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https://www.readbyqxmd.com/read/28547012/how-do-the-type-of-qtl-effect-and-the-form-of-the-residual-term-influence-qtl-detection-in-multi-parent-populations-a-case-study-in-the-maize-eu-nam-population
#1
Vincent Garin, Valentin Wimmer, Sofiane Mezmouk, Marcos Malosetti, Fred van Eeuwijk
In the QTL analysis of multi-parent populations, the inclusion of QTLs with various types of effects can lead to a better description of the phenotypic variation and increased power. For the type of QTL effect in QTL models for multi-parent populations (MPPs), various options exist to define them with respect to their origin. They can be modelled as referring to close parental lines or to further away ancestral founder lines. QTL models for MPPs can also be characterized by the homo- or heterogeneity of variance for polygenic effects...
May 25, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28546436/quantifying-wheat-sensitivities-to-environmental-constraints-to-dissect-g-x-e-in-the-field
#2
Boris Parent, Julien Bonneau, Lance Maphosa, Alex Kovalchuk, Peter Langridge, Delphine Fleury
Yield is subject to strong Genotype by Environment interactions (G x E) in the field, especially under abiotic constraints such as soil water deficit (Drought, D) and high temperature (Heat, H). Since environmental conditions show strong fluctuations during the whole crop cycle, geneticists usually do not consider the environmental measures as quantitative variables, but rather as factors in multi-environment analyses. Based on 11 experiments in a field platform with contrasted temperature and soil water deficit, we determined the periods of sensitivity to drought and heat constraints in wheat (Triticum aestivum L...
May 25, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28546385/using-rna-seq-for-genomic-scaffold-placement-correcting-assemblies-and-genetic-map-creation-in-a-common-brassica-rapa-mapping-population
#3
R J Cody Markelz, Michael F Covington, Marcus T Brock, Upendra K Devisetty, Daniel J Kliebenstein, Cynthia Weinig, Julin N Maloof
Brassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here we describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population derived from field collected RNA-seq data. This high-density genotype data enables the detection and correction of putative genome mis-assemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated Brassica rapa genome...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28544613/qtl-and-systems-genetics-analysis-of-mouse-grooming-and-behavioral-responses-to-novelty-in-an-open-field
#4
Anna Delprato, Marie-Paule Algéo, Brice Bonheur, Jason A Bubier, Lu Lu, Robert W Williams, Elissa J Chesler, Wim E Crusio
The open field is a classic test used to assess exploratory behavior, anxiety, and locomotor activity in rodents. Here we mapped quantitative trait loci (QTLs) underlying behaviors displayed in an open field, using a panel of 53 BXD recombinant inbred mouse strains with deep replication (10 per strain and sex). The use of these strains permits the integration and comparison of data obtained in different laboratories, and also offers the possibility to study trait covariance by exploiting powerful bioinformatics tools and resources...
May 24, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28542571/quantitative-trait-loci-for-yield-and-grain-plumpness-relative-to-maturity-in-three-populations-of-barley-hordeum-vulgare-l-grown-in-a-low-rain-fall-environment
#5
Bulti Tesso Obsa, Jason Eglinton, Stewart Coventry, Timothy March, Maxime Guillaume, Thanh Phuoc Le, Matthew Hayden, Peter Langridge, Delphine Fleury
Identifying yield and grain plumpness QTL that are independent of developmental variation or phenology is of paramount importance for developing widely adapted and stable varieties through the application of marker assisted selection. The current study was designed to dissect the genetic basis of yield performance and grain plumpness in southern Australia using three doubled haploid (DH) populations developed from crosses between adapted parents that are similar in maturity and overall plant development. Three interconnected genetic populations, Commander x Fleet (CF), Commander x WI4304 (CW), and Fleet x WI4304 (FW) developed from crossing of Australian elite barley genotypes, were used to map QTL controlling yield and grain plumpness...
2017: PloS One
https://www.readbyqxmd.com/read/28542488/dissecting-the-old-mediterranean-durum-wheat-genetic-architecture-for-phenology-biomass-and-yield-formation-by-association-mapping-and-qtl-meta-analysis
#6
Jose Miguel Soriano, Marcos Malosetti, Martina Roselló, Mark Earl Sorrells, Conxita Royo
Association mapping was used to identify genome regions affecting yield formation, crop phenology and crop biomass in a collection of 172 durum wheat landraces representative of the genetic diversity of ancient local durum varieties from the Mediterranean Basin. The collection was genotyped with 1,149 DArT markers and phenotyped in Spanish northern and southern locations during three years. A total of 245 significant marker trait associations (MTAs) (P<0.01) were detected. Some of these associations confirmed previously identified quantitative trait loci (QTL) and/or candidate genes, and others are reported for the first time here...
2017: PloS One
https://www.readbyqxmd.com/read/28542459/identification-and-evaluation-of-resistance-to-powdery-mildew-and-yellow-rust-in-a-wheat-mapping-population
#7
Lijun Yang, Xuejiang Zhang, Xu Zhang, Jirui Wang, Mingcheng Luo, Mujun Yang, Hua Wang, Libo Xiang, Fansong Zeng, Dazhao Yu, Daolin Fu, Garry M Rosewarne
Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM) and yellow rust (YR). Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR). The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines) was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines...
2017: PloS One
https://www.readbyqxmd.com/read/28542451/mapping-genes-for-resistance-to-stripe-rust-in-spring-wheat-landrace-pi-480035
#8
Jinita Sthapit Kandel, Vandhana Krishnan, Derick Jiwan, Xianming Chen, Daniel Z Skinner, Deven R See
Stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikks. is an economically important disease of wheat (Triticum aestivum L.). Hexaploid spring wheat landrace PI 480035 was highly resistant to stripe rust in the field in Washington during 2011 and 2012. The objective of this research was to identify quantitative trait loci (QTL) for stripe rust resistance in PI 480035. A spring wheat, "Avocet Susceptible" (AvS), was crossed with PI 480035 to develop a biparental population of 110 recombinant inbred lines (RIL)...
2017: PloS One
https://www.readbyqxmd.com/read/28540573/optimization-of-multi-environment-trials-for-genomic-selection-based-on-crop-models
#9
R Rincent, E Kuhn, H Monod, F-X Oury, M Rousset, V Allard, J Le Gouis
We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters...
May 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28540572/characterization-and-mapping-of-dt1-locus-which-co-segregates-with-cctfl1-for-growth-habit-in-pigeonpea
#10
Rachit K Saxena, Jimmy Obala, Andrey Sinjushin, C V Sameer Kumar, K B Saxena, Rajeev K Varshney
We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait...
May 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28539927/a-comprehensive-analysis-of-alternative-splicing-in-paleopolyploid-maize
#11
Wenbin Mei, Sanzhen Liu, James C Schnable, Cheng-Ting Yeh, Nathan M Springer, Patrick S Schnable, William B Barbazuk
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28536597/fine-mapping-of-qtls-for-ascochyta-blight-resistance-in-pea-using-heterogeneous-inbred-families
#12
Ambuj B Jha, Krishna K Gali, Bunyamin Tar'an, Thomas D Warkentin
Ascochyta blight (AB) is an important disease of pea which can cause severe grain yield loss under wet conditions. In our previous study, we identified two quantitative trait loci (QTLs) abIII-1 and abI-IV-2 for AB resistance and these QTLs were consistent across locations and/or years in an inter-specific pea population (PR-19) developed from a cross between Alfetta (Pisum sativum) and P651 (P. fulvum). The objectives of this study were to fine map the abIII-1 and abI-IV-2 QTLs using a high density single nucleotide polymorphism (SNP)-based genetic linkage map and analyze identified markers in heterogeneous inbred family (HIF) populations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28536586/ancestral-qtl-alleles-from-wild-emmer-wheat-enhance-root-development-under-drought-in-modern-wheat
#13
Lianne Merchuk-Ovnat, Tzion Fahima, Jhonathan E Ephrath, Tamar Krugman, Yehoshua Saranga
A near-isogenic line (NIL-7A-B-2), introgressed with a quantitative trait locus (QTL) on chromosome 7AS from wild emmer wheat (Triticum turgidum ssp. dicoccoides) into the background of bread wheat (T. aestivum L.) cv. BarNir, was recently developed and studied in our lab. NIL-7A-B-2 exhibited better productivity and photosynthetic capacity than its recurrent parent across a range of environments. Here we tested the hypothesis that root-system modifications play a major role in NIL-7A-B-2's agronomical superiority...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28534096/genomic-prediction-ability-for-yield-related-traits-in-german-winter-barley-elite-material
#14
Patrick Thorwarth, Jutta Ahlemeyer, Anne-Marie Bochard, Kerstin Krumnacker, Hubert Blümel, Eberhard Laubach, Nadine Knöchel, László Cselényi, Frank Ordon, Karl J Schmid
Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L...
May 22, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28533786/high-density-linkage-map-construction-and-mapping-of-yield-trait-qtls-in-maize-zea-mays-using-the-genotyping-by-sequencing-gbs-technology
#15
Chengfu Su, Wei Wang, Shunliang Gong, Jinghui Zuo, Shujiang Li, Shizhong Xu
Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28533785/qtl-mapping-for-yield-and-resistance-against-mediterranean-corn-borer-in-maize
#16
José C Jiménez-Galindo, Bernardo Ordás, Ana Butrón, Luis F Samayoa, Rosa A Malvar
Introduction: The Mediterranean corn borer (MCB), Sesamia nonagrioides, is a major pest of maize, Zea mays, in Mediterranean countries, inflicting significant kernel yield losses. For that reason, it necessary to know the genetic mechanisms that regulate the agronomic and resistance traits. A quantitative trait loci (QTL) mapping study for yield, resistance against MCB attack, and other relevant agronomic traits was performed using a recombinant inbred line (RIL) population derived from the cross A637 × A509 that is expected to segregate for yield, and ear, and stalk resistance to MCB...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28529518/genetic-variability-genotype-%C3%A3-environment-interaction-correlation-and-gge-biplot-analysis-for-grain-iron-and-zinc-concentration-and-other-agronomic-traits-in-ril-population-of-sorghum-sorghum-bicolor-l-moench
#17
Rahul M Phuke, Kotla Anuradha, Kommineni Radhika, Farzana Jabeen, Ghanta Anuradha, Thatikunta Ramesh, K Hariprasanna, Shivaji P Mehtre, Santosh P Deshpande, Gaddameedi Anil, Roma R Das, Abhishek Rathore, Tom Hash, Belum V S Reddy, Are Ashok Kumar
The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28528868/pleiotropic-effects-of-trait-associated-genetic-variation-on-dna-methylation-utility-for-refining-gwas-loci
#18
Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O'Donovan, Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation...
May 13, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28523639/association-mapping-of-yield-and-yield-related-traits-under-reproductive-stage-drought-stress-in-rice-oryza-sativa-l
#19
B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz, Arvind Kumar
BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%...
December 2017: Rice
https://www.readbyqxmd.com/read/28523008/genetic-interaction-between-arabidopsis-qpm3-1-locus-and-bacterial-effector-gene-hopw1-1-underlies-natural-variation-in-quantitative-disease-resistance-to-pseudomonas-infection
#20
Qi Luo, Wei-Wei Liu, Ke-Di Pan, You-Liang Peng, Jun Fan
Wide quantitative variation in plant disease resistance across Arabidopsis wild populations has been documented and the underlying mechanisms remain largely unknown. To investigate the genetic and molecular basis of this variation, Arabidopsis recombinant inbred lines (RILs) derived from Aa-0 × Col-0 and Gie-0 × Col-0 crosses were constructed and used for inoculation with Pseudomonas syringae pathovars maculicola ES4326 (ES4326) and tomato DC3000 (DC3000). Bacterial growth assays revealed continuous distribution across the large differences between the most and the least susceptible lines in the RILs...
2017: Frontiers in Plant Science
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