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1. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)

Author:
Lee‐Yaw, Julie A.; Grassa, Christopher J.; Joly, Simon; Andrew, Rose L.; Rieseberg, Loren H.
Source:
Thenew phytologist 2019 v.221 no.1 pp. 515-526
ISSN:
0028-646X
Subject:
single nucleotide polymorphism,   etc   ; Helianthus annuus; biogeography; chloroplasts; gene flow; introgression; phylogeny;     Show all 7 Subjects
Abstract:
... Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole‐chloroplast sequence data in combination with over 1000 nuclear single‐nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to tes ...
DOI:
10.1111/nph.15386

2. Comparison of diversity parameters from SNP, microsatellites and pedigree records in the Lidia cattle breed

Author:
Cortés, O.; Eusebi, P.; Dunner, S.; Sevane, N.; Cañón, J.
Source:
Livestock science 2019 v.219 pp. 80-85
ISSN:
1871-1413
Subject:
single nucleotide polymorphism,   etc   ; genetic drift; genetic variation; homozygosity; inbreeding; loss of heterozygosity; microsatellite repeats; pedigree;     Show all 8 Subjects
Abstract:
... Genetic drift, loss of heterozygosity and decrease in genetic variability are consequences of high rates of inbreeding over generations.. High density single nucleotide polymorphisms arrays offered new possibilities to estimate inbreeding coefficients more accurately than those from pedigree records or microsatellites genotypes. In the present study different inbreeding coefficients were estimated ...
DOI:
10.1016/j.livsci.2018.11.006

3. Copy Number Variation in Domestication

Author:
Lye, Zoe N.; Purugganan, Michael D.
Source:
Trends in plant science 2019
ISSN:
1360-1385
Subject:
single nucleotide polymorphism,   etc   ; animals; copy number variation; domestication; evolution; genes; models;     Show all 7 Subjects
Abstract:
... Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as ...
DOI:
10.1016/j.tplants.2019.01.003

4. The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis)

Author:
O'Connell, Kyle A.; Smith, Eric N.
Source:
Molecular phylogenetics and evolution 2018 v.127 pp. 356-366
ISSN:
1055-7903
Subject:
single nucleotide polymorphism,   etc   ; Masticophis; taxonomic revisions;     Show all 3 Subjects
Abstract:
... A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use ...
DOI:
10.1016/j.ympev.2018.03.018

5. Genomic architecture of complex traits in loblolly pine

Author:
De La Torre, Amanda R.; Puiu, Daniela; Crepeau, Marc W.; Stevens, Kristian; Salzberg, Steven L.; Langley, Charles H.; Neale, David B.
Source:
Thenew phytologist 2019 v.221 no.4 pp. 1789-1801
ISSN:
0028-646X
Subject:
single nucleotide polymorphism,   etc   ; Pinus taeda; data collection; gene frequency; genes; genetic variation; genomics; genotype; inheritance (genetics); metabolites; phenotype; xylem;     Show all 12 Subjects
Abstract:
... Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance. Whole‐genome resequencing data were used to generate high‐resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda ...
DOI:
10.1111/nph.15535

6. Interactions of CDH13 gene polymorphisms and ambient PM10 air pollution exposure with blood pressure and hypertension in Korean men

Author:
Kim, Hyun-Jin; Seo, Yong-Seok; Sung, Joohon; Son, Ho-Young; Yun, Jae Moon; Kwon, Hyuktae; Cho, Belong; Kim, Jong-Il; Park, Jin-Ho
Source:
Chemosphere 2019 v.218 pp. 292-298
ISSN:
0045-6535
Subject:
single nucleotide polymorphism,   etc   ; Koreans; adults; air pollution; alleles; diastolic blood pressure; homozygosity; hypertension; men; particulates; risk; systolic blood pressure;     Show all 12 Subjects
Abstract:
... Associations between air pollution and blood pressure (BP) traits can be modified by several candidate genes, which might explain differences in individual genetic susceptibility. Based on recent evidence hypothesized to link air pollution and BP traits, we examined whether the polymorphisms of CDH13—a candidate gene—would modify the relationship between them in adult Korean men. A total of 1816 s ...
DOI:
10.1016/j.chemosphere.2018.11.125

7. Signs of adaptation to trace metal contamination in a common urban bird

Author:
Andrew, Samuel C.; Taylor, Mark Patrick; Lundregan, Sarah; Lien, Sigbjørn; Jensen, Henrik; Griffith, Simon C.
Source:
The Science of the total environment 2019 v.650 pp. 679-686
ISSN:
0048-9697
Subject:
single nucleotide polymorphism,   etc   ; Passer domesticus; birds; cell membranes; genes; genomics; humans; lead; loci; metalloids; mining; toxicity; transporters; wildlife; zinc;     Show all 15 Subjects
Abstract:
... Metals and metalloids at elevated concentrations can be toxic to both humans and wildlife. In particular, lead exposure can act as a stressor to wildlife and cause negative effects on fitness. Any ability to adapt to stress caused by the negative effects of trace metal exposure would be beneficial for species living in contaminated environments. However, mechanisms for responding adaptively to met ...
DOI:
10.1016/j.scitotenv.2018.09.052

8. Identification and validation of single-nucleotide polymorphism markers linked to first flower node in kenaf by using combined specific-locus amplified fragment sequencing and bulked segregant analysis

Author:
Li, Hui; Li, Defang; Zhao, Lining
Source:
Industrial crops and products 2019 v.128 pp. 566-571
ISSN:
0926-6690
Subject:
single nucleotide polymorphism,   etc   ; DNA; Hibiscus cannabinus; flowers; genetic markers; genotype; industrial crops; kenaf; loci; marker-assisted selection; phenotype;     Show all 11 Subjects
Abstract:
... It is important to develop DNA markers closely linked to the first flower node for molecular marker-assisted selection in kenaf breeding. Kenaf (Hibiscus cannabinus L.) is an annual, multipurpose industrial crop with a worldwide distribution. The higher the node of the first flower, the greater is the fiber yield. In this study, a population of 130 F2 individuals was constructed through the cross ...
DOI:
10.1016/j.indcrop.2018.11.055

9. High-throughput blood sample preparation for single nucleotide polymorphism genotyping in less than 25 min

Author:
Wang, Jidong; Zheng, Jiaying; Zhang, Shaohua; Du, Jihui; Chen, Yongxin; Liu, Xiaolei; Zhang, Huisheng; Jiang, Xingyu; Chen, Wenwen
Source:
Talanta 2019 v.191 pp. 119-125
ISSN:
0039-9140
Subject:
single nucleotide polymorphism,   etc   ; DNA; blood sampling; blood serum; genotyping; leukocyte count; protocols; quantitative polymerase chain reaction; triacylglycerols; uric acid;     Show all 10 Subjects
Abstract:
... Straightforward, rapid and high-throughput pretreatment for single nucleotide polymorphisms (SNP) genotyping is critically needed in clinical practice. However, all existing SNP genotyping methods require DNA purification step, which is labor-intensive and time-consuming. We develop a protocol for SNP genotyping by combining whole blood lysis (WBL) with qPCR and justify the practicality of our met ...
DOI:
10.1016/j.talanta.2018.08.051

10. Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms

Author:
Zeng, Xiang; Vonk, Judith M.; van der Plaat, Diana A.; Faiz, Alen; Paré, Peter D.; Joubert, Philippe; Nickle, David; Brandsma, Corry-Anke; Kromhout, Hans; Vermeulen, Roel; Xu, Xijin; Huo, Xia; de Jong, Kim; Boezen, H. Marike
Source:
Environment international 2019 v.122 pp. 263-269
ISSN:
0160-4120
Subject:
single nucleotide polymorphism,   etc   ; cough; dyspnea; environmental factors; gender; gene expression; genes; loci; lungs; meta-analysis; quantitative trait loci; regression analysis;     Show all 12 Subjects
Abstract:
... Respiratory symptoms are important indicators of respiratory diseases. Both genetic and environmental factors contribute to respiratory symptoms development but less is known about gene-environment interactions. We aimed to assess interactions between single nucleotide polymorphisms (SNPs) and occupational exposures on respiratory symptoms cough, dyspnea and phlegm. As identification cohort LifeLi ...
DOI:
10.1016/j.envint.2018.11.017

11. Genomic-polygenic and polygenic predictions for milk yield, fat yield, and age at first calving in Thai multibreed dairy population using genic and functional sets of genotypes

Author:
Laodim, Thawee; Elzo, Mauricio A.; Koonawootrittriron, Skorn; Suwanasopee, Thanathip; Jattawa, Danai
Source:
Livestock science 2019 v.219 pp. 17-24
ISSN:
1871-1413
Subject:
single nucleotide polymorphism,   etc   ; calving; cows; databases; genes; genetic correlation; genotype; heritability; heterosis; milk yield; models; pedigree; phenotype; prediction; sires; variance;     Show all 16 Subjects
Abstract:
... The objectives of this research were to estimate genomic-polygenic and polygenic variance components and parameters, and to compare prediction accuracies and rankings of animals for 305-d milk yield (MY), 305-d fat yield (FY), and age at first calving (AFC) using three genomic-polygenic models and a polygenic model (PM). Data came from 8361 first-lactation cows from the Thai multibreed dairy popul ...
DOI:
10.1016/j.livsci.2018.11.008

12. Identification of sorghum grain mold resistance loci through genome wide association mapping

Author:
Nida, Habte; Girma, Gezahegn; Mekonen, Moges; Lee, Sanghun; Seyoum, Amare; Dessalegn, Kebede; Tadesse, Taye; Ayana, Getachew; Senbetay, Tsegau; Tesso, Tesfaye; Ejeta, Gebisa; Mengiste, Tesfaye
Source:
Journal of cereal science 2019 v.85 pp. 295-304
ISSN:
0733-5210
Subject:
single nucleotide polymorphism,   etc   ; Sorghum bicolor; biosynthesis; chromosome mapping; flavonoids; fungi; genes; genome-wide association study; landraces; loci; spores; transcription factors;     Show all 12 Subjects
Abstract:
... Grain mold, caused by a consortium of pathogenic fungal species, is the most important disease of sorghum [Sorghum bicolor (L.) Moench]. Genome wide association study on 1425 diverse Ethiopian sorghum landraces identified a major grain mold resistance locus containing tightly linked and sequence related MYB transcription factor genes. The locus contains YELLOW SEED1 (Y1), a likely non-functional p ...
DOI:
10.1016/j.jcs.2018.12.016

13. Correction to: High density marker panels, SNPs prioritizing and accuracy of genomic selection

Author:
Chang, Ling-Yun; Toghiani, Sajjad; Ling, Ashley; Aggrey, Sammy E.; Rekaya, Romdhane
Source:
BMC genetics 2018 v.19 no.1 pp. 13
ISSN:
1471-2156
Subject:
single nucleotide polymorphism,   etc   ; data analysis; genetic markers; marker-assisted selection;     Show all 4 Subjects
Abstract:
... CORRECTION TO: BMC GENETICS (2018) 19:4 DOI: 10.1186/S12863-017-0595-2: The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. The original article has been updated. ...
DOI:
10.1186/s12863-018-0598-7

14. Cryptic natural hybridization between two species of Protea

Author:
Mitchell, N.; Holsinger, K.E.
Source:
South African journal of botany 2018 v.118 pp. 306-314
ISSN:
0254-6299
Subject:
single nucleotide polymorphism,   etc   ; Protea; genotyping by sequencing; introgression; mountains; seedlings;     Show all 6 Subjects
Abstract:
... Protea punctata and P. venusta are closely related, but morphologically distinct, species that naturally hybridize in the wild. Here we examined patterns of hybridization and cryptic introgression in seedlings grown from seeds collected at Blesberg Mountain in the Swartberg Mountain range. We used restriction site associated genotyping by sequencing (RAD-Seq) to identify 7185 single nucleotide pol ...
DOI:
10.1016/j.sajb.2017.12.002

15. Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum

Author:
Blanc-Jolivet, Céline; Kersten, Birgit; Bourland, Nils; Guichoux, Erwan; Delcamp, Adline; Doucet, Jean-Louis; Degen, Bernd
Source:
Conservation genetics resources 2018 v.10 no.3 pp. 539-541
ISSN:
1877-7252
Subject:
single nucleotide polymorphism,   etc   ; Entandrophragma cylindricum; loci; provenance; sequence analysis; trees;     Show all 6 Subjects
Abstract:
... We describe the development of new nuclear SNP markers for the genetic timber tracking of the geographical origin of Sapelli, Entandrophragma cylindricum (Meliaceae). Restriction associated DNA sequencing (RADseq) of two reference individuals yielded 1131 putative SNPs. Among those, 131 were selected to design four MassARRAY multiplexes and screened at 178 individuals. Seventy-two loci were select ...
DOI:
10.1007/s12686-017-0872-4

16. The role of introns in the conservation of the metabolic genes of Arabidopsis thaliana

Author:
Mukherjee, Dola; Saha, Deeya; Acharya, Debarun; Mukherjee, Ashutosh; Chakraborty, Sandip; Ghosh, Tapash Chandra
Source:
Genomics 2018 v.110 no.5 pp. 310-317
ISSN:
0888-7543
Subject:
single nucleotide polymorphism,   etc   ; Arabidopsis thaliana; alternative splicing; exons; introns;     Show all 5 Subjects
Abstract:
... In Arabidopsis thaliana, primary metabolic genes (PMGs) are more evolutionarily conserved and intron-rich than secondary metabolic genes. We observed that PMGs are more primitive and pan-taxonomically persistent as compared to secondary (SMGs) and non-metabolic genes (NMGs). This difference in primitiveness and persistence is primarily correlated with intron number and is independent of gene expre ...
DOI:
10.1016/j.ygeno.2017.12.003

17. RIT2: responsible and susceptible gene for neurological and psychiatric disorders

Author:
Daneshmandpour, Yousef; Darvish, Hossein; Emamalizadeh, Babak
Source:
Molecular genetics and genomics 2018 v.293 no.4 pp. 785-792
ISSN:
1617-4615
Subject:
single nucleotide polymorphism,   etc   ; Parkinson disease; autism; genes; humans; pathophysiology; schizophrenia;     Show all 7 Subjects
Abstract:
... RIT2 gene was recently introduced as a susceptibility gene in neurological disorders, a group of major problems in human society affecting millions of people worldwide. Several variants, including single nucleotide polymorphisms and CNVs, have been identified and studied in different populations. In this review, we have summarized the studies relevant to the RIT2 gene and its related disorders, in ...
DOI:
10.1007/s00438-018-1451-4

18. Changing the Guard at a Prostate Cancer SNP

Author:
Bulger, Michael
Source:
Cell 2018 v.174 no.3 pp. 501-502
ISSN:
0092-8674
Subject:
single nucleotide polymorphism,   etc   ; non-coding RNA; prostatic neoplasms; transcription factors;     Show all 4 Subjects
Abstract:
... The molecular underpinnings of a prostate-cancer-associated SNP are investigated in a pair of papers in this issue of Cell. Together, Gao et al. and Hua et al. paint a picture of competition between transcription factors that, in turn, toggle the function of a regulatory region from a promoter to an enhancer and induce a switch in noncoding RNA isoforms. ...
DOI:
10.1016/j.cell.2018.07.014

19. Molecular Approaches To Address the Challenges of RNA Analysis in Complex Matrices

Author:
Lansing, Shan S.; Matlapudi, Susmitha; Burrows, Sean M.
Source:
Analytical chemistry 2018 v.90 no.15 pp. 9156-9164
ISSN:
1520-6882
Subject:
single nucleotide polymorphism,   etc   ; biosensors; non-coding RNA; nucleases; polyethylene glycol;     Show all 5 Subjects
Abstract:
... We present on a design change and addition of an internal polyethylene glycol (PEG) spacer to an existing biosensor. There were two reasons for changing the sensor design. The first was to increase the stability of the biosensor to avoid binding off-analytes with single nucleotide polymorphisms. The second was to prevent sensor degradation by nucleases. The biosensor, designed for detection of sho ...
DOI:
10.1021/acs.analchem.8b01621

20. A simple and ultrasensitive fluorescence assay for single-nucleotide polymorphism

Author:
Ma, Qian; Gao, Zhiqiang
Source:
Analytical and bioanalytical chemistry 2018 v.410 no.13 pp. 3093-3100
ISSN:
1618-2642
Subject:
single nucleotide polymorphism,   etc   ; DNA; fluorescence; gene amplification; genes; mutants; nucleotides;     Show all 7 Subjects
Abstract:
... In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). Briefly, a designed padlock probe is first circularized by a DNA ligase when it perfectly complements to a mutant gene. Then, the mutant gene functions as a primer to initiate branched rolling circle amplification reaction ...
DOI:
10.1007/s00216-018-0874-4