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Genes
Special Issues
From QTL Mapping to QTG and QTN Identification
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From QTL Mapping to QTG and QTN Identification

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (25 February 2023) | Viewed by 11498

Special Issue Editor

Dr. Akira Ishikawa

E-Mail Website
Guest Editor
Laboratory of Animal Genetics and Breeding, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
Interests: animal; QTL; QTG; genetics; genomics; breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Most traits of great importance in medicine, agriculture and evolution are quantitative in nature. These traits include traditional quantitative traits (e.g., complex human diseases and livestock products) and molecular traits (e.g., gene expression, protein expression, DNA methylation and metabolites). These traits are controlled by many quantitative trait loci (QTLs), environmental factors and their interactions. A deep understanding of the genetic and molecular mechanisms for such traits can dramatically improve human health and animal production.

A great number of QTLs affecting a variety of quantitative traits have so far been mapped to almost all chromosomal regions of animals, including humans, model animals, livestock and poultry. Recent advances in QTL studies that are integrated with next-generation sequencing, multi-omics approaches and/or causality analysis have allowed us to identify the candidates of causal quantitative trait genes (QTGs) and causal quantitative trait nucleotides (QTNs). However, it is still challenging to identify true QTGs and QTNs, because common QTLs with relatively small phenotypic effects are usually located in noncoding genomic regions. In this Special Issue, any original and review articles related to QTL, QTG or QTN identification in animals are welcomed.

Dr. Akira Ishikawa
Guest Editor

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Keywords

  • quantitative traits
  • molecular traits
  • QTL
  • QTG
  • QTN
  • humans
  • model animals
  • livestock
  • poultry

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Published Papers (5 papers)

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Research

11 pages, 2017 KiB  
Article
Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation
by Moran Gershoni, Andrey Shirak, Yehoshav Ben-Meir, Ariel Shabtay, Miri Cohen-Zinder and Eyal Seroussi
Genes 2023, 14(3), 547; https://doi.org/10.3390/genes14030547 - 22 Feb 2023
Viewed by 1788
Abstract
In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution [...] Read more.
In dairy cattle, identifying polymorphisms that contribute to complex economical traits such as residual feed intake (RFI) is challenging and demands accurate genotyping. In this study, we compared imputed genotypes (n = 192 cows) to those obtained using the TaqMan and high-resolution melting (HRM) methods (n = 114 cows), for mutations in the FABP4 gene that had been suggested to have a large effect on RFI. Combining the whole genome sequence (n = 19 bulls) and the cows’ BovineHD BeadChip allowed imputing genotypes for these mutations that were verified by Sanger sequencing, whereas, an error rate of 11.6% and 10.7% were encountered for HRM and TaqMan, respectively. We show that this error rate seriously affected the linkage-disequilibrium analysis that supported this gene candidacy over other BTA14 gene candidates. Thus, imputation produced superior genotypes and should also be regarded as a method of choice to validate the reliability of the genotypes obtained by other methodologies that are prone to genotyping errors due to technical conditions. These results support the view that RFI is a complex trait and that searching for the causative sequence variation underlying cattle RFI should await the development of statistical methods suitable to handle additive and epistatic interactions. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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11 pages, 308 KiB  
Article
Genetic Polymorphism at 15 Codons of the Prion Protein Gene in 156 Goats from Romania
by Maria Rodica Gurau, Elena Negru, Teodor Ionescu, Anca Amalia Udriste, Călina Petruța Cornea and Stelian Baraitareanu
Genes 2022, 13(8), 1316; https://doi.org/10.3390/genes13081316 - 23 Jul 2022
Cited by 1 | Viewed by 1862
Abstract
Background: The variability of prion protein gene (PRNP) codons and the frequency of alleles (K222, D146, and S146) that appear to confer genetic resistance to classical scrapie are still unknown in several goat populations/breeds prevalent in Romania. This work aims to [...] Read more.
Background: The variability of prion protein gene (PRNP) codons and the frequency of alleles (K222, D146, and S146) that appear to confer genetic resistance to classical scrapie are still unknown in several goat populations/breeds prevalent in Romania. This work aims to assess the genetic polymorphism at 15 PRNP codons in Romanian goat populations to inform the development of goat breeding programs for scrapie resistance. Methods: Whole blood and hair follicles from Carpathian (50), French Alpine (53), and Banat’s White (53) breed goats were sampled to extract genomic DNA for genetic analyses and Sanger sequencing. In the targeted goat groups, one classical scrapie-positive Banat’s White goat was included. Results: The codons without polymorphisms were G37G, W102W, N146N, R151R, S173S, and I218I. The following non-synonymous polymorphisms of PRNP were recorded: P110P, P110S, P110T, T110T, G127G, G127S, I142I, I142M, T142I, H143H, P143P, R143R, R154R, H154R, P168P, Q168Q, Q211Q, Q211R, Q222Q, H222Q, K222K, S240S, P240P, P240S, and S240P. Conclusions: PRNP polymorphism was recorded in 60% (9/15) of codons. The scrapie-positive Banat’s White goat had G37G, W102W, T110T, G127G, I142I, H143H, N146N, R151R, R154R, P168P, S173S, R211R, I218I, Q222Q, and S240S. The K222 allele had a frequency of 6% (3/50) in Carpathian, 9.43% (5/53) in Banat’s White, and 15.09% (8/53) in French Alpine. Therefore, the polymorphisms detected in this sample of Romanian goat breeds are too rare to design a breeding program at the current time. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
9 pages, 1944 KiB  
Article
Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations
by Shinji Sasazaki, Raito Yamamoto, Shintaro Toyomoto, Hina Kondo, Takayuki Akiyama, Namiko Kohama, Emi Yoshida, Fuki Kawaguchi, Kenji Oyama and Hideyuki Mannen
Genes 2022, 13(7), 1190; https://doi.org/10.3390/genes13071190 - 1 Jul 2022
Cited by 3 | Viewed by 1962
Abstract
In our previous study, we used genome resequencing to detect all candidate polymorphisms within a quantitative trait loci (QTL) region for beef marbling reported previously at 10–30 Mbp on bovine chromosome 7, and we selected 6044 polymorphisms as candidate quantitative trait nucleotides (QTNs). [...] Read more.
In our previous study, we used genome resequencing to detect all candidate polymorphisms within a quantitative trait loci (QTL) region for beef marbling reported previously at 10–30 Mbp on bovine chromosome 7, and we selected 6044 polymorphisms as candidate quantitative trait nucleotides (QTNs). In the present study, we aimed to identify quantitative trait genes (QTGs) and QTNs in this QTL region by verifying the effect of SNPs on beef marbling in two Japanese Black cattle populations using a Dynamic Array integrated fluidic circuit. In total, 96 selected SNPs were genotyped in 441 and 529 animals in Hyogo and Miyazaki cattle populations, respectively. The most significant p-values were detected in a SNP in a splice region of ALDH7A1 (SNP93_ALDH7A1; p = 3.46 × 10−5) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (ICAM1) (SNP37_ICAM1; p = 3.33 × 10−4) in Miyazaki cattle. Interestingly, SNP93_ALDH7A1 was not significant (p = 0.459) in Miyazaki cattle, and SNP37_ICAM1 showed a weakly significant association (p = 0.043) in Hyogo cattle. Thus, each population would likely have different QTGs and QTNs for beef marbling in the QTL region. In the Hyogo population, it was not possible to determine the accurate range of the linkage disequilibrium (LD) block in LD block analysis because of a strong LD structure throughout the assessed region. In Miyazaki cattle, however, an LD block containing SNP37_ICAM1 had a range of 15.8–16.1 Mbp, suggesting that QTNs would be located within this region. The functions of 19 genes in the LD block were investigated. ICAM1 is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37_ICAM1 was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_ICAM1 on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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14 pages, 2658 KiB  
Article
QTL Mapping for Age-Related Eye Pigmentation in the Pink-Eyed Dilution Castaneus Mutant Mouse
by Takaya Nakano, Momoko Takenaka, Makoto Sugiyama and Akira Ishikawa
Genes 2022, 13(7), 1138; https://doi.org/10.3390/genes13071138 - 24 Jun 2022
Viewed by 2493
Abstract
Pink-eyed dilution castaneus (Oca2p-cas) is a mutant gene on mouse chromosome 7 that arose spontaneously in wild Mus musculus castaneus. Homozygotes for Oca2p-cas exhibit pink eyes and a light gray coat throughout life. In an ordinary [...] Read more.
Pink-eyed dilution castaneus (Oca2p-cas) is a mutant gene on mouse chromosome 7 that arose spontaneously in wild Mus musculus castaneus. Homozygotes for Oca2p-cas exhibit pink eyes and a light gray coat throughout life. In an ordinary mutant strain carrying Oca2p-cas, we previously discovered a novel spontaneous mutation that gradually increases melanin pigmentation in the eyes and coat with aging, and we developed a novel mutant strain that was fixed for the novel phenotype. The purpose of this study was to map major quantitative trait loci (QTLs) for the novel pigmentation phenotype and for expression levels of four important melanogenesis genes, microphthalmia-associated transcription factor (Mitf), tyrosinase (Tyr), tyrosinase-related protein-1 (Tyrp1) and dopachrome tautomerase (Dct). We developed 69 DNA markers and created 303 F2 mice from two reciprocal crosses between novel and ordinary mutant strains. The QTL analysis using a selective genotyping strategy revealed a significant QTL for eye pigmentation between 34 and 64 Mb on chromosome 13. This QTL explained approximately 20% of the phenotypic variance. The QTL allele derived from the novel strain increased pigmentation. Although eye pigmentation was positively correlated with Dct expression, no expression QTLs were found, suggesting that the pigmentation QTL on chromosome 13 may not be directly in the pathway of any of the four melanogenesis genes. This study is the first step toward identifying a causal gene for the novel spontaneous phenotype in mice and is expected to discover a new regulatory mechanism for complex melanin biosynthesis during aging. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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10 pages, 1583 KiB  
Article
Fine Mapping of the Mouse Ath28 Locus Yields Three Atherosclerosis Modifying Sub-Regions
by Juying Han, Brian Ritchey, Emmanuel Opoku and Jonathan D. Smith
Genes 2022, 13(1), 70; https://doi.org/10.3390/genes13010070 - 28 Dec 2021
Cited by 1 | Viewed by 1889
Abstract
A mouse strain intercross between Apoe−/− AKR/J and DBA/2J mice identified three replicated atherosclerosis quantitative trait loci (QTLs). Our objective was to fine map mouse atherosclerosis modifier genes within a genomic region known to affect lesion development in apoE-deficient (Apoe−/− [...] Read more.
A mouse strain intercross between Apoe−/− AKR/J and DBA/2J mice identified three replicated atherosclerosis quantitative trait loci (QTLs). Our objective was to fine map mouse atherosclerosis modifier genes within a genomic region known to affect lesion development in apoE-deficient (Apoe−/−) mice. We dissected the Ath28 QTL on the distal end of chromosome 2 by breeding a panel of congenic strains and measuring aortic root lesion area in 16-week-old male and female mice fed regular laboratory diets. The parental congenic strain contained ~9.65 Mb of AKR/J DNA from chromosome 2 on the DBA/2J genetic background, which had lesions 55% and 47% smaller than female and male DBA/2J mice, respectively (p < 0.001). Seven additional congenic lines identified three separate regions associated with the lesion area, named Ath28.1, Ath28.2, and Ath28.3, where the AKR/J alleles were atherosclerosis-protective for two regions and atherosclerosis-promoting for the other region. These results were replicated in both sexes, and in combined analysis after adjusting for sex. The congenic lines did not greatly impact total and HDL cholesterol levels or body weight. Bioinformatic analyses identified all coding and non-coding genes in the Ath28.1 sub-region, as well as strain sequence differences that may be impactful. Even within a <10 Mb region of the mouse genome, evidence supports the presence of at least three atherosclerosis modifier genes that differ between the AKR/J and DBA/2J mouse strains, supporting the polygenic nature of atherosclerosis susceptibility. Full article
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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