Fa'asologa o Vaega Fa'aopoopo Fa'apitoa-Locus (SLAF-Seq)
Fa'asologa o galuega
Fuafuaga Fa'atekinisi
Vaega Auaunaga
● Fa'asologa ile NovaSeq ile PE150.
● Sauniuniga faletusi ma fa'ailoga fa'alua fa'alua, e mafai ai ona tu'ufa'atasia le silia ma le 1000 fa'ata'ita'iga.
● O lenei metotia e mafai ona faʻaogaina pe leai se genome faʻasino, faʻatasi ai ma laina paipa bioinformatic eseese mo tulaga taʻitasi:
Fa'atasi ai ma fa'amatalaga genome: SNP ma InDel mauaina
A aunoa ma le fa'asinomaga genome: fa'ata'ita'iga fa'aputuina ma le su'esu'ega SNP
● I lei silicoa'o le'i fa'ata'atia le tele o fa'aputuga ole enzyme e su'esu'e e su'e ai mea e fa'atupuina ai le tufatufaina tutusa o pine SLAF ile genome.
● I le taimi o le faʻataʻitaʻiga muamua, e tolu faʻatasiga enzyme e faʻataʻitaʻiina i faʻataʻitaʻiga 3 e faʻatupu ai faletusi 9 SLAF, ma o lenei faʻamatalaga e faʻaaogaina e filifili ai le tuʻufaʻatasiga o le enzyme faʻatapulaʻa sili ona lelei mo le poloketi.
Tulaga Auaunaga
●Su'esu'ega Fa'ailoga Fa'aa'e Maualuga: O le tu'ufa'atasia o se faiga fa'amaufa'ailoga fa'alua fa'alua e mafai ai le fa'asologa fa'atasi o le faitau aofa'i o tagata, ma le fa'alauteleina o nofoaga fa'apitoa e fa'aleleia ai le lelei, fa'amautinoaina o numera fa'ailoga e fetaui ma mana'oga eseese o fesili su'esu'e eseese.
● Fa'alagolago maualalo ile Genome: E mafai ona faʻaoga i ituaiga o loʻo i ai pe leai foi se genome faʻasino.
●Fuafuaga Fuafuaga Fuafuaga: E tasi-enzyme, lua-enzyme, multi-enzyme digestion, ma ituaiga eseese o enzymes e mafai ona filifilia uma e faʻafetaui sini suʻesuʻega eseese poʻo ituaiga. O lei silicoe faia muamua le mamanu ina ia mautinoa ai se mamanu sili ona lelei o le enzyme.
● Malosi maualuga ile Enzymatic Digestion: O le faatinoga o sei silicomua'i mamanu ma se fa'ata'ita'iga fa'ata'ita'iga fa'amautinoa lelei le fa'ata'ita'iga fa'atasi ma le tufatufaina o pine SLAF i luga ole chromosome (1 SLAF tag/4Kb) ma fa'aitiitia le fa'asologa toe fai (<5%).
●Tomai Tele: O la matou 'au e aumaia le tamaoaiga o le poto masani i galuega faatino uma, faatasi ai ma se faamaumauga o le tapunia o galuega faatino 5000 SLAF-Seq i luga o le selau o ituaiga, e aofia ai laau toto, mammals, manulele, iniseti, ma meaola vai.
● Fausia e le tagata lava ia Bioinformatic Workflow: BMKGENE atiaʻe se suʻesuʻega bioinformatic tuʻufaʻatasia mo SLAF-Seq e faʻamautinoa ai le faʻamaoni ma le saʻo o le gaioiga mulimuli.
Fa'amatalaga Auaunaga
| Ituaiga su'esu'ega | Fautuaina le faitau aofai o tagata | Fuafuaga fa'asologa | |
| Le loloto o le fa'asologa o fa'ailoga | Numera fa'ailoga | ||
| Fa'afanua Genetic | 2 matua ma >150 fanau | Matua: 20x WGS Fanau: 10x | Tele ole Genome: <400 Mb: WGS ua fautuaina <1Gb: 100K pine 1-2Gb:: 200K pine >2Gb: 300K pine Max 500k pine |
| Genome-Wide Association Studies (GWAS) | ≥200 faʻataʻitaʻiga | 10x | |
| Genetic Evolution | ≥30 faʻataʻitaʻiga, faʻatasi ma> 10 faʻataʻitaʻiga mai vaega laiti taʻitasi | 10x | |
Manaoga Auaunaga
Fa'asa'o ≥ 5 ng/µL
Aofaʻi aofaʻi ≥ 80 ng
Nanodrop OD260/280=1.6-2.5
Agarose gel: leai pe faʻatapulaʻaina le faʻaleagaina poʻo le faʻaleagaina
Fautuaina Fa'ata'ita'iga Tu'uina atu
Pusa: 2 ml centrifuge paipa
(Mo le tele o faʻataʻitaʻiga, matou te fautuaina e aua le teuina i le ethanol)
Fa'ailoga fa'ata'ita'iga: E mana'omia le fa'ailoga manino o fa'ata'ita'iga ma ia tutusa ma fa'amatalaga fa'ata'ita'iga ua tu'uina atu.
La'uina: Fa'amamago-aisa: Fa'ata'ita'iga e mana'omia ona teu muamua i taga ma tanu i le aisa-mago.
Au'aunaga Galuega
Fa'ata'ita'iga QC
Fa'ata'ita'iga pailate
SLAF-faʻataʻitaʻiga
Sauniuniga Faletusi
Fa'asologa
Fa'amatalaga Fa'amatalaga
Au'aunaga ina ua uma ona fa'atau
E aofia ai le au'ili'iliga nei:
- Fa'asologa o fa'amaumauga QC
- Atina'e fa'ailoga SLAF
Fa'afanua e fa'asino i le genome
A aunoa ma se genome faʻasino: faʻapipiʻi
- Iloiloga o pine SLAF.: fuainumera, tufatufaina i le genome
- Su'esu'ega fa'ailoga: SNP, InDel, SNV, CV vala'au ma fa'amatalaga
Tufatufaina o pine SLAF i chromosomes:
Tufatufaina o SNP i chromosomes:
SNP fa'amatalaga
| Tausaga | Tusitala | IF | Ulutala | Talosaga |
| 2022 | Fesootaiga faanatura | 17.694 | Genomic faavae o giga-chromosomes ma giga-genome o laau peony Paeonia ostii | SLAF-GWAS |
| 2015 | Phytologist Fou | 7.433 | O tulagavae o fale e taula ai itulagi genomic e taua agronomic i soya | SLAF-GWAS |
| 2022 | Tusitala o Su'esu'ega Maualuga | 12.822 | Genome-lautele fa'aoso introgressions o Gossypium barbadense i G. hirsutum fa'aalia loci sili atu mo le fa'aleleia fa'atasi o le lelei o alava ma fua uiga | SLAF-Evolutionary genetics |
| 2019 | La'au Molecular | 10.81 | Population Genomic Analysis ma De Novo Assembly Fa'aalia le Afuaga o Weedy Alaisa o se Taaloga Evolutionary | SLAF-Evolutionary genetics |
| 2019 | Natura Genetics | 31.616 | Genome sequence ma kenera eseese o le carp masani, Cyprinus carpio | SLAF-So'oga fa'afanua |
| 2014 | Natura Genetics | 25.455 | Ole genome ole pinati fa'ato'aina e maua ai le fa'amatalaga ile karyotypes legume, polyploid evolusione ma fa'ato'aga fa'ato'aga. | SLAF-So'oga fa'afanua |
| 2022 | La'au Biotechnology Journal | 9.803 | O le fa'ailoaina ole ST1 o lo'o fa'ailoa mai ai se filifiliga e a'afia ai le fa'asa'oina o fatu fatu ma le suau'u o lo'o iai i le taimi o le fa'atauina o soya | SLAF-Fa'ailoga atina'e |
| 2022 | Tusitala Faava o Malo o Saienisi Molecular | 6.208 | Fa'ailoaina ma le Atina'eina o Fa'ailoga DNA mo se Wheat-Leymus mollis 2Ns (2D) Suiga Disomic Chromosome | SLAF-Fa'ailoga atina'e |
| Tausaga | Tusitala | IF | Ulutala | Talosaga |
| 2023 | Tuaoi i le faasaienisi laau | 6.735 | Fa'afanua QTL ma su'esu'ega transcriptome o le suka i le taimi o fuala'au fua o Pyrus pyrifolia | Fa'afanua Genetic |
| 2022 | La'au Biotechnology Journal | 8.154 | O le fa'ailoaina o le ST1 o lo'o fa'aalia ai se filifiliga e aofia ai le fa'atauina o fatu fatu ma le suau'u o lo'o iai i le taimi o le fa'atosinaina o soya.
| SNP valaau |
| 2022 | Tuaoi i le faasaienisi laau | 6.623 | Genome-Wide Association Mapping of Hulless Barely Phenotypes in Drought Siosiomaga.
| GWAS |
