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https://www.readbyqxmd.com/read/28647327/genomic-analysis-of-cow-mortality-and-milk-production-using-a-threshold-linear-model
#1
S Tsuruta, D A L Lourenco, I Misztal, T J Lawlor
The objective of this study was to investigate the feasibility of genomic evaluation for cow mortality and milk production using a single-step methodology. Genomic relationships between cow mortality and milk production were also analyzed. Data included 883,887 (866,700) first-parity, 733,904 (711,211) second-parity, and 516,256 (492,026) third-parity records on cow mortality (305-d milk yields) of Holsteins from Northeast states in the United States. The pedigree consisted of up to 1,690,481 animals including 34,481 bulls genotyped with 36,951 SNP markers...
June 21, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28646171/a-new-type-of-homodiploid-fish-derived-from-the-interspecific-hybridization-of-female-common-carp%C3%A2-%C3%A3-%C3%A2-male-blunt-snout-bream
#2
Shi Wang, Xiaolan Ye, Yude Wang, Yuting Chen, Bowen Lin, Zhenfeng Yi, Zhuangwen Mao, Fangzhou Hu, Rurong Zhao, Juan Wang, Rong Zhou, Li Ren, Zhanzhou Yao, Min Tao, Chun Zhang, Jun Xiao, Qinbo Qin, Shaojun Liu
It is commonly believed that hybridization might lead to the formation of new polyploidy species, but it is unclear whether hybridization can produce a new homodiploid species. Here, we report the spontaneous occurrence of a new crucian carp-like homodiploid fish (2n = 100) that originated from the interspecific hybridization of female common carp (Cyprinus carpio, Cyprininae, 2n = 100) × male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48). The phenotype and reproductive traits of this new crucian carp-like homodiploid fish were found to be very similar to those of the existing diploid species (diploid crucian carp; Carassius auratus)...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28643617/preselection-statistics-and-random-forest-classification-identify-population-informative-single-nucleotide-polymorphisms-in-cosmopolitan-and-autochthonous-cattle-breeds
#3
F Bertolini, G Galimberti, G Schiavo, S Mastrangelo, R Di Gerlando, M G Strillacci, A Bagnato, B Portolano, L Fontanesi
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna)...
June 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28642784/novel-miscanthus-germplasm-based-value-chains-a-life-cycle-assessment
#4
Moritz Wagner, Andreas Kiesel, Astley Hastings, Yasir Iqbal, Iris Lewandowski
In recent years, considerable progress has been made in miscanthus research: improvement of management practices, breeding of new genotypes, especially for marginal conditions, and development of novel utilization options. The purpose of the current study was a holistic analysis of the environmental performance of such novel miscanthus-based value chains. In addition, the relevance of the analyzed environmental impact categories was assessed. A Life Cycle Assessment was conducted to analyse the environmental performance of the miscanthus-based value chains in 18 impact categories...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642589/multiple-origins-and-a-narrow-genepool-characterise-the-african-tea-germplasm-concordant-patterns-revealed-by-nuclear-and-plastid-dna-markers
#5
Moses Cheloti Wambulwa, Muditha Kasun Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Möller, Jie Liu, Jian-Chu Xu, De-Zhu Li, Lian-Ming Gao
Despite the highly economic value of tea in Africa, its genetic and geographic origins remain largely unexplored. Here we address this by collecting 439 samples across 11 countries in Africa and Asia to investigate the origin and genepool composition of African tea based on 23 nuclear microsatellites loci (nSSRs) and three cpDNA intergenic spacer regions. Our results indicated that the African tea represents a potpourri originating from multiple introductions over time. The nSSR analysis revealed that the majority (79%) of tea accessions collected in Africa belong to Indian Assam tea which have likely originated from India and/or Sri Lanka...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28638387/predicting-flowering-behavior-and-exploring-its-genetic-determinism-in-an-apple-multi-family-population-based-on-statistical-indices-and-simplified-phenotyping
#6
Jean-Baptiste Durand, Alix Allard, Baptiste Guitton, Eric van de Weg, Marco C A M Bink, Evelyne Costes
Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28638317/emergence-time-and-skin-melanin-spot-patterns-do-not-correlate-with-growth-performance-social-competitive-ability-or-stress-response-in-farmed-rainbow-trout
#7
Manuel Gesto, Peter V Skov, Alfred Jokumsen
In wild salmonid fish, specific individual behavioral traits have been correlated with the timing of fry emergence from their gravel spawning nests; Early emerging fish display more aggressive behavior and have a higher probability of becoming socially dominant, compared to fish that emerge at a later stage. Apart from aggression and dominance, other behavioral and metabolic traits, such as boldness, metabolic rate, or growth, have also been linked to emergence time. Altogether, the traits of early- and late-emerging fish resemble those of the proactive and reactive stress-coping style, respectively...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28637429/effects-of-selection-for-fast-growth-on-survival-rate-during-grow-out-phase-in-giant-freshwater-prawn-macrobrachium-rosenbergii
#8
Nguyen Thanh Vu, Trinh Quoc Trong, Nguyen Hong Nguyen
BACKGROUND: Correlated genetic response in survival to selection for high growth has not been reported in giant freshwater prawn (GFP) (Macrobrachium rosenbergii). The main aim of this study was to measure genetic changes and estimate heritability for this character (survival rate) and its genetic associations with body traits in a GFP population selected over eight generations from 2008 to 2015. Statistical analyses were conducted on 106,696 data records, using threshold logistic mixed model...
June 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28637257/effects-of-a-chromosome-9-quantitative-trait-locus-for-ascites-on-economically-important-traits-in-broilers
#9
Sriram Krishna, Katy J Tarrant, Douglas D Rhoads, Nicholas B Anthony
A quantitative trait locus on chromosome 9 was previously shown to be associated with ascites in multiple experimental and commercial populations. A study to evaluate the association of the QTL, based on variable number tandem repeat genotypes, with economically important traits was carried out on a commercial male elite line. Results indicated the highest fat and the lowest fillet mean were associated with the most resistant ascites genotype. All other traits measured for this genotype showed no trend towards positive or negatively impacting production values...
June 15, 2017: Poultry Science
https://www.readbyqxmd.com/read/28633685/cross-validation-analysis-for-genetic-evaluation-models-for-ranking-in-endurance-horses
#10
S García-Ballesteros, L Varona, M Valera, J P Gutiérrez, I Cervantes
Ranking trait was used as a selection criterion for competition horses to estimate racing performance. In the literature the most common approaches to estimate breeding values are the linear or threshold statistical models. However, recent studies have shown that a Thurstonian approach was able to fix the race effect (competitive level of the horses that participate in the same race), thus suggesting a better prediction accuracy of breeding values for ranking trait. The aim of this study was to compare the predictability of linear, threshold and Thurstonian approaches for genetic evaluation of ranking in endurance horses...
June 21, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28633351/data-compression-can-discriminate-broilers-by-selection-line-detect-haplotypes-and-estimate-genetic-potential-for-complex-phenotypes
#11
N J Hudson, R J Hawken, R Okimoto, R L Sapp, A Reverter
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers...
June 15, 2017: Poultry Science
https://www.readbyqxmd.com/read/28630621/development-of-snp-genotyping-assays-for-seed-composition-traits-in-soybean
#12
Gunvant Patil, Juhi Chaudhary, Tri D Vuong, Brian Jenkins, Dan Qiu, Suhas Kadam, Grover J Shannon, Henry T Nguyen
Seed composition is one of the most important determinants of the economic values in soybean. The quality and quantity of different seed components, such as oil, protein, and carbohydrates, are crucial ingredients in food, feed, and numerous industrial products. Soybean researchers have successfully developed and utilized a diverse set of molecular markers for seed trait improvement in soybean breeding programs. It is imperative to design and develop molecular assays that are accurate, robust, high-throughput, cost-effective, and available on a common genotyping platform...
2017: International Journal of Plant Genomics
https://www.readbyqxmd.com/read/28626887/using-numerical-plant-models-and-phenotypic-correlation-space-to-design-achievable-ideotypes
#13
Victor Picheny, Pierre Casadebaig, Ronan Trépos, Robert Faivre, David Da Silva, Patrick Vincourt, Evelyne Costes
Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality...
June 18, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28624281/short-communication-genetic-parameters-for-milk-protein-composition-predicted-using-mid-infrared-spectroscopy-in-the-french-montb%C3%A3-liarde-normande-and-holstein-dairy-cattle-breeds
#14
M P Sanchez, M Ferrand, M Gelé, D Pourchet, G Miranda, P Martin, M Brochard, D Boichard
Genetic parameters for the major milk proteins were estimated in the 3 main French dairy cattle breeds (i.e. Montbéliarde, Normande, and Holstein) as part of the PhénoFinlait program. The 6 major milk protein contents as well as the total protein content (PC) were estimated from mid-infrared spectrometry on 133,592 test-day milk samples from 20,434 cows in first lactation. Lactation means, expressed as a percentage of milk (protein contents) or of protein (protein fractions), were analyzed with an animal mixed model including fixed environmental effects (herd, year × month of calving, and spectrometer) and a random genetic effect...
June 14, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28620261/single-nucleotide-polymorphism-based-genetic-diversity-analysis-of-the-kilakarsal-and-vembur-sheep-breeds
#15
Rathinasamy Selvam, Nagarajan Murali, A Kannan Thiruvenkadan, Ramesh Saravanakumar, Gurusamy Ponnudurai, Thilak Pon Jawahar
AIM: The present study was thus undertaken to analyze the genetic diversity of Kilakarsal and Vembur sheep breeds using single-nucleotide polymorphism (SNP) markers within Toll-like receptor (TLR) 3, 5, 6, 9, and 10 genes. MATERIALS AND METHODS: Competitive allele-specific polymerase chain reaction (PCR)-based end-point genotyping was performed using real-time PCR to type the SNPs. Allele discrimination module implemented in real-time PCR was utilized to call the genotypes based on fluorescence intensity recorded for each of the two alleles...
May 2017: Veterinary World
https://www.readbyqxmd.com/read/28619006/tag-snp-selection-for-prediction-of-tick-resistance-in-brazilian-braford-and-hereford-cattle-breeds-using-bayesian-methods
#16
Bruna P Sollero, Vinícius S Junqueira, Cláudia C G Gomes, Alexandre R Caetano, Fernando F Cardoso
BACKGROUND: Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. RESULTS: BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil...
June 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28615148/echocardiographic-assessments-of%C3%A2-longitudinal-left-ventricular-function-in%C3%A2-healthy-english-springer-spaniels
#17
D Dickson, R Shave, M Rishniw, M Patteson
OBJECTIVES: To establish reference intervals for echocardiographic measures of longitudinal left ventricular function in adult English Springer spaniel (ESS) dogs. ANIMALS: This study involved 42 healthy adult ESS. METHODS: Animals were prospectively recruited from a general practice population in the United Kingdom. Dogs were examined twice, at least 12 months apart, to exclude dogs with progressive cardiac disease. Mitral annular plane systolic excursion, tissue Doppler imaging mitral annular velocities and two-dimensional speckle-tracking echocardiographic left ventricular longitudinal strain and strain rate were measured...
June 11, 2017: Journal of Veterinary Cardiology: the Official Journal of the European Society of Veterinary Cardiology
https://www.readbyqxmd.com/read/28613378/genetic-diversity-of-desmanthus-sp-accessions-using-issr-markers-and-morphological-traits
#18
J C Costa, G G M Fracetto, F J C Fracetto, M V F Santos, M A Lira Júnior
Desmanthus is a genus of forage legumes with high nutritional value, productive potential, and ability to obtain nitrogen in association with diazotrophic bacteria. The use of accurate techniques for genotype identification and characterization is essential for breeding programs. Morphological markers are widely used to know the genetic diversity and the molecular markers are fundamental in these studies. We investigated the genetic diversity among Desmanthus sp genotypes in Pernambuco (Brazilian Northeast State), using morphological traits and ISSR markers...
May 31, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28611852/cnv-analysis-of-host-responses-to-porcine-reproductive-and-respiratory-syndrome-virus-infection
#19
El Hamidi A Hay, Igseo Choi, Lingyang Xu, Yang Zhou, Robert R R Rowland, Joan K Lunney, George E Liu
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28611254/patterns-of-genetic-structure-and-linkage-disequilibrium-in-a-large-collection-of-pea-germplasm
#20
Mathieu Siol, Françoise Jacquin, Marianne Chabert-Martinello, Petr Smýkal, Marie-Christine Le Paslier, Grégoire Aubert, Judith Burstin
Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions gathering elite cultivars, landraces and wild relatives using an array of ~13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types and spring types...
June 13, 2017: G3: Genes—Genomes—Genetics
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