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Marker assisted selection

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https://www.readbyqxmd.com/read/28822146/-dna-marker-assisted-selection-of-medicinal-plants-%C3%A2-evaluation-of-disease-resistance-of-miaoxiang-kangqi-1-a-new-cultivar-of-panax-notoginseng
#1
Zhong-Jian Chen, Xiao-Han Ma, Lin-Lin Dong, Lian-Juan Zhang, Guang-Fei Wei, Li-Na Xiao, Yong Wang, Fu-Gang Wei, Wei-Lin Liu, Yu-Qi Yu, Shi-Lin Chen
DNA marked-assisted selection of medicinal plants accelerated the breeding and promotion of new cultivars, and guaranteed the healthy development of Chinese medicinal materials industry. The first disease-resistant cultivar of notoginseng, namely "Miaoxiang Kangqi 1", served as the object of study. We evaluated the Kangqi's resistance of seeds, seedlings and root against the pathological bacteria (Fusarum oxysporum) of root rot. Compared to the traditional cultivars, the disease index of notoginseng seeds declined by 52...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28821187/genetic-dissection-of-seedling-stage-salinity-tolerance-in-rice-using-introgression-lines-of-a-salt-tolerant-landrace-nona-bokra
#2
Venkata Ramana Rao Puram, John Ontoy, Steven Linscombe, Prasanta K Subudhi
Salinity is an important abiotic stress affecting rice production worldwide. Development of salt tolerant varieties is the most feasible approach for improving rice productivity in salt affected soils. In rice, seedling stage salinity tolerance is crucial for better crop establishment. Quantitative trait loci (QTL) mapping using introgression lines (ILs) is useful for identification and simultaneous transfer of desirable alleles into elite genetic background. In the present study, 138 ILs derived from the cross between a high yielding elite salt susceptible japonica rice cultivar Jupiter and a salt tolerant indica landrace Nona Bokra were evaluated for salt tolerance at seedling stage in a hydroponics experiment and were genotyped using 126 simple sequence repeat markers...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28817683/genome-wide-association-analysis-of-cold-tolerance-at-germination-in-temperate-japonica-rice-oryza-sativa-l-varieties
#3
Ester Sales, Juan Viruel, Concha Domingo, Luis Marqués
A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature...
2017: PloS One
https://www.readbyqxmd.com/read/28813631/rapid-and-targeted-introgression-of-fgr-gene-through-marker-assisted-backcrossing-in-rice-oryza-sativa-l
#4
Acga Cheng, Ismanizan Ismail, Mohamad Osman, Habibuddin Hashim, Nur Samahah Mohd Zainual
While it is crucial for developing countries like Malaysia to achieve self-sufficiency in rice (Oryza sativa L.), it is equally critical to be able to produce high-quality rice, specifically fragrant rice, which demands are often met through importation. The present study was aimed at developing high-yielding fragrant rice, in a timely and cost-effective manner. A marker-assisted backcross (MABC) approach was optimised to introgress the fragrance gene (fgr) into two high-yielding Malaysian varieties; MR84 and MR219, within two years utilising less than fifty molecular markers...
August 16, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28812937/genetic-and-molecular-characterization-of-leaf-rust-resistance-in-two-durum-wheat-landraces
#5
Naeela Qureshi, Harbans Bariana, James A Kolmer, Hanif Miah, Urmil Bansal
Leaf rust, caused by Puccinia triticina, is a constraint to durum wheat (Triticum turgidum subsp. durum) production, and landraces are reported to be an important source of resistance. Two Portuguese landraces (Aus26582 and Aus26579) showed resistance against durum-specific P. triticina races and were crossed with a susceptible landrace (Bansi) to develop recombinant inbred line (RIL) populations. Monogenic segregation for leaf rust resistance was observed among both RIL populations. The underlying locus, temporarily named LrAW2, was mapped to the short arm of chromosome 6B in the Aus26582/Bansi population and five DArTseq markers cosegregated with LrAW2...
August 16, 2017: Phytopathology
https://www.readbyqxmd.com/read/28812232/introgression-of-heat-shock-protein-hsp70-and-shsp-genes-into-the-malaysian-elite-chilli-variety-kulai-capsicum-annuum-l-through-the-application-of-marker-assisted-backcrossing-mab
#6
Magaji G Usman, Mohd Y Rafii, Mohammad Y Martini, Oladosu A Yusuff, Mohd R Ismail, Gous Miah
Backcrossing together with simple sequence repeat marker strategy was adopted to improve popular Malaysian chilli Kulai (Capsicum annuum L.) for heat tolerance. The use of molecular markers in backcross breeding and selection contributes significantly to overcoming the main drawbacks such as increase linkage drag and time consumption, in the ancient manual breeding approach (conventional), and speeds up the genome recovery of the recurrent parent. The strategy was adopted to introgress heat shock protein gene(s) from AVPP0702 (C...
August 15, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28811498/genome-re-sequencing-reveals-the-history-of-apple-and-supports-a-two-stage-model-for-fruit-enlargement
#7
Naibin Duan, Yang Bai, Honghe Sun, Nan Wang, Yumin Ma, Mingjun Li, Xin Wang, Chen Jiao, Noah Legall, Linyong Mao, Sibao Wan, Kun Wang, Tianming He, Shouqian Feng, Zongying Zhang, Zhiquan Mao, Xiang Shen, Xiaoliu Chen, Yuanmao Jiang, Shujing Wu, Chengmiao Yin, Shunfeng Ge, Long Yang, Shenghui Jiang, Haifeng Xu, Jingxuan Liu, Deyun Wang, Changzhi Qu, Yicheng Wang, Weifang Zuo, Li Xiang, Chang Liu, Daoyuan Zhang, Yuan Gao, Yimin Xu, Kenong Xu, Thomas Chao, Gennaro Fazio, Huairui Shu, Gan-Yuan Zhong, Lailiang Cheng, Zhangjun Fei, Xuesen Chen
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28809947/high-density-genetic-linkage-map-construction-by-f2-populations-and-qtl-analysis-of-early-maturity-traits-in-upland-cotton-gossypium-hirsutum-l
#8
Libei Li, Shuqi Zhao, Junji Su, Shuli Fan, Chaoyou Pang, Hengling Wei, Hantao Wang, Lijiao Gu, Chi Zhang, Guoyuan Liu, Dingwei Yu, Qibao Liu, Xianlong Zhang, Shuxun Yu
Due to China's rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213...
2017: PloS One
https://www.readbyqxmd.com/read/28806927/mapping-of-a-major-qtl-for-salt-tolerance-of-mature-field-grown-maize-plants-based-on-snp-markers
#9
Meijie Luo, Yanxin Zhao, Ruyang Zhang, Jinfeng Xing, Minxiao Duan, Jingna Li, Naishun Wang, Wenguang Wang, Shasha Zhang, Zhihui Chen, Huasheng Zhang, Zi Shi, Wei Song, Jiuran Zhao
BACKGROUND: Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. RESULTS: To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462...
August 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28802838/identification-of-immune-correlates-of-protection-in-shigella-infection-by-application-of-machine-learning
#10
Jorge M Arevalillo, Marcelo B Sztein, Karen L Kotloff, Myron M Levine, Jakub K Simon
BACKGROUND: Immunologic correlates of protection are important in vaccine development because they give insight into mechanisms of protection, assist in the identification of promising vaccine candidates, and serve as endpoints in bridging clinical vaccine studies. Our goal is the development of a methodology to identify immunologic correlates of protection using the Shigella challenge as a model. METHODS: The proposed methodology utilizes the Random Forests (RF) machine learning algorithm as well as Classification and Regression Trees (CART) to detect immune markers that predict protection, identify interactions between variables, and define optimal cutoffs...
August 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28801681/nrf1-and-zscan10-bind-to-the-promoter-region-of-the-six1-gene-and-their-effects-body-measurements-in-qinchuan-cattle
#11
Da-Wei Wei, Lin-Sheng Gui, Sayed Haidar Abbas Raza, Song Zhang, Rajwali Khan, Li Wang, Hong-Fang Guo, Lin-Sen Zan
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5' deletion promoter plasmid luciferase reporter assays and 5'-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region -216/-28 relative to the transcriptional start site (TSS)...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798766/toward-genomics-based-breeding-in-c3-cool-season-perennial-grasses
#12
REVIEW
Shyamal K Talukder, Malay C Saha
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28797222/genetic-architecture-and-temporal-patterns-of-biomass-accumulation-in-spring-barley-revealed-by-image-analysis
#13
Kerstin Neumann, Yusheng Zhao, Jianting Chu, Jens Keilwagen, Jochen C Reif, Benjamin Kilian, Andreas Graner
BACKGROUND: Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. RESULTS: With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions...
August 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28795219/development-of-25-near-isogenic-lines-nils-with-ten-bph-resistance-genes-in-rice-oryza-sativa-l-production-resistance-spectrum-and-molecular-analysis
#14
Kshirod K Jena, Sherry Lou Hechanova, Holden Verdeprado, G D Prahalada, Sung-Ryul Kim
A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection...
August 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28793327/qtl-mapping-for-nine-drought-responsive-agronomic-traits-in-bread-wheat-under-irrigated-and-rain-fed-environments
#15
Vijay Gahlaut, Vandana Jaiswal, Bhudeva S Tyagi, Gyanendra Singh, Sindhu Sareen, Harindra S Balyan, Pushpendra Kumar Gupta
In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits...
2017: PloS One
https://www.readbyqxmd.com/read/28791437/saturation-mapping-of-regions-determining-resistance-to-ascochyta-blight-and-broomrape-in-faba-bean-using-transcriptome-based-snp-genotyping
#16
S Ocaña-Moral, N Gutiérrez, A M Torres, E Madrid
Transcriptome-based SNP markers were genotyped in a faba bean map to saturate regions bearing QTL for Ascochyta fabae and broomrape and distinguish positional and functional candidates underlying both resistances. Faba bean is an important food crop worldwide. Marker-assisted selection for disease resistance is a top priority in current faba bean research programs, with pathogens such as Ascochyta fabae and broomrape (Orobanche crenata) being among the major constraints in global faba bean production. However, progress in genetics and genomics in this species has lagged behind that of other grain legumes...
August 8, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28771560/comparative-genome-wide-methylation-analysis-of-longissimus-dorsi-muscles-between-japanese-black-wagyu-and-chinese-red-steppes-cattle
#17
Xibi Fang, Zhihui Zhao, Haibin Yu, Guangpeng Li, Ping Jiang, Yuwei Yang, Runjun Yang, Xianzhong Yu
DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS)...
2017: PloS One
https://www.readbyqxmd.com/read/28769968/association-and-genetic-identification-of-loci-for-four-fruit-traits-in-tomato-using-indel-markers
#18
Xiaoxi Liu, Xiaolin Geng, Hongchi Zhang, Huolin Shen, Wencai Yang
Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28758171/qtl-mapping-for-resistance-to-iridovirus-in-asian-seabass-using-genotyping-by-sequencing
#19
Le Wang, Bin Bai, Shuqing Huang, Peng Liu, Zi Yi Wan, Baoqing Ye, Jinlu Wu, Gen Hua Yue
Identifying quantitative trait loci (QTL) for viral disease resistance is of particular importance in selective breeding programs of fish species. Genetic markers linked to QTL can be useful in marker-assisted selection (MAS) for elites resistant to specific pathogens. Here, we conducted a genome scan for QTL associated with Singapore grouper iridovirus (SGIV) resistance in an Asian seabass (Lates calcarifer) family, using a high-density linkage map generated with genotyping-by-sequencing. One genome-wide significant and three suggestive QTL were detected at LG21, LG6, LG13, and LG15, respectively...
July 31, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28753861/e2f1-signalling-is-predictive-of-chemoresistance-and-lymphogenic-metastasis-in-penile-cancer-a-pilot-functional-study-reveals-new-prognostic-biomarkers
#20
Ferdinand Fenner, Deborah Goody, Chris Protzel, Andreas Erbersdobler, Christin Richter, Juliane M Hartz, Carsten M Naumann, Holger Kalthoff, Ottmar Herchenröder, Oliver W Hakenberg, Brigitte M Pützer
BACKGROUND: For penile cancer (PC) there are no known molecular predictors of lymphatic spread and/or chemoresistance. OBJECTIVE: To identify functional biomarkers that can predict malignant progression and treatment responsiveness. DESIGN, SETTING, AND PARTICIPANTS: We used four patient-derived PC cell lines and measured invasion and capillary tube formation, chemoresponsiveness, and mRNA and protein expression. Data were further validated in E2F1 transcription factor knockdown and overexpression experiments...
March 1, 2017: European Urology Focus
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