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https://www.readbyqxmd.com/read/28899355/genetic-tests-for-estimating-dairy-breed-proportion-and-parentage-assignment-in-east-african-crossbred-cattle
#1
Eva M Strucken, Hawlader A Al-Mamun, Cecilia Esquivelzeta-Rabell, Cedric Gondro, Okeyo A Mwai, John P Gibson
BACKGROUND: Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application...
September 12, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28866789/population-data-and-forensic-efficiency-of-21-autosomal-str-loci-included-in-agcu-ex22-amplification-system-in-the-wanzhou-han-population
#2
Xing Zou, Yongguo Li, Zehong Wei, Ting Wang, Yue Hu, Ying Zhu, Jianbo Li, Renkuan Tang
Autosomal short tandem repeats (STRs), widely distributed in the whole human genome, play an important role in personal identification and parentage testing. In this study, the allele frequencies and forensic efficiency parameters of 21 autosomal STR loci included in the AGCU EX22 kit were obtained from 433 Chinese Han individuals residing in the Wanzhou District in the north of Chongqing Municipality, Southwest China. No deviation from Hardy-Weinberg equilibrium was observed in all of the 21 STR loci. A total of 241 alleles were observed with allele frequencies ranging from 0...
September 2, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28861717/estimates-of-heritability-for-growth-and-shell-color-traits-and-their-genetic-correlations-in-the-black-shell-strain-of-pacific-oyster-crassostrea-gigas
#3
Lan Xu, Qi Li, Hong Yu, Lingfeng Kong
The Pacific oyster Crassostrea gigas has been introduced widely and massively and became an economically important aquaculture species on a global scale. We estimated heritabilities of growth and shell color traits and their genetic correlations in black shell strain of C. gigas. Analyses were performed on 22 full-sib families in a nested mating design including 410 individuals at harvest (24 months of age). The parentage assignment was inferred based on four panels of multiplex PCR markers including 10 microsatellite loci and 94...
August 31, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28855677/no-evidence-for-parental-age-effects-on-offspring-leukocyte-telomere-length-in-free-living-soay-sheep
#4
H Froy, E J Bird, R V Wilbourn, J Fairlie, S L Underwood, E Salvo-Chirnside, J G Pilkington, C Bérénos, J M Pemberton, D H Nussey
In humans, the effect of paternal age at conception (PAC) on offspring leukocyte telomere length (LTL) is well established, with older fathers thought to pass on longer telomeres to their offspring in their sperm. Few studies have looked for PAC effects in other species, but it has been hypothesised that the effect will be exacerbated in polygamous species with higher levels of sperm competition and production. We test for maternal (MAC) and paternal age at conception effects on offspring LTL in Soay sheep, a primitive breed experiencing strong sperm competition...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28854191/use-of-noninvasive-bug-eggs-to-enable-comparative-inferences-on-genetic-mating-system-with-and-without-parental-information-a-study-in-a-cattle-egret-colony
#5
Carolina Isabel Miño, Elaine Dantas de Souza, Emmanuel Moralez-Silva, Talita Alvarenga Valdes, Vera Lúcia Cortiço Corrêa Rodrigues, Sílvia Nassif Del Lama
Colonial waterbirds such as herons, egrets and spoonbills exhibit ecological characteristics that could have promoted the evolution of conspecific brood parasitism and extra-pair copulation. However, an adequate characterization of the genetic mating systems of this avian group has been hindered by the lack of samples of elusive candidate parents which precluded conducting conventional parentage allocation tests. Here, we investigate the genetic mating system of the invasive cattle egret using hematophagous insects contained in fake eggs to collect blood from incubating adults in a wild breeding colony...
2017: PloS One
https://www.readbyqxmd.com/read/28797302/development-and-characterization-of-microsatellite-markers-for-diploid-populations-of-the-wind-pollinated-herb-mercurialis-annua
#6
Ana Paula Machado, John R Pannell, Jeanne Tonnabel
OBJECTIVE: Mercurialis annua is a wind-pollinated annual plant that has long been used as a model for the study of ploidy and sexual-systems evolution. However, no molecular markers are yet available for genetic studies of its diploid populations. Here, we develop and characterize a set of eight polymorphic microsatellite markers for diploid dioecious M. annua. RESULTS: Following an SSR-enrichment protocol, 13 microsatellite markers were proposed, eight of which yielded successful amplification and polymorphism...
August 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28776934/development-of-genome-and-transcriptome-derived-microsatellites-in-related-species-of-snapping-shrimps-with-highly-duplicated-genomes
#7
Kaitlyn M Gaynor, Joseph W Solomon, Stefanie Siller, Linnet Jessell, J Emmett Duffy, Dustin R Rubenstein
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication...
August 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28735584/genomic-differentiation-between-swamp-and-river-buffalo-using-a-cattle-high-density-single-nucleotide-polymorphisms-panel
#8
L Pérez-Pardal, S Chen, V Costa, X Liu, J Carvalheira, A Beja-Pereira
Buffalo (Bubalus bubalis) is an important livestock species in many tropical and subtropical regions. In recent decades, the interest in buffalo's milk have expanded and intensive buffalo farms start to emerge. However, breeding programs and population genetics information for this species is scarce or inexistent. The present study aims to test the suitability of the commercial high-density single nucleotide polymorphisms (SNP) genotyping panel, the Illumina BovineHD BeadChip, to estimate population genetics parameters, pedigree control and identification of common variants in major production candidate genes...
July 24, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28619083/on-marker-based-parentage-verification-via-non-linear-optimization
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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