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TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik

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https://www.readbyqxmd.com/read/28220206/a-user-guide-to-the-brassica-60k-illumina-infinium%C3%A2-snp-genotyping-array
#1
REVIEW
Annaliese S Mason, Erin E Higgins, Rod J Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, Isobel A P Parkin
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies...
February 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28215025/analysis-of-the-genetic-architecture-of-maize-ear-and-grain-morphological-traits-by-combined-linkage-and-association-mapping
#2
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/28204843/bread-wheat-milling-behavior-effects-of-genetic-and-environmental-factors-and-modeling-using-grain-mechanical-resistance-traits
#3
François-Xavier Oury, P Lasme, C Michelet, A Dubat, O Gardet, E Heumez, B Rolland, M Rousset, J Abecassis, C Bar L'Helgouac'h, V Lullien-Pellerin
Genetic (Pinb-D1 alleles) and environment (through vitreousness) have important effects on bread wheat milling behavior. SKCS optimal values corresponding to soft vitreous or hard mealy grains were defined to obtain the highest total flour yield. Near-isogenic lines of bread wheat that differ in hardness, due to distinct puroindoline-b alleles (the wild type, Pinb-D1a, or the mutated forms, Pinb-D1b or Pinb-D1d), were grown in different environments and under two nitrogen fertilization levels, to study genetic and environmental effects on milling behavior...
February 15, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28194473/tapping-the-genetic-diversity-of-landraces-in-allogamous-crops-with-doubled-haploid-lines-a-case-study-from-european-flint-maize
#4
Juliane Böhm, Wolfgang Schipprack, H Friedrich Utz, Albrecht E Melchinger
Using landraces for broadening the genetic base of elite maize germplasm is hampered by heterogeneity and high genetic load. Production of DH line libraries can help to overcome these problems. Landraces of maize (Zea mays L.) represent a huge reservoir of genetic diversity largely untapped by breeders. Genetic heterogeneity and a high genetic load hamper their use in hybrid breeding. Production of doubled haploid line libraries (DHL) by the in vivo haploid induction method promises to overcome these problems...
February 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28188333/use-of-modern-tomato-breeding-germplasm-for-deciphering-the-genetic-control-of-agronomical-traits-by-genome-wide-association-study
#5
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato...
February 10, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28184981/association-mapping-utilizing-diverse-barley-lines-reveals-net-form-net-blotch-seedling-resistance-susceptibility-loci
#6
Jonathan K Richards, Timothy L Friesen, Robert S Brueggeman
A diverse collection of barley lines was phenotyped with three North American Pyrenophora teres f. teres isolates and association analyses detected 78 significant marker-trait associations at 16 genomic loci. Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resistance and susceptibility...
February 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28168408/ssr-enriched-genetic-linkage-maps-of-bermudagrass-cynodon-dactylon%C3%A2-%C3%A3-%C3%A2-transvaalensis-and-their-comparison-with-allied-plant-genomes
#7
Sameer Khanal, Changsoo Kim, Susan A Auckland, Lisa K Rainville, Jeevan Adhikari, Brian M Schwartz, Andrew H Paterson
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents...
February 6, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28144699/fine-mapping-of-rymv3-a-new-resistance-gene-to-rice-yellow-mottle-virus-from-oryza-glaberrima
#8
Hélène Pidon, Alain Ghesquière, Sophie Chéron, Souley Issaka, Eugénie Hébrard, François Sabot, Olufisayo Kolade, Drissa Silué, Laurence Albar
A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV...
January 31, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28144698/fine-mapping-qfs07-1-controlling-fiber-strength-in-upland-cotton-gossypium-hirsutum-l
#9
Xiaomei Fang, Xueying Liu, Xiaoqin Wang, Wenwen Wang, Dexin Liu, Jian Zhang, Dajun Liu, Zhonghua Teng, Zhaoyun Tan, Fang Liu, Fengjiao Zhang, Maochao Jiang, Xiuling Jia, Jianwei Zhong, Jinghong Yang, Zhengsheng Zhang
KEY MESSAGE: qFS07.1 controlling fiber strength was fine-mapped to a 62.6-kb region containing four annotated genes. RT-qPCR and sequence of candidate genes identified an LRR RLK gene as the most likely candidate. Fiber strength is an important component of cotton fiber quality and is associated with other properties, such as fiber maturity, fineness, and length. Stable QTL qFS07.1, controlling fiber strength, had been identified on chromosome 7 in an upland cotton recombinant inbred line (RIL) population from a cross (CCRI35 × Yumian1) described in our previous studies...
January 31, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28116459/homoeologous-recombination-based-transfer-and-molecular-cytogenetic-mapping-of-powdery-mildew-resistant-gene-pm57-from-aegilops-searsii-into-wheat
#10
Wenxuan Liu, Dal-Hoe Koo, Qing Xia, Chunxin Li, Fuqiang Bai, Yuli Song, Bernd Friebe, Bikram S Gill
Pm57, a novel resistant gene against powdery mildew, was transferred into common wheat from Ae. searsi and further mapped to 2S (s) #1L at an interval of FL0.75 to FL0.87. Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici, is one of the most severe foliar diseases of wheat causing reduction in grain yield and quality. Host plant resistance is the most effective and environmentally safe approach to control this disease. Tests of a set of Chinese Spring-Ae. searsii (S(s)S(s), 2n = 2x = 14) Feldman & Kislev ex K...
January 23, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28097399/segregation-for-fertility-and-meiotic-stability-in-novel-brassica-allohexaploids
#11
Margaret W Mwathi, Mehak Gupta, Chaya Atri, Surinder S Banga, Jacqueline Batley, Annaliese S Mason
Allohexaploid Brassica populations reveal ongoing segregation for fertility, while genotype influences fertility and meiotic stability. Creation of a new Brassica allohexaploid species is of interest for the development of a crop type with increased heterosis and adaptability. At present, no naturally occurring, meiotically stable Brassica allohexaploid exists, with little data available on chromosome behaviour and meiotic control in allohexaploid germplasm. In this study, 100 plants from the cross B. carinata × B...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28097398/mapping-quantitative-trait-loci-for-root-development-under-hypoxia-conditions-in-soybean-glycine-max-l-merr
#12
Loc Van Nguyen, Ryoji Takahashi, Stephen Mwangi Githiri, Tito O Rodriguez, Nobuko Tsutsumi, Sayuri Kajihara, Takasi Sayama, Masao Ishimoto, Kyuya Harada, Keisuke Suematsu, Tomomi Abiko, Toshihiro Mochizuki
Greatest potential, QTLs for hypoxia and waterlogging tolerance in soybean roots were detected using a new phenotypic evaluation method. Waterlogging is a major environmental stress limiting soybean yield in wet parts of the world. Root development is an important indicator of hypoxia tolerance in soybean. However, little is known about the genetic control of root development under hypoxia. This study was conducted to identify quantitative trait loci (QTLs) responsible for root development under hypoxia. Recombinant inbred lines (RILs) developed from a cross between a hypoxia-sensitive cultivar, Tachinagaha, and a tolerant landrace, Iyodaizu, were used...
January 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28093630/brassica-napus-ds-3-encoding-a-della-protein-negatively-regulates-stem-elongation-through-gibberellin-signaling-pathway
#13
Bo Zhao, Haitao Li, Juanjuan Li, Bo Wang, Cheng Dai, Jing Wang, Kede Liu
Identification and characterization of a semi-dwarfing gene ds-3 encoding a mutant DELLA protein regulating plant height through gibberellin signaling pathway. Lodging is one of the most important factors causing severe yield loss in oilseed rape. Utilization of semi-dwarf varieties has been proved the most effective way to increase lodging resistance and yield in many crops. To develop semi-dwarf germplasm in oilseed rape, we identified a semi-dwarf mutant ds-3 which showed a reduced response to phytohormones gibberellins (GAs)...
January 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28070610/automated-tetraploid-genotype-calling-by-hierarchical-clustering
#14
Cari A Schmitz Carley, Joseph J Coombs, David S Douches, Paul C Bethke, Jiwan P Palta, Richard G Novy, Jeffrey B Endelman
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall...
January 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28050618/clubroot-resistance-qtl-are-modulated-by-nitrogen-input-in-brassica-napus
#15
A Laperche, Y Aigu, M Jubault, M Ollier, S Guichard, P Glory, S E Strelkov, A Gravot, M J Manzanares-Dauleux
Nitrogen levels can modulate the effectiveness of clubroot resistance in an isolate- and host-specific manner. While the same QTL were detected under high and low nitrogen, their effects were altered. Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of oilseed rape and is known to be affected by nitrogen fertilization. However, the genetic factors involved in clubroot resistance have not been characterized under nitrogen-limiting conditions. This study aimed to assess the variability of clubroot resistance under different nitrogen levels and to characterize the impact of nitrogen supply on genetic resistance factors...
January 3, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28039516/defeating-the-warrior-genetic-architecture-of-triticale-resistance-against-a-novel-aggressive-yellow-rust-race
#16
Dominik Losert, Hans Peter Maurer, Willmar L Leiser, Tobias Würschum
Genome-wide association mapping of resistance against the novel, aggressive 'Warrior' race of yellow rust in triticale revealed a genetic architecture with some medium-effect QTL and a quantitative component, which in combination confer high levels of resistance on both leaves and ears. Yellow rust is an important destructive fungal disease in small grain cereals and the exotic 'Warrior' race has recently conquered Europe. The aim of this study was to investigate the genetic architecture of yellow rust resistance in hexaploid winter triticale as the basis for a successful resistance breeding...
December 30, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28039515/genome-wide-association-mapping-for-seedling-and-field-resistance-to-puccinia-striiformis-f-sp-tritici-in-elite-durum-wheat
#17
Weizhen Liu, Marco Maccaferri, Peter Bulli, Sheri Rynearson, Roberto Tuberosa, Xianming Chen, Michael Pumphrey
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs...
December 30, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28028582/genetic-dissection-of-sorghum-grain-quality-traits-using-diverse-and-segregating-populations
#18
Richard E Boyles, Brian K Pfeiffer, Elizabeth A Cooper, Bradley L Rauh, Kelsey J Zielinski, Matthew T Myers, Zachary Brenton, William L Rooney, Stephen Kresovich
Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage...
December 27, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28004134/genetic-analysis-and-mapping-of-adult-plant-resistance-loci-to-leaf-rust-in-durum-wheat-cultivar-bairds
#19
Caixia Lan, Bhoja R Basnet, Ravi P Singh, Julio Huerta-Espino, Sybil A Herrera-Foessel, Yong Ren, Mandeep S Randhawa
New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds. CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP...
December 21, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27995275/genome-wide-mapping-and-prediction-suggests-presence-of-local-epistasis-in-a-vast-elite-winter-wheat-populations-adapted-to-central-europe
#20
Sang He, Jochen C Reif, Viktor Korzun, Reiner Bothe, Erhard Ebmeyer, Yong Jiang
Genome-wide association mapping as well as marker- and haplotype-based genome-wide selection unraveled a complex genetic architecture of grain yield with absence of large effect QTL and presence of local epistatic effects. The genetic architecture of grain yield determines to a large extent the optimum design of genomic-assisted wheat breeding programs. The main goal of our study was to examine the potential and limitations to dissect the genetic architecture of grain yield in wheat using a large experimental data set...
December 19, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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