Taxanaha Jajabka La Weyneeyay ee Gaarka ah-Locus (SLAF-Seq)
Socodka shaqada
Adeeggu waxa uu leeyahay nakhshad horudhac ah oo silico ah si loo dammaanad qaado xulashada enzyme ugu fiican ee diyaarinta maktabadda.
Qorshaha Farsamada
Tilmaamaha Adeegga
● Ku darida NovaSeq ee leh PE150.
● Diyaarinta maktabadda oo leh barcodeing labanlaab ah, oo awood u siinaya in ka badan 1000 muunado.
● Ka madax-bannaan genome tixraaceed:
Iyada oo leh genome tixraac: SNP iyo daahfurka InDel
Iyadoo aan lahayn genome tixraac: ururinta muunada iyo SNP daahfurka
● Gudahasiliko ahMarxaladda hore-naqshadeynta isku darka enzyme xaddidan ee badan ayaa la baaray si loo helo kuwa abuura qaybinta isku midka ah ee sumadaha SLAF ee weheliya genome.
● Inta lagu jiro tijaabada hore, saddex isku darka ensaymes ayaa lagu tijaabiyay 3 muunado si loo soo saaro 9 maktabadaha SLAF, macluumaadkan waxaa loo isticmaalaa in lagu doorto isku darka enzyme xaddidan ee ugu fiican ee mashruuca.
Faa'iidooyinka Adeegga
●Helitaanka Calaamadaha Hiddaha ee Sare: Waxaan isku darsanay nidaamka barcode-ka labanlaaban-sare ah oo u oggolaanaya isku-xigxiga isku mar ee dad badan, iyo kordhinta goobta-gaar ah ee kor u qaadeysa waxtarka, hubinta in lambarrada summada ay buuxiyaan shuruudaha kala duwan ee su'aalaha cilmi-baarista ee kala duwan.
● Ku-tiirsanaanta Hoose ee Genome: Waxaa lagu dabaqi karaa noocyada leh ama aan lahayn genome tixraaceed.
●Naqshadaynta Qorshaha Dabacsan: Hal-enzyme, dual-enzyme, dheef-shiid kiimikaad badan, iyo noocyo kala duwan oo ensaymes ah ayaa dhammaantood loo dooran karaa si loo daboolo yoolalka cilmi-baarista ee kala duwan ama noocyada.
● Waxtarka sare ee dheefshiidka enzymatic: Qabashada ahsiliko ahNaqshad horudhac ah iyo tijaabo hore ayaa xaqiijinaysa naqshadaynta ugu fiican iyadoo xitaa qaybinta calaamadaha SLAF ee koromosoomyada (1 SLAF tag / 4Kb) iyo hoos u dhigista isku xigxiga soo noqnoqda (<5%).
●Khibrad BalaadhanMashruuc kasta waxa aanu u keenaynaa waayo-aragnimo badan, iyada oo aan haysanno rikoodho ah in la xidho in ka badan 5000 mashruuc oo SLAF-Seq ah oo lagu samaynayo boqollaal nooc, oo ay ku jiraan dhirta, naasleyda, shimbiraha, cayayaanka, iyo noolaha biyaha.
● Socod-shaqeedka Bioinformatic-ka ee is-horumariyay: Waxaan u sameynay isku-dhafka bioinformatic-ka isku-dhafka ah ee SLAF-Seq si loo hubiyo kalsoonida iyo saxnaanta wax-soo-saarka kama dambaysta ah.
Tilmaamaha Adeegga
| Nooca falanqaynta | Qiyaasta dadweynaha ee lagu taliyay | Istaraatiijiyada isku xigxiga | |
| Qoto dheer ee isku xigxiga tag | Lambarka tag | ||
| Khariidadaha Hiddaha | 2 waalid iyo>150 farac | Waalidiinta: 20x WGS Dhisidda: 10x | Cabbirka hiddaha: <400 Mb: WGS ayaa lagula talinayaa <1Gb: 100k tags 1-2Gb:: 200k tags >2Gb: 300k tags ugu badnaan 500k tags |
| Daraasadaha Ururka Guud ee Genome-Wide (GWAS) | ≥200 oo muunado | 10x | |
| Evolution Hidde | ≥30 muunado, oo leh> 10 muunado koox-hoosaad kasta | 10x | |
Shuruudaha Adeegga
Xooga saarista ≥ 5 ng/µL
Wadarta qaddarka ≥ 80 ng
Nandrop OD260/280=1.6-2.5
Agarose gel: maya ama xaddidan hoos u dhac ama wasakh
Tusaalaha keenista lagu taliyay
Weelka: 2 ml tuubo centrifuge
(Samballada intooda badan, waxaan kugula talineynaa inaan lagu keydin ethanol)
Calaamadaynta Tusaalaha: Muunaduhu waxay u baahan yihiin in si cad loo calaamadiyo oo la mid ah foomka macluumaadka muunada ee la gudbiyay.
Shixnadda: Barafka qallalan: Muunadodu waxay u baahan yihiin in marka hore bac lagu shubo oo lagu aaso baraf qallalan.
Socodka Shaqada Adeegga
Tusaalaha QC
Tijaabada tijaabada
SLAF-tijaabo
Diyaarinta Maktabadda
Isku xigxiga
Falanqaynta Xogta
Adeegyada iibka kadib
Falanqayntayada bioinformatical waxay ka kooban tahay:
Xogta QC iyo jarista xogta si meesha looga saaro akhrinta N-hodanka ah, akhrinta adabtarada ama akhrinta tayada hoose.
Xakamaynta tayada labaad ee nadiifka ah waxay akhridaa si loo hubiyo qaybinta saldhigga, tayada isku xigxiga iyo qiimeynta xogta, laakiin sidoo kale si loo hubiyo waxtarka dheefshiidka iyo gelinta la helay.
Marka akhrinta la hubiyo, waxaa jira laba ikhtiyaar:
- Khariidaynta tixraaca genome
- Iyadoo aan lahayn genome tixraac: kooxaysi
Intaa ka dib, falanqaynta calaamadaha SLAF waxaa loo isticmaalaa in lagu sameeyo wicitaano kala duwan si looga caawiyo helitaanka calaamadeeyaha: SNP, InDel, SNV, wacitaanka CV iyo sharraxaad
Qaybinta summada SLAF ee koromosoomyada:
Qaybinta SNP-yada koromosoomyada:
Tusmada ugu hooseysa ee SNP
Jiang S, Li S, Luo J.Pyrus pyrifolia.Hore. Dhirta Sci.14:1137104. doi: 10.3389/fpls.2023.1137104
Li, J., Zhang, Y., Ma, R., Huang, W., Hou, J., Fang, C., & Sun, L. (2022). Aqoonsiga st1 wuxuu daaha ka qaadayaa xulashada ku lug leh ku-dhufashada qaab-dhismeedka abuurka iyo waxa ku jira saliidda inta lagu jiro dhaqashada soybean.Wargeyska Biotechnology ee dhirta, 20 (6), 1110-1121. https://doi.org/10.1111/pbi.13791
Xu, P., Zhang, X., Wang, X.iyo al.Isku xigxiga genome iyo kala duwanaanshaha hidde-sidaha carp-ka caadiga ah,Cyprinus carpio.Nat Genet 46, 1212-1219 (2014). https://doi.org/10.1038/ng.3098
Zhuang, W., Chen, H., Yang, M.iyo al.Hiddo-sidaha lawska la beeray waxa uu siinaya aragti ku saabsan karyotypes legume, kobcinta polyploid iyo guriynta dalagga.Nat Genet 51, 865-876 (2019). https://doi.org/10.1038/s41588-019-0402-2
| Sannadka | Joornaal | IF | Ciwaanka | Codsiyada |
| 2022 | Isgaarsiinta dabeecadda | 17.694 | Asalkii genomic ee giga-chromosomes iyo giga-genome of peony geed Paeonia ostii | SAF-GWAS |
| 2015 | Cilmi-nafsiga cusub | 7.433 | Raad-raacyada gurigu waxay ku xidhaan gobollada genomic ee muhiimadda beeralayda gudaha digirta | SAF-GWAS |
| 2022 | Joornaalka Cilmi-baarista Sare | 12.822 | Genom-ballaaran hordhaca macmalka ah ee Gossypium barbadense galay G. hirsutum Muujin heer sare ah oo loogu talagalay hagaajinta tayada fiber suufka iyo wax-soo-saarka isku mar ah sifooyinka | SLAF-horumarka hiddaha |
| 2019 | Warshada Molecular | 10.81 | Falanqaynta Genomic Dadweynaha iyo Golaha De Novo ayaa Muujiyay Asalka Weedy Bariiska sida Ciyaar Horumarineed | SLAF-horumarka hiddaha |
| 2019 | Hiddaha Dabeecada | 31.616 | Taxanaha hiddo-wadaha iyo kala duwanaanshaha hidde-sidaha ee carp-ka caadiga ah, Cyprinus carpio | Khariidadda SLAF-Likage |
| 2014 | Hiddaha Dabeecada | 25.455 | Hiddo-sidaha lawska la beeray wuxuu bixiyaa aragti ku saabsan legume karyotypes, polyploid kobcinta iyo dalagyada guri-guritaan. | Khariidadda SLAF-Likage |
| 2022 | Wargeyska Biotechnology ee dhirta | 9.803 | Aqoonsiga ST1 wuxuu muujinayaa xulashada ku lug leh garaacista qaab-dhismeedka abuurka iyo waxa ku jira saliidda inta lagu jiro dhaqashada soybean | Horumarinta SLF-Marker |
| 2022 | Joornaalka Caalamiga ah ee Cilmiga Molecular | 6.208 | Aqoonsiga iyo Horumarinta Calaamadaha DNA ee Qamadiga-Leymus mollis 2Ns (2D) Beddelka Kala-duwan ee Chromosome | Horumarinta SLF-Marker |
| Sannadka | Joornaal | IF | Ciwaanka | Codsiyada |
| 2023 | Xuduudaha sayniska dhirta | 6.735 | Khariidadda QTL iyo falanqaynta qoraalka qoraalka ee nuxurka sonkorta inta lagu jiro bislaanshaha miraha ee Pyrus pyrifolia | Khariidadda Hidde |
| 2022 | Wargeyska Biotechnology ee dhirta | 8.154 | Aqoonsiga ST1 waxay daaha ka qaadaysaa xulashada ku lug leh ku-dhufashada qaab-dhismeedka abuurka iyo waxa ku jira saliidda inta lagu jiro dhaqashada soybean
| SNP wac |
| 2022 | Xuduudaha sayniska dhirta | 6.623 | Khariidaynta Ururka Genome-Wide ee Qaababka Hulless Barely Phenotypes ee Deegaanka Abaaraha.
| GWAS |
