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Ming-Li Wu, Qing Li, Jiang Xu, Xi-Wen Li
Background: Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position of A. compactum is not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. Methods: The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform...
2018: Chinese Medicine
Scott L Sydenham, Annelie Barnard
Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance...
2018: Frontiers in Plant Science
Jun-Liang Yin, Zheng-Wu Fang, Cai Sun, Peng Zhang, Xing Zhang, Chen Lu, Shu-Ping Wang, Dong-Fang Ma, Yong-Xing Zhu
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat. Resistant cultivars are the preferred strategy to control the disease. Space-induced wheat mutant R39 has adult-plant resistance (APR) to Pst. Genetic analysis indicated that a single recessive gene, designated YrR39, was responsible for the APR of R39 to Pst. Bulked segregant analysis (BSA) combined with a SLAF sequencing (SLAF-seq) strategy was used to fine-map YrR39 to a 17.39 Mb segment on chromosome 4B...
February 15, 2018: Scientific Reports
Peng Qiao, Wei Tian, Peigui Liu, Fuqiang Yu, Juan Chen, Xiaojuan Deng, Shanping Wan, Ran Wang, Yun Wang, Hongen Guo
Tuber indicum is an ectomycorrhizal ascomycete that produces edible ascocarps. Based on a number of specimens with known exact origin, we investigate the speciation of the Tuber indicum complex in southwest China. Internal transcribed spacer (ITS) and simple sequence repeat (SSR) markers were used in the study. Phylogeography and population genetics analyses were combined to detect 31 wild populations of the T. indicum complex. Two distinct lineages, Tuber cf. indicum and Tuber cf. himalayense, were identified in the T...
February 12, 2018: Fungal Genetics and Biology: FG & B
Manosh Kumar Biswas, Ujjal Kumar Nath, Jewel Howlader, Mita Bagchi, Sathishkumar Natarajan, Md Abdul Kayum, Hoy-Taek Kim, Jong-In Park, Jong-Goo Kang, Ill-Sup Nou
Lilies ( Lilium sp.) are commercially important horticultural crops widely cultivated for their flowers and bulbs. Here, we conducted large-scale data mining of the lily transcriptome to develop transcription factor (TF)-associated microsatellite markers (TFSSRs). Among 216,768 unigenes extracted from our sequence data, 6966 unigenes harbored simple sequence repeats (SSRs). Seventy-one SSRs were associated with TF genes, and these were used to design primers and validate their potential as markers. These 71 SSRs were accomplished with 31 transcription factor families; including bHLH, MYB, C2H2, ERF, C3H, NAC, bZIP, and so on...
February 14, 2018: Genes
Sima Taheri, Thohirah Lee Abdullah, Mohd Rafii Yusop, Mohamed Musa Hanafi, Mahbod Sahebi, Parisa Azizi, Redmond Ramin Shamshiri
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development...
February 13, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Priscila Rodríguez-Rodríguez, Pedro Luis Pérez de Paz, Pedro A Sosa
Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia...
February 12, 2018: Genetica
B Kalyana Babu, Salej Sood, Dinesh Kumar, Anjeli Joshi, A Pattanayak, Lakshmi Kant, H D Upadhyaya
Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them...
February 2018: 3 Biotech
Z G Wang, T Z Dong, J Li, G Chen
Objectives: To explore the critical values of temperature perception in various mucosa sites of oral cavity and to draw the perceptive temperature threshold maps in healthy volunteers. To observe the interrelationship between subjective cognitive perception and sympathetic skin response (SSR) under various levels of thermal stimuli. Methods: Forty-two healthy volunteers (recruited from the students of Tianjin Medical University, 16 females and 26 males) were enrolled in the present study. The whole oral mucosa of each subject was divided into multiple partitions according to the mucosa type as well as tooth position...
February 9, 2018: Zhonghua Kou Qiang Yi Xue za Zhi, Zhonghua Kouqiang Yixue Zazhi, Chinese Journal of Stomatology
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
Min Du, Na Li, Baozhen Niu, Yanhong Liu, Dongjing You, Defu Jiang, Congquan Ruan, Zhengquan Qin, Taowen Song, Wentao Wang
BACKGROUND: The yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited. METHODOLOGY AND PRINCIPAL FINDINGS: Illumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp...
2018: PloS One
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
Yi Zhou, Gaofeng Zhou, Sue Broughton, Sharon Westcott, Xiaoqi Zhang, Yanhao Xu, Le Xu, Chengdao Li, Wenying Zhang
Tiller angle, an important agronomic trait, contributes to crop production and plays a vital role in breeding for plant architecture. A barley line V-V-HD, which has prostrate tillers during vegetative growth and erect tillers after booting, is considered the ideal type for repressing weed growth and increasing leaf area during early growth. Genetic analysis identified that the prostrate trait in V-V-HD is controlled by a single gene. A double haploid population with 208 lines from V-V-HD × Buloke was used to map the prostrate growth gene...
2018: PloS One
XiaoLei Shi, Long Yan, ChunYan Yang, WeiWen Yan, David Octor Moseley, Tao Wang, BingQiang Liu, Rui Di, PengYin Chen, MengChen Zhang
BACKGROUND: Identification of the quantitative trait locus (QTL) underlying salt tolerance is a prerequisite for marker-assisted selection in the salt-tolerant breeding process. METHODS: In this study, the recombinant inbred lines derived from the salt-tolerant elite soybean cultivar 'Jidou 12' and the salt-sensitive elite cultivar 'Ji NF 58' were used to identify the QTL associated with salt tolerance, using both salt tolerance rating (STR) and leaf chlorophyll content (SPAD) as indicators...
February 5, 2018: BMC Research Notes
Marcus Unterrainer, Cornelius Maihoefer, Clemens C Cyran, Peter Bartenstein, Maximilian Niyazi, Nathalie Lisa Albert
In this case of suspected sphenoid wing meningioma, Ga-DOTATATE PET/CT showed a somatostatin receptor (SSR)-expressing tumor with extension to the nasopharynx and SSR-expressing cervical lymph nodes. Subsequent biopsy from the nasopharynx revealed an Epstein-Barr virus (EBV)-associated, undifferentiated World Health Organization type 3 nasopharyngeal carcinoma (NPC), a potential clinical pitfall due to the reported high SSR expression of this tumor subtype. In consideration of the high target-to-background contrast, SSR ligands might be superior to F-FDG for EBV-associated NPC PET imaging, particularly at the skull base...
February 3, 2018: Clinical Nuclear Medicine
Masahiro Kishine, Katsuji Tsutsumi, Kazumi Kitta
Simple sequence repeat (SSR) is a popular tool for individual fingerprinting. The long-core motif (e.g. tetra-, penta-, and hexa-nucleotide) simple sequence repeats (SSRs) are preferred because they make it easier to separate and distinguish neighbor alleles. In the present study, a new set of 8 tetra-nucleotide SSRs in potato (Solanum tuberosum) is reported. By using these 8 markers, 72 out of 76 cultivars obtained from Japan and the United States were clearly discriminated, while two pairs, both of which arose from natural variation, showed identical profiles...
December 2017: Breeding Science
Kengo Matsumoto, Yuya Ota, Satomi Seta, Yukinori Nakayama, Teppei Ohno, Ritsuko Mizobuchi, Hiroyuki Sato
Rice brown spot (BS), caused by Bipolaris oryzae, is one of the major diseases of rice in Japan. Quantitative resistance has been observed in local cultivars (e.g., CH45), but no economically useful resistant variety has been bred. Using simple sequence repeat (SSR) polymorphic markers, we conducted quantitative trait locus (QTL) analysis of BS resistance in backcross inbred lines (BILs) from a cross between indica CH45 (resistant) and japonica Koshihikari (susceptible). On the basis of field disease evaluations in 2015 and 2016, four QTLs contributing to BS resistance were identified on chromosomes 2 (qBSR2-kc), 7 (qBSR7-kc), 9 (qBSR9-kc), and 11 (qBSR11-kc)...
December 2017: Breeding Science
Theophile Odjo, Yohei Koide, Drissa Silue, Seiji Yanagihara, Takashi Kumashiro, Yoshimichi Fukuta
The genetic variation in resistance to blast (Pyricularia oryzae Cavara) in 195 rice accessions comprising 3 species of the AA genome complex (Asian rice [Oryza sativa L.], African rice [Oryza glaberrima Steud.] and wild rice [Oryza barthii]) was investigated based on their patterns of reaction to standard differential blast isolates (SDBIs) and SSR marker polymorphism data. Cluster analysis of the polymorphism data of 61 SSR markers identified 3 major clusters: cluster A (mainly Japonica Group or upland accessions), cluster B (mainly Indica Group or lowland accessions) and cluster C (O...
December 2017: Breeding Science
Mohammad Ashik Iqbal Khan, Mohammad Abdul Latif, Mohammad Khalequzzaman, Asami Tomita, Mohammad Ansar Ali, Yoshimichi Fukuta
Genetic variation in blast resistance was clarified in 334 Bangladesh rice accessions from 4 major ecotypes (Aus, Aman, Boro and Jhum). Cluster analysis of polymorphism data of 74 SSR markers separated these accessions into cluster I (corresponding to the Japonica Group) and cluster II (corresponding to the Indica Group). Cluster II accessions were represented with high frequency in all ecotypes. Cluster II was further subdivided into subclusters IIa and IIb. Subcluster IIa accessions were represented with high frequency in only Aus and Jhum ecotypes...
December 2017: Breeding Science
Özlem Ateş Sönmezoğlu, Begüm Terzi
Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey...
February 2018: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
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