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Marker assisted selection

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https://www.readbyqxmd.com/read/29224171/genetic-mapping-and-validation-of-the-loci-controlling-7s-%C3%AE-and-11s-a-type-storage-protein-subunits-in-soybean-glycine-max-l-merr
#1
Jeffrey D Boehm, Vi Nguyen, Rebecca M Tashiro, Dale Anderson, Chun Shi, Xiaoguang Wu, Lorna Woodrow, Kangfu Yu, Yuhai Cui, Zenglu Li
Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F2 population, which were validated with an F5 RIL population. The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs...
December 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29218378/efficiency-of-multi-trait-indirect-and-trait-assisted-genomic-selection-for-improvement-of-biomass-sorghum
#2
Samuel B Fernandes, Kaio O G Dias, Daniel F Ferreira, Patrick J Brown
We compare genomic selection methods that use correlated traits to help predict biomass yield in sorghum, and find that trait-assisted genomic selection performs best. Genomic selection (GS) is usually performed on a single trait, but correlated traits can also help predict a focal trait through indirect or multi-trait GS. In this study, we use a pre-breeding population of biomass sorghum to compare strategies that use correlated traits to improve prediction of biomass yield, the focal trait. Correlated traits include moisture, plant height measured at monthly intervals between planting and harvest, and the area under the growth progress curve...
December 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29218375/genetic-analysis-of-multi-environmental-spring-wheat-trials-identifies-genomic-regions-for-locus-specific-trade-offs-for-grain-weight-and-grain-number
#3
Sivakumar Sukumaran, Marta Lopes, Susanne Dreisigacker, Matthew Reynolds
GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa...
December 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29217731/genome-wide-analysis-of-grain-yield-stability-and-environmental-interactions-in-a-multiparental-soybean-population
#4
Alencar Xavier, Diego Jarquin, Reka Howard, Vishnu Ramasubramanian, James E Specht, George L Graef, William D Beavis, Brian W Diers, Qijian Song, Perry Cregan, Randall Nelson, Rouf Mian, J G Shannon, Leah McHale, Dechun Wang, William Schapaugh, Aaron J Lorenz, Shizhong Xu, William Muir, Katy M Rainey
Genetic improvement towards optimized and stable agronomic performance of soybean genotypes is desirable for food security. Understanding how genotypes perform in different environmental conditions helps breeders develop sustainable cultivars adapted to target regions. Complex traits of importance are known to be controlled by a large number of genomic regions with small effects whose magnitude and direction are modulated by environmental factors. Knowledge of the constraints and undesirable effects resulting from genotype by environmental interactions is a key objective in improving selection procedures in soybean breeding programs...
December 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29216923/supervised-learning-for-infection-risk-inference-using-pathology-data
#5
Bernard Hernandez, Pau Herrero, Timothy Miles Rawson, Luke S P Moore, Benjamin Evans, Christofer Toumazou, Alison H Holmes, Pantelis Georgiou
BACKGROUND: Antimicrobial Resistance is threatening our ability to treat common infectious diseases and overuse of antimicrobials to treat human infections in hospitals is accelerating this process. Clinical Decision Support Systems (CDSSs) have been proven to enhance quality of care by promoting change in prescription practices through antimicrobial selection advice. However, bypassing an initial assessment to determine the existence of an underlying disease that justifies the need of antimicrobial therapy might lead to indiscriminate and often unnecessary prescriptions...
December 8, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29213298/reproducible-genomic-dna-preparation-from-diverse-crop-species-for-molecular-genetic-applications
#6
Kelvin T Chiong, Mona B Damaj, Carmen S Padilla, Carlos A Avila, Shankar R Pant, Kranthi K Mandadi, Ninfa R Ramos, Denise V Carvalho, T Erik Mirkov
Background: Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these procedures. Isolating DNA from agronomically important crops, such as sugarcane, rice, citrus, potato and tomato is a challenge due to the presence of high fiber, polysaccharides, or secondary metabolites. We present a simplified, rapid and reproducible SDS-based method that provides high-quality and -quantity of DNA from small amounts of leaf tissue, as required by the emerging biotechnology and molecular genetic applications...
2017: Plant Methods
https://www.readbyqxmd.com/read/29209087/quantitative-trait-loci-mapping-for-feed-conversion-efficiency-in-crucian-carp-carassius-auratus
#7
Meixia Pang, Beide Fu, Xiaomu Yu, Haiyang Liu, Xinhua Wang, Zhan Yin, Shouqi Xie, Jingou Tong
QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208499/identification-of-snp-markers-associated-with-tolerance-to-ammonia-toxicity-by-selective-genotyping-from-de-novo-assembled-transcriptome-in-litopenaeus-vannamei
#8
Xia Lu, Jie Kong, Xianhong Meng, Baoxiang Cao, Kun Luo, Ping Dai, Sheng Luan
The high concentration of ammonia from deteriorated aquaculture environments and the intensive culture system could increase the susceptibility to pathogens and even cause high mortality in Litopenaeus vannamei. In addition, we have revealed that the ammonia-tolerant shrimp also have high disease resistance in L. vannamei. In the present study, in order to identify SNP markers associated with tolerance to ammonia toxicity, we developed and characterized SNPs from our previous transcriptome sequencing data of ammonia-stressed and control groups, and a marker-trait association analysis was performed for marker-assisted selection (MAS) to increase production in L...
December 2, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29208345/multi-class-parkinsonian-disorders-classification-with-quantitative-mr-markers-and-graph-based-features-using-support-vector-machines
#9
Rita Morisi, David Neil Manners, Giorgio Gnecco, Nico Lanconelli, Claudia Testa, Stefania Evangelisti, Lia Talozzi, Laura Ludovica Gramegna, Claudio Bianchini, Giovanna Calandra-Buonaura, Luisa Sambati, Giulia Giannini, Pietro Cortelli, Caterina Tonon, Raffaele Lodi
BACKGROUND AND PURPOSE: In this study we attempt to automatically classify individual patients with different parkinsonian disorders, making use of pattern recognition techniques to distinguish among several forms of parkinsonisms (multi-class classification), based on a set of binary classifiers that discriminate each disorder from all others. METHODS: We combine diffusion tensor imaging, proton spectroscopy and morphometric-volumetric data to obtain MR quantitative markers, which are provided to support vector machines with the aim of recognizing the different parkinsonian disorders...
November 28, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29205390/sustaining-global-agriculture-through-rapid-detection-and-deployment-of-genetic-resistance-to-deadly-crop-diseases
#10
REVIEW
Sambasivam Periyannan
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security...
December 4, 2017: New Phytologist
https://www.readbyqxmd.com/read/29204906/mapping-qtl-for-omega-3-content-in-hybrid-saline-tilapia
#11
Grace Lin, Le Wang, Si Te Ngoh, Lianghui Ji, Laszlo Orbán, Gen Hua Yue
Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F2 family of saline tilapia generated by crossing red tilapia and Mozambique tilapia...
December 4, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/29204079/an-overview-of-signaling-regulons-during-cold-stress-tolerance-in-plants
#12
REVIEW
Amit Pareek, Ashima Khurana, Arun K Sharma, Rahul Kumar
Plants, being sessile organisms, constantly withstand environmental fluctuations, including low-temperature, also referred as cold stress. Whereas cold poses serious challenges at both physiological and developmental levels to plants growing in tropical or sub-tropical regions, plants from temperate climatic regions can withstand chilling or freezing temperatures. Several cold inducible genes have already been isolated and used in transgenic approach to generate cold tolerant plants. The conventional breeding methods and marker assisted selection have helped in developing plant with improved cold tolerance, however, the development of freezing tolerant plants through cold acclimation remains an unaccomplished task...
December 2017: Current Genomics
https://www.readbyqxmd.com/read/29202697/genetic-diversity-and-association-mapping-of-mineral-element-concentrations-in-spinach-leaves
#13
Jun Qin, Ainong Shi, Beiquan Mou, Michael A Grusak, Yuejin Weng, Waltram Ravelombola, Gehendra Bhattarai, Lingdi Dong, Wei Yang
BACKGROUND: Spinach is a useful source of dietary vitamins and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorphism (SNP) markers for mineral element concentrations is necessary to support spinach molecular breeding. The purpose of this study was to conduct a genome-wide association study (GWAS) and to identify SNP markers associated with mineral elements in the USDA-GRIN spinach germplasm collection...
December 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29201033/cell-based-phenotyping-reveals-qtl-for-membrane-potential-maintenance-associated-with-hypoxia-and-salinity-stress-tolerance-in-barley
#14
Muhammad B Gill, Fanrong Zeng, Lana Shabala, Guoping Zhang, Yun Fan, Sergey Shabala, Meixue Zhou
Waterlogging and salinity are two major abiotic stresses that hamper crop production world-wide resulting in multibillion losses. Plant abiotic stress tolerance is conferred by many interrelated mechanisms. Amongst these, the cell's ability to maintain membrane potential (MP) is considered to be amongst the most crucial traits, a positive relationship between the ability of plants to maintain highly negative MP and its tolerance to both salinity and waterlogging stress. However, no attempts have been made to identify quantitative trait loci (QTL) conferring this trait...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29200321/two-new-insertion-deletion-variants-of-the-pitx2-gene-and-their-effects-on-growth-traits-in-sheep
#15
Haidong Zhao, Shuai He, Shuhui Wang, Yanjiao Zhu, Hongwei Xu, Renyun Luo, Xianyong Lan, Yong Cai, Xiuzhu Sun
In China, Tong sheep (TS) and Lanzhou fat-tailed sheep (LFTS) are two closely relative endanger breeds for low meat production and low fecundity, finding some marker-assisted selected (MAS) is our first priority for improving their growth traits. For this purpose, Hu sheep (HS) and small-tailed Han sheep (STHS) were compared with two endangered breeds (TS and LFTS). Paired-liked homeodomain transcription factor 2 (PITX2) gene was the important member of PITX family, which could adjust animal growth through hypothalamic-pituitary-adrenal axis...
December 4, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29199464/sperm-rna-elements-as-markers-of-health
#16
Rayanne B Burl, Stephanie Clough, Edward Sendler, Molly Estill, Stephen A Krawetz
Idiopathic infertility, an etiology not identified as part of standard clinical assessment, represents approximately 20% of all infertility cases. Current male infertility diagnosis focuses on the concentration, motility, and morphology of spermatozoa. This is of limited value when predicting birth success and of limited utility when selecting the optimum treatment. At fertilization, spermatozoa provide their genomic contribution, as well as a set of RNAs and proteins that have distinct roles in development...
December 3, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29194674/a-whole-genome-sequence-association-study-for-puberty-in-a-large-duroc%C3%A2-%C3%A3-%C3%A2-erhualian-f2-population
#17
W S Xin, F Zhang, G R Yan, W W Xu, S J Xiao, Z Y Zhang, L S Huang
A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows' reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome-wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNPs respectively...
December 1, 2017: Animal Genetics
https://www.readbyqxmd.com/read/29188397/comparison-of-machine-learning-and-semi-quantification-algorithms-for-i123-fp-cit-classification-the-beginning-of-the-end-for-semi-quantification
#18
Jonathan Christopher Taylor, John Wesley Fenner
BACKGROUND: Semi-quantification methods are well established in the clinic for assisted reporting of (I123) Ioflupane images. Arguably, these are limited diagnostic tools. Recent research has demonstrated the potential for improved classification performance offered by machine learning algorithms. A direct comparison between methods is required to establish whether a move towards widespread clinical adoption of machine learning algorithms is justified. This study compared three machine learning algorithms with that of a range of semi-quantification methods, using the Parkinson's Progression Markers Initiative (PPMI) research database and a locally derived clinical database for validation...
November 29, 2017: EJNMMI Physics
https://www.readbyqxmd.com/read/29186488/a-putative-r3-myb-repressor-is-the-candidate-gene-underlying-atroviolacium-a-locus-for-anthocyanin-pigmentation-in-tomato-fruit
#19
Xue Cao, Zhengkun Qiu, Xiaotian Wang, Tong Van Giang, Xiaolin Liu, Jing Wang, Xiaoxuan Wang, Jianchang Gao, Yanmei Guo, Yongchen Du, Guoping Wang, Zejun Huang
Anthocyanins are potential health-promoting compounds in the human diet. The atv (atroviolacium) locus, derived from the wild tomato species Solanum cheesmaniae, has been shown to enhance anthocyanin pigmentation in tomato fruit when it co-exists with either the Aft (Anthocyanin fruit) or the Abg (Aubergine) locus. In the present study, the atv locus was fine-mapped to an approximately 5.0-kb interval on chromosome 7. A putative R3 MYB repressor was identified in this interval and is hereby designated as SlMYBATV...
November 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29184565/a-novel-qtl-for-powdery-mildew-resistance-in-nordic-spring-barley-hordeum-vulgare-l-ssp-vulgare-revealed-by-genome-wide-association-study
#20
Therése Bengtsson, Inger Åhman, Outi Manninen, Lars Reitan, Therese Christerson, Jens Due Jensen, Lene Krusell, Ahmed Jahoor, Jihad Orabi
The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region...
2017: Frontiers in Plant Science
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