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1. A hairpin-mediated nicking enzymatic signal amplification for nucleic acids detection

Author:
Zheng, Guoliang; Dai, Jiangshan; Wang, Haiyan; Li, Ling; Yuan, Deyu; Bai, Shujun; Song, Xu; Zhao, Yongyun
Source:
Talanta 2021 v.225 pp. 121991
ISSN:
0039-9140
Subject:
single nucleotide polymorphism,   etc   ; RNA; detection; research; sampling;     Show all 5 Subjects
Abstract:
... A novel signal amplification to detect nucleic acid, called hairpin-mediated nicking enzymatic signal amplification (HNESA), is developed. This method overcomes the limitation of conventional nicking enzymatic signal amplification (NESA) that the target must contain the nicking endonuclease recognition site by using a hairpin probe containing the nicking endonuclease recognition site as an interme ...
DOI:
10.1016/j.talanta.2020.121991

2. Homozygosity stretches around homozygous mutations in autosomal recessive disorders: patients from nonconsanguineous Indian families

Author:
Phadke, Shubha R.; Srivastava, Priyanka; Sharma, Pankaj; Rai, Archana; Masih, Suzena
Source:
Journal of genetics 2021 v.100 no.1 pp. 2
ISSN:
0022-1333
Subject:
single nucleotide polymorphism arrays,   etc   ; ancestry; genomics; homozygosity; marriage; India;     Show all 6 Subjects
Abstract:
... India has a large heterogeneous population with its unique social and genetic characteristics. Tradition of marriage between specific caste groups have produced unique characteristics to the mutation spectrum of genetic disorders and may be a higher prevalence of autosomal recessive (AR) disorders in some communities. We observed that in many nonconsanguineous families with rare autosomal disorder ...
DOI:
10.1007/s12041-020-01250-6

3. Technical note: Genetic groups in single-step single nucleotide polymorphism best linear unbiased predictor

Author:
Vandenplas, Jeremie; Eding, Herwin; Calus, Mario P.L.
Source:
Journal of dairy science 2021 v.104 no.3 pp. 3298-3303
ISSN:
0022-0302
Subject:
single nucleotide polymorphism,   etc   ; dairy cattle; dairy science; genomics; memory; pedigree;     Show all 6 Subjects
Abstract:
... Genetic groups, also called unknown or phantom parents groups, are often used in dairy cattle genetic evaluations to account for selection that cannot be accounted for by known genetic relationships. With the advent of genomic evaluations, the theory of genetic groups was extended to the so-called single-step genomic BLUP (ssGBLUP). In short, genetic groups can be fitted in ssGBLUP through regress ...
DOI:
10.3168/jds.2020-19460

4. Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses

Author:
Sheng, Yan-Ran; Hou, Shun-Yu; Hu, Wen-Ting; Wei, Chun-Yan; Liu, Yu-Kai; Liu, Yu-Yin; Jiang, Lu; Xiang, Jing-Jing; Sun, Xiao-Xi; Lei, Cai-Xia; Wang, Hui-Ling; Zhu, Xiao-Yong
Source:
Genes 2021 v.12 no.2
ISSN:
2073-4425
Subject:
single nucleotide polymorphism arrays,   etc   ; abortion (animals); conception; etiology; pregnancy;     Show all 5 Subjects
Abstract:
... It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscop ...
DOI:
10.3390/genes12020141

5. Confirmation of Paternity despite Three Genetic Incompatibilities at Chromosome 2

Author:
Doniec, Andrzej; Łuczak, Wojciech; Wróbel, Maria; Januła, Miłosz; Ossowski, Andrzej; Grzmil, Paweł; Kupiec, Tomasz
Source:
Genes 2021 v.12 no.1
ISSN:
2073-4425
Subject:
single nucleotide polymorphism,   etc   ; DNA; children; parenting; paternity; sequence analysis;     Show all 6 Subjects
Abstract:
... DNA testing in cases of disputed paternity is a routine analysis carried out in genetic laboratories. The purpose of the test is to demonstrate similarities and differences in analyzed genetic markers between the alleged father, mother, and a child. The existence of differences in the examined loci between the child and the presumed father may indicate the exclusion of biological parenthood. Howev ...
DOI:
10.3390/genes12010062

6. New resources for genetic studies in maize (Zea mays L.): a genome‐wide Maize6H‐60K single nucleotide polymorphism array and its application

Author:
Tian, Hongli; Yang, Yang; Yi, Hongmei; Xu, Liwen; He, Hang; Fan, Yaming; Wang, Lu; Ge, Jianrong; Liu, Yawei; Wang, Fengge; Zhao, Jiuran
Source:
Theplant journal 2021 v.105 no.4 pp. 1113-1122
ISSN:
0960-7412
Subject:
single nucleotide polymorphism; single nucleotide polymorphism arrays,   etc   ; Zea mays; corn; decline; gene frequency; genotyping; germplasm; heterosis; inbreeding; linkage disequilibrium;     Show all 11 Subjects
Abstract:
... Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low‐cost manner is challenging. Here, we present Maize6H‐60K, a genome‐wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million ...
DOI:
10.1111/tpj.15089

7. BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs

Author:
Luhmann, Nina; Holley, Guillaume; Achtman, Mark
Source:
Genome biology 2021 v.22 no.1 pp. 30
ISSN:
1474-760X
Subject:
single nucleotide polymorphism,   etc   ; Salmonella; extracts; fluoroquinolones; genes; genome assembly; graphs; nucleotide sequences; pathogenicity islands;     Show all 9 Subjects
Abstract:
... BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants. We show two ...
DOI:
10.1186/s13059-020-02237-3

8. Convergence behavior of single-step GBLUP and SNPBLUP for different termination criteria

Author:
Vandenplas, Jeremie; Calus, Mario P. L.; Eding, Herwin; van Pelt, Mathijs; Bergsma, Rob; Vuik, Cornelis
Source:
Genetics, selection, evolution 2021 v.53 no.1 pp. 34
ISSN:
1297-9686
Subject:
single nucleotide polymorphism,   etc   ; dairy cattle; data collection; evolution; genomics; prediction; swine;     Show all 7 Subjects
Abstract:
... BACKGROUND: The preconditioned conjugate gradient (PCG) method is the current method of choice for iterative solving of genetic evaluations. The relative difference between two successive iterates and the relative residual of the system of equations are usually chosen as a termination criterion for the PCG method in animal breeding. However, our initial analyses showed that these two commonly used ...
DOI:
10.1186/s12711-021-00626-1

9. Development of a 38 K single nucleotide polymorphism array and application in genomic selection for resistance against Vibrio harveyi in Chinese tongue sole, Cynoglossus semilaevis

Author:
Lu, Sheng; Zhou, Qian; Chen, Yadong; Liu, Yang; Li, Yangzhen; Wang, Lei; Yang, Yingming; Chen, Songlin
Source:
Genomics 2021 v.113 no.4 pp. 1838-1844
ISSN:
0888-7543
Subject:
single nucleotide polymorphism arrays,   etc   ; Cynoglossus semilaevis; Vibrio harveyi; genomics; genotyping; marker-assisted selection; prediction; progeny;     Show all 8 Subjects
Abstract:
... Based on 1572 re-sequenced Chinese tongue sole (Cynoglossus semilaevis), we investigated the accuracy of four genomic methods at predicting genomic estimated breeding values (GEBVs) of Vibrio harveyi resistance in C. semilaevis when SNPs varying from 500 to 500 k. All methods outperformed the pedigree-based best linear unbiased prediction when SNPs reached 50 k or more. Then, we developed an SNP a ...
DOI:
10.1016/j.ygeno.2021.03.034

10. Molecular characterization and analysis of the association of growth hormone 1 gene with growth traits in Chinese indigenous yak (Bos grunniens)

Author:
Gui, Linsheng; Raza, Sayed Haidar Abbas; Sun, Yonggang; Sabek, Ahmed; Abbas, Sayed Qaisar; Shah, Mujahid Ali; Khan, Rajwali; Abdelnour, Sameh A.
Source:
Tropical animal health and production 2021 v.53 no.2 pp. 221
ISSN:
0049-4747
Subject:
single nucleotide polymorphism,   etc   ; animal health; exons; genetic markers; genotype; polymerase chain reaction; somatotropin; yaks;     Show all 8 Subjects
Abstract:
... This study aimed to investigate the effects of polymorphisms in growth hormone 1 (GH1) gene on the growth traits in Chinese indigenous yak. Using the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, one novel single-nucleotide polymorphism (SNP), termed as g.1721G>A, was identified in the exon 4 of GH1 gene in 423 individuals of yak population. Based on the c ...
DOI:
10.1007/s11250-021-02671-w

11. Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34+

Author:
Xu, Feng; Ge, Chongtao; Li, Shaoting; Tang, Silin; Wu, Xingwen; Luo, Hao; Deng, Xiangyu; Zhang, Guangtao; Stevenson, Abigail; Baker, Robert C.
Source:
International journal of food microbiology 2021 v.346 pp. 109167
ISSN:
0168-1605
Subject:
single nucleotide polymorphism,   etc   ; Poecilia; Salmonella choleraesuis Choleraesuis; food industry; food microbiology; genome; models; nanopores; prediction; serotypes;     Show all 10 Subjects
Abstract:
... Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of selected Salmonella serotypes. However, one limitation is that established methods for WGS-based serotype prediction, utilizing data from either ONT or Illumina, cannot differentiate certain serotypes and serotype variants with the ...
DOI:
10.1016/j.ijfoodmicro.2021.109167

12. Transcriptomic analysis suggests candidate genes for hygienic behavior in African-derived Apis mellifera honeybees

Author:
Teixeira, Érica Weinstein; de Paiva Daibert, Raquel Morais; Glatzl Júnior, Luiz Afonso; da Silva, Marcos Vinicius Gualberto Barbosa; Alves, Maria Luisa Teles Marques Florencio; Evans, Jay Daniel; Toth, Amy Lynn
Source:
Apidologie 2021 v.52 no.2 pp. 447-462
ISSN:
0044-8435
Subject:
single nucleotide polymorphism,   etc   ; Apis mellifera; RNA; gene expression regulation; genes; hygiene; transcriptome; transcriptomics;     Show all 8 Subjects
Abstract:
... Hygienic behavior is a social defense mechanism against parasites and pathogens in honeybees. We studied the genetic basis of hygienic behavior in African-derived Apis mellifera by performing RNA sequencing on brains of individual honeybee workers observed performing hygienic behavior, in order to identify expression changes linked with this behavior. We also used the transcriptome data to search ...
DOI:
10.1007/s13592-020-00834-6

13. Genetic factors in the pathogenesis of ameloblastoma, dentigerous cyst and odontogenic keratocyst

Author:
Ghafouri-Fard, Soudeh; Atarbashi-Moghadam, Saede; Taheri, Mohammad
Source:
Gene 2021 v.771 pp. 145369
ISSN:
0378-1119
Subject:
single nucleotide polymorphism,   etc   ; genetic factors; non-coding RNA; odontogenic neoplasms; oncogenes; pathogenesis; tissues; tumor suppressor genes;     Show all 8 Subjects
Abstract:
... Ameloblastoma (AB), dentigerous cyst (DC) and Odontogenic keratocyst (OKC) are odontogenic lesions with propensity to malignant transformation or local invasion. The molecular mechanisms of development of these lesions are not fully understood. However, some researches have reported dysregulation of tumor suppressor genes or oncogenes in these lesions. Down-regulation of P53 gene has been reported ...
DOI:
10.1016/j.gene.2020.145369

14. Combining targeted sequencing and ultra-low-pass whole-genome sequencing for accurate somatic copy number alteration detection

Author:
Fu, Junfeng; Guo, Weihua; Yan, Cheng; Lv, Zhenyang; Wang, Yu; Wang, Ze; Fan, Zhe; Lei, Ting
Source:
Functional & integrative genomics 2021 v.21 no.2 pp. 161-169
ISSN:
1438-793X
Subject:
single nucleotide polymorphism,   etc   ; alleles; aneuploidy; blood; brain; carcinogenesis; cerebrospinal fluid; genomics; lung neoplasms; metastasis; prognosis;     Show all 11 Subjects
Abstract:
... This study investigated the feasibility of combining targeted sequencing and ultra-low-pass whole-genome sequencing (ULP-WGS) for improved somatic copy number alteration (SCNA) detection, due to its role in tumorigenesis and prognosis. Cerebrospinal fluid and matched blood samples were obtained from 29 patients with brain metastasis derived from lung cancer. Samples were subjected to targeted sequ ...
DOI:
10.1007/s10142-021-00767-y

15. Mapping chromosomal regions associated with anther indehiscence with exerted stigmas in CRI-48 and Jasmine 85 cross of rice (Oryza sativa L)

Author:
Abebrese, Samuel Oppong; Amoah, Nana Kofi Abaka; Dartey, Paul Kofi Ayirebi; Bimpong, Isaac Kofi; Akromah, Richard; Gracen, Vernon Edward; Offei, Samuel Kwame; Danquah, Eric Yirenkyi
Source:
Heliyon 2021 v.7 no.3 pp. e06483
ISSN:
2405-8440
Subject:
single nucleotide polymorphism,   etc   ; Oryza glaberrima; Oryza sativa; alleles; ancestry; backcrossing; hybrids; loci; male sterility; rice; stigma;     Show all 11 Subjects
Abstract:
... Anther indehiscence in certain wide crosses combines male sterility with stigma exertion, a phenomenon that is desirable for hybrid rice seed production. This study sought to identify chromosomal region(s) that combine anther indehiscence with exerted stigmas. A mapping population consisting of 189 BC₁F₁ plants was derived from a cross between CRI-48 and Jasmine 85 and backcrossing the resulting F ...
DOI:
10.1016/j.heliyon.2021.e06483

16. Investigating the Effect of Imputed Structural Variants from Whole-Genome Sequence on Genome-Wide Association and Genomic Prediction in Dairy Cattle

Author:
Chen, Long; Pryce, Jennie E.; Hayes, Ben J.; Daetwyler, Hans D.
Source:
Animals 2021 v.11 no.2
ISSN:
2076-2615
Subject:
single nucleotide polymorphism,   etc   ; DNA; Holstein; Jersey; dairy cattle; genetic variance; genome; genomics; milk yield; prediction; variance;     Show all 11 Subjects
Abstract:
... Structural variations (SVs) are large DNA segments of deletions, duplications, copy number variations, inversions and translocations in a re-sequenced genome compared to a reference genome. They have been found to be associated with several complex traits in dairy cattle and could potentially help to improve genomic prediction accuracy of dairy traits. Imputation of SVs was performed in individual ...
DOI:
10.3390/ani11020541

17. Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Author:
Mehrban, Hossein; Naserkheil, Masoumeh; Lee, Deuk Hwan; Cho, Chungil; Choi, Taejeong; Park, Mina; Ibáñez-Escriche, Noelia
Source:
Genes 2021 v.12 no.2
ISSN:
2073-4425
Subject:
single nucleotide polymorphism,   etc   ; backfat; beef cattle; carcass weight; genomics; genotyping; marbling; phenotype; prediction; quantitative traits; yearlings;     Show all 11 Subjects
Abstract:
... The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait bes ...
DOI:
10.3390/genes12020266

18. SNP in Potentially Defunct Tetrahydrocannabinolic Acid Synthase Is a Marker for Cannabigerolic Acid Dominance in Cannabis sativa L.

Author:
Garfinkel, Andrea R.; Otten, Matthew; Crawford, Seth
Source:
Genes 2021 v.12 no.2
ISSN:
2073-4425
Subject:
single nucleotide polymorphism,   etc   ; Cannabis sativa; cannabinoids; chemotypes; cultivars; genetic markers; genotyping; recessive genes;     Show all 8 Subjects
Abstract:
... The regulation of cannabinoid synthesis in Cannabis sativa is of increasing research interest as restrictions around the globe loosen to allow the plant’s legal cultivation. Of the major cannabinoids, the regulation of cannabigerolic acid (CBGA) production is the least understood. The purpose of this study was to elucidate the inheritance of CBGA dominance in C. sativa and describe a marker relate ...
DOI:
10.3390/genes12020228

19. Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Author:
Chawla, Harmeet Singh; Lee, HueyTyng; Gabur, Iulian; Vollrath, Paul; Tamilselvan‐Nattar‐Amutha, Suriya; Obermeier, Christian; Schiessl, Sarah V.; Song, Jia‐Ming; Liu, Kede; Guo, Liang; Parkin, Isobel A. P.; Snowdon, Rod J.
Source:
Plant biotechnology journal 2021 v.19 no.2 pp. 240-250
ISSN:
1467-7644
Subject:
single nucleotide polymorphism,   etc   ; Brassica napus; allopolyploidy; biotechnology; crops; disease resistance; ecology; evolution; genes;     Show all 9 Subjects
Abstract:
... Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However ...
DOI:
10.1111/pbi.13456

20. Population Structure Assessed Using Microsatellite and SNP Data: An Empirical Comparison in West African Cattle

Author:
Álvarez, Isabel; Fernández, Iván; Traoré, Amadou; Menéndez-Arias, Nuria A.; Goyache, Félix
Source:
Animals 2021 v.11 no.1
ISSN:
2076-2615
Subject:
single nucleotide polymorphism,   etc   ; genetic background; genetic variation; microsatellite repeats; population structure; taurine; zebu; Benin;     Show all 8 Subjects
Abstract:
... A sample of 185 West African cattle belonging to nine different taurine, sanga, and zebu populations was typed using a set of 33 microsatellites and the BovineHD BeadChip of Illumina. The information provided by each type of marker was summarized via clustering methods and principal component analyses (PCA). The aim was to assess differences in performance between both marker types for the identif ...
DOI:
10.3390/ani11010151