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https://www.readbyqxmd.com/read/28924510/development-of-est-ssr-markers-for-taxillus-nigrans-loranthaceae-in-southwestern-china-using-next-generation-sequencing
#1
Ning Miao, Lei Zhang, Maoping Li, Liqiang Fan, Kangshan Mao
PREMISE OF THE STUDY: We developed transcriptome microsatellite markers (simple sequence repeats) for Taxillus nigrans (Loranthaceae) to survey the genetic diversity and population structure of this species. METHODS AND RESULTS: We used Illumina HiSeq data to reconstruct the transcriptome of T. nigrans by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them amplified successfully and demonstrated polymorphisms...
August 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28922359/a-first-linkage-map-and-downy-mildew-resistance-qtl-discovery-for-sweet-basil-ocimum-basilicum-facilitated-by-double-digestion-restriction-site-associated-dna-sequencing-ddradseq
#2
Robert Pyne, Josh Honig, Jennifer Vaiciunas, Adolfina Koroch, Christian Wyenandt, Stacy Bonos, James Simon
Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew...
2017: PloS One
https://www.readbyqxmd.com/read/28902884/development-of-est-ssr-markers-in-flowering-chinese-cabbage-brassica-campestris-l-ssp-chinensis-var-utilis-tsen-et-lee-based-on-de-novo-transcriptomic-assemblies
#3
Jingfang Chen, Ronghua Li, Yanshi Xia, Guihua Bai, Peiguo Guo, Zhiliang Wang, Hua Zhang, Kadambot H M Siddique
Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs)...
2017: PloS One
https://www.readbyqxmd.com/read/28890721/development-and-application-of-transcriptome-derived-microsatellites-in-actinidia-eriantha-actinidiaceae
#4
Rui Guo, Jacob B Landis, Michael J Moore, Aiping Meng, Shuguang Jian, Xiaohong Yao, Hengchang Wang
Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28886152/molecular-cytogenetic-identification-of-a-novel-wheat-agropyron-elongatum-chromosome-translocation-line-with-powdery-mildew-resistance
#5
Xiaojun Li, Xiaoling Jiang, Xiangdong Chen, Jie Song, Cuicui Ren, Yajuan Xiao, Xiaohui Gao, Zhengang Ru
Agropyron elongatum (Host.) Neviski (synonym, Thinopyrum ponticum Podp., 2n = 70) has been used extensively as a valuable source for wheat breeding. Numerous chromosome fragments containing valuable genes have been successfully translocated into wheat from A. elongatum. However, reports on the transfer of powdery mildew resistance from A. elongatum to wheat are rare. In this study, a novel wheat-A. elongatum translocation line, 11-20-1, developed and selected from the progenies of a sequential cross between wheat varieties (Lankaoaizaoba, Keyu 818 and BainongAK 58) and A...
2017: PloS One
https://www.readbyqxmd.com/read/28878504/analysis-of-spatial-distribution-of-genetic-diversity-and-validation-of-indian-foxtail-millet-core-collection
#6
Subhash Chander, K V Bhat, Ratna Kumari, Sanjay Sen, A B Gaikwad, M V C Gowda, N Dikshit
Foxtail millet [Setaria italica (L.) P. Beauv.] is an important small millet, grown as a short duration, drought tolerant crop across the world. This crop can be grown on wide ranges of soil conditions and has an immense potential for food and fodder in rainfed and arid regions of the India. In the present study, 31 primer pairs (27 SSR and 4 EST-SSR) were used to analyse the genetic diversity in 223 core collection accessions. Analysis resulted in detection of a total of 136 alleles with an average of 4.38 alleles per locus...
July 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/28839254/comparative-transcriptome-analysis-identified-candidate-genes-related-to-bailinggu-mushroom-formation-and-genetic-markers-for-genetic-analyses-and-breeding
#7
Yongping Fu, Yueting Dai, Chentao Yang, Peng Wei, Bing Song, Yang Yang, Lei Sun, Zhi-Wu Zhang, Yu Li
Bailinggu (Pleurotus tuoliensis) is a major, commercially cultivated mushroom and widely used for nutritional, medicinal, and industrial applications. Yet, the mushroom's genetic architecture and the molecular mechanisms underlying its formation are largely unknown. Here we performed comparative transcriptomic analysis during Bailinggu's mycelia, primordia, and fruiting body stages to identify genes regulating fruiting body development and develop EST-SSR markers assessing the genetic value of breeding materials...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28829885/genetic-diversity-analysis-in-malaysian-giant-prawns-using-expressed-sequence-tag-microsatellite-markers-for-stock-improvement-program
#8
K H Atin, A Christianus, N Fatin, A C Lutas, M Shabanimofrad, B Subha
The Malaysian giant prawn is among the most commonly cultured species of the genus Macrobrachium. Stocks of giant prawns from four rivers in Peninsular Malaysia have been used for aquaculture over the past 25 years, which has led to repeated harvesting, restocking, and transplantation between rivers. Consequently, a stock improvement program is now important to avoid the depletion of wild stocks and the loss of genetic diversity. However, the success of such an improvement program depends on our knowledge of the genetic variation of these base populations...
August 17, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28791211/development-and-characterization-of-polymorphic-est-based-ssr-markers-in-barley-hordeum-vulgare
#9
Won-Sam Jo, Hye-Yeong Kim, Kyung-Min Kim
In barley, breeding using good genetic characteristics can improve the quality or quantity of crop characters from one generation to the next generation. The development of effective molecular markers in barley is crucial for understanding and analyzing the diversity of useful alleles. In this study, we conducted genetic relationship analysis using expressed sequence tag-simple sequence repeat (EST-SSR) markers for barley identification and assessment of barley cultivar similarity. Seeds from 82 cultivars, including 31 each of naked and hulled barley from the Korea Seed and Variety Service and 20 of malting barley from the RDA-Genebank Information Center, were analyzed in this study...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28791205/development-of-est-derived-microsatellite-markers-in-the-aquatic-macrophyte-ranunculus-bungei-ranunculaceae
#10
Zhigang Wu, Jinwei Wu, Yalin Wang, Hongwei Hou
PREMISE OF THE STUDY: Microsatellite or simple sequence repeat (SSR) markers were developed to investigate the influence of ecological factors on gene flow and spatial genetic structuring of the submerged plant Ranunculus bungei (Ranunculaceae), which is regarded as an important species for understanding how plants adapt to an aquatic environment. METHODS AND RESULTS: Twenty-two microsatellite loci were identified from an expressed sequence tag (EST) library. The number of alleles per locus ranged from one to five, and the expected heterozygosity varied from 0...
July 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28769972/the-first-molecular-identification-of-an-olive-collection-applying-standard-simple-sequence-repeats-and-novel-expressed-sequence-tag-markers
#11
Soraya Mousavi, Roberto Mariotti, Luca Regni, Luigi Nasini, Marina Bufacchi, Saverio Pandolfi, Luciana Baldoni, Primo Proietti
Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG), established in the years' 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28686183/development-and-evaluation-of-a-novel-set-of-est-ssr-markers-based-on-transcriptome-sequences-of-black-locust-robinia-pseudoacacia-l
#12
Qi Guo, Jin-Xing Wang, Li-Zhuo Su, Wei Lv, Yu-Han Sun, Yun Li
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification...
July 7, 2017: Genes
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#13
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28630801/characterization-of-the-transcriptome-and-est-ssr-development-in-boea-clarkeana-a-desiccation-tolerant-plant-endemic-to-china
#14
Ying Wang, Kun Liu, De Bi, Shoubiao Zhou, Jianwen Shao
BACKGROUND: Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28545396/transcriptomic-resources-for-the-medicinal-legume-mucuna-pruriens-de-novo-transcriptome-assembly-annotation-identification-and-validation-of-est-ssr-markers
#15
N Sathyanarayana, Ranjith Kumar Pittala, Pankaj Kumar Tripathi, Ratan Chopra, Heikham Russiachand Singh, Vikas Belamkar, Pardeep Kumar Bhardwaj, Jeff J Doyle, Ashley N Egan
BACKGROUND: The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28529834/development-and-characterization-of-est-ssr-markers-for-begonia-luzhaiensis-begoniaceae
#16
Yu-Hsin Tseng, Han-Yau Huang, Wei-Bin Xu, Hsun-An Yang, Yan Liu, Ching-I Peng, Kuo-Fang Chung
PREMISE OF THE STUDY: Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure. METHODS AND RESULTS: Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0...
May 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28526937/molecular-confirmation-of-intraspecific-tomato-solanum-lycopersicum-hybrids-and-their-evaluation-against-late-blight-and-cucumber-mosaic-virus
#17
Amjad Hameed, Muhammad Yussouf Saleem, Khalid Pervaiz Akhtar, Muhammad Shoaib, Qumer Iqbal, Muhammad Asghar
Tomato is one of the most consumed vegetables in the world. Diseases are the number one concern in the development of high-yield and disease-resistant tomato hybrids which is the foremost priority of breeders. Present study was conducted (1) to develop DNA-based markers for genetic confirmation of tomato F1 hybrids, (2) to utilize sequenced characterized amplified region (SCAR) marker linked to the Ph-3 gene for Phytophthora infestans resistance in tomato and (3) to evaluate male and female parental genotypes and their F1 hybrids against late blight (LB) and cucumber mosaic virus (CMV)...
May 19, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28510247/characterization-and-development-of-56-est-ssr-markers-derived-from-the-transcriptome-of-odontobutis-potamophila
#18
P P Wang, M Ren, S Q Chen, S W Yin, C Zhao, H Y Zhang, X R Li, Q Q Cao, G Q Zhou
Expressed sequence tags (ETSs) are the sources of microsatellite development. In this study, we isolated and characterized microsatellite markers for Odontobutis potamophila by using Illumina RNA-sequencing. We sequenced a large number of ESTs and screened 200 potential microsatellites. Consequently, a total of 56 novel polymorphic microsatellite repeat markers were identified in thirty-two individuals from a wild population area (Jiande, Zhejiang Province, China). The number of alleles per locus varied from two to eight, the observed heterozygosity (HO) ranged from 0...
May 10, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28500405/est-ssr-marker-revealed-effective-over-biochemical-and-morphological-scepticism-towards-identification-of-specific-turmeric-curcuma-longa-l-cultivars
#19
Ambika Sahoo, Sudipta Jena, Basudeba Kar, Suprava Sahoo, Asit Ray, Subhashree Singh, Raj Kumar Joshi, Laxmikanta Acharya, Sanghamitra Nayak
Turmeric (Curcuma longa L., family Zingiberaceae) is one of the most economically important plants for its use in food, medicine, and cosmetic industries. Cultivar identification is a major constraint in turmeric, owing to high degree of morphological similarity that in turn, affects its commercialization. The present study addresses this constraint, using EST-SSR marker based, molecular identification of 8 elite cultivars and 88 accessions in turmeric. Fifty EST-SSR primers were screened against eight cultivars of turmeric (Suroma, Roma, Lakadong, Megha, Alleppey Supreme, Kedaram, Pratibha, and Suvarna); out of which 11 primers showed polymorphic banding pattern...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28493955/molecular-diversity-analysis-drought-related-marker-traits-association-mapping-and-discovery-of-excellent-alleles-for-100-day-old-plants-by-est-ssrs-in-cassava-germplasms-manihot-esculenta-cranz
#20
Bin Wang, Xin Guo, Pingjuan Zhao, Mengbin Ruan, Xiaoling Yu, Liangping Zou, Yiling Yang, Xiao Li, Deli Deng, Jixiang Xiao, Yiwei Xiao, Chunji Hu, Xue Wang, Xiaolin Wang, Wenquan Wang, Ming Peng
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2...
2017: PloS One
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