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Development of EST-SSR Markers from Saccharina japonica and the Study of the Genetic Diversity

Author: ZuoFengPing
Tutor: LiuTao
School: Ocean University of China
Course: Biological Engineering
Keywords: Saccharina japonica Microsatellite Association Analysis quantitative traitlocus QTL Trait
CLC: S968.421
Type: Master's thesis
Year: 2013
Downloads: 5
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Abstract


Saccharina japonica has a long history of cultivation and it is an important algae,and it is also a high production marine economic algae. Both the production andcultivation scale of Saccharina japonica in our country are ranked first in the world.Heterogenesis, parthenogenesis and apogamy in the life history of Saccharina japonicamake it a favourable model organism for genetics and algology study. Riching inpolysaccharides and phenolic compounds, possessing numerous chromosomes and hugegenome, makes the progress for studying Saccharina japonica molecular genetics moreslowly and difficult. Microsatellite DNA marker is a codominant marker and is widelyused to breed molecular identification population genetic structure assessment geneticmapping and QTL location. The amount of SSR markers is still very limited now and thisis largely restrained development in Saccharina japonica breeding.This research studied microsatellite repeat motif from our own lab sequencedgenome and transcriptome database of Rongfu Saccharina japonica. We find thatmicrosatellite in Saccharina japonica mainly consists of dinucleotide and trinucleotide.Among these different types of microsatellite the AC motif is dominant dinucleotide andthe TGC motif is dominant trinucleotide. The repeat sequence doesn’t show anypreference about certain repeat motif. We designed1120primers from the Saccharinajaponica genome and transcriptome respectively.There are1020EST-SSR and100DNAgenome SSR primers.We choosed four different Saccharina japonica DNA(PengZPingB vegetable DongF Number2and Ellen Bay) to screen1120primers and obtained146polyphonic primers which129primers from transcriptome and17primers fromgenome SSR. And then we choosed10main population and cultivation lines Ellen BayFujian PingB vegetable Sanhai Gaojia Zaohoucheng DongF Number3PengZNumber2Rongfu and DongF Number2in our country to screen the SSR location from146primers. We obtained52pairs polymorphic primers at last. We totoally amplified134alleles from30individuals, and the mean alleles per locus is2.67(ranging from2to5). The mean PIC is0.33,which ranges from0.064to0.66.Among these10populations,Ellen Bay DongF Number3and DongF Number2possess the highest polymorphic siteratio which are all73.08%. Zaohoucheng owns the lowest polymorphic site ratio which is28.85%.The number of polymorphic site range from15~38.The genetic diversity showedthat the genetic distance is among0.07~0.5879among these10populations. The GeneticDifferentiation Index Fst is0.3134, the Fixation index Fis is-0.43and the Geneflow Nm is0.5477.The following research applied developed SSR marker and used association analysisto study main triat in Saccharina japonica.Among6populations Gaojia Fujian SanhaiDongF Number3Zaohoucheng and Rongfu,284individuals, we use software “Tassel”to analysis linkage relationship.And it is also an effective way for gene location andexploring alleles. We try to use association analysis and single sign analysis to look formarkers which related to quantity trait locus.We checked the polymorphic markers in bigpopulations. Finally, we achieved3QTL that concerned with Saccharina japonica’strait.1QTL that concerned with frond length trait frond width trait thickness traitwave-fold thickness and wet weight trait.1QTL that concerned thickness trait and wetweight trait.1QTL that concerned with frond width trait.

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CLC: > Agricultural Sciences > Aquaculture, fisheries > Aquaculture technology > A variety of seafood, animal and plant breeding > Algae farming > Brown algae > Kelp
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