Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in tiger puffer Takifugu rubripes

Liu, Zhifeng; Wang, Xinan; Ma, Aijun; Zhu, Liguang; Chang, Haowen; Sun, Zhibin

doi:10.1016/j.aquaculture.2022.738613

Cited by 5 publications

(3 citation statements)

References 63 publications

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“…With the development of technology, genetic mapping has been widely applied to aquatic animal breeding [19]. So far, genetic linkage maps have been constructed for many aquatic animals, such as tiger puffer Takifugu rubripes [20], Chinese Giant salamander [21]. Selection of mapping population is a prerequisite for constructing genetic linkage map.…”

Section: High-resolution Genetic Mapmentioning

confidence: 99%

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Zhang

Liu

Chu

et al. 2023

Preprint

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Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline of T. fasciatus germplasm resources. This study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LG), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. QTL (quantitative trait locus) localization analysis showed that a total of 19 QTL associated with growth traits of T. fasciatus were identified in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Further, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HMGB1, HMGB1) related to cold tolerance of T. fasciatus. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growth T. fasciatus.

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Section: High-resolution Genetic Mapmentioning

confidence: 99%

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Zhang

Liu

Chu

et al. 2023

Preprint

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“…WGR SNP data offers greater marker densities, comprehensive genome coverage [ 27 ], robust detection of rare variants [ 28 – 31 ], higher resolution, and more extensive information than traditional QTL methods, revealing the genetic basis of numerous quantitative traits. QTL analysis based on WGR has been widely used in aquatic biology [ 32 ], such as Takifugu rubripes [ 33 ], Andrias davidianus [ 34 ], Seriola dumerili [ 35 ], Oreochromis [ 36 ] and Oncorhynchus mykiss [ 37 ]. Body weight and wool production related traits in sheep are economically important.…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

Zhang,

Lu,

Guo

et al. 2024

BMC Genomics

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Background The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program. Results In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers). Conclusions The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

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“…With the rapid development of molecular biology and sequencing technology, modern breeding techniques attempt to target the regulatory genes underpinning desired phenotypes and achieve superior varieties via the selection or manipulation of these genes, i.e., molecular-assisted breeding ( Eze, 2019 ; Liu et al, 2022 ). Therefore, it has become increasingly important to understand the regulatory mechanisms and major genes behind desired phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami

Yin

Zhang

Zhong³

et al. 2023

Front. Genet.

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Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.

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Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in tiger puffer Takifugu rubripes

Cited by 5 publications

References 63 publications

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami

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