Zogulitsa

Evolutionary Genetics

Evolutionary genetics ndi ntchito yotsatizana yomwe idapangidwa kuti ipereke kutanthauzira kwatsatanetsatane pazachisinthiko zazinthu zoperekedwa motengera kusiyanasiyana kwa majini, kuphatikiza ma SNP, InDels, SVs ndi CNVs.Lili ndi zofufuza zonse zofunika pofotokoza za kusintha kwa chisinthiko ndi maonekedwe a anthu, monga chiwerengero cha anthu, kusiyana kwa majini, maubwenzi a phylogeny, ndi zina zotero. Lilinso ndi maphunziro okhudza kutuluka kwa majini, zomwe zimapereka mphamvu kuyerekezera kukula kwa chiwerengero cha anthu, nthawi ya kusiyana.

Lumikizanani nafe

Tsatanetsatane wa Utumiki

Zotsatira za Demo

Nkhani Yophunzira

Ubwino wa Utumiki

Takagi et al.,Magazini ya zomera, 2013

● Kuyerekeza nthawi ya kusiyana kwa mitundu ndi liwiro potengera kusiyanasiyana kwa ma nucleotide ndi ma amino acid.
● Kuwulula za ubale wodalirika wa phylogenetic pakati pa zamoyo zomwe zili ndi mphamvu zochepa za kusinthika kosinthika komanso kusinthika kofanana
● Kupanga maulalo pakati pa kusintha kwa ma genetic ndi ma phenotypes kuti avumbulutse majini okhudzana ndi chikhalidwe
● Kuyerekezera mitundu yosiyanasiyana ya majini, yomwe imasonyeza kuti zamoyo zinachita kusintha kuchokera ku zinthu zina
● Nthawi yosinthira mofulumira
● Zochitika zambiri: BMK yapeza zambiri zokhudzana ndi chiwerengero cha anthu ndi ntchito zokhudzana ndi chisinthiko kwa zaka zoposa 12, zomwe zikukhudza mazana a mitundu, ndi zina zotero.

Mafotokozedwe a Utumiki

Zida:

Nthawi zambiri, timagulu ting'onoting'ono titatu (monga timagulu tating'onoting'ono) tikulimbikitsidwa.Pagulu lililonse liyenera kukhala ndi anthu osachepera 10 (Zomera ＞15, zitha kuchepetsedwa pamitundu yosowa).

Njira yotsatirira:

* WGS itha kugwiritsidwa ntchito ku mitundu yokhala ndi ma genome apamwamba kwambiri, pomwe SLAF-Seq imagwira ntchito ku zamoyo zomwe zili ndi kapena popanda genome, kapena genome yoyipa.

Imagwira pa kukula kwa ma genome	WGS	SLAF-Tag (×10,000)
≤ 500 Mb	10 ×/payekha	WGS ndiyomwe ikulimbikitsidwa
500 Mb - 1 Gb		10
1 GB - 2 GB		20
≥2 Gb		30

Bioinformatics kusanthula

● Kusanthula kwachisinthiko

● Kusesa kosankha

● Kuthamanga kwa majini

● Mbiri ya anthu

● Nthawi yosiyana

Zitsanzo Zofunika ndi Kutumiza

Zitsanzo Zofunika:

Mitundu	Minofu	WGS-NGS	SLAF
Nyama	Matenda a Visceral	0.5-1g	0.5g pa
	Minofu ya minofu
	Magazi a nyamakazi	1.5 ml	1.5 ml
	Magazi a Nkhuku/Nsomba
Chomera	Tsamba Latsopano	1-2g pa	0.5-1g
	Petal / tsinde
	Muzu/Mbewu
Maselo	Selo yokhazikika

gDNA

Kukhazikika
(ndi/ul)

Ndalama

(ug)

OD260/OD280

SLAF

≥35

≥1.6

1.6-2.5

WGS-NGS

≥1

≥0.1

Kuyenda kwa Ntchito Yantchito

Kuyesera kupanga

Kupereka zitsanzo

Kumanga laibulale

Kutsata

Kusanthula deta

Pambuyo pogulitsa ntchito

Zam'mbuyo: Bulked Segregant kusanthula

Ena: Metabolomics

*Zotsatira zawonetsero zomwe zawonetsedwa pano zonse zidachokera ku ma genome omwe adasindikizidwa ndi BMKGENE

1.Kusanthula kwachisinthiko kumakhala ndi zomangamanga za mtengo wa phylogenetic, chiwerengero cha anthu ndi PCA zochokera ku mitundu yosiyanasiyana ya majini.

Mtengo wa Phylogenetic umayimira ubale wa taxonomic ndi chisinthiko pakati pa zamoyo ndi makolo wamba.
PCA ikufuna kuwonetsa kuyandikana pakati pa anthu ochepa.
Kuchuluka kwa anthu kumawonetsa kukhalapo kwa anthu ochepa mosiyanasiyana malinga ndi ma frequency a allele.

3-1 Phylogenetic-mtengo 3-2 PCA 3-3Kamangidwe ka anthu

Chen, ndi.al.,PNAS, 2020

2.Kusesa kosankha

Kusesa kosankha kumatanthawuza njira yomwe malo abwino amasankhidwira ndikuchulukira kwa malo omwe salowerera ndale kumachulukidwa ndipo omwe ali osalumikizidwa amachepetsedwa, zomwe zimapangitsa kuchepa kwa madera.

Kuzindikira kwamtundu wa genome pazigawo zosankhidwa bwino kumakonzedwa powerengera kuchuluka kwa chibadwa cha anthu (π，Fst, Tajima's D) mwa ma SNP onse mkati mwa zenera lotsetsereka (100Kb) pamlingo wina (10 KB).

Mitundu ya Nucleotide (π)
4 Nucleotide-zosiyanasiyana (π)

Tajima D
5Tajima's-D

Fixation index (Fst)

6Fixation-index(Fst)

Wu, ndi.al.,Chomera cha Molecular, 2018

3.Gene Flow

7 Kutuluka kwa majini

Wu, ndi.al.,Chomera cha Molecular, 2018

Mbiri ya 4.Demographic

8Demographic-mbiri

Zhang, ndi.al.,Nature Ecology & Evolution, 2021

5.Divergence nthawi

9 Nthawi yosiyana

Zhang, ndi.al.,Nature Ecology & Evolution, 2021

BMK Case

Mapu osintha ma genomic amapereka zidziwitso pamaziko amtundu wa Spring Chinese kabichi (Brassica rapa ssp. Pekinensis) kusankha.

Lofalitsidwa: Chomera cha Molecular, 2018

Njira yotsatirira:

Kutsatizana: kutsatizana kwakuya: 10 ×

Zotsatira zazikulu

Mu kafukufukuyu, makabichi 194 aku China adakonzedwa kuti atsatidwenso ndikuzama kwapakati pa 10×, zomwe zidapereka 1,208,499 SNPs ndi 416,070 InDels.Kusanthula kwa Phylogenetic pamizere iyi ya 194 kumasonyeza kuti mizere iyi ikhoza kugawidwa mu mitundu itatu ya ecotypes, masika, chilimwe ndi autumn.Kuphatikiza apo, kuchuluka kwa anthu komanso kusanthula kwa PCA kunawonetsa kuti kabichi waku China wa masika adachokera ku kabichi yophukira ku Shandong, China.Izi pambuyo pake zidadziwitsidwa ku Korea ndi Japan, zidawoloka ndi mizere yakumaloko ndipo mitundu ina yotsekera mochedwa idabweretsedwanso ku China ndipo pamapeto pake idakhala kabichi waku China.

Kusanthula kwa ma genome pa makabichi aku China a kasupe ndi makabichi a m'dzinja pakusankhidwa kudavumbulutsa malo 23 a genomic omwe adasankhidwa mwamphamvu, awiri mwa iwo adalumikizana ndi madera owongolera nthawi yotengera mapu a QTL.Madera awiriwa adapezeka kuti ali ndi majini ofunikira omwe amayendetsa maluwa, BrVIN3.1 ndi BrFLC1.Majini awiriwa adatsimikiziridwa kuti akutenga nawo gawo pakusunga nthawi ndi kafukufuku wa transcriptome ndi kuyesa kwa transgenic.

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

Kusanthula kamangidwe ka anthu pa kabichi waku China

Zambiri zamtundu wakusankha kabichi waku China

Buku

Tongbing, et al."Mapu Osiyanasiyana a Genomic Amapereka Chidziwitso pa Maziko a Genetic a Spring Chinese Kabichi (Brassica rapa ssp.pekinensis)Kusankha."Zomera za Molecular,11(2018):1360-1376.