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Isabel Rodríguez-Quilón, Luis Santos-Del-Blanco, María Jesús Serra-Varela, Jarkko Koskela, Santiago C González-Martínez, Ricardo Alía
Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
Angelica Giancaspro, Stefania L Giove, Daniela Zito, A Blanco, Agata Gadaleta
Fusarium head blight (scab) is one of the most widespread and damaging diseases of wheat, causing grain yield and quality losses and production of harmful mycotoxins. Development of resistant varieties is hampered by lack of effective resistance sources in the tetraploid wheat primary gene pool. Here we dissected the genetic basis of resistance in a new durum wheat (Triticum turgidum ssp. durum) Recombinant inbred lines (RILs) population obtained by crossing an hexaploid resistant line and a durum susceptible cultivar...
2016: Frontiers in Plant Science
Feng Chang, Lijun Li, Gang Gao, Shengqiang Ding, Jincai Yang, Ting Zhang, Genle Zuo
BACKGROUND: Our study was aimed at finding out if Runx2 SNPs (single-nucleotide polymorphisms) are related to susceptibility to and prognosis of ossification of posterior longitudinal ligament (OPLL). METHODS: We selected 80 OPLL patients and another 80 independent patients without OPLL from September 2013 to November 2014. Serum was collected to detect the genotypes of rs1321075, rs12333172, and rs1406846 on Runx2 with direct sequencing analysis. RESULTS: Differences in clinical characteristics, including age, weight, height, sex ratio, as well as smoking and drinking history, between OPLL and control groups appeared to be insignificant (all P-value >...
October 5, 2016: Journal of Clinical Laboratory Analysis
Teruaki Tozaki, Fumio Sato, Mutsuki Ishimaru, Mio Kikuchi, Hironaga Kakoi, Kei-Ichi Hirota, Shun-Ichi Nagata
Ligand-dependent nuclear receptor compressor-like (LCORL) encodes a transcription factor, and its polymorphisms are associated with measures of skeletal frame size and adult height in several species. Recently, the single nucleotide polymorphism (SNP) BIEC2-808543 located upstream of LCORL was identified as a genetic diagnostic marker associated with withers height in Thoroughbreds. In this study, 322 Thoroughbreds-in-training were genotyped for BIEC2-808543 to evaluate the association between genotype and body composition traits, including body weight, withers height, the ratio of body weight to withers height, chest circumference, and cannon circumference...
2016: Journal of Equine Science
Teresa B De Leon, Steven Linscombe, Prasanta K Subudhi
BACKGROUND: Salinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage...
December 2016: Rice
Erik P A van Iperen, Suthesh Sivapalaratnam, Michael V Holmes, G Kees Hovingh, Aeilko H Zwinderman, Folkert W Asselbergs
BACKGROUND AND AIMS: Type 2 diabetes (T2D), low-density lipoprotein-cholesterol (LDL-c), body mass index (BMI), blood pressure and smoking are established risk factors that play a causal role in coronary artery disease (CAD). Numerous common genetic variants associating with these and other risk factors have been identified, but their association with CAD has not been comprehensively examined in a single study. Our goal was to comprehensively evaluate the associations of established and emerging risk factors with CAD using genetic variants identified from Genome-wide Association Studies (GWAS)...
September 13, 2016: Atherosclerosis
Huma Butt, Shabana, Shahida Hasnain
BACKGROUND: Diabetes is a socioeconomic burden in Pakistan. International diabetes federation reported 6.9 million cases of diabetes and 87,548 deaths due to diabetes in Pakistan in 2014. Peroxisome proliferators-activated receptors are transcription factors, regulating several physiological processes. AIM: The aim of the current study was to determine the prevalence of silent variant C1431T in exon 6 of PPAR-y and analyze its effect on various anthropometric and biochemical parameters in a Pakistani cohort...
2016: Diabetology & Metabolic Syndrome
Harold A Nieuwboer, René Pool, Conor V Dolan, Dorret I Boomsma, Michel G Nivard
Here we present a method of genome-wide inferred study (GWIS) that provides an approximation of genome-wide association study (GWAS) summary statistics for a variable that is a function of phenotypes for which GWAS summary statistics, phenotypic means, and covariances are available. A GWIS can be performed regardless of sample overlap between the GWAS of the phenotypes on which the function depends. Because a GWIS provides association estimates and their standard errors for each SNP, a GWIS can form the basis for polygenic risk scoring, LD score regression, Mendelian randomization studies, biological annotation, and other analyses...
October 6, 2016: American Journal of Human Genetics
Marissa A H den Hoed, Saskia M F Pluijm, Lisette Stolk, André G Uitterlinden, Rob Pieters, Marry M van den Heuvel-Eibrink
PURPOSE: Despite similarities in upfront treatment of childhood cancer, not every adult survivor of childhood cancer (CCS) has an impaired bone mineral density (BMD). No data are available on the role of genetic variation on impairment of BMD in CCS. METHODS: This cross-sectional single-center cohort study included 334 adult CCSs (median follow-up time after cessation of treatment: 15 years; median age at follow-up: 26 years). Total body BMD (BMDTB ) and lumbar spine BMD (BMDLS ) were measured by dual x-ray absorptiometry...
August 31, 2016: Pediatric Blood & Cancer
Yankun Wang, Wenjing Chen, Pu Chu, Shubei Wan, Mao Yang, Mingming Wang, Rongzhan Guan
BACKGROUND: Key genes related to plant type traits have played very important roles in the "green revolution" by increasing lodging resistance and elevating the harvest indices of crop cultivars. Although there have been numerous achievements in the development of dwarfism and plant type in Brassica napus breeding, exploring new materials conferring oilseed rape with efficient plant types that provide higher yields is still of significance in breeding, as well as in elucidating the mechanisms underlying plant development...
2016: BMC Plant Biology
Yansong Ma, Jochen C Reif, Yong Jiang, Zixiang Wen, Dechun Wang, Zhangxiong Liu, Yong Guo, Shuhong Wei, Shuming Wang, Chunming Yang, Huicai Wang, Chunyan Yang, Weiguo Lu, Ran Xu, Rong Zhou, Ruizhen Wang, Zudong Sun, Huaizhu Chen, Wanhai Zhang, Jian Wu, Guohua Hu, Chunyan Liu, Xiaoyan Luan, Yashu Fu, Tai Guo, Tianfu Han, Mengchen Zhang, Bincheng Sun, Lei Zhang, Weiyuan Chen, Cunxiang Wu, Shi Sun, Baojun Yuan, Xinan Zhou, Dezhi Han, Hongrui Yan, Wenbin Li, Lijuan Qiu
Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers...
2016: Molecular Breeding: New Strategies in Plant Improvement
Liane Fischer, Caroline Wilde, Torsten Schöneberg, Ines Liebscher
BACKGROUND: A large number of human inherited and acquired diseases and phenotypes are caused by mutations in G protein-coupled receptors (GPCR). Genome-wide association studies (GWAS) have shown that variations in the ADGRD1 (GPR133) locus are linked with differences in metabolism, human height and heart frequency. ADGRD1 is a Gs protein-coupled receptor belonging to the class of adhesion GPCRs. RESULTS: Analysis of more than 1000 sequenced human genomes revealed approximately 9000 single nucleotide polymorphisms (SNPs) in the human ADGRD1 as listed in public data bases...
2016: BMC Genomics
Jérôme Bartholomé, Joost Van Heerwaarden, Fikret Isik, Christophe Boury, Marjorie Vidal, Christophe Plomion, Laurent Bouffier
BACKGROUND: Genomic selection (GS) is a promising approach for decreasing breeding cycle length in forest trees. Assessment of progeny performance and of the prediction accuracy of GS models over generations is therefore a key issue. RESULTS: A reference population of maritime pine (Pinus pinaster) with an estimated effective inbreeding population size (status number) of 25 was first selected with simulated data. This reference population (n = 818) covered three generations (G0, G1 and G2) and was genotyped with 4436 single-nucleotide polymorphism (SNP) markers...
2016: BMC Genomics
Enid Perez-Lara, Kassa Semagn, Hua Chen, Muhammad Iqbal, Amidou N'Diaye, Atif Kamran, Alireza Navabi, Curtis Pozniak, Dean Spaner
We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population...
2016: PloS One
Chengming Sun, Benqi Wang, Lei Yan, Kaining Hu, Sheng Liu, Yongming Zhou, Chunyun Guan, Zhenqian Zhang, Jiana Li, Jiefu Zhang, Song Chen, Jing Wen, Chaozhi Ma, Jinxing Tu, Jinxiong Shen, Tingdong Fu, Bin Yi
Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5...
2016: Frontiers in Plant Science
Lindsay V Clark, Elena Dzyubenko, Nikolay Dzyubenko, Larisa Bagmet, Andrey Sabitov, Pavel Chebukin, Douglas A Johnson, Jens Bonderup Kjeldsen, Karen Koefoed Petersen, Uffe Jørgensen, Ji Hye Yoo, Kweon Heo, Chang Yeon Yu, Hua Zhao, Xiaoli Jin, Junhua Peng, Toshihiko Yamada, Erik J Sacks
BACKGROUND AND AIMS: Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. METHODS: A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M...
July 24, 2016: Annals of Botany
Michel G Nivard, Christel M Middeldorp, Gitta Lubke, Jouke-Jan Hottenga, Abdel Abdellaoui, Dorret I Boomsma, Conor V Dolan
Heritability may be estimated using phenotypic data collected in relatives or in distantly related individuals using genome-wide single nucleotide polymorphism (SNP) data. We combined these approaches by re-parameterizing the model proposed by Zaitlen et al and extended this model to include moderation of (total and SNP-based) genetic and environmental variance components by a measured moderator. By means of data simulation, we demonstrated that the type 1 error rates of the proposed test are correct and parameter estimates are accurate...
July 20, 2016: European Journal of Human Genetics: EJHG
Manman Shen, Liang Qu, Meng Ma, Taocun Dou, Jian Lu, Jun Guo, Yuping Hu, Guoqiang Yi, Jingwei Yuan, Congjiao Sun, Kehua Wang, Ning Yang
The comb, as a secondary sexual character, is an important trait in chicken. Indicators of comb length (CL), comb height (CH), and comb weight (CW) are often selected in production. DNA-based marker-assisted selection could help chicken breeders to accelerate genetic improvement for comb or related economic characters by early selection. Although a number of quantitative trait loci (QTL) and candidate genes have been identified with advances in molecular genetics, candidate genes underlying comb traits are limited...
2016: PloS One
Charlotte N Miller, Andrea L Harper, Martin Trick, Peter Werner, Keith Waldron, Ian Bancroft
BACKGROUND: The current approach to reducing the tendency for wheat grown under high fertilizer conditions to collapse (lodge) under the weight of its grain is based on reducing stem height via the introduction of Rht genes. However, these reduce the yield of straw (itself an important commodity) and introduce other undesirable characteristics. Identification of alternative height-control loci is therefore of key interest. In addition, the improvement of stem mechanical strength provides a further way through which lodging can be reduced...
2016: BMC Genomics
M N Li, X Guo, P J Bao, X Y Wu, X Z Ding, M Chu, C N Liang, P Yan
ATP citrate lyase (ACLY) is the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA, which is a key precursor of both fatty acid and mevalonate synthesis pathways. Genetic variation of the ACLY gene may influence multiple traits associated with animal production. Here, we identified three non-synonymous mutations in ACLY exons in five beef cattle populations using DNA pool sequencing and high-resolution melting analysis. Results from association analyses revealed that the single nucleotide polymorphism (SNP) g...
2016: Genetics and Molecular Research: GMR
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