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Quantitative trait loci

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https://www.readbyqxmd.com/read/29779872/the-maternal-effect-gene-wds-controls-wolbachia-titer-in-nasonia
#1
Lisa J Funkhouser-Jones, Edward J van Opstal, Ananya Sharma, Seth R Bordenstein
Maternal transmission of intracellular microbes is pivotal in establishing long-term, intimate symbioses. For germline microbes that exert negative reproductive effects on their hosts, selection can theoretically favor the spread of host genes that counteract the microbe's harmful effects. Here, we leverage a major difference in bacterial (Wolbachia pipientis) titers between closely related wasp species with forward genetic, transcriptomic, and cytological approaches to map two quantitative trait loci that suppress bacterial titers via a maternal effect...
May 4, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29775500/endosperm-sugar-accumulation-caused-by-mutation-of-phs8-isa1-leads-to-pre-harvest-sprouting-in-rice
#2
Lin Du, Fan Xu, Jun Fang, Shaopei Gao, Jiuyou Tang, Shuang Fang, Hongru Wang, Hongning Tong, Fengxia Zhang, Jinfang Chu, Guodong Wang, Chengcai Chu
Pre-harvest sprouting (PHS) is an unfavorable trait in cereal crops which could seriously decrease grain yield and quality. Although some PHS-associated quantitative trait loci (QTL) or genes in cereals have been reported, the molecular mechanism underlying PHS remains largely elusive. Here, we characterized a rice mutant, phs8, which exhibits PHS phenotype accompanied by sugary endosperm. Map-based cloning revealed that PHS8 encodes a starch debranching enzyme named isoamylase1. Mutation in PHS8 resulted in the phytoglycogen breakdown and sugar accumulation in the endosperm...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29774565/local-and-systemic-regulation-of-psii-efficiency-in-triticale-infected-by-the-hemibiotrophic-pathogen-microdochium-nivale
#3
Mateusz Dyda, Iwona Wąsek, Mirosław Tyrka, Maria Wędzony, Magdalena Szechyńska-Hebda
Microdochium nivale is a fungal pathogen that causes yield losses of cereals during winter. Cold hardening under light conditions induces genotype-dependent resistance of a plant to infection. We aim to show how photosystem II (PSII) regulation contributes to plant resistance. Using mapping population of triticale doubled haploid lines, three M. nivale strains and different infection assays, we demonstrate that plants that maintain a higher maximum quantum efficiency of PSII show less leaf damage upon infection...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29773962/discovery-and-validation-of-genomic-regions-associated-with-resistance-to-maize-lethal-necrosis-in-four-biparental-populations
#4
Manje Gowda, Yoseph Beyene, Dan Makumbi, Kassa Semagn, Michael S Olsen, Jumbo M Bright, Biswanath Das, Stephen Mugo, L M Suresh, Boddupalli M Prasanna
In sub-Saharan Africa, maize is the key determinant of food security for smallholder farmers. The sudden outbreak of maize lethal necrosis (MLN) disease is seriously threatening the maize production in the region. Understanding the genetic basis of MLN resistance is crucial. In this study, we used four biparental populations applied linkage mapping and joint linkage mapping approaches to identify and validate the MLN resistance-associated genomic regions. All populations were genotyped with low to high density markers and phenotyped in multiple environments against MLN under artificial inoculation...
2018: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/29771937/construction-and-characterization-of-a-bacterial-artificial-chromosome-library-for-gossypium-mustelinum
#5
Yuling Liu, Baohong Zhang, Xinpeng Wen, Shulin Zhang, Yangyang Wei, Quanwei Lu, Zhen Liu, Kunbo Wang, Fang Liu, Renhai Peng
A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD4) was constructed. Intact nuclei from G. mustelinum (AD4) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G...
2018: PloS One
https://www.readbyqxmd.com/read/29770990/pool-based-genome-wide-association-study-identified-novel-candidate-regions-on-bta9-and-14-for-oleic-acid-percentage-in-japanese-black-cattle
#6
Fuki Kawaguchi, Hiroto Kigoshi, Ayaka Nakajima, Yuta Matsumoto, Yoshinobu Uemoto, Moriyuki Fukushima, Emi Yoshida, Eiji Iwamoto, Takayuki Akiyama, Namiko Kohama, Eiji Kobayashi, Takeshi Honda, Kenji Oyama, Hideyuki Mannen, Shinji Sasazaki
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1...
May 17, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29766219/association-study-of-genetic-variants-in-estrogen-metabolic-pathway-genes-and-colorectal-cancer-risk-and-survival
#7
Shuwei Li, Lisheng Xie, Mulong Du, Kaili Xu, Lingjun Zhu, Haiyan Chu, Jinfei Chen, Meilin Wang, Zhengdong Zhang, Dongying Gu
Although studies have investigated the association of genetic variants and the abnormal expression of estrogen-related genes with colorectal cancer risk, the evidence remains inconsistent. We clarified the relationship of genetic variants in estrogen metabolic pathway genes with colorectal cancer risk and survival. A case-control study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in ten candidate genes with colorectal cancer risk in a Chinese population. A logistic regression model and Cox regression model were used to calculate SNP effects on colorectal cancer susceptibility and survival, respectively...
May 16, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29766218/qtl-mapping-and-epistatic-interaction-analysis-of-field-resistance-to-sudden-death-syndrome-fusarium-virguliforme-in-soybean
#8
Ruijuan Tan, Bradley Serven, Paul J Collins, Zhongnan Zhang, Zixiang Wen, John F Boyse, Cuihua Gu, Martin I Chilvers, Brian W Diers, Dechun Wang
Two interactive quantitative trait loci (QTLs) controlled the field resistance to sudden death syndrome (SDS) in soybean. The interaction between them was confirmed. Sudden death syndrome (SDS), caused by Fusarium virguliforme, is a major disease of soybean [Glycine max (L.) Merr.] in the United States. Breeding for soybean resistance to SDS is the most cost-effective method to manage the disease. The objective of this study was to identify and characterize quantitative trait loci (QTLs) underlying field resistance to SDS in a recombinant inbred line population from the cross GD2422 × LD01-5907...
May 15, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29764961/genome-wide-search-for-quantitative-trait-loci-controlling-important-plant-and-flower-traits-in-petunia-using-an-interspecific-recombinant-inbred-population-of-petunia-axillaris-and-petunia-exserta
#9
Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M Warner, Zhanao Deng
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia...
May 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#10
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29761461/bovine-genome-database-tools-for-mining-the-bos-taurus-genome
#11
Darren E Hagen, Deepak R Unni, Aditi Tayal, Gregory W Burns, Christine G Elsik
The Bovine Genome Database (BGD; http://bovinegenome.org ) is a web-accessible resource that supports bovine genomics research by providing genome annotation and data mining tools. BovineMine is a tool within BGD that integrates BGD data, including the genome, genes, precomputed gene expression levels and variant consequences, with external data sources that include quantitative trait loci (QTL), orthologues, Gene Ontology, gene interactions, and pathways. BovineMine enables researchers without programming skills to create custom integrated datasets for use in downstream analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761460/a-primer-for-the-rat-genome-database-rgd
#12
Stanley J F Laulederkind, G Thomas Hayman, Shur-Jen Wang, Jennifer R Smith, Victoria Petri, Matthew J Hoffman, Jeff De Pons, Marek A Tutaj, Omid Ghiasvand, Monika Tutaj, Jyothi Thota, Melinda R Dwinell, Mary Shimoyama
The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, http://rgd.mcw.edu ) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761429/guidelines-for-sample-normalization-to-minimize-batch-variation-for-large-scale-metabolic-profiling-of-plant-natural-genetic-variance
#13
Saleh Alseekh, Si Wu, Yariv Brotman, Alisdair R Fernie
Recent methodological advances in both liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) have facilitated the profiling highly complex mixtures of primary and secondary metabolites in order to investigate a diverse range of biological questions. These techniques usually face a large number of potential sources of technical and biological variation. In this chapter we describe guidelines and normalization procedures to reduce the analytical variation, which are essential for the high-throughput evaluation of metabolic variance used in broad genetic populations which commonly entail the evaluation of hundreds or thousands of samples...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760201/a-high-resolution-genetic-map-for-the-laboratory-rat
#14
John Littrell, Shirng-Wern Tsaih, Amelie Baud, Pasi Rastas, Leah Solberg-Woods, Michael J Flister
An accurate and high-resolution genetic map is critical for mapping complex traits, yet the resolution of the current rat genetic map is far lower than human and mouse, and has not been updated since the original Jensen-Seaman map in 2004. For the first time, we have refined the rat genetic map to sub-centimorgan (cM) resolution (<0.02 cM) by using 95,769 genetic markers and 870 informative meiosis from a cohort of 528 heterogeneous stock (HS) rats. Global recombination rates in the revised sex-averaged map (0...
May 14, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29757987/genomic-regions-analysis-of-seedling-root-traits-and-their-regulation-in-responses-to-phosphorus-deficiency-tolerance-in-cssl-population-of-elite-super-hybrid-rice
#15
Galal Bakr Anis, Yingxin Zhang, Huimin Wang, Zihe Li, Weixun Wu, Lianping Sun, Aamir Riaz, Liyong Cao, Shihua Cheng
Phosphorus (P) is the essential macro-element supporting rice productivity. Quantitative trait loci (QTL) underlying related traits at the seedling stage under two different phosphorus levels was investigated in rice using a population of 76 Chromosomal Sequence Substitution Lines (CSSLs) derived from a cross between the maintainer variety XieqingzaoB (P stress tolerant) and the restorer variety Zhonghui9308 (P stress sensitive); the parents of super hybrid rice Xieyou9308. A genetic linkage map with 120 DNA marker loci was constructed...
May 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29754326/acid-phosphatase-gene-gmhad1-linked-to-low-phosphorus-tolerance-in-soybean-through-fine-mapping
#16
Zhandong Cai, Yanbo Cheng, Peiqi Xian, Qibin Ma, Ke Wen, Qiuju Xia, Gengyun Zhang, Hai Nian
Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments...
May 12, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29753465/short-communication-uncovering-quantitative-trait-loci-associated-with-resistance-to-mycobacterium-avium-ssp-paratuberculosis-infection-in-holstein-cattle-using-a-high-density-single-nucleotide-polymorphism-panel
#17
Sanjay Mallikarjunappa, M Sargolzaei, L F Brito, K G Meade, N A Karrow, S D Pant
Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection...
May 9, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29752522/meta-qtl-analysis-of-seed-iron-and-zinc-concentration-and-content-in-common-bean-phaseolus-vulgaris-l
#18
Paulo Izquierdo, Carolina Astudillo, Matthew W Blair, Asif M Iqbal, Bodo Raatz, Karen A Cichy
Twelve meta-QTL for seed Fe and Zn concentration and/or content were identified from 87 QTL originating from seven population grown in sixteen field trials. These meta-QTL include 2 specific to iron, 2 specific to zinc and 8 that co-localize for iron and zinc concentrations and/or content. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption worldwide and it is an important source of microelements, especially iron and zinc. Bean biofortification breeding programs develop new varieties with high levels of Fe and Zn targeted for countries with human micronutrient deficiencies...
May 11, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29751743/dissecting-closely-linked-association-signals-in-combination-with-the-mammalian-phenotype-database-can-identify-candidate-genes-in-dairy-cattle
#19
Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
BACKGROUND: Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identifying the causal variants and revealing underlying mechanisms have proven complicated. In dairy cattle populations, we face a challenge due to long-range linkage disequilibrium (LD) arising from close familial relationships in the studied individuals. Long range LD makes it difficult to distinguish if one or multiple quantitative trait loci (QTL) are segregating in a genomic region showing association with a phenotype...
May 11, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29751669/mapping-grain-iron-and-zinc-content-quantitative-trait-loci-in-an-iniadi-derived-immortal-population-of-pearl-millet
#20
Sushil Kumar, Charles Tom Hash, Thirunavukkarasu Nepolean, Mahesh D Mahendrakar, Chellapilla Tara Satyavathi, Govind Singh, Abhishek Rathore, Rattan S Yadav, Rajeev Gupta, Rakesh K Srivastava
Pearl millet is a climate-resilient nutritious crop requiring low inputs and is capable of giving economic returns in marginal agro-ecologies. In this study, we report large-effect iron (Fe) and zinc (Zn) content quantitative trait loci ( QTLs) using diversity array technology (DArT) and simple sequence repeats (SSRs) markers to generate a genetic linkage map using 317 recombinant inbred line (RIL) population derived from the (ICMS 8511-S1-17-2-1-1-B-P03 × AIMP 92901-S1-183-2-2-B-08) cross. The base map [seven linkage groups (LGs)] of 196 loci was 964...
May 11, 2018: Genes
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