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est-ssr marker

Zongyu Zhang, Wengang Xie, Junchao Zhang, Xuhong Zhao, Yongqiang Zhao, Yanrong Wang
Elymus nutans and Elymus sibiricus are two important perennial forage grasses of the genus Elymus , widely distributed in high altitude regions of Western and Northern China, especially on the Qinghai-Tibetan Plateau. Information on phenotypic and genetic diversity is limited, but necessary for Elymus germplasm collection, conservation, and utilization. In the present study, the phenotypic and genetic differentiation of 73 accessions of the two species were evaluated using 15 phenotypic traits and 40 expressed sequence tag derived simple sequence repeat markers (EST-SSRs)...
March 7, 2018: Genes
S Parthiban, P Govindaraj, S Senthilkumar
Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome...
March 2018: 3 Biotech
Subramani Pandian, Lakkakula Satish, Ramakrishnan Rameshkumar, Pandiyan Muthuramalingam, Arockiam Sagina Rency, Periyasamy Rathinapriya, Manikandan Ramesh
Finger millet (Eleusine coracana (L.) Geartn.) is one of the important small millets serves as a food security crop because of its high nutritional values. The complex tetraploid genome of finger millet requires a large number of informative, functional DNA markers for different applications in genetics and breeding. Yet, less number of simple sequence repeat (SSR) markers have been developed from expressed sequence tags in finger millet. In the present study, 56 new genic SSR markers were developed from publicly available drought related ESTs...
February 8, 2018: Gene
Reza Pournosrat, Selma Kaya, Salar Shaaf, Benjamin Kilian, Hakan Ozkan
Despite the global value of barley, compared to its wild progenitor, genetic variation in this crop has been drastically reduced due to the process of domestication, selection and improvement. In the medium term, this will negatively impact both the vulnerability and yield stability of barley against biotic and abiotic stresses under climate change. Returning to the crop wild relatives (CWR) as sources of new and beneficial alleles is a clear option for enhancing the resilience of diversity and adaptation to climate change...
2018: PloS One
Sudhakar Pandey, Waquar Akhter Ansari, Maneesh Pandey, Bijendra Singh
In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0...
February 2018: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
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
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 (h2 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...
February 2018: Journal of Applied Genetics
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
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
Zuo-Zhou Li, Hua Tian, Jin-Ju Zhang
Premise of the study: Polymorphic microsatellite markers were developed to reveal the genetic diversity of extant populations and the mating system of Sinowilsonia henryi (Hamamelidaceae). Methods and Results: In this study, nuclear simple sequence repeat (SSR) markers were developed using the Illumina high-throughput sequencing technique (RNA-Seq). The de novo-assembled transcriptome generated a total of 64,694 unique sequences with an average length of 601 bp...
November 2017: Applications in Plant Sciences
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 NextSeqTM 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
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
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
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
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
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
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
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
Haleh Salimi, Masoud Bahar, Aghafakhr Mirlohi, Majid Talebi
BACKGROUND: Potato has a narrow genetic base which is due to its development, as it takes its genetic root from a few genotypes originated from South America. OBJECTIVES: The objective of this study was to assess the genetic relationships among potato (Solanum tuberosum L.) genotypes originated from different geographical regions. MATERIALS AND METHODS: This study has rendered 25 useful SSRs and EST-SSRs that were located in pre-existing genetic maps, fingerprinted in a collection of the 47 potato genotypes from America, Europe and Iran...
December 2016: Iranian Journal of Biotechnology
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
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