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https://www.readbyqxmd.com/read/28619083/on-marker-based-parentage-verification-via-non-linear-optimization
#1
Vinzent Boerner
BACKGROUND: Parentage verification by molecular markers is mainly based on short tandem repeat markers. Single nucleotide polymorphisms (SNPs) as bi-allelic markers have become the markers of choice for genotyping projects. Thus, the subsequent step is to use SNP genotypes for parentage verification as well. Recent developments of algorithms such as evaluating opposing homozygous SNP genotypes have drawbacks, for example the inability of rejecting all animals of a sample of potential parents...
June 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28560110/isolation-and-characterization-of-microsatellite-markers-for-sturnira-parvidens-and-cross-species-amplification-in-sturnira-species
#2
Edgar G Gutiérrez, Giovani Hernández Canchola, Livia S León Paniagua, Norberto Martínez Méndez, Jorge Ortega
BACKGROUND: Sturnira is one of the most species-rich genera in the Neotropics, and it is found from Mexico and the Lesser Antilles to Argentina. This genus forms a well-supported monophyletic clade with at least twenty-one recognized species, as well as several others under taxonomic review. Sturnira parvidens is a widespread frugivorous bat of the deciduous forests of the Neotropics, is highly abundant, and is a major component in fruit dispersal to regenerate ecosystems. METHODS: We used a technique based on Illumina paired-end sequencing of a library highly enriched for microsatellite repeats to develop loci for S...
2017: PeerJ
https://www.readbyqxmd.com/read/28549462/development-of-a-snp-panel-dedicated-to-parentage-assignment-in-french-sheep-populations
#3
F Tortereau, C R Moreno, G Tosser-Klopp, B Servin, J Raoul
BACKGROUND: The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values...
May 26, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28448554/evaluation-of-efficiency-of-controlled-pollination-based-parentage-analysis-in-a-larix-gmelinii-var-principis-rupprechtii-mayr-seed-orchard
#4
Wenting Sun, Dade Yu, Mingliang Dong, Jian Zhao, Xiaoping Wang, Hongjing Zhang, Jinfeng Zhang
Controlled pollination (CP) is an important tool for breeding programs to improve seed quality, as it rapidly generates desirable genotypes and maximizes genetic gains. However, few studies have evaluated the success rate of CP, especially in Larix gmelinii var. principis-rupprechtii Mayr. seed orchards. In this study, we estimated the rate of correct parentage in 257 CP progeny in an L. gmelinii var. principis-rupprechtii seed orchard from ten candidate parents using 13 microsatellites. The parentage exclusion probabilities of all combined loci in the single parent and parent pair tests were > 0...
2017: PloS One
https://www.readbyqxmd.com/read/28444756/e7-1057%C3%AE-ta-mutation-of-the-acidic-%C3%AE-glucosidase-gene-causes-pompe-s-disease-in-droughtmaster-cattle
#5
R E Lyons, D J Johnston, M R McGowan, A Laing, B Robinson, H Owen, B D Hill, B M Burns
OBJECTIVE: To determine whether known loss-of-function alleles of the acidic α-glucosidase gene (GAA) are present in the Droughtmaster breed and, if so, whether the clinical signs and pathology of generalised glycogenosis (Pompe's disease) previously reported in other affected cattle are also seen in homozygous Droughtmasters. DESIGN: Existing genomic and other diagnostic tests developed for generalised glycogenosis in cattle were used to test for the presence of the three known loss-of-function alleles of GAA in a herd of Droughtmaster cattle...
May 2017: Australian Veterinary Journal
https://www.readbyqxmd.com/read/28405751/developmental-validation-of-a-6-dye-str-kit-with-27-loci
#6
Shuanglin Li, Ling Chen, Yanfang Wang, Quyi Xu, Hong Liu, Yue Li, Chao Liu
The EX27 System is a 6-dye (i.e., FAM, HEX, TAMAR, ROX, VIG, and SIZ-500) kit that combines the 24 autosomal STR loci (i.e., D3S1358, D13S317, D7S820, D16S539, D1S1656, Penta E, TPOX, TH01, D2S1338, CSF1PO, Penta D, D10S1248, D19S433, vWA, D21S11, D18S51, D6S1043, D8S1179, D5S818, D12S391, FGA, D22S1045, D2S441, SE33) with a Y-STR locus (DYS391), an Indel site (YIndel) and Amelogenin, which is designed to amplify DNA from extracts as well as direct amplification from substrates. The new system contains most of the widely used autosomal STR loci around the world and is sensitive to the male component in mixtures and is more accurate in gender determination owing to the DYS391 and YIndel...
April 12, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28346672/congenital-bilateral-anterior-nasal-atresia-in-16-half-sibling-holstein-friesian-calves
#7
M McGowan, C Smith, A Ferguson, B Stone, D Vankan, R Allavena
CASE REPORT: Cases of bilateral anterior nasal atresia, sometimes referred to as arhinia or partial arhinia, are extremely rare in cattle and have only been reported as single events. This report describes the birth of 16 Holstein Friesian calves over a 3-month period, all affected with bilateral atresia of the nares and anterior nasal cavity, with 2 calves having additional severe deviation of the nasomaxillary bones and nasal septum. One affected calf was born with an anatomically normal twin...
April 2017: Australian Veterinary Journal
https://www.readbyqxmd.com/read/28344897/testing-of-microsatellite-multiplexes-for-individual-identification-of-cape-parrots-poicephalus-robustus-paternity-testing-and-monitoring-trade
#8
Willem G Coetzer, Colleen T Downs, Mike R Perrin, Sandi Willows-Munro
BACKGROUND: Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade...
2017: PeerJ
https://www.readbyqxmd.com/read/28342005/genetic-polymorphisms-for-19-autosomal-str-loci-of-chongqing-han-ethnicity-and-phylogenetic-structure-exploration-among-28-chinese-populations
#9
Xing Zou, YongGuo Li, Ping Li, QianYun Nie, Ting Wang, Yue Hu, Ying Zhu, JianBo Li, RenKuan Tang
The allele frequencies and forensic statistical parameters of 19 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D6S1043, Penta D, Penta E, and D12S391) included in the Goldeneye™ DNA ID system 20A kit were obtained in 671 Chinese Han individuals residing in Chongqing, Southwest China. All 19 STR loci were identified in agreement with the Hardy-Weinberg equilibrium. A total of 238 alleles were observed with corresponding allele frequencies that varied from 0...
March 24, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28295384/noninvasive-fetal-genotyping-of-paternally-inherited-alleles-using-targeted-massively-parallel-sequencing-in-parentage-testing-cases
#10
Donggui Yang, Hao Liang, Yu Gao, Shaobin Lin, Zhiming He, Jun Gao, Hongyu Sun, Qing Li, Xiaoyan Ma, Xueling Ou
BACKGROUND: Researchers have sought to develop a noninvasive protocol for paternity analysis that uses fetal cell-free DNA (cfDNA) in maternal plasma. Massively parallel sequencing (MPS) is expected to overcome this challenge because it enables the analysis of millions of DNA molecules at a single-base resolution. STUDY DESIGN AND METHODS: Seven women were involved in prenatal paternity testing cases. Before conventional invasive procedures, cfDNA was isolated from maternal plasma...
March 10, 2017: Transfusion
https://www.readbyqxmd.com/read/28271620/pedigree-reconstruction-from-snp-data-parentage-assignment-sibship-clustering-and-beyond
#11
Jisca Huisman
Data on hundreds or thousands of Single Nucleotide Polymorphisms (SNPs) provides detailed information about the relationships between individuals, but currently few tools can turn this information into a multi-generational pedigree. I present the R package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent, and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first, second and third degree relationships between the focal individuals, as well as the traditional alter native of being unrelated...
March 7, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28213940/estimating-mating-rates-in-wild-drosophila-melanogaster-females-by-decay-rates-of-male-reproductive-proteins-in-their-reproductive-tracts
#12
Thomas J Giardina, Andrew G Clark, Anthony C Fiumera
Female Drosophila melanogaster frequently mate with multiple males in nature as shown through parentage analysis. Although polyandry is well documented, we know little about the timing between mating events in wild Drosophila populations due to the challenge of following behaviors of individual females. In this study we used the presence of a male reproductive protein that is transferred to the female during mating (Sex Peptide, SP) to determine whether she had recently mated. We sampled females throughout the day, conducted control matings to determine the decay rate of SP within the female reproductive tract and performed computer simulations to fit the observed proportion of mated females to a non-homogenous Poisson process that defined the expected time between successive matings for a given female...
February 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28170027/snp-discovery-and-characterisation-in-white-rhino-ceratotherium-simum-with-application-to-parentage-assignment
#13
Christiaan Labuschagne, Desiré L Dalton, J Paul Grobler, Antoinette Kotzé
The white rhino is one of the great success stories of modern wildlife conservation, growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns is adding constant pressure on remaining populations. Captive management of ex situ populations of endangered species using molecular methods can contribute to improving the management of the species. Here we compare for the first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine microsatellites (MS) in isolation and in combination for assigning parentage in captive White Rhinoceros...
January 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28095776/genetic-and-economic-benefits-of-selection-based-on-performance-recording-and-genotyping-in-lower-tiers-of-multi-tiered-sheep-breeding-schemes
#14
Bruno F S Santos, Julius H J van der Werf, John P Gibson, Timothy J Byrne, Peter R Amer
BACKGROUND: Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. METHODS: The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection...
January 17, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28049866/genetic-diversity-of-the-yonaguni-horse-based-on-polymorphisms-in-microsatellites-and-mitochondrial-dna
#15
Natsuko Senju, Teruaki Tozaki, Hironaga Kakoi, Akihisa Shinjo, Ryota Matsuyama, Julio Almunia, Masaki Takasu
Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0...
February 28, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28018637/from-resource-to-female-defence-the-impact-of-roosting-ecology-on-a-bat-s-mating-strategy
#16
Linus Günther, Marlena D Lopez, Mirjam Knörnschild, Kyle Reid, Martina Nagy, Frieder Mayer
With their extraordinary species richness and diversity in ecological traits and social systems, bats are a promising taxon for testing socio-ecological hypotheses in order to get new insights into the evolution of animal social systems. Regarding its roosting habits, proboscis bats form an extreme by occupying sites which are usually completely exposed to daylight (e.g. tree trunks, vines or rocks). This is accompanied by morphological and behavioural adaptations to remain cryptic in exposed day roosts. With long-term behavioural observations and genetic parentage analyses of individually marked proboscis bats, we assessed its social dispersion and male mating strategy during day and night...
November 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27992828/validation-of-the-microreader%C3%A2-23sp-id-system-a-new-str-23-plex-system-for-forensic-application
#17
Jienan Li, Haibo Luo, Feng Song, Lushun Zhang, Chuncao Deng, Zailiang Yu, Tianzhen Gao, Miao Liao, Yiping Hou
Microreader™ 23sp ID system is a new 23-plex STR genotyping system that amplified 21 non-CODIS STR loci (D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D7S3048, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D12S391, D2S1338, D17S1290 and D5S2500), one CODIS STR locus (D16S539) and the amelogenin locus in one reaction. Microreader™ 23sp ID system was validated according to the guidelines of "Validation Guidelines for DNA Analysis Methods (2012)" described by the Scientific Working Group on DNA Analysis Methods (SWGDAM), including PCR-based studies, sensitivity study, precision and accuracy evaluation, stutter percentage and peak height ratio, inhibitors, species specificity and DNA mixture studies...
March 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27902727/hybrid-origins-of-citrus-varieties-inferred-from-dna-marker-analysis-of-nuclear-and-organelle-genomes
#18
Tokurou Shimizu, Akira Kitajima, Keisuke Nonaka, Terutaka Yoshioka, Satoshi Ohta, Shingo Goto, Atsushi Toyoda, Asao Fujiyama, Takako Mochizuki, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins...
2016: PloS One
https://www.readbyqxmd.com/read/27890101/genetic-polymorphism-studies-on-22-autosomal-str-loci-of-the-powerplex-fusion-system-in-bangladeshi-population
#19
Tania Hossain, Mahamud Hasan, Ashish K Mazumder, Pilu Momtaz, Abu Sufian, Jabedul Alam Khandaker, Sharif Akhteruzzaman
Genetic polymorphism of 22 autosomal STR loci included in PowerPlex® Fusion System (D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA and D22S1045) was studied in 188 unrelated Bangladeshi Bengali individuals. Allele frequencies and forensic efficiency parameters such as, the power of discrimination (PD), observed and expected heterozygosity (Ho & He), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE) and typical paternity index was calculated for the loci...
November 2016: Legal Medicine
https://www.readbyqxmd.com/read/27864914/the-lek-mating-system-of-the-worm-pipefish-nerophis-lumbriciformis-a-molecular-maternity-analysis-and-test-of-the-phenotype-linked-fertility-hypothesis
#20
N M Monteiro, D Carneiro, A Antunes, N Queiroz, M N Vieira, A G Jones
The origin and maintenance of mating preferences continues to be an important and controversial topic in sexual selection research. Leks and lek-like mating systems, where individuals gather in particular spots for the sole purpose of mate choice, are particularly puzzling, because the strong directional selection imposed by mate choice should erode genetic variation among competing individuals and negate any benefit for the choosing sex. Here, we take advantage of the lek-like mating system of the worm pipefish (Nerophis lumbriciformis) to test the phenotype-linked fertility hypothesis for the maintenance of mating preferences...
November 19, 2016: Molecular Ecology
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