Construction of the first high-density genetic linkage map of pikeperch (Sander lucioperca) using specific length amplified fragment (SLAF) sequencing and QTL analysis of growth-related traits

Guo, Jian; Li, Caijuan; Teng, Teng; Shen, Fanfan; Wang, Yunfeng; Pan, Chenglong; Ling, Qufei

doi:10.1016/j.aquaculture.2018.07.047

Cited by 27 publications

(17 citation statements)

References 45 publications

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“…LGs ( Table 5), indicating that growth-related traits are controlled by multiple QTL loci or regions in S. argus. Similar results were found in some other fish species and multiple QTLs were identified for one trait, e.g., 10 QTLs for body weight were detected on two LGs of P. ussuriensis [9], 14 QTLs for body height of T. blochii were were detected on two LGs [20], 4 QTLs for head length of common carp were detected on four LGs [3], and 5 significant QTLs for body length were detected on three LGs in Sander lucioperca [63]. These findings suggest that the growth traits are regulated by numerous loci or genes in fish, a few of these loci may have major effects and the remaining loci may possess minor effects.…”

Section: Qtl Mapping and Candidate Genes For Growth Traitssupporting

confidence: 85%

“…In the present study for S. argus, ddRADseq-based SNPs discovery in a F1 full-sib family was performed for the first time. A total of 1753.7 M pair-end reads and 293,309 original RAD markers were generated, including 88,789 polymorphic SNP loci with a polymorphism ratio of 30.27%, which was higher than that found in common carp (21.1%) [12] and pikeperch (14.63%) [63]. According to our preliminary population genetic analysis (unpublished data), we have inferred that the higher polymorphism rate is due to a high genetic diversity of S. argus.…”

Section: Discussion Ddradseq and Snps Genotypingmentioning

confidence: 95%

“…4), reflecting that these genomic regions may have key roles in growth regulation. Multifactorial QTLs for growth traits have also been detected in common carp [1,3], L. calcarifer [18], S. chuatsi [59], S. lucioperca [63], bighead carp [66] and so on, implicating the pleiotropic effect of a QTL for multiple traits. Based on critical factors that control various traits through diverse metabolic pathways, pleiotropy may contribute to multifactorial QTLs [4].…”

Section: Qtl Mapping and Candidate Genes For Growth Traitsmentioning

confidence: 99%

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ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

et al. 2020

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Background: Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. Results: Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. Conclusions: The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growthrelated traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.

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Section: Qtl Mapping and Candidate Genes For Growth Traitssupporting

confidence: 85%

Section: Discussion Ddradseq and Snps Genotypingmentioning

confidence: 95%

Section: Qtl Mapping and Candidate Genes For Growth Traitsmentioning

confidence: 99%

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ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

et al. 2020

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“…Most of the early genetic linkage maps were constructed by using labor-intensive or dominant markers such as RFLP (restriction fragment length polymorphism), AFLP (amplified fragment length polymorphism), RAPD (random amplified polymorphic DNA), and SSR (simple sequence repeats) (Cheng, et al, 2010; Yue, 2014; Tong and Sun, 2015). Traditional genetic marker systems have played important roles in genetic linkage map construction; however, unsatisfied marker density, dominant expression, and not repeatable in different maps have limited their ability of fine mapping as well as the identification of QTLs with important genetic traits (Guo et al, 2018; Zhang et al, 2019). SNP is the most abundant and stable form of genetic variation with a high polymorphism in most genomes (Leonforte et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

2019

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Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.

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“…Comparatively, linkage maps have provided a framework for genomic and genetic studies, such as molecular marker-assisted selection (MAS) for quality [27] and quantitative traits (QTL), as well as chromosomal frameworks for genome scaffolds. The genetic maps for many aquaculture species have been published [14,15,[28][29][30][31]. A high-density genetic linkage map can provide a more precise localization of the loci related to target traits and mount more genomic contigs.…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

et al. 2020

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Background: Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture. Results: In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents. Conclusion: A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

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Construction of the first high-density genetic linkage map of pikeperch (Sander lucioperca) using specific length amplified fragment (SLAF) sequencing and QTL analysis of growth-related traits

Cited by 27 publications

References 45 publications

ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

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