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https://www.readbyqxmd.com/read/29299397/development-of-est-ssr-markers-for-primula-ovalifolia-primulaceae-by-transcriptome-sequencing
#1
Shuai Yuan, Gui Zeng, Miaomiao Shi, Dianxiang Zhang
Premise of the study: Microsatellite primers were developed for Primula ovalifolia, a member of Primula section Petiolares (Primulaceae), to study the population genetics and species delimitation in this section. Methods and Results: A total of 4753 markers were successfully designated from 5139 putative simple sequence repeat loci. We isolated 38 expressed sequence tag-simple sequence repeat markers from 220 selected marker sites and tested polymorphism in three populations of P...
December 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29230682/association-of-functional-markers-with-flowering-time-in-lentil
#2
Jitendra Kumar, Sunanda Gupta, Revanappa S Biradar, Priyanka Gupta, Sonali Dubey, Narendra Pratap Singh
In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h 2 bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus...
December 11, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29192443/-est-ssr-identification-markers-development-of-ligusticum-chuanxiong-based-on-ligusticum-chuanxiong-transcriptome-sequences
#3
Can Yuan, Fang Peng, Ze-Mao Yang, Wen-Juan Zhong, Fang-Sheng Mou, Yi-Yun Gong, Pei-Cheng Ji, De-Qiang Pu, Hai-Yan Huang, Xiao Yang, Chao Zhang
Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29188147/development-and-characterization-of-est-ssr-markers-for-ottelia-acuminata-var-jingxiensis-hydrocharitaceae
#4
Zhi-Zhong Li, Meng-Xue Lu, Josphat K Saina, Andrew W Gichira, Qing-Feng Wang, Jin-Ming Chen
Premise of the study: Simple sequence repeat (SSR) markers were derived from transcriptomic data for Ottelia acuminata (Hydrocharitaceae), a species comprising five endemic and highly endangered varieties in China. Methods and Results: Sixteen novel SSR markers were developed for O. acuminata var. jingxiensis. One to eight alleles per locus were found, with a mean of 2.896. The observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.793, respectively...
November 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29163598/an-rna-sequencing-transcriptome-analysis-of-grasspea-lathyrus-sativus-l-and-development-of-ssr-and-kasp-markers
#5
Xiaopeng Hao, Tao Yang, Rong Liu, Jinguo Hu, Yang Yao, Marina Burlyaeva, Yan Wang, Guixing Ren, Hongyan Zhang, Dong Wang, Jianwu Chang, Xuxiao Zong
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeq(TM) 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29158639/mining-and-characterization-of-est-ssr-markers-for-zingiber-officinale-roscoe-with-transferability-to-other-species-of-zingiberaceae
#6
Praveen Awasthi, Ashish Singh, Gulfam Sheikh, Vidushi Mahajan, Ajai Prakash Gupta, Suphla Gupta, Yashbir S Bedi, Sumit G Gandhi
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29149037/development-of-novel-polymorphic-est-ssr-markers-in-bailinggu-pleurotus-tuoliensis-for-crossbreeding
#7
Yueting Dai, Wenying Su, Chentao Yang, Bing Song, Yu Li, Yongping Fu
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29125846/characterization-of-the-lycium-barbarum-fruit-transcriptome-and-development-of-est-ssr-markers
#8
Chunling Chen, Meilong Xu, Cuiping Wang, Gaixia Qiao, Wenwen Wang, Zhaoyun Tan, Tiantian Wu, Zhengsheng Zhang
Lycium barbarum, commonly known as goji, is important in Chinese herbal medicine and its fruit is a very important agricultural and biological product. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. Moreover, this species lacks SSR markers due to lack of genomic and transcriptomic information. In this study, a total of 139,333 unigenes with average length of 1049 bp and N50 of 1579 bp are obtained by trinity assembly from Illumina sequencing reads...
2017: PloS One
https://www.readbyqxmd.com/read/29109921/development-and-characterization-of-est-ssr-markers-via-transcriptome-sequencing-in-brainea-insignis-aspleniaceae-s-l
#9
Haijun Liu, Zhihua Yan, Hualing Xu, Chunmei Li, Qiang Fan, Wenbo Liao, Boyong Liao
Premise of the study: Brainea insignis (Aspleniaceae) is an endangered tree fern in China whose wild populations have been seriously damaged due to overexploitation. Expressed sequence tag-simple sequence repeat (EST-SSR) primers were developed to investigate its genetic diversity and provide resources for future conservation studies. Methods and Results: We obtained 72,897 unigenes of B. insignis using transcriptome sequencing and detected 15,006 SSRs in 12,058 unigenes...
October 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29025415/genetic-evidence-of-multiple-invasions-and-a-small-number-of-founders-of-asian-palmyra-palm-borassus-flabellifer-in-thailand
#10
Kwanjai Pipatchartlearnwong, Akarapong Swatdipong, Supachai Vuttipongchaikij, Somsak Apisitwanich
BACKGROUND: Borassus flabellifer or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years. B. flabellifer is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear...
October 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29020092/construction-of-a-genetic-map-using-est-ssr-markers-and-qtl-analysis-of-major-agronomic-characters-in-hexaploid-sweet-potato-ipomoea-batatas-l-lam
#11
Jin-Hee Kim, Il Kyung Chung, Kyung-Min Kim
The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29018469/de-novo-assembly-of-transcriptome-and-development-of-novel-est-ssr-markers-in-rhododendron-rex-l%C3%A3-vl-through-illumina-sequencing
#12
Yue Zhang, Xue Zhang, Yue-Hua Wang, Shi-Kang Shen
Transcriptome sequences generated by next-generation sequencing (NGS) technologies can be utilized to rapidly detect and characterize a large number of gene-based microsatellites from different plants. Rhododendron rex Lévl. is a perennial woody species from the family Ericaceae and an endangered plant with high ornamental value endemic to Southwestern China. Nevertheless, the genetic and genomic information of R. rex remain unknown. In this study, we performed transcriptome sequencing for R. rex leaf samples, and generated large transcript sequences for functional characterization and development gene-associated SSR markers...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28924510/development-of-est-ssr-markers-for-taxillus-nigrans-loranthaceae-in-southwestern-china-using-next-generation-sequencing
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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