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https://www.readbyqxmd.com/read/28230237/parasitism-drives-host-genome-evolution-insights-from-the-pasteuria-ramosa-daphnia-magna-system
#1
Yann Bourgeois, Anne C Roulin, Kristina Müller, Dieter Ebert
Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28228439/loss-of-pollen-specific-phospholipase-not-like-dad-triggers-gynogenesis-in-maize
#2
Laurine M Gilles, Abdelsabour Khaled, Jean-Baptiste Laffaire, Sandrine Chaignon, Ghislaine Gendrot, Jérôme Laplaige, Hélène Bergès, Genséric Beydon, Vincent Bayle, Pierre Barret, Jordi Comadran, Jean-Pierre Martinant, Peter M Rogowsky, Thomas Widiez
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein...
February 22, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28222685/evaluation-of-the-accuracy-of-imputed-sequence-variant-genotypes-and-their-utility-for-causal-variant-detection-in-cattle
#3
Hubert Pausch, Iona M MacLeod, Ruedi Fries, Reiner Emmerling, Phil J Bowman, Hans D Daetwyler, Michael E Goddard
BACKGROUND: The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants. RESULTS: We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute...
February 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28222201/linkage-and-mapping-of-quantitative-trait-loci-associated-with-angular-leaf-spot-and-powdery-mildew-resistance-in-common-beans
#4
Denis Bassi, Boris Briñez, Juliana Santa Rosa, Paula Rodrigues Oblessuc, Caléo Panhoca de Almeida, Stella Maris Nucci, Larissa Chariel Domingos da Silva, Alisson Fernando Chiorato, Rosana Pereira Vianello, Luis Eduardo Aranha Camargo, Matthew Wohlgemuth Blair, Luciana Lasry Benchimol-Reis
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28220807/field-based-high-throughput-phenotyping-rapidly-identifies-genomic-regions-controlling-yield-components-in-rice
#5
Paul Tanger, Stephen Klassen, Julius P Mojica, John T Lovell, Brook T Moyers, Marietta Baraoidan, Maria Elizabeth B Naredo, Kenneth L McNally, Jesse Poland, Daniel R Bush, Hei Leung, Jan E Leach, John K McKay
To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220139/genome-wide-single-nucleotide-polymorphism-discovery-and-the-construction-of-a-high-density-genetic-map-for-melon-cucumis-melo-l-using-genotyping-by-sequencing
#6
Che-Wei Chang, Yu-Hua Wang, Chih-Wei Tung
Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#7
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219341/integrating-genetic-maps-in-bambara-groundnut-vigna-subterranea-l-verdc-and-their-syntenic-relationships-among-closely-related-legumes
#8
Wai Kuan Ho, Hui Hui Chai, Presidor Kendabie, Nariman Salih Ahmad, Jaeyres Jani, Festo Massawe, Andrzej Kilian, Sean Mayes
BACKGROUND: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata)...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218981/the-genetic-architecture-of-amino-acids-dissection-by-association-and-linkage-analysis-in-maize
#9
Min Deng, Dongqin Li, Jingyun Luo, Yingjie Xiao, Haijun Liu, Qingchun Pan, Xuehai Zhang, Minliang Jin, Mingchao Zhao, Jianbing Yan
Amino acids are both constituents of proteins, providing the essential nutrition for humans and animals, and signaling molecules regulating the growth and development of plants. Most cultivars of maize are deficient in essential amino acids such as lysine and tryptophan. Here, we measured the levels of 17 different total amino acids, and created 48 derived traits in mature kernels from a maize diversity inbred collection and three recombinant inbred line (RIL) populations. By GWAS, 247 and 281 significant loci were identified in two different environments, 5...
February 20, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28216997/genetic-mapping-and-qtl-analysis-of-botrytis-resistance-in-gerbera-hybrida
#10
Yiqian Fu, Alex van Silfhout, Arwa Shahin, Ronny Egberts, Martin Beers, Ans van der Velde, Adrie van Houten, Jaap M van Tuyl, Richard G F Visser, Paul Arens
Gerbera hybrida is an economically important cut flower. In the production and transportation of gerbera with unavoidable periods of high relative humidity, grey mould occurs and results in losses in quality and quantity of flowers. Considering the limitations of chemical use in greenhouses and the impossibility to use these chemicals in auction or after sale, breeding for resistant gerbera cultivars is considered as the best practical approach. In this study, we developed two segregating F1 populations (called S and F)...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28215025/analysis-of-the-genetic-architecture-of-maize-ear-and-grain-morphological-traits-by-combined-linkage-and-association-mapping
#11
Chaoshu Zhang, Zhiqiang Zhou, Hongjun Yong, Xiaochong Zhang, Zhuanfang Hao, Fangjun Zhang, Mingshun Li, Degui Zhang, Xinhai Li, Zhenhua Wang, Jianfeng Weng
Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments...
February 18, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28213475/wheat-landrace-genome-diversity
#12
Luzie U Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Cai-Yun Yang, Julie King, Alexandra M Allen, Amanda Burridge, Keith J Edwards, Simon Griffiths
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28211577/genetic-dissection-of-adaptive-form-and-function-in-rapidly-speciating-cichlid-fishes
#13
Frederico Henning, Gonzalo Machado-Schiaffino, Lukas Baumgarten, Axel Meyer
Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly-evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and H. nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected...
February 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28207056/identification-of-the-submergence-tolerance-qtl-come-quick-drowning1-cqd1-in-arabidopsis-thaliana
#14
Melis Akman, Rogier Kleine, Peter H van Tienderen, M Eric Schranz
No abstract text is available yet for this article.
February 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28202015/variant-discovery-in-the-sheep-milk-transcriptome-using-rna-sequencing
#15
Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp, Juan José Arranz
BACKGROUND: The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199342/meta-qtl-for-resistance-to-white-mold-in-common-bean
#16
Renato C C Vasconcellos, O Blessing Oraguzie, Alvaro Soler, Haidar Arkwazee, James R Myers, Juan J Ferreira, Qijian Song, Phil McClean, Phillip N Miklas
White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature)...
2017: PloS One
https://www.readbyqxmd.com/read/28198669/ulfasqtl-an-ultra-fast-method-of-composite-splicing-qtl-analysis
#17
Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
BACKGROUND: Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198421/tawrky70-transcription-factor-in-wheat-qtl-2dl-regulates-downstream-metabolite-biosynthetic-genes-to-resist-fusarium-graminearum-infection-spread-within-spike
#18
Udaykumar Kage, Kalenahalli N Yogendra, Ajjamada C Kushalappa
A semi-comprehensive metabolomics was used to identify the candidate metabolites and genes to decipher mechanisms of resistance in wheat near-isogenic lines (NILs) containing QTL-2DL against Fusarium graminearum (Fg). Metabolites, with high fold-change in abundance, belonging to hydroxycinnamic acid amides (HCAAs): such as coumaroylagmatine, coumaroylputrescine and Fatty acids: phosphatidic acids (PAs) were identified as resistance related induced (RRI) metabolites in rachis of resistant NIL (NIL-R), inoculated with Fg...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196526/the-genetic-architecture-of-low-temperature-adaptation-in-the-wine-yeast-saccharomyces-cerevisiae
#19
Estéfani García-Ríos, Miguel Morard, Leopold Parts, Gianni Liti, José M Guillamón
BACKGROUND: Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci. RESULTS: In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193175/genome-wide-association-mapping-for-milk-fat-composition-and-fine-mapping-of-a-qtl-for-de-novo-synthesis-of-milk-fatty-acids-on-bovine-chromosome-13
#20
Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens, Sigbjørn Lien
BACKGROUND: Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle...
February 13, 2017: Genetics, Selection, Evolution: GSE
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