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

Li, Congyan; Li, Yuying; Zheng, Jie; Guo, Zhiqiang; Mei, Xiuli; Lei, Min; Ren, Yongjun; Zhang, Xiangyu; Zhang, Cuixia; Tang, Li; Yang, Jicheng; Yang, Rui; Yu, Jifeng; Xie, Xiaohong; Kuang, Liangde

doi:10.3390/ani12162052

Cited by 2 publications

(1 citation statement)

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“…In our study, GBS fragments have been positioned and their relationship to genic regions under selection has been ascertained. Similarly, recent GWAS studies have successfully revealed candidate genes under selection in camels (Bitaraf et al, 2022), pigs (Chen et al, 2019) and rabbits (Li et al, 2022). The most important selection signal obtained in our results was detected on OAR20 involving 12 SNPs mapped on the genomic region ~50.3–50.6 Mbp.…”

Section: Discussionmentioning

confidence: 97%

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

et al. 2023

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In developing countries, the use of simple and cost‐efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme‐ reduced representational sequencing, is an efficient, cost‐effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two‐enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi‐allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome‐wide association study contrasting fat vs. thin‐tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail‐type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost‐efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.

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Section: Discussionmentioning

confidence: 97%

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

et al. 2023

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Genome Polymorphism Analysis and Selected Sweep Regions Detection via the Genome Resequencing of 91 Cabbage (Brassica oleracea) Accessions

Cai

Zhang

et al. 2023

Horticulturae

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The completion of more and more high-quality cabbage genome sequencing attempts provides an important reference genome sequence for resequencing a large proportion of B. oleracea populations. This has laid a foundation for the study of the population diversity of B. oleracea and the excavation of genes related to important agronomic traits. Here, we performed genome resequencing of 91 B. oleracea accessions from 14 countries. We produced a total of 983.84 Gb of high-quality sequencing data, and the average sequencing depth of the genomes was over 15.71 among the 91 accessions. A total of 3,432,341 high-quality SNPs were detected in these B. oleracea accessions. A phylogenetic tree indicated that the leaf ball shapes of “Gaobian” accessions and most “Jianqiu” accessions converge with “Bianqiu” accessions, while “Yuanqiu” accessions were individually assigned to a branch. The principal component analysis (PCA) result was consistent with the phylogenetic relationships. The LD distance of “Yuanqiu” was 38.69 Kb, while that of “Bianqiu” was 30.16 Kb. This result indicated that the linkage degree of the “Yuanqiu” population is greater than that of the “Bianqiu” population, which may indicate that the “Yuanqiu” population has received more positive selection. Our analysis showed that, for the 91 accessions, the best population structure number was four. A total of 560 genes were identified across the 203 selected sweep regions identified in the “Yuanqiu” accessions. Similarly, 682 genes were identified across the 304 selective sweep regions in the “Bianqiu” accessions. Finally, several functional terms were identified via enrichment analysis of the genes in the selective sweep regions. In conclusion, this study will provide rich resources for studies on gene function related to leaf ball development and the population diversity of B. olearcea.

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

Cited by 2 publications

References 44 publications

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

Genome Polymorphism Analysis and Selected Sweep Regions Detection via the Genome Resequencing of 91 Cabbage (Brassica oleracea) Accessions

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