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Quantitative trait loci

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https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#1
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149250/modeling-the-causal-role-of-dna-methylation-in-the-association-between-cigarette-smoking-and-inflammation-in-african-americans-a-2-step-epigenetic-mendelian-randomization-study
#2
Min A Jhun, Jennifer A Smith, Erin B Ware, Sharon L R Kardia, Thomas H Mosley, Stephen T Turner, Patricia A Peyser, Sung Kyun Park
The association between cigarette smoking and inflammation is well known. However, the biological mechanisms behind the association are not fully understood, particularly the role of DNA methylation, which is known to be affected by smoking. Using 2-step epigenetic Mendelian randomization, we investigated the role of DNA methylation in the association between cigarette smoking and inflammation. In 822 African Americans from the Genetic Epidemiology Network of Arteriopathy, phase 2 (Jackson, Mississippi; 2000-2005), study population, we examined the association of cigarette smoking with DNA methylation using single nucleotide polymorphisms identified in previous genome-wide association studies of cigarette smoking...
November 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29147737/genetic-dissection-of-early-season-cold-tolerance-in-sorghum-genome-wide-association-studies-for-seedling-emergence-and-survival-under-field-and-controlled-environment-conditions
#3
Sebastian Parra-Londono, Karin Fiedler, Mareike Kavka, Birgit Samans, Silke Wieckhorst, Arndt Zacharias, Ralf Uptmoor
A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions. Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker-trait associations controlling temperature-related seedling establishment...
November 16, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29146906/qtl-mapping-and-molecular-characterization-of-the-classical-d-locus-controlling-seed-and-flower-color-in-linum-usitatissimum-flax
#4
Gurudatt Pavagada Sudarshan, Manoj Kulkarni, Leonid Akhov, Paula Ashe, Hamid Shaterian, Sylvie Cloutier, Gordon Rowland, Yangdou Wei, Gopalan Selvaraj
The flowers of flax (linseed) are blue-hued, ephemeral and self-pollinating, and the seeds are typically brown. A century-old interest in natural yellow seed variants and a historical model point to recessive alleles in B1, D and G loci being responsible, but the functional aspects had remained unknown. Here, we characterized the "D" locus by quantitative trait loci (QTL) mapping and identified a FLAVONOID 3'5' HYDROXYLASE (F3'5'H) gene therein. It does not belong to the F3'5'H clade, but resembles biochemically characterized F3'Hs (flavonoid 3' hydroxylase) but without F3'H activity...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29145412/mapping-and-verification-of-grain-shape-qtls-based-on-an-advanced-backcross-population-in-rice
#5
Duo Xia, Hao Zhou, Lei Qiu, Haichao Jiang, Qinglu Zhang, Guanjun Gao, Yuqing He
Grain shape is a key factor that influences both the appearance quality and grain yield of rice. To clarify the genetic basis of grain shape, an advanced backcross population was developed from the cross of a slender indica variety Jin23B and a round japonica variety QingGuAi, and a total of 10 quantitative trait loci (QTLs) for grain shape were detected over 2 years. Three QTLs, qGW1, qGS3 and qGS7 have large effects on grain shape and were detected in both years. To further validate their effects, the BC4F2 populations of the three QTLs were constructed...
2017: PloS One
https://www.readbyqxmd.com/read/29143610/development-of-f1-hybrid-population-and-the-high-density-linkage-map-for-european-aspen-populus-tremula-l-using-radseq-technology
#6
Anatoly V Zhigunov, Pavel S Ulianich, Marina V Lebedeva, Peter L Chang, Sergey V Nuzhdin, Elena K Potokina
BACKGROUND: Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe. RESULTS: We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143602/molecular-and-agro-morphological-characterization-of-ancient-wheat-landraces-of-turkey
#7
Kahraman Gurcan, Fatih Demirel, Mehmet Tekin, Serap Demirel, Taner Akar
BACKGROUND: Turkey is one of the important gene centers for many crop species. In this research, some ancient wheats such as tetraploid and diploid hulled wheats together with hexaploid tir wheats (Triticum aestivum ssp. leucospermum Korn.) landraces mainly adapted to harsh winter conditions of Eastern Anatolian region of Turkey were characterized at agro-morphological and molecular level. Totally 50 hulled wheat population from Kastamonu, Konya and Kayseri provinces and 15 tir wheats from Kars provinces of Turkey were in-situ collected for characterization in 2013...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29142307/genetic-polymorphism-related-to-monocyte-macrophage-function-is-associated-with-graft-versus-host-disease
#8
Kati Hyvärinen, Jarmo Ritari, Satu Koskela, Riitta Niittyvuopio, Anne Nihtinen, Liisa Volin, David Gallardo, Jukka Partanen
Despite detailed human leukocyte antigen (HLA) matching and modern immunosuppressive therapy, severe graft-versus-host disease (GvHD) remains a major hurdle for successful allogeneic hematopoietic stem cell transplantation (HSCT). As the genetic diversity in GvHD complicates the systematic discovery of associated variants across populations, we studied 122 GvHD-associated single nucleotide polymorphisms (SNPs) in 492 HLA-matched sibling HSCT donor-recipient pairs from Finland and Spain. The association between these candidate SNPs and grade III-IV acute GvHD and extensive chronic GvHD was assessed...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142238/mapping-qtls-conferring-salt-tolerance-and-micronutrient-concentrations-at-seedling-stagein-wheat
#9
Babar Hussain, Stuart James Lucas, Levent Ozturk, Hikmet Budak
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#10
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29141988/genotyping-by-sequencing-in-almond-snp-discovery-linkage-mapping-and-marker-design
#11
Shashi N Goonetilleke, Timothy J March, Michelle G Wirthensohn, Pere Arús, Amanda R Walker, Diane E Mather
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond [Prunus dulcis (Mill.) D.A. Webb], application of a double pseudo-testcross mapping approach to the F1 progeny of a bi-parental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping-by-sequencing to discover and map single-nucleotide polymorphisms in the almond cultivars 'Nonpareil' and 'Lauranne'...
November 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29138903/next-generation-sequencing-to-identify-candidate-genes-and-develop-diagnostic-markers-for-a-novel-phytophthora-resistance-gene-rpshc18-in-soybean
#12
Chao Zhong, Suli Sun, Yinping Li, Canxing Duan, Zhendong Zhu
A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates...
November 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29138689/clarifying-sub-genomic-positions-of-qtls-for-flowering-habit-and-fruit-quality-in-u-s-strawberry-fragaria%C3%A3-ananassa-breeding-populations-using-pedigree-based-qtl-analysis
#13
Sujeet Verma, Jason D Zurn, Natalia Salinas, Megan M Mathey, Beatrice Denoyes, James F Hancock, Chad E Finn, Nahla V Bassil, Vance M Whitaker
The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29136656/genetic-diversity-linkage-disequilibrium-and-association-mapping-analyses-of-gossypium-barbadense-l-germplasm
#14
Alisher A Abdullaev, Ilkhom B Salakhutdinov, Sharof S Egamberdiev, Ernest E Khurshut, Sofiya M Rizaeva, Mauricio Ulloa, Ibrokhim Y Abdurakhmonov
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers...
2017: PloS One
https://www.readbyqxmd.com/read/29131514/quantitative-trait-loci-associated-with-soybean-seed-weight-and-composition-under-different-phosphorus-levels
#15
Gokhan Hacisalihoglu, Amy L Burton, Jeffery L Gustin, Selim Eker, Safiye Asikli, Elif Hakli Heybet, Levent Ozturk, Ismail Cakmak, Atilla Yazici, Kent O Burkey, James Orf, A Mark Settles
Seed size and composition are important traits in food crops and can be affected by nutrient availability in the soil. Phosphorus (P) is a non-renewable, essential macronutrient, and P deficiency limits soybean (Glycine max) yield and quality. To investigate the associations of seed traits in low- and high-P environments, soybean recombinant inbred lines (RILs) from the cross of cultivars Fiskeby III and Mandarin (Ottawa) were grown under contrasting P availability environments. Traits including individual seed weight, seed number, and intact mature pod weight were significantly affected by soil P levels and showed transgressive segregation among the RILs...
November 13, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29128518/verification-of-genetic-loci-responsible-for-the-resistance-susceptibility-to-the-sendai-virus-infection-using-congenic-mice
#16
Raghda Mohamed Fathi Abbas, Daisuke Torigoe, Yayoi Kameda, Hassan T Tag-El-Din-Hassan, Nobuya Sasaki, Masami Morimatsu, Takashi Agui
Sendai virus (SeV) is one of the most important pathogens in the specific-pathogen free rodents. It is known that there are some inbred mouse strains susceptible or resistant to SeV infection. The C57BL/6 (B6) and DBA/2 (D2) mice are representative of the resistant and susceptible strains, respectively. Previous study with the quantitative trait locus (QTL) analysis identified three QTLs responsible for resistance or susceptibility to SeV infection on different chromosomes and indicated that resistance or susceptibility to SeV infection was almost predicted by genotypes of these three QTLs...
November 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29128211/genome-wide-association-studies-to-identify-quantitative-trait-loci-affecting-milk-production-traits-in-water-buffalo
#17
J J Liu, A X Liang, G Campanile, G Plastow, C Zhang, Z Wang, A Salzano, B Gasparrini, M Cassandro, L G Yang
Water buffalo is the second largest resource of milk supply around the world, and it is well known for its distinctive milk quality in terms of fat, protein, lactose, vitamin, and mineral contents. Understanding the genetic architecture of milk production traits is important for future improvement by the buffalo breeding industry. The advance of genome-wide association studies (GWAS) provides an opportunity to identify potential genetic variants affecting important economical traits. In the present study, GWAS was performed for 489 buffaloes with 1,424 lactation records using the 90K Affymetrix Buffalo SNP Array (Affymetrix/Thermo Fisher Scientific, Santa Clara, CA)...
November 8, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29127523/identification-of-quantitative-trait-loci-for-resistance-to-rsivd-in-red-sea-bream-pagrus-major
#18
Eitaro Sawayama, Shiho Tanizawa, Shin-Ichi Kitamura, Kei Nakayama, Kohei Ohta, Akiyuki Ozaki, Motohiro Takagi
Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated...
November 10, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/29127429/a-high-density-consensus-linkage-map-of-white-lupin-highlights-synteny-with-narrow-leafed-lupin-and-provides-markers-tagging-key-agronomic-traits
#19
Michał Książkiewicz, Nelson Nazzicari, Hua'an Yang, Matthew N Nelson, Daniel Renshaw, Sandra Rychel, Barbara Ferrari, Maria Carelli, Magdalena Tomaszewska, Stanisław Stawiński, Barbara Naganowska, Bogdan Wolko, Paolo Annicchiarico
White lupin (Lupinus albus L.) is a valuable source of seed protein, carbohydrates and oil, but requires genetic improvement to attain its agronomic potential. This study aimed to (i) develop a new high-density consensus linkage map based on new, transcriptome-anchored markers; (ii) map four important agronomic traits, namely, vernalization requirement, seed alkaloid content, and resistance to anthracnose and Phomopsis stem blight; and, (iii) define regions of synteny between the L. albus and narrow-leafed lupin (L...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29127305/cis-snps-set-testing-and-predixcan-analysis-for-gene-expression-data-using-linear-mixed-models
#20
Ping Zeng, Ting Wang, Shuiping Huang
Understanding the functional mechanism of SNPs identified in GWAS on complex diseases is currently a challenging task. The studies of expression quantitative trait loci (eQTL) have shown that regulatory variants play a crucial role in the function of associated SNPs. Detecting significant genes (called eGenes) in eQTL studies and analyzing the effect sizes of cis-SNPs can offer important implications on the genetic architecture of associated SNPs and interpretations of the molecular basis of diseases. We applied linear mixed models (LMM) to the gene expression level and constructed likelihood ratio tests (LRT) to test for eGene in the Geuvadis data...
November 10, 2017: Scientific Reports
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