Paretage Assigment Gene Expressio Of Growth Related Gene In Snakehead Murrel, Channa Striata
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Date
2020-03
Authors
Fong, Pooi Har
Journal Title
Journal ISSN
Volume Title
Publisher
Universiti Sains Malaysia
Abstract
Haruan (Channa striata) is a fresh water fish known for its medicinal value
and is an important source of protein in Southeast Asia. The demand for this fish is
still high; hence this species has good market potential for aquaculture industry in
Malaysia. Furthermore, snakehead farming is not popular and there is yet a selective
breeding as well as systematic hatchery programmes developed in Malaysia. Hence,
the first objective of this study was to investigate the feasibility of using the existing
microsatellite markers in genotyping C. striata for parentage identification and
pedigree management. The next objective is to establish a reference for
transcriptome library for gene expression study. With the transcriptome library,
differentially expressed genes in response of fast and slow growth could be identified
and applied in snakehead murrel selective breeding programmes. Accurate parentage
identification for pedigree management is integral to a successful systematic
hatchery programme especially in aquaculture industry to prevent inbreeding
depression. Hence, the feasibility of seven pairs of microsatellite markers
characterized previously for a population genetics study of C. striata was evaluated
in this study. A total of 211 offspring from 22 brood stocks kept in six separated
tanks were genotyped according to tanks and were later assigned back to these 22
brood stocks using five different parentage assignment software. Among these
software, Colony was the best software to successfully allocate the offspring back to
their parents. In addition, the results of the parentage allocations revealed that mating
behaviour of this species is polygamous and polyandry. De novo transcriptome library of C. striata was successfully constructed with seven high qualities of RNAseq
data and yielded 1045123 contigs after transcript assembly and 155973 were
annotated with at least one data database hits. There were 33556 transcripts unique to
UniProt IDs, 5313 transcripts unique to Pfam domains and 14727 unique transcripts
to Gene Ontology terms. A sample from each group was excluded from the
differential expression analysis due to low correlation to other biological replicates in
their respective groups in replicates quality assessment. In the differential gene
expression analysis with two biological replicates in each group, there were a total of
5113 transcripts were significant differentially expressed. There were 1749
transcripts were expressed in both fast and slow growing groups while 550 and 1199
were up-regulated in slow and fast growing group respectively. A total of two
transcripts of the down-regulated and three transcripts of the up-regulated in the slow
growing groups were pick randomly to validate the RNA-seq results using qPCR.
The 18S gene was used as the housekeeping gene as well as the reference gene. The
validation results were congruent with the RNA-seq results. The five selected genes
were then used as the candidate of biomarkers to screen for fast growing C. striata
fingerlings. The results of the fingerlings physical measurements and expression
levels of these five candidate biomarkers showed that LIFR, HPHL1 and TPM2 were
potential markers for screening of fast growing fingerlings for C. striata.
Description
Keywords
Natural history