Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

Wong, Li Lian; Razali, Siti Aisyah; Deris, Zulaikha Mat; Danish-Daniel, Muhd; Tan, Min Pau; Nor, Siti Azizah Mohd; Ma, Hongyu; Wang, Min; Liang, Yantao; Asaduzzaman, Md; Sung, Yeong Yik; Liu, Zhanjiang; Sorgeloos, Patrick; Peer, Yves Van de; Afiqah‐Aleng, Nor

doi:10.1016/j.aquaculture.2021.737633

Cited by 22 publications

(14 citation statements)

References 405 publications

(415 reference statements)

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“…It is possible that genetic decline, genetic drift, and inbreeding result in low genetic variability in farmed stocks ( Jorge et al, 2018 ). Additionally, the domesticated stocks are subjected to artificial selection in a selective breeding program, which may show reduced effective population size, thus leading to a decline in genetic diversity ( Wong et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Duan

Guan

et al. 2022

Front. Genet.

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P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise FST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.

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Section: Discussionmentioning

confidence: 99%

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Duan

Guan

et al. 2022

Front. Genet.

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“…Molecular markers are DNA segments associated with specific genes or traits, enabling researchers to identify and select individuals with desirable characteristics and differentiate between various families, populations, and species (Hsu et al, 2011; Hsu & Gwo, 2017; Hsu, Huang, Lee, et al, 2020; Hsu, Huang, Lin, et al, 2020). They are now widely used in fisheries and aquaculture research (Hsu et al, 2022; Wong et al, 2022; You et al, 2020). Molecular markers can be employed to track the inheritance of traits within populations, providing valuable information for breeding programs (Chen et al, 2022; Chu et al, 2021; Hsu et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Molecular markers can be employed to track the inheritance of traits within populations, providing valuable information for breeding programs (Chen et al, 2022; Chu et al, 2021; Hsu et al, 2021). The successful application of molecular markers in various aquaculture species has facilitated the development of improved strains with enhanced growth rates and other desirable traits (You et al, 2020; Wong et al, 2022). High‐throughput next‐generation sequencing (NGS) technologies have greatly advanced molecular marker‐assisted breeding by enabling the rapid identification and genotyping of numerous molecular markers.…”

Section: Introductionmentioning

confidence: 99%

Utilizing ISSRseq genotyping to assist growth selection in tomato grouper (Cephalopholis sonnerati) without broodstock information

Hsu,

Chu,

Gong

et al. 2023

J World Aquaculture Soc

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Growth selection in fish is essential for aquaculture; however, long generation times and artificial breeding limitations present challenges for breeding endeavors. The tomato grouper (Cephalopholis sonnerati) is an emerging aquaculture species with a generation cycle of at least 5 to 10 years. Mixed culture of broodstocks and natural mating are commonly employed in hatcheries. To expedite the selection process for tomato grouper, we utilized ISSRseq technology for assisted future growth selection. After 6 months of rearing, we selected 48 individuals, including 24 fast‐growing and 24 slow‐growing individuals (representing the top and bottom 10% of samples). These samples produced 932 SNPs. Although specific broodstock pairing information is unavailable, our results suggest that these fry likely originated from multiple broodstock exhibiting considerable diversity. Further analysis of genetic relationships among individuals revealed three main clades. One clade contained a higher proportion of faster‐growing individuals (80%), while another featured a lower proportion of rapidly growing individuals (28.6%). Through the relatedness network and further exclusion of individuals, the faster‐growth clade comprised 92.3% of fast‐growing individuals. The faster‐growth clade is appropriate for further development into a high‐growth strain. Our findings demonstrate that molecular markers can advance population selective breeding to family selection in aquaculture breeding research.

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“…Compared with second-generation sequencing (SGS), TGS provides longer read lengths, which makes it very suitable for unsolved problems in genomic, transcriptome and epigenetic research [ 8 ]. PacBio® SMRT sequencing generates high fidelity (HiFi) long reads with lengths up to 25 kb with high read accuracy (>99.9%) [ 9 , 10 ]. These long-read data can cover different exon boundaries to obtain full-length transcripts [ 9 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…The type I receptor is defined by the cytoplasmic GS box and a serine kinase that activates the cellular smad1 and smad5 signaling proteins. The type II receptor activates a type I receptor serine kinase by transphosphorylating the GS box segment [ 10 ]. The type II receptor phosphorylates the type I receptor on a Gly/Ser motif, called the GS region, that lies on the amino-terminal side of the kinase domain [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome and analysis of bmp-related genes in Platypharodon extremus

Wu¹,

Gong²,

Chen³

et al. 2022

Heliyon

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Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

Cited by 22 publications

References 405 publications

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Utilizing ISSRseq genotyping to assist growth selection in tomato grouper (Cephalopholis sonnerati) without broodstock information

Full-length transcriptome and analysis of bmp-related genes in Platypharodon extremus

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