Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream

Wan, Shiming; Liu, Hong; Zhao, Bowen; Nie, Chun‐Hong; Wang, Weimin; Gao, Zexia

doi:10.1038/srep46509

Cited by 25 publications

(15 citation statements)

References 59 publications

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“…QTLs were detected using composite interval mapping (CIM) algorithm on Windows QTL Cartographer version 2.5 (Statistical Genetics, NC State University). The model and parameters used for CIM analysis were as described (Wan et al, 2017 ). We calculated trait-specific LOD scores using 1000 permutations at genome wide statistical threshold ( P ≤ 0.05).…”

Section: Methodsmentioning

confidence: 99%

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping

et al. 2018

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Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22–0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.

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Section: Methodsmentioning

confidence: 99%

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping

et al. 2018

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“…With the increase of sequencing depth and cost reduction of NGS, RADseq has now been widely applied in construction of linkage maps and QTL fine mapping of genetic traits for commercial fishes. For example, genetic map and growth-related QTLs in turbot (6647 SNPs) [56], blunt snout bream (14,648 SNPs) [57], Yangtze River common carp (7820 SNPs and 295 SSRs) [3], golden pompano (12,358 SNPs) [20],Yellow River common carp (6230 SNPs and 65 SSRs) [1], and P. ussuriensis (7435 SNPs) [9]; genetic map and sex determination QTLs in hāpuku (1575 SNPs) [58], mandarin fish (3283 SNPs) [59], channel catfish (4768 SNPs) [60]; linkage map and disease resistance-related QTLs in Asian seabass (6425 SNPs) [61], Japanese flounder (12,712 SNPs) [16]; genetic map and fatty acid compositions-related QTLs in Asian Seabass (2424 SNPs) [62]. Accumulating achievement has reinforced the consensus among geneticist about the advantage of RADseq technology.…”

Section: Discussion Ddradseq and Snps Genotypingmentioning

confidence: 99%

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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“…Using the interval mapping algorithm, no significant QTLs were associated with BW/ED. A total of 11 QTLs that associated with weight-related traits were detected in 6 LGs, including 1 significant GW QTL (qBL/ HL5-a; Fig. 3d) and 10 significant CW QTLs, with LOD scores ranging from 3.1 to 5.1 ( Table 3).…”

Section: Qtl Mapping Of Significant Economic Traitsmentioning

confidence: 99%

“…Newly developed genotyping methods, such as reduced-representation sequencing, SNP arrays, and re-sequencing, have allowed for the discovery and simultaneous scoring of thousands of SNP markers from a single sequencing run for dozens of individuals. These techniques have already been applied in some fish species, such as Ictalurus punctatus [2], Siniperca chuatsi [3], Scophthalmus maximus [4], Paralichthys olivaceus [5], and Megalobrama amblycephala [6]. In addition, significant QTLs for weight, gender and disease resistance in these fish species have been detected.…”

Section: Introductionmentioning

confidence: 99%

A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

Zhang

et al. 2020

BMC Genomics

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Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

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Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream

Cited by 25 publications

References 59 publications

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping

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 SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

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