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1. Exploring and Exploiting Pan-genomics for Crop Improvement

Author:
Tao, Yongfu; Zhao, Xianrong; Mace, Emma; Henry, Robert; Jordan, David
Source:
Molecular plant 2019 v.12 no.2 pp. 156-169
ISSN:
1674-2052
Subject:
single nucleotide polymorphism,   etc   ; bioactive properties; genes; genetic variation; landscapes;     Show all 5 Subjects
Abstract:
... Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic diversity of a species. Pan-genome analysis offers a platform to evaluate the genetic diversity of ...
DOI:
10.1016/j.molp.2018.12.016

2. Allele frequency‐free inference of close familial relationships from genotypes or low‐depth sequencing data

Author:
Waples, Ryan K.; Albrechtsen, Anders; Moltke, Ida
Source:
Molecular ecology 2019 v.28 no.1 pp. 35-48
ISSN:
0962-1083
Subject:
single nucleotide polymorphism,   etc   ; alleles; gene frequency; genomics; genotype; human population;     Show all 6 Subjects
Abstract:
... Knowledge of how individuals are related is important in many areas of research, and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data are limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants ...
DOI:
10.1111/mec.14954

3. Accuracy of imputation to whole-genome sequence in sheep

Author:
Bolormaa, Sunduimijid; Chamberlain, Amanda J.; Khansefid, Majid; Stothard, Paul; Swan, Andrew A.; Mason, Brett; Prowse-Wilkins, Claire P.; Duijvesteijn, Naomi; Moghaddar, Nasir; van der Werf, Julius H.; Daetwyler, Hans D.; MacLeod, Iona M.
Source:
Genetics, selection, evolution 2019 v.51 no.1 pp. 1
ISSN:
1297-9686
Subject:
single nucleotide polymorphism,   etc   ; Border Leicester; Merino; alleles; chromosomes; computer software; genomics; genotype; genotyping; heritability; prediction; sheep;     Show all 12 Subjects
Abstract:
... BACKGROUND: The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a range of breeds provides the opportunity to impute sheep genotyped with single nucleotide polymorphism (SNP) arrays to WGS. This study evaluated the accuracy of imputation from SNP g ...
DOI:
10.1186/s12711-018-0443-5

4. A genome wide association study for the number of animals born dead in domestic pigs

Author:
Wu, Pingxian; Wang, Kai; Zhou, Jie; Yang, Qiang; Yang, Xidi; Jiang, Anan; Jiang, Yanzhi; Li, Mingzhou; Zhu, Li; Bai, Lin; Li, Xuewei; Tang, Guoqing
Source:
BMC genetics 2019 v.20 no.1 pp. 4
ISSN:
1471-2156
Subject:
single nucleotide polymorphism,   etc   ; Large White; genes; genome-wide association study; genotyping; landraces; loci; nucleoproteins; sows;     Show all 9 Subjects
Abstract:
... BACKGROUND: The number of animals born dead, which includes the number of mummified (NM) and stillborn (NS) animals, is the most important trait to directly quantify the reproductive loss in domestic pigs. In this study, 282 Landrace sows and 250 Large White sows were genotyped by sequencing (GBS). A total of 816 and 1068 litter records for NM and NS were collected from them. A genome-wide associa ...
DOI:
10.1186/s12863-018-0692-x

5. Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

Author:
Wang, Xiao; Lund, Mogens Sandø; Ma, Peipei; Janss, Luc; Kadarmideen, Haja N.; Su, Guosheng
Source:
Journal of animal science and biotechnology 2019 v.10 no.1 pp. 8
ISSN:
2049-1891
Subject:
single nucleotide polymorphism,   etc   ; genomics; genotyping by sequencing; genotyping errors; homozygosity; livestock; loci; prediction; quality control;     Show all 9 Subjects
Abstract:
... BACKGROUND: Genotyping by sequencing (GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes, dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic pr ...
DOI:
10.1186/s40104-019-0315-z

6. Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs

Author:
Milan, Massimo; Maroso, Francesco; Dalla Rovere, Giulia; Carraro, Lisa; Ferraresso, Serena; Patarnello, Tomaso; Bargelloni, Luca; Cardazzo, Barbara; Fariselli, Piero
Source:
Food chemistry 2019 v.286 pp. 413-420
ISSN:
0308-8146
Subject:
single nucleotide polymorphism,   etc   ; Ruditapes philippinarum; artificial intelligence; clams; cost effectiveness; harvesting; microbiome; provenance; seafoods; traceability;     Show all 10 Subjects
Abstract:
... Developing reliable tools to trace food origin represents a major goal for producers and control authorities. Here, we test the hypothesis whether NGS-generated data could provide a reliable tool to ensure seafood traceability. As a test case, we used the Manila clam Ruditapes philippinarum, a bivalve mollusk of high commercial interest with worldwide distribution, collected in the Venice lagoon s ...
DOI:
10.1016/j.foodchem.2019.02.037

7. Comparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan

Author:
Okutani, Akiko; Inoue, Satoshi; Morikawa, Shigeru
Source:
Infection, genetics, and evolution 2019 v.71 pp. 128-139
ISSN:
1567-1348
Subject:
single nucleotide polymorphism,   etc   ; Bacillus anthracis; anthrax; cattle; genome; genomics; horses; imports; phylogeny; swine; vaccines; zoonoses; Japan;     Show all 13 Subjects
Abstract:
... Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core ...
DOI:
10.1016/j.meegid.2019.03.022

8. Genomic basis of delayed reward discounting

Author:
Gray, Joshua C.; Sanchez-Roige, Sandra; de Wit, Harriet; MacKillop, James; Palmer, Abraham A.
Source:
Behavioural processes 2019 v.162 pp. 157-161
ISSN:
0376-6357
Subject:
single nucleotide polymorphism,   etc   ; cognition; genetic correlation; genome-wide association study; genomics; heritability; obesity; rodents;     Show all 8 Subjects
Abstract:
... Delayed reward discounting (DRD) is a behavioral economic measure of impulsivity, reflecting how rapidly a reward loses value based on its temporal distance. In humans, more impulsive DRD is associated with susceptibility to a number of psychiatric diseases (e.g., addiction, ADHD), health outcomes (e.g., obesity), and lifetime outcomes (e.g., educational attainment). Although the determinants of D ...
DOI:
10.1016/j.beproc.2019.03.006

9. Recent advances on application of peptide nucleic acids as a bioreceptor in biosensors development

Author:
Saadati, Arezoo; Hassanpour, Soodabeh; Guardia, Miguel de la; Mosafer, Jafar; Hashemzaei, Mahmoud; Mokhtarzadeh, Ahad; Baradaran, Behzad
Source:
Trends in analytical chemistry 2019 v.114 pp. 56-68
ISSN:
0165-9936
Subject:
single nucleotide polymorphism,   etc   ; DNA; RNA; bacteria; biosensors; chemical species; electrochemistry; nucleic acid hybridization; peptides; proteinases; viruses;     Show all 11 Subjects
Abstract:
... The analogs of DNA are unique biomedical tools that are broadly utilized to develop different types of biosensors. Peptide nucleic acids (PNA) are an individual and notable class of nucleic acid analogs due to their unique, novel physicochemical and biochemical characteristics, stability and resistance to nuclease and protease enzymes, significant interactions with complementary strands and remark ...
DOI:
10.1016/j.trac.2019.02.030

10. Across-years prediction of hybrid performance in maize using genomics

Author:
Schrag, Tobias A.; Schipprack, Wolfgang; Melchinger, Albrecht E.
Source:
Theoretical and applied genetics 2019 v.132 no.4 pp. 933-946
ISSN:
0040-5752
Subject:
single nucleotide polymorphism,   etc   ; Zea mays; breeding programs; corn; data collection; genomics; genotype; hybrids; pedigree; phenotype; prediction;     Show all 11 Subjects
Abstract:
... KEY MESSAGE: Inclusion of historical training data improved the genomics-based prediction of performance of maize hybrids, the extent depending on the phenotypic trait and genotype-by-year interaction. Prediction of hybrid performance using existing phenotypic data on previous hybrids combined with molecular data collected on the parent lines allows to identify the most promising candidates from a ...
DOI:
10.1007/s00122-018-3249-5

11. Genome‐wide association study of growth traits in Jinghai Yellow chicken hens using SLAF‐seq technology

Author:
Wang, W. H.; Wang, J. Y.; Zhang, T.; Wang, Y.; Zhang, Y.; Han, K.
Source:
Animal genetics 2019 v.50 no.2 pp. 175-176
ISSN:
0268-9146
Subject:
single nucleotide polymorphism,   etc   ; body weight; genes; genome-wide association study; growth traits; hens; quantitative trait loci;     Show all 7 Subjects
Abstract:
... In this study, we performed a new genome‐wide association study using SLAF‐seq technology. A total of 19 single nucleotide polymorphism effects involving nine different SNP markers reached 5% Bonferroni‐corrected genome‐wide significance. In addition, a 5‐Mb region spanning 72.9–77.9 Mb on GGA4, exhibiting many significant SNP effects, was identified. The LDB2 gene in this region had a very strong ...
DOI:
10.1111/age.12346

12. Short communication: Calculating analytical reliabilities for single-step predictions

Author:
Edel, C.; Pimentel, E.C.G.; Erbe, M.; Emmerling, R.; Götz, K.-U.
Source:
Journal of dairy science 2019 v.102 no.4 pp. 3259-3265
ISSN:
0022-0302
Subject:
single nucleotide polymorphism,   etc   ; Simmental; animal models; cattle; genes; genomics; genotype; genotyping; pedigree; prediction;     Show all 10 Subjects
Abstract:
... It has been shown that single-step genomic BLUP (ssGBLUP) can be reformulated, resulting in an equivalent SNP model that includes the explicit imputation of gene contents of all ungenotyped animals in the pedigree. This reformulation reveals the underlying mechanism enabling ungenotyped animals to contribute information to genotyped animals via estimates of marker effects and consequently to the r ...
DOI:
10.3168/jds.2018-15707

13. A novel SNP of PLAG1 gene and its association with growth traits in Chinese cattle

Author:
Zhong, Jia-Lin; Xu, Jia-Wei; Wang, Jian; Wen, Yi-fan; Niu, Hui; Zheng, Li; He, Hua; Peng, Kun; He, Pan; Shi, Shu-Yue; Huang, Yin-Qi; Lei, Chu-Zhao; Dang, Rui-Hua; Lan, Xian-Yong; Qi, Xing-Lei; Chen, Hong; Huang, Yong-Zhen
Source:
Gene 2019 v.689 pp. 166-171
ISSN:
0378-1119
Subject:
single nucleotide polymorphism,   etc   ; adenoma; beef cattle; breeding; chest; genes; genotype; growth traits; transcription (genetics); transcription factors;     Show all 10 Subjects
Abstract:
... Genetic polymorphism has great influences on the improvement of cattle traits. The polymorphism of the same gene family will greatly change the growth traits of cattle, such as the pleomorphic adenoma gene (PLAG) family. Many studies have shown that the PLAG family proteins are the transcription regulators of nuclear protein, which mainly regulates the expression of many important genes in the bod ...
DOI:
10.1016/j.gene.2018.12.018

14. Identification of male-specific SNP markers and development of PCR-based genetic sex identification technique in crucifix crab (Charybdis feriatus) with implication of an XX/XY sex determination system

Author:
Fang, Shaobin; Zhang, Yin; Shi, Xi; Zheng, Huaiping; Li, Shengkang; Zhang, Yueling; Fazhan, Hanafiah; Waiho, Khor; Tan, Huaqiang; Ikhwanuddin, Mhd; Ma, Hongyu
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; Charybdis feriatus; breeding programs; females; heterozygosity; homozygosity; males; polymerase chain reaction; sex determination;     Show all 9 Subjects
Abstract:
... In this study, we first identified male-specific SNP markers using restriction site-associated DNA sequencing, and further developed a PCR-based sex identification technique for Charybdis feriatus. A total of 296.96 million clean reads were obtained, with 114.95 and 182.01 million from females and males. After assembly and alignment, 10 SNP markers were identified being heterozygous in males but h ...
DOI:
10.1016/j.ygeno.2019.03.003

15. Identification of deleterious SNPs and their effects on BCL11A, the master regulator of fetal hemoglobin expression

Author:
Das, Sankha Subhra; Chakravorty, Nishant
Source:
Genomics 2019
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; B-cell lymphoma; binding sites; genes; hemoglobin; leukemia; ligands; mutants; post-translational modification;     Show all 9 Subjects
Abstract:
... The B-cell lymphoma/leukemia 11A protein (encoded by BCL11A gene) is a key regulator of fetal-to-adult hemoglobin switching as seen in post-natal life. Although genetic polymorphisms like SNPs in BCL11A gene are expected to affect fetal hemoglobin (HbF) expression levels, yet their implications are poorly studied. This study utilizes a computational approach to identify the deleterious SNPs which ...
DOI:
10.1016/j.ygeno.2019.03.002

16. Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

Author:
Berry, D.P.; McHugh, N.; Wall, E.; McDermott, K.; O’Brien, A.C.
Source:
Irish journal of agricultural and food research 2019 v.58 no.1 pp. 1-12
ISSN:
2009-9029
Subject:
single nucleotide polymorphism,   etc   ; alleles; artificial insemination; chromosomes; dams (mothers); genotype; genotyping; lambing; parentage; purebreds; sheep; sires;     Show all 12 Subjects
Abstract:
... The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was ...
DOI:
10.2478/ijafr-2019-0001

17. An evaluation of the methods to estimate effective population size from measures of linkage disequilibrium

Author:
García‐Cortés, Luis Alberto; Austerlitz, Frederic; de Cara, M. Angeles R.
Source:
Journal of evolutionary biology 2019 v.32 no.3 pp. 267-277
ISSN:
1010-061X
Subject:
single nucleotide polymorphism,   etc   ; effective population size; empirical research; equations; genome; genomics; linkage disequilibrium; mating systems;     Show all 8 Subjects
Abstract:
... In 1971, John Sved derived an approximate relationship between linkage disequilibrium (LD) and effective population size for an ideal finite population. This seminal work was extended by Sved and Feldman (Theor Pop Biol 4, 129, 1973) and Weir and Hill (Genetics 95, 477, 1980) who derived additional equations with the same purpose. These equations yield useful estimates of effective population size ...
DOI:
10.1111/jeb.13411

18. A targeted gene approach to SNP discovery in the blue (Connochaetes taurinus) and black wildebeest (C. gnou)

Author:
van Wyk, Anna M.; Labuschagne, Christiaan; Kropff, Anna S.; Kotzé, Antoinette; Grobler, J. Paul; van Vuuren, Bettine Jansen; Dalton, Desiré L.
Source:
Conservation genetics resources 2019 v.11 no.1 pp. 35-38
ISSN:
1877-7252
Subject:
single nucleotide polymorphism,   etc   ; Connochaetes taurinus; gene flow; gene frequency; genes; heterozygosity; hybridization; loci; population structure; wildebeest;     Show all 10 Subjects
Abstract:
... We report the characterization of 23 single nucleotide polymorphism (SNP) markers for the blue (Connochaetes taurinus) and black wildebeest (C. gnou) based on a targeted gene approach. The polymorphisms of these SNP loci were assessed using a captive population of blue and black wildebeest comprising 30 individuals. The minor allele frequency per SNP ranged from 0.000 to 0.458 and the observed and ...
DOI:
10.1007/s12686-017-0959-y

19. International bull evaluations by genomic BLUP with a prediction population

Author:
Fragomeni, B.; Masuda, Y.; Bradford, H.L.; Lourenco, D.A.L.; Misztal, I.
Source:
Journal of dairy science 2019 v.102 no.3 pp. 2330-2335
ISSN:
0022-0302
Subject:
single nucleotide polymorphism,   etc   ; bulls; genetic correlation; genetic variance; genomics; genotype; genotyping; phenotype; prediction;     Show all 9 Subjects
Abstract:
... The purpose of this study was to determine whether multi-country genomic evaluation can be accomplished by multiple-trait genomic best linear unbiased predictor (GBLUP) without sharing genotypes of important animals. Phenotypes and genotypes with 40k SNP were simulated for 25,000 animals, each with 4 traits assuming the same genetic variance and 0.8 genetic correlations. The population was split i ...
DOI:
10.3168/jds.2018-15554

20. Association of genetic polymorphisms with age at menarche in Russian women

Author:
Ponomarenko, Irina; Reshetnikov, Evgeny; Altuchova, Oksana; Polonikov, Alexey; Sorokina, Inna; Yermachenko, Anna; Dvornyk, Volodymyr; Golovchenko, Oleg; Churnosov, Mikhail
Source:
Gene 2019 v.686 pp. 228-236
ISSN:
0378-1119
Subject:
single nucleotide polymorphism,   etc   ; body mass index; females; genes; loci; menarche; models; tissues; women;     Show all 9 Subjects
Abstract:
... Examine the association of genetic polymorphisms with age at menarche (AAM) in Russian women.A total of 1613 Russian females were recruited for the study.Fifty two polymorphisms were analyzed for their association with AAM, height, and BMI.The associations were analyzed assuming the additive, dominant, and recessive models and using the log-linear regression as implemented in PLINK v. 2.050. The 2 ...
DOI:
10.1016/j.gene.2018.11.042