Usoro Mpempe Mpempe Akọwapụtara kpọmkwem-Locus (SLAF-Seq)
Usoro ọrụ
Ọrụ ahụ nwere ụfọdụ nhazi mbụ na silico iji kwe nkwa nhọrọ enzyme kacha mma na nkwadebe nke ọba akwụkwọ.
Atụmatụ nka
Atụmatụ ọrụ
● Usoro na NovaSeq na PE150.
● Nkwadebe nke ọba akwụkwọ nwere koodu nzuzo abụọ, na-enyere aka ikpokọta ihe karịrị 1000 sample.
● N'adabereghị na genome ntụaka:
Site na genome ntụaka: nchọpụta SNP na InDel
Enweghị genome ntụaka: nchịkọta nlele na nchọpụta SNP
● N'imena silikiA na-enyocha usoro nhazi nke ọtụtụ mgbochi enzyme iji chọta ndị na-emepụta nkesa otu nke mkpado SLAF n'akụkụ genome.
● N'oge nnwale ahụ, a na-anwale ngwakọta enzyme atọ na nlele 3 iji mepụta ọba akwụkwọ SLAF 9, a na-eji ozi a họrọ ngwakọta enzyme mmachi kacha mma maka ọrụ ahụ.
Uru ọrụ
●Nchọpụta ihe nrịbama mkpụrụ ndụ ihe nketa: Anyị na-ejikọta usoro koodu koodu abụọ dị elu nke na-enye ohere maka nhazi oge nke ọnụ ọgụgụ buru ibu, na mmụba mpaghara mpaghara na-eme ka arụmọrụ dịkwuo mma, na-eme ka ọnụ ọgụgụ mkpado na-egbo mkpa dị iche iche nke ajụjụ nyocha dị iche iche.
● Ndabere dị ala na Genome: Enwere ike itinye ya na ụdị ndị nwere ma ọ bụ na-enweghị akwụkwọ genome.
●Nhazi atụmatụ na-agbanwe agbanwe: Otu-enzyme, dual-enzyme, multi-enzyme digestion, na ụdị dị iche iche nke enzymes nwere ike ịhọrọ iji kwado ihe mgbaru ọsọ nyocha ma ọ bụ ụdị dị iche iche.
● Ịrụ ọrụ dị elu na mgbaze Enzymatic: Nduzi nke ihena silikipre-design na a pre-nnwale na-ekwe nkwa kacha mma na ọbụna nkesa nke SLAF mkpado na chromosome (1 SLAF mkpado / 4Kb) na ibelata ugboro ugboro usoro (<5%).
●Ọkachamara sara mbara: Anyị na-eweta ahụmahụ bara ụba na ọrụ ọ bụla, yana ndekọ ndekọ nke imechi ihe karịrị 5000 SLAF-Seq oru na ọtụtụ narị ụdị, gụnyere osisi, mammals, nnụnụ, ụmụ ahụhụ, na aquatic ntule.
● Usoro ọrụ bioinformatic mebere onwe ya: Anyị mepụtara usoro ọrụ bioinformatic agbakwunyere maka SLAF-Seq iji hụ na ntụkwasị obi na izi ezi nke mmepụta ikpeazụ.
Nkọwapụta ọrụ
| Ụdị nyocha | Ọnụ ọgụgụ ndị akwadoro | Usoro usoro | |
| Omimi nke mkpado usoro | Nọmba mkpado | ||
| Maapụ mkpụrụ ndụ ihe nketa | 2 nne na nna na>150 ụmụ | Ndị nne na nna: 20x WGS Agba: 10x | Nha genome: <400 Mb: WGS ka akwadoro <1Gb: mkpado 100k 1-2Gb:: mkpado 200K > 2Gb: mkpado 300k Mkpado kacha 500k |
| Ọmụmụ ihe gbasara otu Genome-Wide (GWAS) | ≥200 samples | 10x | |
| Genetic Evolution | ≥30 samples, na> 10 samples si ọ bụla subgroup | 10x | |
Ihe achọrọ ọrụ
Ntinye uche ≥ 5 ng/µL
Mkpokọta ego ≥ 80 ng
Nanodrop OD260/280=1.6-2.5
Agarose gel: enweghị ma ọ bụ oke mmebi ma ọ bụ mmetọ
Nnyefe nlele akwadoro
Akpa: 2 ml centrifuge tube
(Maka ọtụtụ n'ime ihe atụ, anyị na-akwado ka ị ghara ichekwa na ethanol)
Ịkpọ aha nlele: Ọ dị mkpa ka e depụta ihe nlere anya nke ọma yana otu n'ụdị ozi nlele etinyere.
Mbupu: ice-akọrọ: A ga-ebu ụzọ tinye ihe nlele n'ime akpa wee lie ya na ice-akọrọ.
Usoro ọrụ ọrụ
Ihe atụ QC
Nnwale pilot
SLAF-nnwale
Nkwadebe ụlọ akwụkwọ
Usoro
Nyocha data
Ọrụ ire ere
Nyocha bioinformatical anyị nwere:
Data QC na mbelata data iji wepu N-ọgaranya agụ, ihe nkwụnye agụ ma ọ bụ agụ dị ala.
Njikwa mma nke abụọ nke dị ọcha na-agụ iji lelee nkesa isi, ogo usoro na nyocha data, kamakwa iji lelee arụmọrụ mgbaze na ntinye enwetara.
Ozugbo enyochara agụ, enwere nhọrọ abụọ:
- Ịtụ aka na genome
- Enweghị genome ntụaka: nchịkọta
Mgbe nke ahụ gasịrị, a na-eji nyocha nke mkpado SLAF mee ụfọdụ ọkpụkpọ dị iche iche iji nyere aka na nchọpụta akara: SNP, InDel, SNV, oku CV na nkọwa.
Nkesa nke mkpado SLAF na chromosomes:
Nkesa SNP na chromosomes:
Mgbanwe nke ọnụahịa SNP
Jiang S, Li S, Luo J, Wang X na Shi C (2023) QTL maapụ na nyocha transcriptome nke ọdịnaya shuga n'oge mfri eke.Pyrus pyrifolia.N'ihu. Osisi Sci.14:1137104. doi: 10.3389/fpls.2023.1137104
Li, J., Zhang, Y., Ma, R., Huang, W., Hou, J., Fang, C., & Sun, L. (2022). Nchọpụta nke st1 na-ekpughe nhọrọ metụtara ịkụ mkpụrụ morphology na ọdịnaya mmanụ n'oge ụlọ soybean.Akwụkwọ akụkọ ihe ọkụkụ nke biotechnology, 20 (6), 1110-1121. https://doi.org/10.1111/pbi.13791
Xu, P., Zhang, X., Wang, X.et al.Usoro genome na ụdị mkpụrụ ndụ ihe nketa dị iche iche nke carp nkịtị,Cyprinus carpio.Na Genet 46, 1212–1219 (2014). https://doi.org/10.1038/ng.3098
Zhuang, W., Chen, H., Yang, M.et al.Mkpụrụ ndụ ihe nketa nke ahụekere na-akọ na-enye nghọta banyere ụdị karyotypes legume, evolushọn polyploid na ihe ọkụkụ.Na Genet 51, 865–876 (2019). https://doi.org/10.1038/s41588-019-0402-2
| Afọ | Akwụkwọ akụkọ | IF | Aha | Ngwa |
| 2022 | Nkwukọrịta okike | 17.694 | Genomic ndabere nke giga-chromosomes na giga-genome nke osisi peony Paeonia ostii | SLF-GWAS |
| 2015 | Ọkachamara gbasara ahụike ọhụrụ | 7,433 | Akara ukwu nke ụlọ na-akwado mpaghara genomic nke mkpa agronomic dị na soybean | SLF-GWAS |
| 2022 | Akwụkwọ akụkọ nyocha dị elu | 12.822 | Genom-wide artificial introgressions nke Gossypium barbadense n'ime G. hirsutum kpughee loci dị elu maka imeziwanye ogo na mkpụrụ nke eriri owu n'otu oge àgwà | SAF-Evolutionary genetics |
| 2019 | Osisi Molecular | 10.81 | Ọnụọgụ Genomic Analysis na De Novo Assembly na-ekpughe mmalite nke ahịhịa Rice dị ka egwuregwu evolushọn | SAF-Evolutionary genetics |
| 2019 | Genetics okike | 31.616 | Usoro genome na ụdị mkpụrụ ndụ ihe nketa dị iche iche nke carp nkịtị, Cyprinus carpio | SLF-njikọ map |
| 2014 | Genetics okike | 25,455 | Mkpụrụ ndụ ihe nketa nke ahụekere na-akọ na-enye nghọta na legume karyotypes, polyploid evolushọn na ihe ubi domestication. | SLF-njikọ map |
| 2022 | Akwụkwọ akụkọ ihe ọkụkụ nke biotechnology | 9,803 | Nchọpụta nke ST1 na-ekpughe nhọrọ metụtara ịkụ mkpụrụ morphology mkpụrụ na mmanụ dị n'ime ya n'oge anụ ụlọ soybean | SLF-Marker mmepe |
| 2022 | Akwụkwọ akụkọ International nke Science Molecular | 6.208 | Nchọpụta na Mmepe Ihe nrịbama DNA maka Wheat-Leymus mollis 2Ns (2D) Ngbanwe chromosome Disomik | SLF-Marker mmepe |
| Afọ | Akwụkwọ akụkọ | IF | Aha | Ngwa |
| 2023 | Frontiers na sayensị osisi | 6,735 | Maapụ QTL na nyocha transcriptome nke ọdịnaya shuga n'oge mfri eke Pyrus pyrifolia | Maapụ mkpụrụ ndụ ihe nketa |
| 2022 | Akwụkwọ akụkọ ihe ọkụkụ nke biotechnology | 8.154 | Nchọpụta nke ST1 na-ekpughe nhọrọ metụtara ịkụ mkpụrụ morphology na ọdịnaya mmanụ n'oge a na-elekọta soybean.
| SNP na-akpọ |
| 2022 | Frontiers na sayensị osisi | 6,623 | Nkewa otu Genome-Wide Association nke Hulless Barely Phenotypes na gburugburu ọkọchị.
| GWAS |
