Imikhiqizo

I-Evolutionary Genetics

I-Evolutionary genetics iyisevisi egcwele yokulandelana eyenzelwe ukuhlinzeka ngencazelo ebanzi yolwazi lokuziphendukela kwemvelo lwezinto ezinikeziwe ngokusekelwe ezinhlobonhlobo zofuzo, okuhlanganisa ama-SNP, ama-InDels, ama-SV nama-CNV.Ihlinzeka ngakho konke ukuhlaziya okuyisisekelo okudingekayo ekuchazeni izinguquko zokuziphendukela kwemvelo kanye nezici zofuzo zabantu, njengesakhiwo sabantu, ukuhlukahluka kofuzo, ubudlelwano be-phylogeny, njll. Futhi iqukethe izifundo ngokugeleza kwezakhi zofuzo, okunika amandla ukulinganiswa kobukhulu besibalo esisebenzayo, isikhathi sokuhlukana.

Xhumana nathi

Imininingwane Yesevisi

Imiphumela yedemo

Ucwaningo lwesigameko

Izinzuzo Zesevisi

1Izakhi zofuzo zokuziphendukela kwemvelo

Takagi et al.,Ijenali yezitshalo, 2013

● Ukulinganisa isikhathi sokuhlukana kwezinhlobo zezilwane nesivinini ngokusekelwe ezinhlobonhlobo zeleveli yama-nucleotide nama-amino acid.
● Ukwembulwa kobudlelwane obuthembeke kakhulu be-phylogenetic phakathi kwezinhlobo zezilwane ezinethonya elincishisiwe lokuguquguquka okuguquguqukayo kanye nokuziphendukela kwemvelo okufanayo
● Ukwakha izixhumanisi phakathi kwezinguquko zofuzo nama-phenotypes ukuze kwambulwe izakhi zofuzo ezihlobene nezici
● Ukulinganisa ukuhlukahluka kwezakhi zofuzo, okubonisa amandla okuziphendukela kwemvelo kwezinhlobo zezinto eziphilayo
● Isikhathi sokushintsha esisheshayo
● Okuhlangenwe nakho okubanzi: I-BMK iqongelele ulwazi olukhulu ngenani labantu kanye namaphrojekthi ahlobene nokuziphendukela kwemvelo iminyaka engaphezu kwengu-12, ehlanganisa amakhulu ezinhlobo zezilwane, njll. futhi yanikela kumaphrojekthi wezinga eliphezulu angaphezu kuka-80 ashicilelwe ku-Nature Communications, Izitshalo Zemolekyuli, I-Plant Biotechnology Journal, njll.

Imininingwane Yesevisi

Izinto zokwakha:

Ngokujwayelekile, kunconywa okungenani izigaba ezintathu ezincane (isib. izinhlobonhlobo noma izinhlobo).Inani elincane ngalinye kufanele libe nabantu abangekho ngaphansi kuka-10 (Izitshalo ＞15, zingancishiselwa izinhlobo ezingavamile).

Isu lokulandelanisa:

* I-WGS ingaqashwa ezinhlotsheni ezine-genome yereferensi yekhwalithi ephezulu, kuyilapho i-SLAF-Seq isebenza ezinhlotsheni ezine-genome eyisithenjwa noma ezingenayo, noma i-genome eyireferensi yekhwalithi embi.

Isebenza kusayizi wofuzo	WGS	Amathegi e-SLAF (×10,000)
≤ 500 Mb	10×/ngamunye	I-WGS inconywa kakhulu
500 Mb - 1 Gb		10
1 Gb - 2 Gb		20
≥2 Gb		30

I-Bioinformatics ihlaziya

● Ukuhlaziya kokuziphendukela kwemvelo

● Ukushanela okukhethekile

● Ukugeleza kofuzo

● Umlando wezibalo zabantu

● Isikhathi sokuhlukana

Izidingo Zesampula Nokulethwa

Izimfuneko zesampula:

Izinhlobo	Izicubu	I-WGS-NGS	I-SLAF
Isilwane	Izicubu ze-Visceral	0.5~1g	0.5g
	Izicubu zemisipha
	Igazi lezilwane ezincelisayo	1.5mL	1.5mL
	Igazi lezinkukhu/Inhlanzi
Isitshalo	Iqabunga Elisha	1~2g	0.5~1g
	I-Petal/Isiqu
	Impande/Imbewu
Amaseli	Iseli Cultured

gDNA

Ukugxila
(ng/ul)

Inani

(ug)

OD260/OD280

I-SLAF

≥35

≥1.6

1.6-2.5

I-WGS-NGS

≥1

≥0.1

Ukugeleza Komsebenzi Wesevisi

Idizayini yokuhlola

Ukulethwa kwesampula

Ukwakhiwa komtapo wolwazi

Ukulandelanisa

Ukuhlaziywa kwedatha

Amasevisi angemuva kokuthengisa

Okwedlule: Ukuhlaziywa kwe-Bulked Segregant

Olandelayo: I-Metabolomics

*Imiphumela yedemo eboniswe lapha yonke ivela kuzakhi zofuzo ezishicilelwe nge-BMKGENE

Ukuhlaziywa kwe-1.Evolution kuqukethe ukwakhiwa kwesihlahla se-phylogenetic, isakhiwo sabantu kanye ne-PCA ngokusekelwe ezinhlobonhlobo zofuzo.

Isihlahla se-Phylogenetic simele ubudlelwano be-taxonomic kanye nokuziphendukela kwemvelo phakathi kwezinhlobo ezinokhokho oyedwa.
I-PCA ihlose ukubona ngeso lengqondo ukusondelana phakathi kwabantu abancane.
Ukwakheka kwenani labantu kubonisa ukuba khona kwenani labantu abancane abahlukene ngokofuzo ngokuya ngamaza e-allele.

3-1Isihlahla se-Phylogenetic 3-2PCA 3-3Isakhiwo-sabantu

Chen, njll.al.,I-PNAS, 2020

2.Ukushanela okukhethiwe

Ukushanela okukhethiwe kusho inqubo lapho kukhethwa khona isayithi elinenzuzo futhi amaza amasayithi axhumene angathathi hlangothi ayanda futhi lawo amasayithi angaxhunywanga ancipha, okuholela ekuncishisweni kwesifunda.

Ukutholwa okubanzi kwe-genome ezindaweni ezishanelayo ezikhethiwe kucubungula ngokubala inkomba yofuzo labantu (π，Fst, Tajima's D) yawo wonke ama-SNP ngaphakathi kwewindi elislayidayo (100 Kb) esinyathelweni esithile (10 KB).

Ukuhlukahluka kwe-Nucleotide (π)
I-4Nucleotide-diversity(π)

UTajima D
5Tajima's-D

Inkomba yokulungisa(Fst)

I-6Fixation-index(Fst)

Wu, et.al.,Isitshalo samangqamuzana, 2018

3.Ukugeleza kweGene

7Ukugeleza kofuzo

Wu, et.al.,Isitshalo samangqamuzana, 2018

4.Umlando wezibalo zabantu

8Umlando wabantu

Zhang, njll.al.,I-Nature Ecology & Evolution, 2021

5.Isikhathi sokuhlukana

9Isikhathi sokuhlukana

Zhang, njll.al.,I-Nature Ecology & Evolution, 2021

Icala le-BMK

Imephu yokuhlukahluka kofuzo inikeza imininingwane ngesisekelo sofuzo se-Spring Chinese Cabbage(Brassica rapa ssp. Pekinensis)

Kushicilelwe: Isitshalo samangqamuzana, 2018

Isu lokulandelanisa:

Ukulandelanisa: ukujula kokulandelana: 10×

Imiphumela esemqoka

Kulolu cwaningo, amaklabishi aseShayina angu-194 acutshungulwa ukuze aphinde alandelane ngokujula okuphakathi kuka-10×, okukhiqize ama-SNP angu-1,208,499 kanye nama-InDels angu-416,070.Ukuhlaziywa kwe-Phylogenetic kule migqa engu-194 kuboniswe ukuthi le migqa ingahlukaniswa ngezinhlobo ezintathu ze-ecotypes, intwasahlobo, ihlobo kanye nekwindla.Ukwengeza, ukwakheka kwenani labantu kanye nokuhlaziywa kwe-PCA kubonise ukuthi iklabishi laseShayina lasentwasahlobo lavela ekwindla yeklabishi eShandong, eChina.Lezi zabe zethulwa e-Korea nase-Japan, zaphambana nemigqa yasendaweni futhi ezinye izinhlobo zazo ezifakwa sekwephuzile zalethwa emuva e-China futhi ekugcineni zaba iklabishi lase-Spring Chinese.

Ukuskena okubanzi kwe-genome kumaklabishi asentwasahlobo aseShayina kanye neklabishi yasekwindla ekukhethweni kwembula izindawo ezingama-23 ze-genomic eziye zakhethwa ngokuqinile, ezimbili zazo zigqitshwe ngesifunda sokulawula isikhathi sokubhowula okusekelwe kumephu ye-QTL.Lezi zifunda ezimbili zitholwe zinezakhi zofuzo ezibalulekile ezilawula ukuqhakaza, i-BrVIN3.1 kanye ne-BrFLC1.Lezi zakhi zofuzo ezimbili zaqinisekiswa futhi ukuthi ziyabandakanyeka ekuhlanganiseni isikhathi ngocwaningo lwe-transcriptome kanye nokuhlolwa kwe-transgenic.

I-PB-full-length-RNA-Sequencing-case-study

Ukuhlaziywa kwesakhiwo sabantu kumaklabishi aseShayina

I-PB-full-length-RNA-alternative-splicing

Ulwazi lwezofuzo ekukhethweni kweklabishi laseShayina

Ireferensi

Tongbing, et al."Imephu Yokuhlukahluka Kwe-Genomic Ihlinzeka Ngemininingwane Ngesisekelo Sofuzo Se-Spring Chinese Cabbage (Brassica rapa ssp.pekinensis)Selection."Izitshalo zamangqamuzana,11(2018):1360-1376.