Ka Hoʻonohonoho ʻĀpana Hoʻonui ʻia o ka Locus Kūikawā (SLAF-Seq)
Kaʻina hana
Loaʻa i ka lawelawe kekahi hoʻolālā mua ma silico e hōʻoia i ke koho enzyme kūpono loa ma ka hoʻomākaukau ʻana o ka waihona puke.
Papahana ʻenehana
Nā Hiʻohiʻona Lawelawe
● Ka hoʻonohonoho ʻana ma NovaSeq me PE150.
● Hoʻomākaukau ʻana i ka waihona puke me ka pākā pālua, e hiki ai ke hōʻuluʻulu ʻia ma luna o 1000 mau laʻana.
● Kūʻokoʻa mai ka genome kuhikuhi:
Me ka genome kuhikuhi: ʻike ʻana o SNP a me InDel
Me ka ʻole o ka genome kuhikuhi: ka hoʻohuihui laʻana a me ka ʻike ʻana o SNP
● I loko o kei loko o ka silicoUa nānā ʻia nā hui pū ʻana o nā enzyme hoʻopulapula he nui ma ke kahua hoʻolālā ma mua e ʻike i nā mea e hoʻopuka ai i kahi hoʻolaha like o nā lepili SLAF ma ke genome.
● I ka wā o ka hoʻokolohua mua, ua hoʻāʻo ʻia ʻekolu mau hui enzyme i loko o 3 mau laʻana e hana i 9 mau waihona puke SLAF, a hoʻohana ʻia kēia ʻike e koho i ka hui enzyme restriction kūpono no ka papahana.
Nā Pōmaikaʻi o ka Lawelawe
●Ka ʻIke ʻana i ka Māka Genetic KiʻekiʻeHoʻohui mākou i kahi ʻōnaehana barcode pālua kiʻekiʻe e ʻae ana i ka hoʻonohonoho like ʻana o nā heluna nui, a me ka hoʻonui ʻana i ka locus-specific e hoʻonui ana i ka pono, e hōʻoia ana e hoʻokō nā helu tag i nā koi like ʻole o nā nīnau noiʻi like ʻole.
● Hilinaʻi Haʻahaʻa ma ka GenomeHiki ke hoʻopili ʻia i nā ʻano me a i ʻole me ka ʻole o kahi genome kuhikuhi.
●Hoʻolālā Papahana MaʻalahiHiki ke koho ʻia ka hoʻoheheʻe ʻana o ka enzyme hoʻokahi, enzyme pālua, enzyme multi-enzyme, a me nā ʻano enzyme like ʻole e hoʻokō i nā pahuhopu noiʻi like ʻole a i ʻole nā ʻano like ʻole.
● Ka Hana Kiʻekiʻe ma ka Hoʻoheheʻe Enzymatic: Ke alakaʻi ʻana o kahii loko o ka silicoʻO ka hoʻolālā mua a me ka hoʻokolohua mua e hōʻoiaʻiʻo i ka hoʻolālā kūpono me ka hoʻolaha like ʻana o nā lepili SLAF ma ka chromosome (1 lepili SLAF / 4Kb) a me ka hoʻemi ʻia ʻana o ke kaʻina hana hou (<5%).
●Ka ʻIke LoaLawe mai mākou i ka nui o ka ʻike i kēlā me kēia papahana, me kahi moʻolelo o ka pani ʻana ma mua o 5000 mau papahana SLAF-Seq ma nā haneli o nā ʻano, me nā mea kanu, nā mammals, nā manu, nā pepeke, a me nā meaola wai.
● Kahe Hana Bioinformatic i hoʻomohala ponoʻī ʻiaUa hoʻomohala mākou i kahi kaʻina hana bioinformatic i hoʻohui ʻia no SLAF-Seq e hōʻoia i ka hilinaʻi a me ka pololei o ka hopena hope loa.
Nā Kikoʻī Hana
| ʻAno loiloi | Ka nui o ka heluna kanaka i manaʻo ʻia | Hoʻolālā hoʻonohonoho | |
| Ka hohonu o ke kaʻina hana lepili | Helu lepili | ||
| Nā Palapala ʻĀina Genetic | 2 mau mākua a me nā keiki ma mua o 150 | Nā Mākua: 20x WGS Hoʻokuʻu ʻana: 10x | Ka nui o ka genome: <400 Mb: Paipai ʻia ʻo WGS <1Gb: 100K mau lepili 1-2Gb:: 200K mau lepili >2Gb: 300K mau lepili Nā lepili 500k kiʻekiʻe loa |
| Nā Haʻawina Hui Pū ʻIa Genome (GWAS) | ≥200 mau laʻana | 10x | |
| Ka Hoʻomohala ʻana o nā Kino | ≥30 mau laʻana, me >10 mau laʻana mai kēlā me kēia hui liʻiliʻi | 10x | |
Nā Koina Lawelawe
Ka nui o ka hui ʻana ≥ 5 ng/µL
Huina nui ≥ 80 ng
ʻO ka gel Agarose: ʻaʻohe a i ʻole ka palena o ka hōʻino a i ʻole ka haumia
Hoʻouna Laʻana i Manaʻo ʻia
Pahu: ʻōmole centrifuge 2 ml
(No ka hapa nui o nā laʻana, ke paipai nei mākou ʻaʻole e mālama i loko o ka ethanol)
Ka lepili laʻana: Pono e lepili maopopo ʻia nā laʻana a like me ka palapala ʻike laʻana i waiho ʻia.
Hoʻouna: Hau maloʻo: Pono e hoʻopaʻa mua ʻia nā laʻana i loko o nā ʻeke a kanu ʻia i loko o ka hau maloʻo.
Kaʻina Hana Lawelawe
QC Laʻana
Hoʻokolohua hoʻāʻo
Hoʻokolohua SLAF
Hoʻomākaukau Hale Waihona Puke
Ka hoʻonohonoho ʻana
Ka Nānā ʻIkepili
Nā lawelawe ma hope o ke kūʻai aku
ʻO kā mākou loiloi bioinformatical e komo pū ana me kēia:
ʻIkepili QC a me ka ʻoki ʻana i ka ʻikepili e wehe i nā heluhelu N-waiwai, nā heluhelu adapter a i ʻole nā heluhelu haʻahaʻa.
ʻO ka lua o ka mana hoʻomalu maikaʻi o ka heluhelu maʻemaʻe e nānā i ka hoʻolaha kumu, ka maikaʻi o ke kaʻina a me ka loiloi ʻikepili, akā e nānā pū i ka pono o ka hoʻoheheʻe ʻana a me nā mea i hoʻokomo ʻia.
Ke nānā ʻia nā heluhelu, aia ʻelua mau koho:
- Ke palapala ʻāina ʻana i ka genome kuhikuhi
- Me ka ʻole o kahi genome kuhikuhi: clustering
Ma hope o ia mea, hoʻohana ʻia ka nānā ʻana o nā lepili SLAF e hana i kekahi mau kāhea ʻano like ʻole e kōkua i ka ʻike ʻana o ka māka: SNP, InDel, SNV, kāhea CV a me ka annotation.
Ka hoʻolaha ʻana o nā lepili SLAF ma nā chromosomes:
Ka hoʻolaha ʻana o nā SNP ma nā chromosomes:
Palapala hōʻike SNP
ʻO Jiang S, Li S, Luo J, Wang X lāua ʻo Shi C (2023) QTL mapping a me ka transcriptome analysis o ka nui o ke kō i ka wā o ka pala ʻana o ka huaʻO Pyrus pyrifolia.Mua. ʻIke Mea kanu.14:1137104. doi: 10.3389/fpls.2023.1137104
Li, J., Zhang, Y., Ma, R., Huang, W., Hou, J., Fang, C., & Sun, L. (2022). Hōʻike ka ʻike ʻana o st1 i kahi koho e pili ana i ka hitchhiking o ke ʻano o ka hua a me ka nui o ka ʻaila i ka wā o ka hoʻoulu ʻana i ka soybean.Ka Nūpepa ʻenehana Mea kanu, 20(6), 1110-1121. https://doi.org/10.1111/pbi.13791
Xu, P., Zhang, X., Wang, X.a me nā mea ʻē aʻe.Ka moʻo genome a me ke ʻano like ʻole o ka genetic o ke carp maʻamau,ʻO Cyprinus carpio.ʻO Nat Genet 46, 1212–1219 (2014). https://doi.org/10.1038/ng.3098
Zhuang, W., Chen, H., Yang, M.a me nā mea ʻē aʻe.Hāʻawi ka genome o ka pīnati i mahi ʻia i ka ʻike i nā karyotypes legume, ka ulu ʻana o ka polyploid a me ka hoʻomoe ʻana i nā mea kanu.ʻO Nat Genet 51, 865–876 (2019). https://doi.org/10.1038/s41588-019-0402-2
| Makahiki | Puke Pai | IF | Poʻo Inoa | Nā noi |
| 2022 | Nā kamaʻilio kūlohelohe | 17.694 | Ke kumu genomic o nā giga-chromosomes a me ka giga-genome o ka peony lāʻau Paeonia ʻōstii | SLAF-GWAS |
| 2015 | Kauka Lapaʻau Hou | 7.433 | Hoʻopaʻa nā kapuaʻi home i nā wahi genomic o ke koʻikoʻi agronomic i loko nā soya | SLAF-GWAS |
| 2022 | Ka Nūpepa o ka Noiʻi Kiʻekiʻe | 12.822 | Nā hoʻokomo hana ʻia o Gossypium barbadense ma ka genome i loko o G. hirsutum hōʻike i nā loci kiʻekiʻe no ka hoʻomaikaʻi like ʻana o ka maikaʻi o ka fiber pulupulu a me ka hua nā ʻano | SLAF-Hoʻomohala ʻana o ka genetics |
| 2019 | Mea kanu Molekala | 10.81 | Hōʻike ka loiloi genomic heluna kanaka a me ka ʻAhahui ʻo De Novo i ke kumu o ka Weedy ʻO ka laiki ma ke ʻano he pāʻani hoʻomohala | SLAF-Hoʻomohala ʻana o ka genetics |
| 2019 | ʻIkepili Kūlohelohe | 31.616 | Ka moʻo genome a me ke ʻano like ʻole o ka genetic o ka carp maʻamau, ʻo Cyprinus carpio | Palapala ʻāina SLAF-Linkage |
| 2014 | ʻIkepili Kūlohelohe | 25.455 | Hāʻawi ka genome o ka pīnati i mahi ʻia i ka ʻike i nā karyotypes legume, polyploid ka ulu ʻana a me ka hoʻoulu ʻana i nā mea kanu. | Palapala ʻāina SLAF-Linkage |
| 2022 | Ka Nūpepa ʻenehana Mea kanu | 9.803 | Hōʻike ka ʻike ʻana o ST1 i kahi koho e pili ana i ka hitchhiking o ke ʻano o ka hua a me ka nui o ka aila i ka wā o ka hoʻoulu ʻana i ka soybean | Ka hoʻomohala ʻana o ka SLAF-Marker |
| 2022 | Ka Nūpepa Honua o nā ʻEpekema Molekala | 6.208 | Ka Hoʻomohala ʻana i ka ʻIke a me ka DNA Marker no kahi Wheat-Leymus mollis 2Ns (2D) Hoʻololi ʻana i ka Chromosome Disomic | Ka hoʻomohala ʻana o ka SLAF-Marker |
| Makahiki | Puke Pai | IF | Poʻo Inoa | Nā noi |
| 2023 | Nā palena i ka ʻepekema mea kanu | 6.735 | ʻO ka palapala ʻāina QTL a me ka nānā ʻana o ka transcriptome o ka nui o ke kō i ka wā o ka pala ʻana o ka hua o Pyrus pyrifolia | Palapala ʻĀina Hoʻoilina |
| 2022 | Ka Nūpepa ʻenehana Mea kanu | 8.154 | Hōʻike ka ʻike ʻana o ST1 i kahi koho e pili ana i ka hitchhiking o ke ʻano o ka hua a me ka ʻike o ka ʻaila i ka wā o ka hoʻoulu ʻana i ka soybean
| Kāhea ʻana o SNP |
| 2022 | Nā palena i ka ʻepekema mea kanu | 6.623 | Palapala ʻĀina Hui Pū ʻIa o nā ʻAno Hulless Barely ma ke Kaiapuni Maloʻo.
| GWAS |
