Imikhiqizo

I-Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

I-genotyping ephezulu kakhulu, ikakhulukazi kubantu abaningi, iyisinyathelo esibalulekile ezifundweni zenhlangano yofuzo, ehlinzeka ngesisekelo sofuzo sokutholwa kwezakhi zofuzo ezisebenzayo, ukuhlaziya kokuziphendukela kwemvelo, njll. Esikhundleni sokulandelanisa kabusha kwegenome ejulile, kuncishiswe ukulandelana kofuzo lokumelela (RRGS). ) yethulwa ukuze kuncishiswe izindleko zokulandelanisa isampula ngayinye, kuyilapho kugcinwe ukusebenza kahle okunengqondo ekutholweni komaka wofuzo.Lokhu ngokuvamile kufinyelelwa ngokukhipha isinqamu esikhawulelwe ngaphakathi kobubanzi obunikeziwe bosayizi, obuqanjwe ngokuthi umtapo wolwazi oncishisiwe (RRL).I-Specific-locus amplified fragment sequencing (SLAF-Seq) isu lokuzithuthukisa le-SNP genotyping ene-reference genome noma ngaphandle kwayo.
Ipulatifomu: I-Illumina NovaSeq Platform

Xhumana nathi

Imininingwane Yesevisi

Imiphumela yedemo

Okushicilelwe Okufakiwe

Imininingwane Yesevisi

Uhlelo Lokusebenza

Ukugeleza komsebenzi

Izinzuzo Zesevisi

Ukusebenza kahle kokutholwa komaka- Ubuchwepheshe bokulandelana komkhiqizo ophezulu busiza i-SLAF-Seq ekutholeni amakhulu ezinkulungwane zamathegi kulo lonke uhlobo lofuzo.

Ukuncika okuphansi ku-genome- Ingasetshenziswa ezinhlotsheni ezine-genome noma ngaphandle kwayo.

Idizayini yesikimu eguquguqukayo- I-enzyme eyodwa, ama-enzyme amabili, ukugaya kwama-enzyme amaningi kanye nezinhlobo ezahlukahlukene zama-enzyme, konke kungakhethwa ukubhekelela umgomo ohlukile wocwaningo noma izinhlobo.Ukuhlola kwangaphambili ku-silico kusetshenziselwa ukuqinisekisa ukwakheka kwe-enzyme efanele.

Ukugaya okusebenzayo kwe-enzymatic- Ukuhlola kwangaphambili kwenziwa ukuze kulungiswe izimo, okwenza ukuhlola okusemthethweni kuzinze futhi kuthembeke.Ukusebenza kahle kokuqoqwa kweziqephu kungafinyelela ngaphezu kwama-95%.

Omaka abasatshalaliswe ngokulinganayo be-SLAF- Omaka be-SLAF basakazwa ngokulinganayo kuwo wonke ama-chromosome ngezinga elikhulu kakhulu, kufinyelelwa isilinganiso esingu-1 SLAF ngo-4 kb.

Ukugwema okuphumelelayo kokuphindaphinda- Ukulandelana okuphindaphindayo kudatha ye-SLAF-Seq kwehliswa kwaba ngaphansi kuka-5%, ikakhulukazi ezinhlotsheni ezinezinga eliphezulu lokuphindaphinda, njengokolweni, ummbila, njll.

Okuhlangenwe nakho okubanzi-Angaphezu kuka-2000 amaphrojekthi avaliwe e-SLAF-Seq kumakhulu ezinhlobo ezihlanganisa izitshalo, izilwane ezincelisayo, izinyoni, izinambuzane, izinto eziphilayo zasemanzini, njll.

Ukuzithuthukisa kwe-bioinformamatic workflow- Ukugeleza komsebenzi okuhlanganisiwe kwe-bioinformamatic ye-SLAF-Seq kwathuthukiswa yi-BMKGENE ukuze kuqinisekiswe ukwethembeka nokunemba kokuphumayo kokugcina.

Imininingwane Yesevisi

Inkundla	Conc.(ng/gl)	Isamba (ug)	OD260/280
Illumina NovaSeq	>35	>1.6(Umqulu>15μl)	1.6-2.5

Qaphela: Amasampula amathathu, ngalinye linezinhlelo ezintathu zama-enzyme, azokwenziwa ukuze kuhlolwe ngaphambilini.

Isu Elinconyiwe Lokulandelanisa

Ukujula kokulandelanisa: 10X/Tag

Usayizi weGenome	Amathegi e-SLAF anconyiwe
<500Mb	100K noma i-WGS
500 Mb-1 Gb	100 K
1 Gb -2 Gb	200 K
Ama-genome amakhulu noma ayinkimbinkimbi	300 - 400K

Izinhlelo zokusebenza

Kunconyiwe

Isikali sabantu

Isu lokulandelanisa nokujula

Ukujula

Inombolo yethegi

I-GWAS

Inombolo yesampula ≥ 200

10X

Ngokuvumelana ne

usayizi we-genome

I-Genetic Evolution

Umuntu ngamunye

iqembu elincane ≥ 10;

isamba samasampuli ≥ 30

10X

Ukulethwa Kwesampula Okunconyiwe

Isitsha: 2 ml centrifuge tube

Kumasampuli amaningi, sincoma ukuthi ungagcini ku-ethanol.

Isampula yokulebula: Amasampuli adinga ukulebula ngokucacile futhi afane nefomu lesampula lolwazi elithunyelwe.

Ukuthunyelwa: Iqhwa elomile: Amasampula adinga ukupakishwa ezikhwameni kuqala futhi agqitshwe eqhweni elomile.

Uhlelo lokusebenza lwesevisi

Isampula ye-QC

Ukuhlolwa komshayeli

SLAF-ukuhlola

Ukulungiselela Umtapowolwazi

Ukulandelanisa

Ukuhlaziywa Kwedatha

Amasevisi angemuva kokuthengisa

Okwedlule: Ukulandelana kwe-DNA/RNA - I-Nanopore Sequencer

Olandelayo: Ukulandelana kwe-Human Whole Exome

1. Izibalo zomphumela wemephu

2. Ukuthuthukiswa komaka we-SLAF

3. Isichasiselo esihlukile

Unyaka	Ijenali	IF	Isihloko	Izinhlelo zokusebenza
2022	Ukuxhumana kwemvelo	17.694	Isisekelo se-genomic se-giga-chromosomes kanye ne-giga-genome ye-peony yesihlahla I-Paeonia ostii	I-SLAF-GWAS
2015	I-Phytologist entsha	7.433	Izinyathelo zasekhaya ziqinisa izifunda ze-genomic ezibalulekile ku-agronomic ubhontshisi wesoya	I-SLAF-GWAS
2022	Ijenali Yocwaningo Oluthuthukile	12.822	I-Genome-wide-wide introgressions yokwenziwa kwe-Gossypium barbadense ku-G. hirsutum veza i-loci ephezulu yokuthuthukisa kanyekanye ikhwalithi yefayibha kakotini kanye nesivuno izici	I-SLAF-Evolutionary genetics
2019	Isitshalo samangqamuzana	10.81	I-Population Genomic Analysis kanye ne-De Novo Assembly Yembula Umsuka Weedy Ilayisi njengomdlalo wokuziphendukela kwemvelo	I-SLAF-Evolutionary genetics
2019	I-Nature Genetics	31.616	Ukulandelana kwe-genome kanye nokuhlukahluka kofuzo kwe-carp evamile, i-Cyprinus carpio	Imephu ye-SLAF-Linkage
2014	I-Nature Genetics	25.455	I-genome ye-peanut etshaliwe inikeza ukuqonda nge-karyotypes ye-legume, i-polyploid ukuziphendukela kwemvelo kanye nokufuywa kwezitshalo.	Imephu ye-SLAF-Linkage
2022	Plant Biotechnology Journal	9.803	Ukukhonjwa kwe-ST1 kuveza ukukhetha okubandakanya ukugitsheliswa kwembewu yokuma kwembewu kanye nokuqukethwe kwamafutha ngesikhathi sokufuywa kukabhontshisi wesoya	Ukuthuthukiswa kwe-SLAF-Marker
2022	Ijenali Yamazwe Ngamazwe Yesayensi Yamangqamuzana	6.208	Ukuhlonzwa kanye Nokuthuthukiswa Kwe-DNA Marker ye-Wheat-Leymus mollis 2Ns (2D) Ukushintshwa kwe-Disomic Chromosome	Ukuthuthukiswa kwe-SLAF-Marker