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https://www.readbyqxmd.com/read/28231525/construction-of-new-est-ssrs-for-fusarium-resistant-wheat-breeding
#1
Aysen Yumurtaci, Hulya Sipahi, Ayed Al-Abdallat, Abdulqader Jighly, Michael Baum
Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28220132/identification-of-marker-trait-associations-for-lint-traits-in-cotton
#2
Muhammad A Iqbal, Mehboob-Ur- Rahman
Harvesting high quality lint, a long-awaited breeding goal-accomplished partly, can be achieved by identifying DNA markers which could be used for diagnosing cotton plants containing the desired traits. In the present studies, a total of 185 cotton genotypes exhibiting diversity for lint traits were selected from a set of 546 genotypes evaluated for fiber traits in 2009. These genotypes were extensively studied for three consecutive years (2011-2013) at three different locations. Significant genetic variations were found for average boll weight, ginning out turn (GOT), micronaire value, staple length, fiber bundle strength, and uniformity index...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28218791/development-and-validation-of-the-first-ssr-markers-for-mimosa-scabrella-benth
#3
F A Saiki, A P Bernardi, M S Reis, H Faoro, E M Souza, F O Pedrosa, A Mantovani, A F Guidolin
Mimosa scabrella Benth., popularly known as ''bracatinga'', is a pioneer and endemic species of Brazil, occurring in Mixed Ombrophilous Forest associated with Brazilian Atlantic Rainforest biomes. It is a fast-growing tree of the Fabaceae family that facilitates the dynamics of ecological succession. SSR development, when there is no genome sequence, is time and labor intensive and there are no molecular markers for M. scabrella. We developed and validated the first microsatellite markers for this tetraploid species, evaluating mother trees and progenies...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28218787/genetic-relationships-in-a-germplasm-collection-of-camellia-japonica-and-camellia-oleifera-using-ssr-analysis
#4
Y Zhao, C J Ruan, G J Ding, S Mopper
Camellia japonica produces different color and bigger flowers, widely being used for gardening green in southern China. However, cultivars were introduced from different regions, but their origin and pedigree information is either not available poorly documented, causing problems in authentication. Many low-yield trees in Camellia oleifera forests have been used as stocks for grafting C. japonica. However, the survival rate of grafts between these two species is related to genetic relationship between stock of C...
February 16, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#5
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28210265/rna-seq-of-guar-cyamopsis-tetragonoloba-l-taub-leaves-de-novo-transcriptome-assembly-functional-annotation-and-development-of-genomic-resources
#6
Umesh K Tanwar, Vikas Pruthi, Gursharn S Randhawa
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28207889/genetic-variation-of-maturity-groups-and-four-e-genes-in-the-chinese-soybean-mini-core-collection
#7
Jicun Li, Xiaobo Wang, Wenwen Song, Xinyang Huang, Jing Zhou, Haiyan Zeng, Shi Sun, Hongchang Jia, Wenbin Li, Xinan Zhou, Suzhen Li, Pengyin Chen, Cunxiang Wu, Yong Guo, Tianfu Han, Lijuan Qiu
The mini core collection (MCC) has been established by streamlining core collection (CC) chosen from China National Genebank including 23,587 soybean (Glycine max) accessions by morphological traits and simple sequence repeat (SSR) markers. Few studies have been focused on the maturity that has been considered as one of the most critical traits for the determination of the adaptation-growing region of the soybean. In the current study, two hundred and ninty-nine accessions of MCC planted for two years at four locations namely in Heihe, Harbin, Jining and Wuhan cities in China were used to assess the variation of maturity in MCC and identify the integrated effect of 4 E loci on flowering and maturity time in soybean...
2017: PloS One
https://www.readbyqxmd.com/read/28192462/development-identification-and-validation-of-caps-marker-for-shell-trait-which-governs-dura-pisifera-and-tenera-fruit-forms-in-oil-palm-elaeis-guineensis-jacq
#8
B Kalyana Babu, R K Mathur, P Naveen Kumar, D Ramajayam, G Ravichandran, M V B Venu, S Sparjan Babu
The oil palm fruit forms (dura, pisifera and tenera) governed by the shell thickness gene (Sh) plays a major role in identification of fruit type and also influences palm oil yield. Identification of desired fruit type is a major asset to the breeders and oil palm workers for applications in breeding, seed certification and to reduce time, space and money spent on identification of fruit form. In the present study, we developed Sh gene specific primer pairs and bulk segregant analysis was done using 300 genomic and 8 genic SSR markers...
2017: PloS One
https://www.readbyqxmd.com/read/28188954/comparative-glandular-trichome-transcriptome-based-gene-characterization-reveals-reasons-for-differential-menthol-biosynthesis-in-mentha-species
#9
Md Qussen Akhtar, Nida Qamar, Pallavi Yadav, Pallavi Kulkarni, Ajay Kumar, Ajit Kumar Shasany
The genes involved in menthol biosynthesis are reported earlier in Mentha × piperita. But the information on these genes is not available in Mentha arvensis. To bridge the gap in knowledge on differential biosynthesis of monoterpenes leading to compositional variation in the essential oil of these species, a comparative transcriptome analysis of the glandular trichome was carried out. In addition to the MVA and MEP pathway genes, about 210 and 196 different terpene synthases (TPS) transcripts were identified from annotation in M...
February 11, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28188068/ssr-and-morphological-trait-based-population-structure-analysis-of-130-diverse-flax-linum-usitatissimum-l-accessions
#10
Shashi Bhushan Choudhary, Hariom Kumar Sharma, Arroju Anil Kumar, Rangappa Thimmaiah Maruthi, Jiban Mitra, Isholeena Chowdhury, Binay Kumar Singh, Pran Gobinda Karmakar
A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous...
February 7, 2017: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/28187714/tipmt-identification-of-pcr-based-taxon-specific-markers
#11
Gabriela F Rodrigues-Luiz, Mariana S Cardoso, Hugo O Valdivia, Edward V Ayala, Célia M F Gontijo, Thiago de S Rodrigues, Ricardo T Fujiwara, Robson S Lopes, Daniella C Bartholomeu
BACKGROUND: Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187131/genome-size-cytogenetic-data-and-transferability-of-est-ssrs-markers-in-wild-and-cultivated-species-of-the-genus-theobroma-l-byttnerioideae-malvaceae
#12
Rangeline Azevedo da Silva, Gustavo Souza, Lívia Santos Lima Lemos, Uilson Vanderlei Lopes, Nara Geórgia Ribeiro Braz Patrocínio, Rafael Moysés Alves, Lucília Helena Marcellino, Didier Clement, Fabienne Micheli, Karina Peres Gramacho
The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized...
2017: PloS One
https://www.readbyqxmd.com/read/28185799/exploring-single-nucleotide-polymorphism-snp-microsatellite-ssr-and-differentially-expressed-genes-in-the-jellyfish-rhopilema-esculentum-by-transcriptome-sequencing
#13
Yunfeng Li, Zunchun Zhou, Meilin Tian, Yi Tian, Ying Dong, Shilei Li, Weidong Liu, Chongbo He
In this study, single nucleotide polymorphism (SNP), microsatellite (SSR) and differentially expressed genes (DEGs) in the oral parts, gonads, and umbrella parts of the jellyfish Rhopilema esculentum were analyzed by RNA-Seq technology. A total of 76.4 million raw reads and 72.1 million clean reads were generated from deep sequencing. Approximately 119,874 tentative unigenes and 149,239 transcripts were obtained. A total of 1,034,708 SNP markers were detected in the three tissues. For microsatellite mining, 5088 SSRs were identified from the unigene sequences...
February 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28184437/an-accurate-and-efficient-method-for-large-scale-ssr-genotyping-and-applications
#14
Lun Li, Zhiwei Fang, Junfei Zhou, Hong Chen, Zhangfeng Hu, Lifen Gao, Lihong Chen, Sheng Ren, Hongyu Ma, Long Lu, Weixiong Zhang, Hai Peng
No abstract text is available yet for this article.
February 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28176848/effect-of-domestication-on-the-genetic-diversity-and-structure-of-saccharina-japonica-populations-in-china
#15
Jie Zhang, Xiuliang Wang, Jianting Yao, Qiuying Li, Fuli Liu, Norishige Yotsukura, Tatiana N Krupnova, Delin Duan
Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S...
February 8, 2017: Scientific Reports
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
#16
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/28167189/neurophysiological-and-clinical-effects-of-dry-needling-in-patients-with-upper-trapezius-myofascial-trigger-points
#17
Maryam Abbaszadeh-Amirdehi, Noureddin Nakhostin Ansari, Soofia Naghdi, Gholamreza Olyaei, Mohammad Reza Nourbakhsh
INTRODUCTION: Dry needling (DN) is a widely used in treatment of myofascial trigger points (MTrPs). The purpose of this pretest-posttest clinical trial was to investigate the neurophysiological and clinical effects of DN in patients with MTrPs. METHODS: A sample of 20 patients (3 man, 17 women; mean age 31.7 ± 10.8) with upper trapezius MTrPs received one session of deep DN. The outcomes of neuromuscular junction response (NMJR), sympathetic skin response (SSR), pain intensity (PI) and pressure pain threshold (PPT) were measured at baseline and immediately after DN...
January 2017: Journal of Bodywork and Movement Therapies
https://www.readbyqxmd.com/read/28166755/testing-the-potential-significance-of-different-scion-rootstock-genotype-combinations-on-the-ecology-of-old-cultivated-olive-trees-in-the-southeast-mediterranean-area
#18
Oz Barazani, Yoni Waitz, Yizhar Tugendhaft, Michael Dorman, Arnon Dag, Mohammed Hamidat, Thameen Hijawi, Zohar Kerem, Erik Westberg, Joachim W Kadereit
BACKGROUND: A previous multi-locus lineage (MLL) analysis of SSR-microsatellite data of old olive trees in the southeast Mediterranean area had shown the predominance of the Souri cultivar (MLL1) among grafted trees. The MLL analysis had also identified an MLL (MLL7) that was more common among rootstocks than other MLLs. We here present a comparison of the MLL combinations MLL1 (scion)/MLL7 (rootstock) and MLL1/MLL1 in order to investigate the possible influence of rootstock on scion phenotype...
February 6, 2017: BMC Ecology
https://www.readbyqxmd.com/read/28166460/an-evaluation-of-increasing-sample-size-based-on-conditional-power
#19
Michael Gaffney, James H Ware
We evaluate properties of sample size re-estimation (SSR) designs similar to the promising zone design considered by Mehta and Pocock (2011). We evaluate these designs under the assumption of a true effect size of 1.1 down to 0.4 of the protocol specified effect size by six measures: 1. The probability of a sample size increase; 2. The mean proportional increase in sample size given an increase; 3 and 4. The mean true conditional power with and without a sample size increase; 5 and 6. The expected increase in sample size and power due to the SSR procedure...
February 6, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28164997/genome-wide-indel-ssr-scanning-reveals-significant-loci-associated-with-excellent-agronomic-traits-of-a-cabbage-brassica-oleracea-elite-parental-line-01-20
#20
Honghao Lv, Qingbiao Wang, Fengqing Han, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yumei Liu, Zhansheng Li, Yangyong Zhang
Elite parental lines are of great significance to crop breeding. To discover unique genomic loci associated with excellent economic traits in the elite cabbage inbred-line '01-20', we performed comparisons of phenotypes as well as whole-genome insertion-deletion/simple sequence repeat loci between '01-20' and each of its five sister lines. '01-20' has a range of excellent agronomic traits, including early-maturing, and improvements in plant type and leaf colour. Eight unique loci were discovered for '01-20' and '01-07-258', another elite line similar to '01-20' at the whole-genome level...
February 6, 2017: Scientific Reports
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