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Quantitative trait loci

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https://www.readbyqxmd.com/read/28724085/quantitative-trait-loci-mapping-for-spike-characteristics-in-hexaploid-wheat
#1
Yaopeng Zhou, Benjamin Conway, Daniela Miller, David Marshall, Aaron Cooper, Paul Murphy, Shiaoman Chao, Gina Brown-Guedira, José Costa
Wheat ( L.) spike characteristics determine the number of grains produced on each spike and constitute key components of grain yield. Understanding of the genetic basis of spike characteristics in wheat, however, is limited. In this study, genotyping-by-sequencing (GBS) and the iSelect 9K assay were used on a doubled-haploid (DH) soft red winter wheat population that showed a wide range of phenotypic variation for spike traits. A genetic map spanning 2934.1 cM with an average interval length of 3.4 cM was constructed...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724080/qtls-associated-with-crown-root-angle-stomatal-conductance-and-maturity-in-sorghum
#2
Jose R Lopez, John E Erickson, Patricio Munoz, Ana Saballos, Terry J Felderhoff, Wilfred Vermerris
Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724072/genome-wide-analysis-of-tar-spot-complex-resistance-in-maize-using-genotyping-by-sequencing-snps-and-whole-genome-prediction
#3
Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M Prasanna, Felix San Vicente, Xuecai Zhang
Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724064/genetic-characterization-of-the-soybean-nested-association-mapping-population
#4
Qijian Song, Long Yan, Charles Quigley, Brandon D Jordan, Edward Fickus, Steve Schroeder, Bao-Hua Song, Yong-Qiang Charles An, David Hyten, Randall Nelson, Katy Rainey, William D Beavis, Jim Specht, Brian Diers, Perry Cregan
A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [ (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#5
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28722705/background-controlled-qtl-mapping-in-pure-line-genetic-populations-derived-from-four-way-crosses
#6
S Zhang, L Meng, J Wang, L Zhang
Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population...
July 19, 2017: Heredity
https://www.readbyqxmd.com/read/28719732/genome-wide-association-meta-analysis-reveals-novel-juvenile-idiopathic-arthritis-susceptibility-loci
#7
Laura A McIntosh, Miranda C Marion, Marc Sudman, Mary E Comeau, Mara L Becker, John F Bohnsack, Tasha E Fingerlin, Thomas A Griffin, J Peter Haas, Daniel J Lovell, Lisa A Maier, Peter A Nigrovic, Sampath Prahalad, Marilynn Punaro, Carlos D Rosé, Carol A Wallace, Carol A Wise, Halima Moncrieffe, Timothy D Howard, Carl D Langefeld, Susan D Thompson
OBJECTIVE: Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. This study focuses on identifying new associations among oligoarticular and polyarticular rheumatoid factor negative (RF(-) ) JIA, which are clinically similar and the most prevalent JIA disease subtypes. METHODS: Three cohorts totaling 2,751 oligoarticular and polyarticular RF(-) JIA cases were genotyped on the Affymetrix Genome-Wide SNP Array 6...
July 18, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28719638/combination-of-twelve-alleles-at-six-quantitative-trait-loci-determines-grain-weight-in-rice
#8
Yuxiang Zeng, Junsheng Shi, Zhijuan Ji, Zhihua Wen, Yan Liang, Changdeng Yang
Grain weight, which is controlled by quantitative trait loci (QTLs), is one of the most important determinants of rice yield. Although many QTLs for grain weight have been identified, little is known about how different alleles in different QTLs coordinate to determine grain weight. In the present study, six grain-weight-QTLs were detected in seven mapping populations (two F2, one F3, and four recombinant inbred lines) developed by crossing 'Lemont', a United States japonica variety, with 'Yangdao 4', a Chinese indica variety...
2017: PloS One
https://www.readbyqxmd.com/read/28719243/genotyping-by-sequencing-based-genetic-analysis-of-african-rice-cultivars-and-association-mapping-of-blast-resistance-genes-against-magnaporthe-oryzae-populations-in-africa
#9
Emmanuel M Mgonja, Chan Ho Park, Houxiang Kang, Elias G Balimponya, Stephen Opiyo, Maria Bellizzi, Samuel K Mutiga, Felix Rotich, Veena Devi Ganeshan, Robert Mabagala, Clay Sneller, Jim Correll, Bo Zhou, Nicholas J Talbot, Thomas K Mitchell, Guo-Liang Wang
Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs)...
July 18, 2017: Phytopathology
https://www.readbyqxmd.com/read/28716969/genetic-determinants-of-susceptibility-to-silver-nanoparticle-induced-acute-lung-inflammation-in-mice
#10
David K Scoville, Dianne Botta, Karen Galdanes, Stefanie C Schmuck, Collin C White, Patricia L Stapleton, Theo K Bammler, James W MacDonald, William A Altemeier, Michelle Hernandez, Steven R Kleeberger, Lung-Chi Chen, Terry Gordon, Terrance J Kavanagh
Silver nanoparticles (AgNPs) are employed in a variety of consumer products; however, in vivo rodent studies indicate that AgNPs can cause lung inflammation and toxicity in a strain- and particle type-dependent manner, but mechanisms of susceptibility remain unclear. The aim of this study was to assess the variation in AgNP-induced lung inflammation and toxicity across multiple inbred mouse strains and to use genome-wide association (GWA) mapping to identify potential candidate susceptibility genes. Mice received doses of 0...
July 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28715421/statistical-correction-of-the-winner-s-curse-explains-replication-variability-in-quantitative-trait-genome-wide-association-studies
#11
Cameron Palmer, Itsik Pe'er
Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication...
July 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28713412/the-emerging-oilseed-crop-sesamum-indicum-enters-the-omics-era
#12
REVIEW
Komivi Dossa, Diaga Diouf, Linhai Wang, Xin Wei, Yanxin Zhang, Mareme Niang, Daniel Fonceka, Jingyin Yu, Marie A Mmadi, Louis W Yehouessi, Boshou Liao, Xiurong Zhang, Ndiaga Cisse
Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713401/genome-wide-association-study-reveals-natural-variations-contributing-to-drought-resistance-in-crops
#13
REVIEW
Hongwei Wang, Feng Qin
Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711251/association-of-candidate-gene-polymorphisms-with-milk-technological-traits-yield-composition-and-somatic-cell-score-in-italian-holstein-friesian-sires
#14
E Viale, F Tiezzi, F Maretto, M De Marchi, M Penasa, M Cassandro
Advances in DNA-based marker technology have enabled the identification of genomic regions underlying complex phenotypic traits in livestock species. The incorporation of detected quantitative trait loci into genetic evaluation provides great potential to enhance selection accuracies, hence expediting the genetic improvement of economically important traits. The objective of the present study was to investigate 96 single nucleotide polymorphisms (SNP) located in 53 candidate genes previously reported to have effects on milk production and quality traits in a population of highly selected Holstein-Friesian bulls...
July 12, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28710696/mesocotyl-elongation-is-essential-for-seedling-emergence-under-deep-seeding-condition-in-rice
#15
Hyun-Sook Lee, Kazuhiro Sasaki, Ju-Won Kang, Tadashi Sato, Won-Yong Song, Sang-Nag Ahn
BACKGROUND: Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by deep-sowing. In rice, mesocotyl and coleoptile are primarily responsible for seedling emergence from deeper levels of soil. RESULTS: Quantitative trait loci (QTLs) for mesocotyl and coleoptile length at 5-cm seeding depth were detected using 98 backcross inbred lines from a cross between Kasalath and Nipponbare...
December 2017: Rice
https://www.readbyqxmd.com/read/28710561/genetic-architecture-of-wild-soybean-glycine-soja-response-to-soybean-cyst-nematode-heterodera-glycines
#16
Hengyou Zhang, Qijian Song, Joshua D Griffin, Bao-Hua Song
The soybean cyst nematode (SCN) is one of the most destructive pathogens of soybean plants worldwide. Host-plant resistance is an environmentally friendly method to mitigate SCN damage. To date, the resistant soybean cultivars harbor limited genetic variation, and some are losing resistance. Thus, a better understanding of the genetic mechanisms of the SCN resistance, as well as developing diverse resistant soybean cultivars, is urgently needed. In this study, a genome-wide association study (GWAS) was conducted using 1032 wild soybean (Glycine soja) accessions with over 42,000 single-nucleotide polymorphisms (SNPs) to understand the genetic architecture of G...
July 14, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28710504/mapping-novel-aphid-resistance-qtl-from-wild-soybean-glycine-soja-85-32
#17
Shichen Zhang, Zhongnan Zhang, Carmille Bales, Cuihua Gu, Chris DiFonzo, Ming Li, Qijian Song, Perry Cregan, Zhenyu Yang, Dechun Wang
Two novel QTLs conferring aphid resistance were mapped and validated on soybean chromosomes 8 and 16, respectively. Closely linked markers were developed to assist breeding for aphid resistance. Soybean aphid, Aphis glycines Matsumura, is a highly destructive pest for soybean production. E08934, a soybean advanced breeding line derived from the wild soybean Glycine soja 85-32, has shown strong resistance to aphids. To dissect the genetic basis of aphid resistance in E08934, a mapping population (070020) consisting of 140 F3-derived lines was developed by crossing E08934 with an aphid-susceptible line E00003...
July 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28710433/high-density-genetic-linkage-map-construction-and-quantitative-trait-locus-mapping-for-hawthorn-crataegus-pinnatifida-bunge
#18
Yuhui Zhao, Kai Su, Gang Wang, Liping Zhang, Jijun Zhang, Junpeng Li, Yinshan Guo
Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28709925/the-infinitesimal-model-definition-derivation-and-implications
#19
N H Barton, A M Etheridge, A Véber
Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution...
July 11, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28706532/identification-of-single-nucleotide-polymorphic-loci-associated-with-biomass-yield-under-water-deficit-in-alfalfa-medicago-sativa-l-using-genome-wide-sequencing-and-association-mapping
#20
Long-Xi Yu
Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa...
2017: Frontiers in Plant Science
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