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https://www.readbyqxmd.com/read/28729817/ssr-marker-variations-in-brassica-species-provide-insight-into-the-origin-and-evolution-of-brassica-amphidiploids
#1
Ajay Kumar Thakur, Kunwar Harendra Singh, Lal Singh, Joghee Nanjundan, Yasin Jeshima Khan, Dhiraj Singh
BACKGROUND: Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. RESULTS: Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B...
2018: Hereditas
https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#2
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724947/marker-trait-association-analysis-of-frost-tolerance-of-672-worldwide-pea-pisum-sativum-l-collections
#3
Rong Liu, Li Fang, Tao Yang, Xiaoyan Zhang, Jinguo Hu, Hongyan Zhang, Wenliang Han, Zeke Hua, Junjie Hao, Xuxiao Zong
Frost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717170/population-structure-of-an-orchid-mycorrhizal-fungus-with-genus-wide-specificity
#4
M P Ruibal, Y Triponez, L M Smith, R Peakall, C C Linde
Fundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks)...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28713419/population-structure-genetic-diversity-and-evolutionary-history-of-kleinia-neriifolia-asteraceae-on-the-canary-islands
#5
Ye Sun, Carlos F Vargas-Mendoza
Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712775/simple-sequence-repeats-showing-length-preference-have-regulatory-functions-in-humans
#6
Jaya Krishnan, Fathima Athar, Tirupaati Swaroopa Rani, Rakesh Kumar Mishra
Simple sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about their functional relevance. Analysis of genomes across various taxa show that despite the instability associated with longer stretches of repeats, few SSRs with specific longer repeat lengths are enriched in the genomes indicating a positive selection. This conserved feature of length dependent enrichment hints at not only sequence but also length dependent functionality for SSRs...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28706300/genetic-analyses-reveal-independent-domestication-origins-of-the-emerging-oil-crop-paeonia-ostii-a-tree-peony-with-a-long-term-cultivation-history
#7
Li-Ping Peng, Chang-Fu Cai, Yuan Zhong, Xing-Xing Xu, Hong-Li Xian, Fang-Yun Cheng, Jian-Feng Mao
Paeonia ostii, a member of tree peony, is an emerging oil crop with important medical and oil uses and widely cultivated in China. Dissolving the genetic diversity and domestication history of this species is important for further genetic improvements and deployments. We firstly selected 29 simple sequence repeats (SSRs) via transcriptome mining, segregation analyses and polymorphism characterizations; then, 901 individuals from the range-wide samples were genotyped using well-characterized SSR markers. We observed moderate genetic diversity among individuals, and Shaanxi Province was identified as the center of genetic diversity for our cultivated plants...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28703120/effects-of-body-habitus-on-internal-radiation-dose-calculations-using-the-5-year-old-anthropomorphic-male-models
#8
Tianwu Xie, Niels Kuster, Habib Zaidi
Computational phantoms are commonly used in internal radiation dosimetry to assess the amount and distribution pattern of energy deposited in various parts of the human body from different internal radiation sources. Radiation dose assessments are commonly performed on predetermined reference computational phantoms while the argument for individualized patient-specific radiation dosimetry exists. This study aims to evaluate the influence of body habitus on internal dosimetry and to quantify the uncertainties in dose estimation correlated with the use of fixed reference models...
July 13, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28702690/molecular-mapping-and-candidate-gene-analysis-of-a-new-epicuticular-wax-locus-in-sorghum-sorghum-bicolor-l-moench
#9
G Anurag Uttam, M Praveen, Y Venkateswara Rao, Vilas A Tonapi, R Madhusudhana
A new epicuticular wax (bloom) locus has been identified and fine mapped to the 207.89 kb genomic region on chromosome 1. A putative candidate gene, Sobic.001G269200, annotated as GDSL-like lipase/acylhydrolase, is proposed as the most probable candidate gene involved in bloom synthesis/deposition. Deposition of epicuticular wax on plant aerial surface is one strategy that plants adapt to reduce non-transpiration water loss. Epicuticular wax (bloom)-less mutants in sorghum with their glossy phenotypes exhibit changes in the accumulation of epicuticular wax on leaf and culm surfaces...
July 12, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28697758/identification-of-qtls-controlling-grain-protein-concentration-using-a-high-density-snp-and-ssr-linkage-map-in-barley-hordeum-vulgare-l
#10
Chaofeng Fan, Huijie Zhai, Huifang Wang, Yafei Yue, Minghu Zhang, Jinghui Li, Shaozhe Wen, Ganggang Guo, Yawen Zeng, Zhongfu Ni, Mingshan You
BACKGROUND: Grain protein concentration (GPC) is a major determinant of quality in barley (Hordeum vulgare L.). Breeding barley cultivars with high GPC has practical value for feed and food properties. The aim of the present study was to identify quantitative trait loci (QTLs) for GPC that could be detected under multiple environments. RESULTS: A population of 190 recombinant inbred lines (RILs) deriving from a cross between Chinese landrace ZGMLEL with high GPC (> 20%) and Australian cultivar Schooner was used for linkage and QTL analyses...
July 11, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28696481/genome-wide-association-study-of-pre-harvest-sprouting-resistance-in-chinese-wheat-founder-parents
#11
Yu Lin, Shihang Liu, Yaxi Liu, Yujiao Liu, Guoyue Chen, Jie Xu, Mei Deng, Qiantao Jiang, Yuming Wei, Yanli Lu, Youliang Zheng
Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and quality, and is caused by an early break in seed dormancy. Association mapping (AM) is used to detect correlations between phenotypes and genotypes based on linkage disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80 Chinese wheat founder parents in five environments and performed a genome-wide association study using 6,057 markers, including 93 simple sequence repeat (SSR), 1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism (SNP) markers...
July 10, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28696392/comparative-transcriptome-analysis-reveals-adaptive-evolution-of-notopterygium-incisum-and-notopterygium-franchetii-two-high-alpine-herbal-species-endemic-to-china
#12
Yun Jia, Mi-Li Liu, Ming Yue, Zhe Zhao, Gui-Fang Zhao, Zhong-Hu Li
The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species...
July 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28695998/co-surgeons-in-breast-reconstructive-microsurgery-what-do-they-bring-to-the-table
#13
Nicholas T Haddock, Samar Kayfan, Ronnie A Pezeshk, Sumeet S Teotia
INTRODUCTION: Current research within other surgical specialties suggests that a co-surgeon approach may reduce operative times and complications associated with complex bilateral procedures, possibly leading to improved patient and surgical outcomes. We sought to evaluate the role of the co-surgery team and its development in free flap breast reconstruction. METHODS: A retrospective review of free-flap breast reconstruction by two surgeons from 2011 to 2016 was conducted...
July 11, 2017: Microsurgery
https://www.readbyqxmd.com/read/28693419/de-novo-transcriptomic-analysis-of-cowpea-vigna-unguiculata-l-walp-for-genic-ssr-marker-development
#14
Honglin Chen, Lixia Wang, Xiaoyan Liu, Liangliang Hu, Suhua Wang, Xuzhen Cheng
BACKGROUND: Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding of cowpea. The objectives of this study were to analyse the cowpea transcriptome and develop genic molecular markers for future genetic studies of this genus. RESULTS: Approximately 54 million high-quality cDNA sequence reads were obtained from cowpea based on Illumina paired-end sequencing technology and were de novo assembled to generate 47,899 unigenes with an N50 length of 1534 bp...
July 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28692124/genetic-variability-of-a-brazilian-capsicum-frutescens-germplasm-collection-using-morphological-characteristics-and-ssr-markers
#15
S I C Carvalho, L B Bianchetti, C F Ragassi, C S C Ribeiro, F J B Reifschneider, G S C Buso, F G Faleiro
Characterization studies provide essential information for the conservation and use of germplasm in plant breeding programs. In this study, 103 Capsicum frutescens L. accessions from the Active Germplasm Bank of Embrapa Hortaliças, representative of all five Brazilian geographic regions, were characterized based on morphological characteristics and microsatellite (or simple sequence repeat - SSR) molecular markers. Morphological characterization was carried out using 57 descriptors, and molecular characterization was based on 239 alleles from 24 microsatellite loci...
July 6, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28690629/genome-wide-analysis-of-simple-sequence-repeats-in-bitter-gourd-momordica-charantia
#16
Junjie Cui, Jiaowen Cheng, Dingguo Nong, Jiazhu Peng, Yafei Hu, Weiming He, Qianjun Zhou, Narinder P S Dhillon, Kailin Hu
Bitter gourd (Momordica charantia) is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo) genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs) in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28690478/genetic-diversity-and-structure-of-core-collection-of-winter-mushroom-flammulina-velutipes-developed-by-genomic-ssr-markers
#17
Xiao Bin Liu, Jing Li, Zhu L Yang
BACKGROUND: A core collection is a subset of an entire collection that represents as much of the genetic diversity of the entire collection as possible. The establishment of a core collection for crops is practical for efficient management and use of germplasm. However, the establishment of a core collection of mushrooms is still in its infancy, and no established core collection of the economically important species Flammulina velutipes has been reported. RESULTS: We established the first core collection of F...
2018: Hereditas
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
#18
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/28684754/a-repeat-length-variation-in-myo-inositol-monophosphatase-gene-contributes-to-seed-size-trait-in-chickpea
#19
Vikas Dwivedi, Swarup Kumar Parida, Debasis Chattopadhyay
Chickpea (Cicer arietinum L.) is the third most important food legume crop. Seed size is the most economically important trait for chickpea. To understand the genetic regulation of seed size in chickpea, the present study established a three-way association of CT repeat length variation of a simple sequence repeat (SSR) in myo-inositol monophosphatase gene (CaIMP) with seed weight and phytic acid content by large scale validation and genotyping in a set of genetically diverse germplasm accessions and two reciprocal intra-specific mapping populations...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28683832/molecular-dating-of-phylogenetic-divergence-between-urochloa-species-based-on-complete-chloroplast-genomes
#20
Marco Pessoa-Filho, Alexandre Magalhães Martins, Márcio Elias Ferreira
BACKGROUND: Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy...
July 6, 2017: BMC Genomics
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