| Farming of Chinese shrimp (Penaeus chinensis) has largely been dependent on the use of wild caught broodstock. There are concerns that harvesting wild shrimp for aquaculture may deplete local shrimp populations or cause by-catch problems, hi addition, the use of wild shrimp poses a serious risk to the shrimp aquaculture industry because they may be carriers of virulent viruses. The life cycle of Chinese shrimp has been closed, paving the way for the establishment of genetic improvement programs. The use of DNA markers can contribute significantly to the development and implementation of genetic improvement programs. DNA markers can be used to verify pedigrees, screen wild populations to maximise diversity in founder animals and to monitor inbreeding levels in breeding populations. Additionally, markers can be used to characterise QTL, thereby enabling marker-assisted selection to be applied as an additional component to a selective breeding program. There are thus compelling reasons for the development of DNA markers in Chinese shrimp breeding. The AFLP and SAMPL analysis offer an alternative to microsatellites and is a powerful technique for genetic fingerprinting, genome mapping and genetic variability. Genetic variation among generations of Chinese shrimp was estimated with AFLP and SAMPL analysis, a search of sex-specific markers and the development of microsatellite based on SAMPL are also tried in this study.SAMPL analysis was used to evaluate the genetic variation among a wild Chinese shrimp population (Wl) and four generations of Chinese shrimp (Gl, G2, G3, G4), which have been selected for resistance against variable pond conditions and specific pathogens (especially to WSSV). The phylogenetic tree constructed based on UPGMA cluster analysis shows that G1, G2, G3, G4 were divided with Wl firstly, thenG2, G3,. G4 were clustered into one group, finally G3, G4 were clustered. New genetic changes has appeared in the selected shrimp generation, at the same time, nogeneration-specific bands were found. In addition, genetic variation among G2, G3 W1, HG were estimated by AFLP and SAMPL, as shown in the UMPGA dendrogram, G2, G3, G4 were clustered into one group, and then G3, G4 were clustered. Whether the data from AFLP and SAMPL were calculated together or respectively, the results were similar with only a little difference from AFLP.Sex-specific DNA sequences in the male and female genomes of Chinese shrimp were compared by AFLP and SAMPL. A total of 15 AFLP primer pairs and 12 SAMPL primer pairs were tested, which produced 1370 bands totally. No sex-specific bands were found in our study. The lack of such markers in this limited search could be due to: (a) weak correlation between the genotypic and phenotypic sex due to autosomal modifier genes; (b) mixed genotypes in pools as a result of environmental sex determination (c) higher than optimal genetic diversity between the individuals studied. Therefore it is proposed that sex chromosomes are either not present or they are weakly differentiated in the genome of the Chinese shrimp.The main difficulty in development of microsatellite (or Simple Sequence Repeats, SSR) is to screen the specific sequences flanking SSR, a method to screen microsatellite based on SAMPL was tested in the Chinese shrimp. Randomly selective bands (S1K S13> S14> S22> S24) were cloned and sequenced, \61bp, I57bp 147bp, 152bp, 298bp sequences were obtained respectively. No SSR were found inSlK S S S22 apart from the SAMPL primers sequence, on the other hand, a SSR sequence of ( GA) 39 were found in S24, which comprises AFLP primers only. Unsatisfactory results in the search could be due to the repeated sequence in SAMPL primers are not abundant in Chinese shrimp genome. In addition, 5 bands may be too few for the analysis. More work need to be done for the microsatellite screening.
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