Te Raupapatanga Wāhanga Whakarei ake o te Wāhi Motuhake (SLAF-Seq)
Rerenga mahi
Kua oti i te ratonga te hoahoa i mua i te whakamahi i te hangarau in silico hei whakarite i te kōwhiringa whākōkī tino pai i te wā e whakaritea ana te whare pukapuka.
Kaupapa Hangarau
Ngā Āhuatanga Ratonga
● Te raupapatanga i runga i te NovaSeq me te PE150.
● Te whakarite whare pukapuka me te tohu pae takirua, e āhei ai te kohikohi i ngā tauira neke atu i te 1000.
● Motuhake mai i te ira tohutoro:
Me te ira tohutoro: Te kitenga SNP me InDel
Kāore he ira tohutoro: te whakarōpūtanga tauira me te kitenga SNP
● I roto i tei roto i te silicoI mua i te hoahoa, ka tātarihia ngā huinga whākōkī here maha hei kimi i ngā mea e whakaputa ana i te tohatoha ōrite o ngā tohu SLAF puta noa i te ira.
● I te wā o mua i te whakamātautau, e toru ngā huinga whākōkī ka whakamatautauria i roto i ngā tauira e 3 hei whakaputa i ngā whare pukapuka SLAF e 9, ā, ka whakamahia ēnei mōhiohio hei whiriwhiri i te huinga whākōkī here tino pai mō te kaupapa.
Ngā Painga Ratonga
●Te Kitea o te Tohu Ira TeiteiKa whakauruhia e mātou he pūnaha waehere pae rua e tere haere ana te tuku, e āhei ai te raupapatanga o ngā taupori nui i te wā kotahi, ā, ka whakarei ake i te whai huatanga o te whakanui motuhake ki ngā tauwāhi, kia mōhio ai ka tutuki i ngā tau tohu ngā whakaritenga rerekē o ngā pātai rangahau rerekē.
● Te iti o te whakawhirinaki ki te iraKa taea te whakamahi ki ngā momo me te ira tohutoro, kāore rānei.
●Hoahoa Kaupapa NgāwariKa taea te tīpako i te nakunaku kotahi-whākōkī, takirua-whākōkī, maha-whākōkī, me ngā momo whākōkī rerekē hei whakatutuki i ngā whāinga rangahau rerekē, i ngā momo rerekē rānei.
● Te Tino Whai Hua i roto i te Nakunaku WhākōkīTe whakahaere o tētahii roto i te silicoMā te hoahoa-mua me te whakamātautau-mua ka tino pai te hoahoa me te tohatoha ōrite o ngā tohu SLAF i runga i te ira (1 tohu SLAF/4Kb) me te whakaiti i te raupapa auau (<5%).
●Tohungatanga WhānuiHe nui ngā wheako e kawea mai ana e mātou ki ia kaupapa, me te hītori o te katinga i ngā kaupapa SLAF-Seq neke atu i te 5000 mō ngā rau momo, tae atu ki ngā tipu, ngā kararehe whakangote, ngā manu, ngā pepeke, me ngā rauropi wai.
● Rerenga Mahi Pūtaiao Koiora-ā-WhaiaroI whakawhanakehia e mātou tētahi rerengamahi koiora-pūnaha whakauru mō te SLAF-Seq hei whakarite i te pono me te tika o te putanga whakamutunga.
Ngā Whakatakotoranga Ratonga
| Momo tātaritanga | Tauine taupori e taunakitia ana | Rautaki raupapatanga | |
| Te hohonutanga o te raupapatanga tohu | Tau tohu | ||
| Ngā Mahere Ira | 2 ngā mātua me ngā uri >150 | Ngā Mātua: 20x WGS Te tukunga: 10x | Rahi o te ira: <400 Mb: E taunakitia ana te WGS <1Gb: 100K ngā tohu 1-2Gb:: 200K ngā tohu >2Gb: 300K ngā tohu Ngā tohu mōrahi 500k |
| Ngā Rangahau Hononga Whānui-Ira (GWAS) | ≥200 tauira | 10x | |
| Te Whanaketanga Ira | ≥30 tauira, me te >10 tauira mai i ia rōpū iti | 10x | |
Ngā Whakaritenga Ratonga
Kukū ≥ 5 ng/µL
Te tapeke o te nui ≥ 80 ng
Nanodrop OD260/280=1.6-2.5
Heri agarose: kāore, he iti noa rānei te pirau, te poke rānei
Tukunga Tauira i Manakohia
Ipu: ngongo centrifuge 2 ml
(Mō te nuinga o ngā tauira, kaua e tiakina ki roto i te etanoru)
Tapanga tauira: Me mārama te tapanga o ngā tauira, ā, me ōrite ki te puka mōhiohio tauira i tukuna.
Tukunga: Hukapapa maroke: Me tākai ngā tauira ki roto i ngā putea i te tuatahi, kātahi ka tanumia ki roto i te hukapapa maroke.
Rerenga Mahi Ratonga
Tauira QC
Whakamātautau whakamātautau
Whakamātautau SLAF
Te Whakaritenga o te Whare Pukapuka
Te raupapatanga
Tātari Raraunga
Ngā Ratonga Whai Muri i te Hoko
Kei roto i tā mātou tātaritanga koiora-pūtaiao:
Te QC raraunga me te kutikuti raraunga hei tango i ngā pānui N-whai rawa, ngā pānui urutau, ngā pānui kounga iti rānei.
Ko te tuarua o ngā mana whakahaere kounga o ngā panui ma hei tirotiro i te tohatoha turanga, te kounga raupapa me te aromatawai raraunga, engari hei tirotiro hoki i te whai huatanga o te nakunaku me ngā whakaurunga i whiwhihia.
Kia oti ngā pānui te tirotiro, e rua ngā kōwhiringa:
- Te mahere ki te ira tohutoro
- Kāore he ira tohutoro: te whakarōpūtanga
Whai muri i tēnā, ka whakamahia te tātaritanga o ngā tohu SLAF hei mahi i ētahi karangatanga rerekē hei āwhina i te kimi tohu: SNP, InDel, SNV, karangatanga CV me te tuhipoka.
Te tohatoha o ngā tohu SLAF i runga i ngā chromosome:
Te tohatoha o ngā SNP i runga i ngā chromosome:
Tuhipoka SNP
Jiang S, Li S, Luo J, Wang X me Shi C (2023) Te mahere QTL me te tātaritanga transcriptome o te ihirangi huka i te wā e maoa haere ana ngā hua oPyrus pyrifolia.Mua. Pūtaiao Tipu.14:1137104. doi: 10.3389/fpls.2023.1137104
Li, J., Zhang, Y., Ma, R., Huang, W., Hou, J., Fang, C., & Sun, L. (2022). Mā te tautuhi i te st1 ka kitea he kōwhiringa e uru ana ki te haereere i te āhua o te purapura me te ihirangi hinu i te wā e whakatōngia ana te pīni soya.Te Hautaka Hangarau Koiora Tipu, 20(6), 1110-1121. https://doi.org/10.1111/pbi.13791
Xu, P., Zhang, X., Wang, X.me ētahi atuTe raupapatanga ira me te kanorau ira o te kāpa noa,Cyprinus carpio.Nat Genet 46, 1212–1219 (2014). https://doi.org/10.1038/ng.3098
Zhuang, W., Chen, H., Yang, M.me ētahi atuMā te ira o te pīnati e whakatōkia ana ka mārama ki ngā karyotypes pīnati, te whanaketanga maha-ploid me te whakawhanaungatanga hua.Nat Genet 51, 865–876 (2019). https://doi.org/10.1038/s41588-019-0402-2
| Tau | Pukapuka | IF | Taitara | Ngā tono |
| 2022 | Ngā whakawhitiwhiti kōrero taiao | 17.694 | Te pūtake ira o ngā ira-kiga me ngā ira-kiga o te peony rākau Paeonia ostii | SLAF-GWAS |
| 2015 | Kairangahau Pūtaiao Hou | 7.433 | Ko ngā tapuwae whakawhanaungatanga e mau ana i ngā rohe ira e whai tikanga nui ana ki te ahuwhenua pīni soya | SLAF-GWAS |
| 2022 | Te Pukapuka Rangahau Matatau | 12.822 | Ngā whakaurunga horihori puta noa i te ira o Gossypium barbadense ki roto i te G. hirsutum whakaatu i ngā wāhi pai rawa atu mō te whakapainga i te kounga me te hua o te muka miro i te wā kotahi ngā āhuatanga | SLAF-Ira whanaketanga |
| 2019 | Te tipu ngota | 10.81 | Te Tātaritanga Ira Taupori me te Huihuinga De Novo e Whakakitea ana te Pūtake o te Weedy Te Raihi hei Kēmu Whanaketanga | SLAF-Ira whanaketanga |
| 2019 | Ngā Ira Taiao | 31.616 | Te raupapatanga ira me te kanorau ira o te kāpa noa, Cyprinus carpio | Mahere Hononga SLAF |
| 2014 | Ngā Ira Taiao | 25.455 | Mā te ira o te pīnati kua whakatōkia ka mārama ki ngā karyotypes legume, polyploid te whanaketanga me te whakawhanaungatanga hua. | Mahere Hononga SLAF |
| 2022 | Te Hautaka Hangarau Koiora Tipu | 9.803 | Ko te tautuhi i te ST1 e whakaatu ana i tētahi kōwhiringa e uru ana ki te haereere i te āhua o te purapura me te nui o te hinu i te wā e whakatōngia ana te pīni soya | Te whanaketanga o te Tohu SLAF |
| 2022 | Te Hautaka ā-Ao mō ngā Pūtaiao Ngota | 6.208 | Te Whakawhanaketanga o te Tautuhi me te Tohu DNA mō te Wiiti-Leymus mollis 2Ns (2D) Te Whakakapinga Ira Tangata Disomic | Te whanaketanga o te Tohu SLAF |
| Tau | Pukapuka | IF | Taitara | Ngā tono |
| 2023 | Ngā rohe o te pūtaiao tipu | 6.735 | Te mahere QTL me te tātaritanga transcriptome o te ihirangi huka i te wā e pakari haere ana ngā hua o Pyrus pyrifolia | Mahere Ira |
| 2022 | Te Hautaka Hangarau Koiora Tipu | 8.154 | Ko te tautuhi i te ST1 e whakaatu ana i tētahi kōwhiringa e uru ana ki te haereere i te āhua o te purapura me te ihirangi hinu i te wā e whakatōngia ana te pīni soya.
| Waea SNP |
| 2022 | Ngā rohe o te pūtaiao tipu | 6.623 | Te Mahere Hononga Whānui o ngā Ira o ngā Āhua Hulless Barely i te Taiao Tauraki.
| GWAS |
