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Marker assisted selection

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https://www.readbyqxmd.com/read/28432412/genotyping-by-sequencing-targeting-of-a-novel-downy-mildew-resistance-gene-pl-20-from-wild-helianthus-argophyllus-for-sunflower-helianthus-annuus-l
#1
G J Ma, S G Markell, Q J Song, L L Qi
Genotyping-by-sequencing revealed a new downy mildew resistance gene, Pl 20 , from wild Helianthus argophyllus located on linkage group 8 of the sunflower genome and closely linked to SNP markers that facilitate the marker-assisted selection of resistance genes. Downy mildew (DM), caused by Plasmopara halstedii, is one of the most devastating and yield-limiting diseases of sunflower. Downy mildew resistance identified in wild Helianthus argophyllus accession PI 494578 was determined to be effective against the predominant and virulent races of P...
April 21, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28430019/characterization-of-rph24-a-gene-conferring-adult-plant-resistance-to-puccinia-hordei-in-barley
#2
Laura A Ziems, Lee T Hickey, Gregory J Platz, Jerome D Franckowiak, Peter M Dracatos, Davinder Singh, Robert F Park
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers...
April 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/28428796/expression-profiling-coupled-with-in-silico-mapping-identifies-candidate-genes-for-reducing-aflatoxin-accumulation-in-maize
#3
Ramesh Dhakal, Chenglin Chai, Ratna Karan, Gary L Windham, William P Williams, Prasanta K Subudhi
Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28422134/genetic-structure-and-signatures-of-selection-in-grey-reef-sharks-carcharhinus-amblyrhynchos
#4
P Momigliano, R Harcourt, W D Robbins, V Jaiteh, G N Mahardika, A Sembiring, A Stow
With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos)...
April 19, 2017: Heredity
https://www.readbyqxmd.com/read/28421095/exploiting-wild-relatives-for-genomics-assisted-breeding-of-perennial-crops
#5
REVIEW
Zoë Migicovsky, Sean Myles
Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28418033/a-genome-wide-snp-based-genetic-map-and-qtl-mapping-for-agronomic-traits-in-chinese-cabbage
#6
Li Huang, Yafei Yang, Fang Zhang, Jiashu Cao
The aim of this work was to construct a high-resolution genetic map for the dissection of complex morphological and agronomic traits in Chinese cabbage (Brassica rapa L. syn. B. campestris). Chinese cabbage, an economically important vegetable, is a good model plant for studies on the evolution of morphologic variation. Herein, two high-generation inbred Chinese cabbage lines, 'Huangxiaoza' and 'Bqq094-11', were crossed. Then restriction-site-associated DNA sequencing (RAD-seq) was performed on the parents and 120 F2 individuals...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28405714/recessive-male-sterility-in-cabbage-brassica-oleracea-var-capitata-caused-by-loss-of-function-of-bocyp704b1-due-to-the-insertion-of-a-ltr-retrotransposon
#7
Jia-Lei Ji, Li-Mei Yang, Zhi-Yuan Fang, Mu Zhuang, Yang-Yong Zhang, Hong-Hao Lv, Yu-Mei Liu, Zhan-Sheng Li
The LTR-retrotransposon insertion in BoCYP704B1 is proved to be the primary cause of the male sterility in cabbage. Effective allele-specific markers were developed for marker-assisted selection of male sterile gene. 83121A is a spontaneous male sterile mutant identified from cabbage. Genetic analysis indicated that male sterility is controlled by a single recessive gene. Pollen wall formation in the 83121A mutant was severely defective, with a lack of sporopollenin or exine. To understand the mechanisms of male sterility in 83121A, transcription analysis using RNA-Seq was carried out in the buds of the male sterile line 83121A and the male fertile line 83121B, which are near-isogenic lines differing only in the fertility trait...
April 12, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28401336/genome-wide-identification-and-characterization-of-nb-arc-resistant-genes-in-wheat-triticum-aestivum-l-and-their-expression-during-leaf-rust-infection
#8
Saket Chandra, Andaleeb Z Kazmi, Zainab Ahmed, Gargi Roychowdhury, Veena Kumari, Manish Kumar, Kunal Mukhopadhyay
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned...
April 11, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28400774/elite-haplotypes-of-a-protein-kinase-gene-tasnrk2-3-associated-with-important-agronomic-traits-in-common-wheat
#9
Lili Miao, Xinguo Mao, Jingyi Wang, Zicheng Liu, Bin Zhang, Weiyu Li, Xiaoping Chang, Matthew Reynolds, Zhenhua Wang, Ruilian Jing
Plant-specific protein kinase SnRK2s play crucial roles in response to various environmental stimuli. TaSnRK2.3, a SnRK2 member, was involved in the response to multiple abiotic stresses in wheat. To facilitate the use of TaSnRK2.3 in wheat breeding, the three genomic sequences of TaSnRK2.3, originating from the A, B, and D genomes of hexaploid wheat, were obtained. Sequence polymorphism assays showing 4 and 10 variations were detected at TaSnRK2.3-1A and at TaSnRK2.3-1B, respectively, yet no variation was identified at TaSnRK2...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28396541/antibiotic-resistance-markers-in-strain-bp1651-of-burkholderia-pseudomallei-identified-by-genome-sequence-analysis
#10
Julia V Bugrysheva, David Sue, Jay E Gee, Mindy G Elrod, Alex R Hoffmaster, Linnell B Randall, Sunisa Chirakul, Apichai Tuanyok, Herbert P Schweizer, Linda M Weigel
Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis including β-lactams such as penicillins (amoxicillin/clavulanic acid), cephalosporins (ceftazidime), carbapenems (imipenem and meropenem), as well as tetracyclines and sulfonamides. We sequenced, assembled, and annotated the Bp1651 genome, and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports...
April 10, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28392793/rapid-introgression-of-the-fusarium-wilt-resistance-gene-into-an-elite-cabbage-line-through-the-combined-application-of-a-microspore-culture-genome-background-analysis-and-disease-resistance-specific-marker-assisted-foreground-selection
#11
Xing Liu, Fengqing Han, Congcong Kong, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Mu Zhuang, Yumei Liu, Zhansheng Li, Honghao Lv
Cabbage is an economically important vegetable worldwide. Cabbage Fusarium Wilt (CFW) is a destructive disease that results in considerable yield and quality losses in cole crops. The use of CFW-resistant varieties is the most effective strategy to mitigate the effects of CFW. 01-20 is an elite cabbage line with desirable traits and a high combining ability, but it is highly susceptible to CFW. To rapidly transfer a CFW resistance gene into 01-20 plants, we used microspore cultures to develop 230 doubled haploid (DH) lines from a cross between 01-20 (highly susceptible) and 96-100 (highly resistant)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28390405/fam-face-sg-a-score-for-risk-stratification-of-frequent-hospital-admitters
#12
Lian Leng Low, Nan Liu, Kheng Hock Lee, Marcus Eng Hock Ong, Sijia Wang, Xuan Jing, Julian Thumboo
BACKGROUND: An accurate risk stratification tool is critical in identifying patients who are at high risk of frequent hospital readmissions. While 30-day hospital readmissions have been widely studied, there is increasing interest in identifying potential high-cost users or frequent hospital admitters. In this study, we aimed to derive and validate a risk stratification tool to predict frequent hospital admitters. METHODS: We conducted a retrospective cohort study using the readily available clinical and administrative data from the electronic health records of a tertiary hospital in Singapore...
April 8, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28389895/rapd-assisted-selection-of-black-gram-vigna-mungo-l-hepper-towards-the-development-of-multiple-disease-resistant-germplasm
#13
B Vishalakshi, B Umakanth, Anirudh P Shanbhag, Arindam Ghatak, Nitish Sathyanarayanan, M S Madhav, G Gopala Krishna, Hari Yadla
Black gram (Vigna mungo L. Hepper), is an extensively studied food crop which is affected by many abiotic and biotic factors, especially diseases. The yield potential of Black gram is shallow due to lack of genetic variability and biotic stress susceptibility. Core biotic stress factors include mung bean yellow mosaic virus (MYMV), urdbean leaf crinkle virus (UCLV), wilt (Fusarium oxysporum) and powdery mildew (Erysiphe polygoni DC). Although many studies determine resistant varieties to a particular disease, however, it is often complimented by low yield and susceptibility to other diseases...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28389769/high-resolution-mapping-of-qtl-for-fatty-acid-composition-in-soybean-using-specific-locus-amplified-fragment-sequencing
#14
Bin Li, Shengxü Fan, Fukuan Yu, Ying Chen, Shengrui Zhang, Fenxia Han, Shurong Yan, Lianzheng Wang, Junming Sun
We constructed a high-density linkage map comprising 3541 markers developed by specific-locus amplified fragment sequencing, and identified 26 stable QTL including nine novel loci, for fatty acid composition in soybean. Soybean oil quality and stability are mainly determined by the fatty acid composition of the seed. In the present study, we constructed a high-density genetic linkage map using 200 recombinant inbred lines derived from a cross between cultivated soybean varieties Luheidou2 and Nanhuizao, and SNP markers developed by specific-locus amplified fragment sequencing (SLAF-seq)...
April 7, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28384189/polymorphisms-of-fst-gene-and-their-association-with-wool-quality-traits-in-chinese-merino-sheep
#15
Guang-Wei Ma, Yan-Kai Chu, Wen-Jian Zhang, Fei-Yue Qin, Song-Song Xu, Hua Yang, En-Guang Rong, Zhi-Qiang Du, Shou-Zhi Wang, Hui Li, Ning Wang
Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep...
2017: PloS One
https://www.readbyqxmd.com/read/28380604/effect-of-a-major-quantitative-trait-locus-for-porcine-reproductive-and-respiratory-syndrome-prrs-resistance-on-response-to-coinfection-with-prrs-virus-and-porcine-circovirus-type-2b-pcv2b-in-commercial-pigs-with-or-without-prior-vaccination-for-prrs
#16
J R Dunkelberger, N V L Serão, M C Niederwerder, M A Kerrigan, J K Lunney, R R R Rowland, J C M Dekkers
A major QTL for host response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection was identified in a previous study. Single nucleotide polymorphism WUR10000125 (WUR), which is in complete linkage disequilibrium with the putative causative mutation, can be used as a tag SNP for the QTL. However, the effect of WUR following PRRS vaccination and/or coinfection with other pathogens is not known. Therefore, objectives of this study were to estimate the effect of WUR on host response following PRRS vaccination and coinfection of PRRSV with porcine circovirus type 2b (PCV2b), to estimate genetic parameters for host response to vaccination and coinfection, and to estimate the effect of previously identified candidate SNP under PRRSV-only or PCV2b-only infection on host response to coinfection...
February 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28376898/identification-of-factors-that-impact-recurrence-in-patients-with-borderline-ovarian-tumors
#17
Xi Chen, Chenyan Fang, Tao Zhu, Ping Zhang, Aijun Yu, Shihua Wang
BACKGROUND: The lack of consensus around best practices for management of borderline ovarian tumors (BOT) is, in part, to the lack of available data and of clarity in interpreting relationships among various factors that impact outcomes. The objective of this study was to identify clinicopathological factors that impact prognosis of patients with borderline ovarian tumors (BOT) and to address features of this disease with the objective of providing clarity in decision making around management of BOT...
April 4, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/28376721/construction-of-a-high-density-genetic-map-and-the-x-y-sex-determining-gene-mapping-in-spinach-based-on-large-scale-markers-developed-by-specific-locus-amplified-fragment-sequencing-slaf-seq
#18
Wei Qian, Guiyan Fan, Dandan Liu, Helong Zhang, Xiaowu Wang, Jian Wu, Zhaosheng Xu
BACKGROUND: Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach...
April 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28374766/reprogramming-mhc-specificity-by-crispr-cas9-assisted-cassette-exchange
#19
William Kelton, Ann Cathrin Waindok, Theresa Pesch, Mark Pogson, Kyle Ford, Cristina Parola, Sai T Reddy
The development of programmable nucleases has enabled the application of new genome engineering strategies for cellular immunotherapy. While targeted nucleases have mostly been used to knock-out or knock-in genes in immune cells, the scarless exchange of entire immunogenomic alleles would be of great interest. In particular, reprogramming the polymorphic MHC locus could enable the creation of matched donors for allogeneic cellular transplantation. Here we show a proof-of-concept for reprogramming MHC-specificity by performing CRISPR-Cas9-assisted cassette exchange...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28367546/delineation-of-disease-phenotypes-associated-with-esophageal-adenocarcinoma-by-maldi-ims-ms-analysis-of-serum-n-linked-glycans
#20
M M Gaye, T Ding, H Shion, A Hussein, Y Hu, S Zhou, Z T Hammoud, B K Lavine, Y Mechref, J C Gebler, D E Clemmer
N-Linked glycans, extracted from patient sera and healthy control individuals, are analyzed by Matrix-assisted laser desorption ionization (MALDI) in combination with ion mobility spectrometry (IMS), mass spectrometry (MS) and pattern recognition methods. MALDI-IMS-MS data were collected in duplicate for 58 serum samples obtained from individuals diagnosed with Barrett's esophagus (BE, 14 patients), high-grade dysplasia (HGD, 7 patients), esophageal adenocarcinoma (EAC, 20 patients) and disease-free control (NC, 17 individuals)...
April 3, 2017: Analyst
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