Characterization and Development of EST-SSR Markers Derived from Transcriptome of Yellow Catfish

Abstract

Yellow catfish (Pelteobagrus fulvidraco) is one of the most important freshwater fish due to its delicious flesh and high nutritional value. However, lack of sufficient simple sequence repeat (SSR) markers has hampered the progress of genetic selection breeding and molecular research for yellow catfish. To this end, we aimed to develop and characterize polymorphic expressed sequence tag (EST)-SSRs from the 454 pyrosequencing transcriptome of yellow catfish. Totally, 82,794 potential EST-SSR markers were identified and distributed in the coding and non-coding regions. 933) is the most abundant motif type, and AC/GT, AAT/ATT, AAAT/ATTT are respective the most frequent di-, tri-, tetra-nucleotide repeats. We designed primer pairs for all of the identified EST-SSRs and randomly selected 300 of these pairs for further validation. Finally, 263 primer pairs were successfully amplified and 57 primer pairs were found to be consistently polymorphic when four populations of 48 individuals were tested. The number of alleles for the 57 loci ranged from 2 to 17, with an average of 8.23. The observed heterozygosity (HO), expected heterozygosity (HE), polymorphism information content (PIC) and fixation index (FIS) values ranged from 0.04 to 1.00, 0.12 to 0.92, 0.12 to 0.91 and −0.83 to 0.93, OPEN ACCESSMolecules 2014, 19 16403 respectively. These EST-SSR markers generated in this study could greatly facilitate future studies of genetic diversity and molecular breeding in yellow catfish.

Development of EST-SSR markers in the relict tree Davidia involucrata (Davidiaceae) using transcriptome sequencing

“…Among its numerous applications, it has significantly advanced the development of transcriptomederived SSR markers in a number of plant and animal species, including tree peony and yellow catfish (Wu et al, 2014;Zhang et al, 2014). In this study, using the Illumina Hiseq-2000 platform, we were able to analyze transcriptome ESTs, generate 142,950 contigs, and design a higher number of potential SSR primers (12,208) compared to previous studies of D. involucrata (Du et al, 2012;Li et al, 2012b;Tao et al, 2012).…”

Parentage determination of yellow catfish (Pelteobagrus Fulvidraco) based on microsatellite DNA markers

“…Eighteen male and eighteen female breeding fishes (1 year old) were selected from the cross-hybridization offspring between one cultured and four wild populations as previously described (Zhang et al 2014). Eighteen full-sib families (named P1 to P18) were obtained by artificial insemination and had been fed with artemia for 3 weeks.…”

“…The offspring from the 18 crosses, and their parents were genotyped with seven SSRs (H20, H147, H152, H159, H160, H259, H260) developed previously (Zhang et al 2014) and two new SSRs (H273, H276) as shown in Table 1. The primer pairs of the microsatellite markers were designed by using the software Primer Premier 5.0.…”

“…Yellow catfish (Pelteobagrus fulvidraco) is an important commercial aquaculture fish in China due to its delicious and tender meat, high nutritional value and no intermuscular bones besides the spine (Zhang et al 2014). The production of yellow catfish was about 300 thousand tons in 2013, with annual increase between 15 and 20 % in recent years.…”

“…But, there is no report on the selected breeding and parentage identification of yellow catfish at present. As recently, we have characterized and developed a number of polymorphic expressed sequence tag (EST)-SSRs from the 454 pyrosequencing transcriptomes of yellow catfish (Zhang et al 2014). The aim of the current study was to assess the efficiency of these polymorphic SSR markers in parentage assignment and individual identity test in yellow catfish, which has potential applications in our selective breeding programs in this species.…”