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Genetic Variation in Biological Traits
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Genetic Variation in Biological Traits

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (10 May 2023) | Viewed by 6133

Special Issue Editor

Dr. Yuwen Liu

E-Mail Website
Guest Editor
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Interests: cis-regulatory elements; fine-mapping; genetic improvement; genomic selection; synthetic biology

Special Issue Information

Dear Colleagues,

Understanding the molecular mechanisms by which genetic variations influence biological traits is the key to comprehensively translating the genetic code of life. Identifying phenotype-associated or causal genetic variants lies the foundation for the development of pharmaceutical products and for the improvement of animal and plant breeding. With the advent of modern genotyping and phenotyping technologies, we are discovering an ever-increasing amount of DNA variants that are associated with biological traits or that are located in regions under potential natural or artificial selection. In the meantime, functional genomics data, such as gene expression, cis-regulatory element activity, protein abundance, and metabolic profiling, have been integrated with genomics data to better pinpoint to potential causal variants at a finer and finer scale. Last but not least, technology breakthroughs in functional validation, such as the application of CRISPR/Cas9-based genetic editing, are providing an unprecedented ease of directly proving the causal relationship between a genetic variant and a trait. In this Special Issue, we welcome original research articles and reviews covering many aspects of the efforts to elucidate how DNA variants might affect biological traits of humans, animals, or plants. These topics include but are not limited to population genetics studies to identify trait-associated DNA variants, evolutionary biology studies to discover DNA regions under potential selection, functional genomics and multi-omics studies to facilitate the fine-mapping of potential causal variants and experimental studies to prove the effects of DNA variants on biological traits.

Dr. Yuwen Liu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • GWAS
  • population genetics
  • selection
  • adaptation
  • functional genomics
  • fine-mapping
  • genetic editing
  • disease etiology
  • animal breeding
  • plant breeding

Published Papers (3 papers)

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Research

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14 pages, 46065 KiB  
Article
Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese
by Guojun Liu, Zhenhua Guo, Xiuhua Zhao, Jinyan Sun, Shan Yue, Manyu Li, Zhifeng Chen, Zhigang Ma and Hui Zhao
Genes 2023, 14(2), 487; https://doi.org/10.3390/genes14020487 - 14 Feb 2023
Cited by 1 | Viewed by 1913
Abstract
The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody [...] Read more.
The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits. Full article
(This article belongs to the Special Issue Genetic Variation in Biological Traits)
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10 pages, 1630 KiB  
Article
Analysis of Copy Number Variation in the Whole Genome of Normal-Haired and Long-Haired Tianzhu White Yaks
by Guangyao Meng, Qi Bao, Xiaoming Ma, Min Chu, Chun Huang, Xian Guo, Chunnian Liang and Ping Yan
Genes 2022, 13(12), 2405; https://doi.org/10.3390/genes13122405 - 18 Dec 2022
Cited by 1 | Viewed by 1737
Abstract
Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome [...] Read more.
Long-haired individuals in the Tianzhu white yak population are a unique genetic resource, and have important landscape value. Copy number variation (CNV) is an important source of phenotypic variation in mammals. In this study, we used resequencing technology to detect the whole genome of 10 long-haired Tianzhu white yaks (LTWY) and 10 normal-haired Tianzhu white yaks (NTWY), and analyzed the differences of CNV in the genome of LTWYs and NTWYs. A total of 110268 CNVs were identified, 2006 CNVRs were defined, and the distribution map of these CNVRs on chromosomes was constructed. The comparison of LTWYs and NTWYs identified 80 differential CNVR-harbored genes, which were enriched in lipid metabolism, cell migration and other functions. Notably, some differential genes were identified as associated with hair growth and hair-follicle development (e.g., ASTN2, ATM, COL22A1, GK5, SLIT3, PM20D1, and SGCZ). In general, we present the first genome-wide analysis of CNV in LTWYs and NTWYs. Our results can provide new insights into the phenotypic variation of different hair lengths in Tianzhu white yaks. Full article
(This article belongs to the Special Issue Genetic Variation in Biological Traits)
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Review

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11 pages, 242 KiB  
Review
Whole Genome Resequencing Helps Study Important Traits in Chickens
by Xinwei Xiong, Jianxiang Liu and Yousheng Rao
Genes 2023, 14(6), 1198; https://doi.org/10.3390/genes14061198 - 30 May 2023
Cited by 3 | Viewed by 1879
Abstract
The emergence of high-throughput sequencing technology promotes life science development, provides technical support to analyze many life mechanisms, and presents new solutions to previously unsolved problems in genomic research. Resequencing technology has been widely used for genome selection and research on chicken population [...] Read more.
The emergence of high-throughput sequencing technology promotes life science development, provides technical support to analyze many life mechanisms, and presents new solutions to previously unsolved problems in genomic research. Resequencing technology has been widely used for genome selection and research on chicken population structure, genetic diversity, evolutionary mechanisms, and important economic traits caused by genome sequence differences since the release of chicken genome sequence information. This article elaborates on the factors influencing whole genome resequencing and the differences between these factors and whole genome sequencing. It reviews the important research progress in chicken qualitative traits (e.g., frizzle feather and comb), quantitative traits (e.g., meat quality and growth traits), adaptability, and disease resistance, and provides a theoretical basis to study whole genome resequencing in chickens. Full article
(This article belongs to the Special Issue Genetic Variation in Biological Traits)
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