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https://www.readbyqxmd.com/read/29777161/genetic-diversity-analysis-reveals-genetic-differentiation-and-strong-population-structure-in-calotropis-plants
#1
Nkatha G Muriira, Alice Muchugi, Anmin Yu, Jianchu Xu, Aizhong Liu
The genus Calotropis (Asclepiadaceae) is comprised of two species, C. gigantea and C. procera, which both show significant economic potential for use of their seed fibers in the textile industry, and of their bioactive compounds as new medicinal resources. The available wild-sourced germplasm contains limited genetic information that restricts further germplasm exploration for the purposes of domestication. We here developed twenty novel EST-SSR markers and applied them to assess genetic diversity, population structure and differentiation within Calotropis...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773972/genetic-diversity-and-structure-of-tea-plant-in-qinba-area-in-china-by-three-types-of-molecular-markers
#2
Yu Zhang, Xiaojuan Zhang, Xi Chen, Wang Sun, Jiao Li
Background: Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea plants. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant ( Camellia sinensis. ) samples collected from Qinb. tea germplasm, assess population structure. Results: In this study, a total of 414 alleles were obtained using 38 pairs of SCoT primers, with an average of 10...
2018: Hereditas
https://www.readbyqxmd.com/read/29732244/development-of-polymorphic-est-ssr-markers-in-itea-chinensis-iteaceae-and-cross-amplification-in-related-species
#3
Xianggang Shi, Haidan Wu, Weixi Li, Wuxia Guo, Yi Zheng, Shixiao Yu, Yelin Huang
Premise of the Study: We isolated and characterized 16 expressed sequence tag-simple sequence repeat (EST-SSR) markers in Itea chinensis (Iteaceae), a common evergreen broadleaf tree, for future studies on the genetic diversity and spatial genetic structure of the species. Methods and Results: Based on transcriptome data of I. chinensis , a total of 36 primer pairs were initially designed and tested. Of these, 16 were successfully amplified and showed clear polymorphism...
January 2018: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29705936/microsatellite-analysis-and-marker-development-in-garlic-distribution-in-est-sequence-genetic-diversity-analysis-and-marker-transferability-across-alliaceae
#4
Karina Barboza, Vanesa Beretta, Perla C Kozub, Cecilia Salinas, Mauro M Morgenfeld, Claudio R Galmarini, Pablo F Cavagnaro
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis...
April 28, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29685108/population-structure-genetic-diversity-and-downy-mildew-resistance-among-ocimum-species-germplasm
#5
Robert M Pyne, Josh A Honig, Jennifer Vaiciunas, Christian A Wyenandt, James E Simon
BACKGROUND: The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii...
April 23, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29649332/development-of-novel-est-ssr-markers-for-ploidy-identification-based-on-de-novo-transcriptome-assembly-for-misgurnus-anguillicaudatus
#6
Bing Feng, Soojin V Yi, Manman Zhang, Xiaoyun Zhou
The co-existence of several ploidy types in natural populations makes the cyprinid loach Misgurnus anguillicaudatus an exciting model system to study the genetic and phenotypic consequences of ploidy variations. A first step in such effort is to identify the specific ploidy of an individual. Currently popular methods of karyotyping via cytological preparation or flow cytometry require a large amount of tissue (such as blood) samples, which can be damaging or fatal to the fishes. Here, we developed novel microsatellite markers (SSR markers) from M...
2018: PloS One
https://www.readbyqxmd.com/read/29626317/mining-and-comparative-survey-of-est-ssr-markers-among-members-of-euphorbiaceae-family
#7
Surojit Sen, Budheswar Dehury, Jagajjit Sahu, Sunayana Rathi, Raj Narain Singh Yadav
Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO...
April 6, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29608956/detection-and-validation-of-est-ssr-markers-associated-with-sugar-related-traits-in-sugarcane-using-linkage-and-association-mapping
#8
Kittipat Ukoskit, Ganlayarat Posudsavang, Nattapat Pongsiripat, Prasert Chatwachirawong, Peeraya Klomsa-Ard, Patthinun Poomipant, Somvong Tragoonrung
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis...
March 31, 2018: Genomics
https://www.readbyqxmd.com/read/29518961/phenotype-and-ssr-based-estimates-of-genetic-variation-between-and-within-two-important-elymus-species-in-western-and-northern-china
#9
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
https://www.readbyqxmd.com/read/29484283/comparison-of-relative-efficiency-of-genomic-ssr-and-est-ssr-markers-in-estimating-genetic-diversity-in-sugarcane
#10
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
https://www.readbyqxmd.com/read/29428798/analysis-of-population-structure-and-genetic-diversity-in-an-exotic-germplasm-collection-of-eleusine-coracana-l-gaertn-using-genic-ssr-markers
#11
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...
May 5, 2018: Gene
https://www.readbyqxmd.com/read/29420597/geographical-and-environmental-determinants-of-the-genetic-structure-of-wild-barley-in-southeastern-anatolia
#12
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
https://www.readbyqxmd.com/read/29398845/genetic-diversity-of-cucumber-estimated-by-morpho-physiological-and-est-ssr-markers
#13
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
https://www.readbyqxmd.com/read/29299397/development-of-est-ssr-markers-for-primula-ovalifolia-primulaceae-by-transcriptome-sequencing
#14
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
#15
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
https://www.readbyqxmd.com/read/29192443/-est-ssr-identification-markers-development-of-ligusticum-chuanxiong-based-on-ligusticum-chuanxiong-transcriptome-sequences
#16
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
#17
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/29188146/characterization-and-development-of-est-derived-ssr-markers-in-sinowilsonia-henryi-hamamelidaceae
#18
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
https://www.readbyqxmd.com/read/29163598/an-rna-sequencing-transcriptome-analysis-of-grasspea-lathyrus-sativus-l-and-development-of-ssr-and-kasp-markers
#19
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
https://www.readbyqxmd.com/read/29158639/mining-and-characterization-of-est-ssr-markers-for-zingiber-officinale-roscoe-with-transferability-to-other-species-of-zingiberaceae
#20
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
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