Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)
Kev ua haujlwm
Cov kev pabcuam muaj qee qhov kev tsim ua ntej hauv silico los lav qhov kev pom zoo enzyme xaiv ntawm kev npaj ntawm lub tsev qiv ntawv.
Tswv yim
Kev Pabcuam Nta
● Sequencing ntawm NovaSeq nrog PE150.
● Kev npaj tsev qiv ntawv nrog ob chav barcoding, ua kom muaj ntau tshaj 1000 tus qauv.
● Kev ywj pheej ntawm kev siv genome:
Nrog kev siv genome: SNP thiab InDel nrhiav pom
Tsis siv cov genome: piv txwv pawg thiab SNP nrhiav pom
● Hauvhauv-silicopre-tsim theem ntau yam txwv enzyme ob peb ua ke raug tshuaj xyuas kom pom cov uas tsim kom muaj ib qho kev faib tawm ntawm SLAF cim npe raws genome.
● Thaum lub sijhawm sim ua ntej, peb qhov kev sib xyaw ua ke enzyme tau sim hauv 3 cov qauv los tsim 9 SLAF cov tsev qiv ntawv, thiab cov ntaub ntawv no yog siv los xaiv qhov kev pom zoo ntawm kev txwv enzyme ua ke rau qhov project.
Kev Pabcuam Zoo
●High Genetic Marker Discovery: Peb koom ua ke qhov kev sib koom ua ke siab tshaj ob chav barcode uas tso cai rau kev sib sau ua ke ntawm cov neeg coob coob, thiab thaj chaw tshwj xeeb ua kom muaj txiaj ntsig zoo, kom ntseeg tau tias cov lej cim ua tau raws li qhov xav tau ntawm ntau yam kev tshawb fawb cov lus nug.
● Tsawg Dependence ntawm Genome: Nws tuaj yeem siv rau hom tsiaj nrog lossis tsis muaj kev siv genome.
●Saj zawg zog Scheme Design: Ib leeg-enzyme, dual-enzyme, ntau-enzyme digestion, thiab ntau hom enzymes tuaj yeem xaiv los ua kom haum rau ntau hom kev tshawb fawb lossis hom.
● High Efficiency hauv Enzymatic Digestion: Kev ua ntawm ibhauv-silicoKev tsim qauv ua ntej thiab kev sim ua ntej ua kom pom kev tsim qauv nrog txawm tias faib ntawm SLAF cim npe ntawm chromosome (1 SLAF tag / 4Kb) thiab txo qis rov ua ntu ntu (<5%).
●Kev txawj ntse: Peb nqa cov kev paub dhau los rau txhua qhov haujlwm, nrog rau cov ntaub ntawv kaw ntau dua 5000 SLAF-Seq cov haujlwm ntawm ntau pua hom, suav nrog cov nroj tsuag, tsiaj txhu, noog, kab, thiab cov kab mob hauv dej.
● Tus kheej tsim Bioinformatic Workflow: Peb tau tsim ib qho kev sib koom ua ke ntawm bioinformatic workflow rau SLAF-Seq los xyuas kom meej qhov kev ntseeg tau thiab qhov tseeb ntawm cov zis kawg.
Service Specifications
| Hom kev tsom xam | Pom zoo ntsuas cov pej xeem | Sequencing tswv yim | |
| Qhov tob ntawm tag sequencing | Tag naj npawb | ||
| Genetic Maps | 2 niam txiv thiab > 150 tus xeeb ntxwv | Cov niam txiv: 20x WGS kev :10x | genome loj: <400 Mb: WGS tau pom zoo <1Gb: 100K tags 1-2Gb:: 200K tags > 2Gb: 300K tags Max 500k tag |
| Genome-Wide Association Studies (GWAS) | ≥200 qauv | 10x ib | |
| Genetic Evolution | ≥30 tus qauv, nrog> 10 qauv los ntawm txhua pab pawg | 10x ib | |
Kev Pabcuam
Cov ntsiab lus ≥ 5 ng / µL
Tag nrho cov nyiaj ≥ 80 ng
Nanodrop OD 260/280 = 1.6-2.5
Agarose gel: tsis muaj los yog txwv tsis pub degradation los yog paug
Pom zoo coj mus kuaj
Ntim: 2 ml centrifuge tube
(Rau feem ntau ntawm cov qauv, peb pom zoo kom tsis txhob khaws cia hauv ethanol)
Sample labeling: Cov qauv yuav tsum tau sau kom meej meej thiab zoo ib yam rau xa cov qauv ntaub ntawv.
Kev Thauj Khoom: Dry-ice: Cov qauv yuav tsum tau ntim rau hauv hnab ua ntej thiab muab faus rau hauv cov dej khov qhuav.
Kev Pabcuam Ua Haujlwm
Qauv QC
Pilot kev sim
SLAF-kev sim
Kev npaj tsev qiv ntawv
Sequencing
Kev txheeb xyuas cov ntaub ntawv
Kev pab cuam tom qab muag
Peb bioinformatical tsom xam muaj xws li:
Cov ntaub ntawv QC thiab cov ntaub ntawv txiav kom tshem tawm N-nplua nuj nyeem, adapter nyeem lossis nyeem tsis zoo.
Kev tswj xyuas qhov zoo thib ob ntawm kev nyeem kom huv los xyuas cov hauv paus kev faib tawm, kev ua ntu zus thiab kev soj ntsuam cov ntaub ntawv, tab sis kuj yuav tsum xyuas cov kev zom zaub mov thiab cov khoom siv tau.
Thaum cov ntawv nyeem tau txheeb xyuas, muaj ob txoj hauv kev:
- Daim ntawv qhia rau siv genome
- Tsis muaj kev siv genome: pawg
Tom qab nws, kev tshuaj xyuas ntawm SLAF cov cim npe yog siv los ua qee qhov kev hu xov tooj los pab nrog cov cim nrhiav pom: SNP, InDel, SNV, CV hu thiab annotation.
Kev faib tawm ntawm SLAF cov cim npe ntawm chromosomes:
Kev faib tawm ntawm SNPs ntawm chromosomes:
SNP annotation
Jiang S, Li S, Luo J, Wang X thiab Shi C (2023) QTL mapping thiab transcriptome tsom xam cov ntsiab lus qab zib thaum lub sij hawm txiv hmab txiv ntoo ripeningPyrus pyrifolia.Pem hauv ntej. Tsob Ntoo Sci.14:1137104 ib. doi: 10.3389/fpls.2023.1137104 ib.
Li, J., Zhang, Y., Ma, R., Huang, W., Hou, J., Fang, C., & Sun, L. (2022). Kev txheeb xyuas ntawm st1 qhia txog kev xaiv nrog hitchhiking ntawm cov noob morphology thiab roj cov ntsiab lus thaum soybean domestication.Plant Biotechnology Journal, 20(6), 1110-1121. https://doi.org/10.1111/pbi.13791
Xu, P., Zhang, X., Wang, X.ua al.Genome sequence thiab genetic ntau haiv neeg ntawm cov carp ntau,Cyprinus carpio.Nat Genet 46, 1212–1219 (2014). https://doi.org/10.1038/ng.3098
Zhuang, W., Chen, H., Yang, M.ua al.Lub genome ntawm cultivated txiv laum huab xeeb muab kev pom rau legume karyotypes, polyploid evolution thiab qoob loo domestication.Nat Genet 51, 865–876 (2019). https://doi.org/10.1038/s41588-019-0402-2
| Xyoo | Phau ntawv | IF | Title | Daim ntawv thov |
| 2022 | Ntuj kev sib txuas lus | 17.694 ib | Genomic hauv paus ntawm giga-chromosomes thiab giga-genome ntawm tsob ntoo peony Paeonia ostii | SLAF-GWAS |
| 2015 | Tshiab Phytologist | 7.433 ib | Domestication footprints thauj tog rau nkoj genomic cheeb tsam ntawm agronomic tseem ceeb hauv taum mog | SLAF-GWAS |
| 2022 | Phau ntawv Journal of Advanced Research | 12.822 Nws | Genome-wide dag introgressions ntawm Gossypium barbadense rau G. hirsutum qhia superior loci rau ib txhij txhim kho ntawm paj rwb fiber zoo thiab tawm los yam ntxwv | SLAF-Evolutionary noob caj noob ces |
| 2019 | Molecular Cog | 10.81 Nws | Population Genomic Analysis thiab De Novo Assembly nthuav tawm lub hauv paus chiv keeb ntawm Weedy Rice raws li Evolutionary Game | SLAF-Evolutionary noob caj noob ces |
| 2019 | Nature Genetics | 31.616 ib | Genome sequence thiab genetic ntau haiv neeg ntawm hom carp, Cyprinus carpio | SLAF-Linkage map |
| Xyoo 2014 | Nature Genetics | 25.455 Nws | Lub genome ntawm cultivated txiv laum huab xeeb muab kev pom rau legume karyotypes, polyploid evolution thiab qoob loo domestication. | SLAF-Linkage map |
| 2022 | Plant Biotechnology Journal | 9.803 ib | Kev txheeb xyuas ntawm ST1 qhia txog kev xaiv uas cuam tshuam nrog kev sib tsoo ntawm cov noob morphology thiab roj cov ntsiab lus thaum soybean domestication | SLAF-Marker kev txhim kho |
| 2022 | International Journal of Molecular Sciences | 6.208 ib | Kev txheeb xyuas thiab DNA Marker Kev Txhim Kho rau Nplej-Leymus mollis 2Ns (2D) Disomic Chromosome Hloov | SLAF-Marker kev txhim kho |
| Xyoo | Phau ntawv | IF | Title | Daim ntawv thov |
| 2023 | Frontiers nyob rau hauv cog science | 6.735 ib | QTL daim ntawv qhia thiab kev txheeb xyuas cov ntsiab lus qab zib thaum lub sij hawm txiv hmab txiv ntoo siav ntawm Pyrus pyrifolia | Daim ntawv qhia caj ces |
| 2022 | Plant Biotechnology Journal | 8.154 ib | Kev txheeb xyuas ntawm ST1 qhia txog kev xaiv uas cuam tshuam nrog kev sib tsoo ntawm cov noob morphology thiab cov ntsiab lus roj thaum lub sij hawm soybean domestication
| SNP hu |
| 2022 | Frontiers nyob rau hauv cog science | 6.623 ib | Genome-Wide Association Mapping ntawm Hulless Ncua Nrab Phenotypes nyob rau hauv Drought Environment.
| GWAS |
