Genomics and Applied Biology 2018, Vol.9, No.4, 19-23
19
Research Report Open Access
Comparative Analysis of Genetic Structure of
Nile tilapia
by SSR and AFLP
Xie Xiaoyong
1
, Zhong Jinxiang
2
, Li Sifa
3
1 Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery
Sciences, Guangzhou, 510300, China
2 Ocean and Fishery Technical Extension Center of Guangdong, Guangzhou, 510220, China
3 Shanghai Ocean University, Shanghai, 201306, China
Corresponding author email:
Genomics and Applied Biology, 2018, Vol.9, No.4 doi:
10.5376/gab.2018.09.0004
Received: 08 May, 2018
Accepted: 22 Jun., 2018
Published: 29 Jun., 2018
Copyright © 2018
Xie et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article
:
Xie X.Y., Zhong J.X., and Li S.F., 2018, Comparative analysis of genetic structure of
Nile tilapia
by SSR and AFLP, Genomics and Applied Biology, 9(4):
19-23 (doi:
10.5376/gab.2018.09.0004
)
Abstract
The genetic structure data of
Nile tilapia
from SSR assay were compared with that from AFLP. The ratio of polymorphic
sites percentage from SSR to AFLP averaged 1.683 17, the average ratio of population specific
Fst
indices was 1.249 87, and the
ratio of gene diversity in group averaged 1.676 60, respectively in 5 populations. The ratio of genetic distance among 5 populations
of
Nile tilapia
from SSR to AFLP averaged 3.972 02, whereas the ratio of genetic identity averaged 0.937 92. The results about SSR
and AFLP could provide reference for other similar studies in this field.
Keywords
Nile tilapia
; Genetic structure; SSR; AFLP; Comparison
Background
In recent decades, research on genetic diversity and genetic structure based on DNA was very active. Marker
techniques of RAPD, RFLP, AFLP, SSR, and ISSR were widely used. Especially AFLP and SSR have been
widely used in genetic diversity, genetic structure and other research fields. SSR technique is often referred to as
microsatellite marker, with the characteristics of well-repeated, highly polymorphic. And it has been proved by
many researches that it could identify a large number of alleles in the genome accurately and efficiently (Zhao et
al., 2014). Compared with other markers, it could reveal the overall characteristics of the whole genome (Song et
al., 2009). AFLP is also called amplified fragment length polymorphism, which combined with the accuracy of
RFLP and the high efficiency of PCR. Compared with other molecular markers, it has the incomparable
advantages (Li et al., 2013). And it is considered to be the most abundant polymorphic technology (Zhang et al.,
2013), has relatively obvious advantages (Guan et al., 2013). And AFLP was used to analyze the genetic diversity
of wild naked carp populations in different tributaries by Wang et al. (2015). However, there were relatively few
reports on the differences and relationships between the results of SSR and AFLP. At present, little is known about
the relationship between genetic diversity and genetic structure data based on SSR and AFLP. The comparative
analysis of SSR and AFLP markers is almost the blind spot of current research on molecular marker application.
Team of Professor Li Sifa from Shanghai Ocean University introduced 5000
Oreochromis niloticus
in 1994,
which has undergone genetic improvement for about 10 years (Xie et al., 2007; 2011). In this study, SSR and
AFLP molecular markers were used to compare and analyze the genetic structure data in the breeding process of
Oreochromis niloticus.
In order to deepen the understanding of the selection of molecular markers and the data of
genetic structure analysis, these two molecular marker methods and their degrees were compared.
1 Results and Analysis
1.1 Calculation of genetic diversity ratio within population based on SSR and AFLP
The results of genetic diversity ratio in population were calculated by SSR and AFLP in this study (Table 1).
According to the two methods, the ratio of polymorphic sites in five selected generations was between 1.603 25
and 1.856 16, with an average of 1.683 17. The ratio of
Fst
in
five selected generations was between 1.081 61 and
1.399 44, with an average of 1.249 87. The ratio of gene diversity in the population was between 1.587 65 and
1.758 33, with an average of 1.676 60.
