Dataset Information

Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data.

ABSTRACT: The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits.

SUBMITTER: Li C

PROVIDER: S-EPMC9404428 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Publications

Trait Analysis in Domestic Rabbits (<i>Oryctolagus cuniculus f. domesticus)</i> Using SNP Markers from Genotyping-by-Sequencing Data.

Li Congyan C Li Yuying Y Zheng Jie J Guo Zhiqiang Z Mei Xiuli X Lei Min M Ren Yongjun Y Zhang Xiangyu X Zhang Cuixia C Yang Chao C Tang Li L Ji Yang Y Yang Rui R Yu Jifeng J Xie Xiaohong X Kuang Liangde L

Animals : an open access journal from MDPI 20220811 16

The domestic rabbit (<i>Oryctolagus cuniculus f. domesticus</i>) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is ...[more]

PMID: 36009642

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Project description:Heat stress causes infertility in male rabbits in summer. This study was conducted to determine the effects of heat stress on semen quality and seminal plasma metabolites of male rabbits. To achieve these objectives, the temperature and humidity index (THI) was used to determine the stress state of male rabbits during different months, thereby the rabbits were divided into heat stress and no heat stress groups. The quality of the semen and the biochemical indices of seminal plasma were then analyzed. Next the plasma metabolites of rabbits in both groups were evaluated using the ultra-high performance liquid chromatography-mass spectroscopy (UPLC-MS)/MS technique. Our results showed that the THI value of the rabbit housing in May was 20.94 (no heat stress). The THI value of the housing in August was 29.10 (heat stress group, n = 10). Compared with the non-heat stress group, the sperm motility, density, and pH in the heat stress group (n = 10) were significantly decreased (P < 0.01); the semen volume decreased significantly (P < 0.05); and the sperm malformation rate increased significantly (P < 0.01). The number of grade A sperm significantly decreased, while the numbers of B and C grade sperm significantly increased (P < 0.01). The total sperm output (TSO), total motile sperm (TMS), and total functional sperm fraction (TFSF) decreased significantly (P < 0.01). Heat stress protein 70 (HSP70) and acid phosphatase (ACP) in the seminal plasma of rabbits in the heat stress group (n = 20) were significantly increased (P < 0.01). Seminal plasma testosterone (T), α-glucosidase (α-Glu), and fructose decreased significantly (P < 0.01). The concentrations of Mg2+ (P < 0.05), Na+ (P < 0.01), and K+ (P < 0.01) in metal ions were significantly decreased. These findings indicated that heat stress severely affected the quality of the male rabbit semen. Furthermore, UPLC-MS/MS technology was used to analyze the seminal plasma samples of rabbits in the heat stress group and non-heat stress group (n = 9 for each group). In total, 346 metabolites were identified, with variable importance in project (VIP) > 1.0, fold change (FC) > 1.5 or < 0.667, and P < 0.05 as the threshold. A total of 71 differential metabolites were matched, including stearic acid, betaine, arachidonic acid, L-malic acid, and indole. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differential metabolites revealed 51 metabolic pathways, including synthesis and degradation of ketones, serine and threonine metabolism, tryptophan metabolism, and the citric acid cycle. Our study has shown that the sperm motility, sperm pH value, and sperm density of male rabbits decreased significantly under heat stress, and the sperm malformation rate increased significantly. Furthermore, the quality of semen was shown to deteriorate and the energy metabolism pathway was disturbed. These findings provide a theoretical reference for alleviating the adaptive heat stress in male rabbits.

Dataset Information

Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data.

Publications

Trait Analysis in Domestic Rabbits (<i>Oryctolagus cuniculus f. domesticus)</i> Using SNP Markers from Genotyping-by-Sequencing Data.

Similar Datasets

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