Genome-wide association study reveals growth-related markers and candidate genes for selection in Chinese longsnout catfish (Leiocassis longirostris)

Mou, Cheng-Yan; Liu, Yu; Zhou, Jian; Li, Qiang; Zhou, Bo; Wei, Zhen; Luo, Hongyu; Ke, Hongyu; Duan, Yuanliang; Zhai, Wan-Ting; Huang, Zhipeng; Zhao, Han; Zhao, Zhi‐Xue; Du, Jun; Ye, Hua; Zhang, Lu

doi:10.1016/j.aquaculture.2022.738513

Cited by 13 publications

(4 citation statements)

References 56 publications

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“…Another gene included in one of these regions was family with sequence similarity 135 member B ( FAM135B ), which encodes for a factor that promotes the secretion of the granulin growth factor, which has high expression in epithelial, immune, chondrocytes, and neuronal cells [ 46 ]. This gene has been reported to affect growth-related traits in livestock species [ 47 ] and in Chinese longsnout catfish [ 48 ]. In this catfish species, this gene has been suggested as a candidate for caudal peduncle depth, which is one of the parameters used to estimate fish growth [ 48 ].…”

Section: Resultsmentioning

confidence: 99%

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Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

Bertolini

Ribani

Capoccioni

et al. 2023

Genes

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The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

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Section: Resultsmentioning

confidence: 99%

“…This gene has been reported to affect growth-related traits in livestock species [ 47 ] and in Chinese longsnout catfish [ 48 ]. In this catfish species, this gene has been suggested as a candidate for caudal peduncle depth, which is one of the parameters used to estimate fish growth [ 48 ].…”

Section: Resultsmentioning

confidence: 99%

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

Bertolini

Ribani

Capoccioni

et al. 2023

Genes

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“…In common carp, a total of 10 SNP loci distributed on LG8 for body mass were identified based on an ultra-high density linkage map and QTL mapping (Peng et al, 2016). In Larimichthys longirostris, the most obvious relationship to growth traits were located on chromosome 16 (Mou et al, 2022). Most growth-associated loci were clustered on chromosomes A8 and B25, suggesting that these two chromosomes may be central to The phylogenetic tree of 200 rice flower carp.…”

Section: Discussionmentioning

confidence: 99%

“…Currently, genome-wide association studies (GWAS) based on a large number of SNP markers have been widely used for identifying markers/genetic variants that are significantly associated with various economic traits in fish, such as sex, stress tolerance, and growth (Berghof et al, 2018;Ji et al, 2019;Gao and Yang, 2021;Luo et al, 2022;Mou et al, 2022). In recent years, SNPs have mainly been detected and genotyped at the genome-wide level using gene chips, simplified genome sequencing, and whole genome resequencing.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study reveals markers and candidate genes associated with growth in the rice flower carp, an economic fish species of integrated rice-fish culture in China

et al. 2023

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The rice flower carp (Cyprinus carpio) is an important fish in integrated rice-fishery farming. Here, we performed the first genome-wide association study (GWAS) for seven growth traits (including body mass, total length, body length, body height, body width, caudal-peduncle depth, and eye spacing) in 200 rice flower carp samples using 369,688 high-quality SNPs and 42,225 indels obtained by double-digest genotyping-by-sequencing (ddGBS). The morphometrics of these traits were highly correlated (Pearson’s correlation coefficients = 0.74–0.99, p < 0.001). GWAS detected 15, 5, 4, 26, 7, 16, and 17 loci significant associated (-log10P ≥ 5) with body mass, total length, body length, body width, body height, caudal-peduncle depth, and eye spacing, respectively. Subsequently, within the 50 kb upstream and downstream regions surrounding these significant loci, 38, 19, 18, 20, 52, 27, and 37 candidate genes for the seven growth traits were detected, respectively. Importantly, B6_4352672 and A8_4978825 were significantly associated with more than five growth traits. These results showed loci significantly associated with more than five growth traits will be helpful for future marker-assisted selection (MAS). Interestingly, chromosomes A8 and B25 had many loci significantly associated with growth traits, most of which were shared among multiple growth-related traits. These results indicated that chromosome A8 and B25 may be closely related to growth traits. Our findings not only help understand the genetic architecture of growth traits in fish but facilitate the identification of candidate genes for marker-assisted selection towards breeding faster-growing rice flower carp in the future.

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Acute hypoxia causes glycolysis and lipid metabolism alterations with HSPs’ persistent activation in Leiocassis longirostris

Hou,

Ke,

Xiang

et al. 2024

Ichthyol Res

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Genome-wide association study reveals growth-related markers and candidate genes for selection in Chinese longsnout catfish (Leiocassis longirostris)

Cited by 13 publications

References 56 publications

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei

Genome-wide association study reveals markers and candidate genes associated with growth in the rice flower carp, an economic fish species of integrated rice-fish culture in China

Acute hypoxia causes glycolysis and lipid metabolism alterations with HSPs’ persistent activation in Leiocassis longirostris

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