Xeeb
| Hom tsom xam | Pom zoo cov pej xeem | Seitencing Lub Tswv Yim | |
| Qhov tob ntawm lossis cov kab sib txuas | Tug naj npawb | ||
| Cov phiajcim caj ces | 2 Niam Txiv thiab> 150 offspring | Cov niam txiv: 20x wgs Offsping: 10 x | Genom Loj Loj: <400 MB: WGS raug pom zoo <1GB: 100k cim npe 1-2Gb :: 200 lis cov cim npe > 2GB: 300k cim npe Max 500k cim npe |
| Genium-Dav Kev Kawm Txog Kev Kawm Koom Tes (GWAS) | ≥200 kuaj | 10 x | |
| Txoj Kev Pom Kev Genolution | ≥30 Cov qauv kuaj, nrog> ntsuas los ntawm txhua pawg pab pawg | 10 x | |
Kev pabcuam yuav tsum tau ua
Kev xav ≥ 5 ng / μl
Tag nrho cov nqi ≥ li 80 ng
Nanodrop Od260 / 280 = 1.6-2.5
Agarose gel: tsis muaj lossis txwv tsis zoo lossis paug
Pom zoo tus qauv xa mus
Thawv: 2 Ml Centrifuge Tube
(Rau feem ntau ntawm cov qauv, peb pom zoo kom tsis txhob khaws cia hauv EJANOL)
Qauv kos npe cim: Cov qauv yuav tsum tau sau cia kom meej meej thiab zoo ib yam rau cov qauv foos.
Cov zaub mov xa tuaj: qhuav-dej khov: Kuaj yuav tsum tau ntim rau hauv cov hnab ua ntej thiab faus rau hauv cov dej khov qhuav.
Kev Pabcuam Workflow
Qauv QC
Kev sim sim
Sauv kev sim
Kev npaj lub tsev qiv ntawv
Ze
Cov Ntaub Ntawv Kev Ntsuam Xyuas
Cov Kev Pab Tom Qab Muag
Xws li kev tsom xam hauv qab no:
- Extreccess QC
- Kev Hlub ncua
Qhia txog kev siv genome
Tsis muaj qhov siv genome: pawg
- Kev tsom xam ntawm SLAF cov cim npe.: Txheeb cais, faib hla cov genome
- Marker Tshawb Nrhiav: SNP, Indel, SNV, CV Hu thiab Tshaj Tawm
Kev faib cov cim npe ntawm cov cim npe:
Kev faib tawm SNPs rau Chromosomes:
SNP Annotation
| Lub xyoo | Phau ceev xwm txheej | IF | Lub npe | Cov Ntawv Thov |
| 2022 | Kev sib txuas lus | 17.694 | Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia Ostii | SLAF-GWAS |
| 2015 | Tus kws txawj txheeb xyuas tshiab phytologist | 7.433 | Domestication hneev taw rau thauj tog rau nkoj genomic ntawm agronomic qhov tseem ceeb hauv taum pauv | SLAF-GWAS |
| 2022 | Phau ntawv Journal ntawm kev tshawb fawb tshaj plaws | 12.822 | Genom-dav artificial intrograms ntawm Goosyy Barbadense rau G. Hirsutum qhia tawm cov kab lus zoo tshaj plaws rau cov kev txhim kho ib txhij ntawm cov paj rwb fiber ntau zoo thiab tawm los tej hauj lwm | SLAF-evolutionary genetics |
| 2019 | Molecular Tsob Nroj | 10.81 | Cov pej xeem cov pej xeem kev tsom xam thiab de novo los ua ke qhia lub keeb kwm ntawm weedy Mov ua kev ua si evolutionary | SLAF-evolutionary genetics |
| 2019 | Xwm Genetics | 31.616 | Genome Seatures thiab kev caj tshuaj genetic ntawm cov carp, cyprinus carpio | Daim Ntawv Qhia Sawb Ntawv |
| 2014 | Xwm Genetics | 25.455 | Qhov Genome ntawm cultivated txiv laum huab xeeb muab kev pom rau hauv legume karyotypes, polyploid Evolution thiab cog qoob loo. | Daim Ntawv Qhia Sawb Ntawv |
| 2022 | Cog Ntawv Biotechnology | 9.803 | Kev txheeb xyuas cov kabmob ST1 qhia tau kev xaiv hitchhiking ntawm noob morphology thiab cov roj cov ntsiab lus thaum nyob hauv domestication | SERF-qhab nia |
| 2022 | Cov Ntaub Ntawv Thoob Ntiaj Teb ntawm Molecular Sciences | 6.208 | Kev cim thiab DNA Marker Kev Tsim Kho rau cov nplej-Leymus mollis 2ns (2D) Disomic Chromosome Hloov Kev | SERF-qhab nia |
| Lub xyoo | Phau ceev xwm txheej | IF | Lub npe | Cov Ntawv Thov |
| 2023 | Frontiever nyob rau hauv cog science | 6.735 | Qtl daim qauv thiab transcriptomea tsom kwm ntawm cov ntsiab lus qab zib thaum lub txiv ntoo ripening ntawm pyriffia | Daim duab qhia caj ces |
| 2022 | Cog Ntawv Biotechnology | 8.154 | Kev txheeb xyuas cov kabmob ST1 qhia tau nrog cov noob morphology thiab roj cov ntsiab lus thaum lub sijhawm ua lag luam
| Snp hu |
| 2022 | Frontiever nyob rau hauv cog science | 6.623 | Genom of Wid Association of Hulless Nus Phenotypes hauv kev thaj chaw ntuj qhuav.
| Lub gwas |
