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Marker assisted selection

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https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#1
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28725940/construction-of-the-first-high-density-genetic-linkage-map-and-analysis-of-quantitative-trait-loci-for-growth-related-traits-in-sinonovacula-constricta
#2
Donghong Niu, Yunchao Du, Ze Wang, Shumei Xie, Haideng Nguyen, Zhiguo Dong, Heding Shen, Jiale Li
The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F1 cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156...
July 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28724085/quantitative-trait-loci-mapping-for-spike-characteristics-in-hexaploid-wheat
#3
Yaopeng Zhou, Benjamin Conway, Daniela Miller, David Marshall, Aaron Cooper, Paul Murphy, Shiaoman Chao, Gina Brown-Guedira, José Costa
Wheat ( L.) spike characteristics determine the number of grains produced on each spike and constitute key components of grain yield. Understanding of the genetic basis of spike characteristics in wheat, however, is limited. In this study, genotyping-by-sequencing (GBS) and the iSelect 9K assay were used on a doubled-haploid (DH) soft red winter wheat population that showed a wide range of phenotypic variation for spike traits. A genetic map spanning 2934.1 cM with an average interval length of 3.4 cM was constructed...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724082/prospective-targeted-recombination-and-genetic-gains-for-quantitative-traits-in-maize
#4
Rex Bernardo
Advances in clustered regularly interspaced short palindromic repeats (CRISPR) technology have allowed targeted recombination in specific DNA sequences in yeast (). My objective was to determine if the selection gains from targeted recombination are large enough to warrant the development of targeted recombination technology in plants. Genomewide marker effects for quantitative traits in two maize ( L.) experiments were used to identify targeted recombination points that would maximize the per-chromosome genetic gains in a given cross...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724072/genome-wide-analysis-of-tar-spot-complex-resistance-in-maize-using-genotyping-by-sequencing-snps-and-whole-genome-prediction
#5
Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M Prasanna, Felix San Vicente, Xuecai Zhang
Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724070/marker-trait-association-analysis-of-iron-and-zinc-concentration-in-lentil-lens-culinaris-medik-seeds
#6
Hamid Khazaei, Rajib Podder, Carolyn T Caron, Shudhangshu S Kundu, Marwan Diapari, Albert Vandenberg, Kirstin E Bett
Lentil ( Medik.) seeds are relatively rich in iron (Fe) and zinc (Zn), making lentil a potential crop to aid in the global battle against human micronutrient deficiency. Understanding the genetic basis for uptake of seed Fe and Zn is required to increase sustainable concentrations of these minerals in seeds. The objectives of this study were to characterize genetic variation in seed Fe and Zn concentration and to identify molecular markers associated with these traits across diverse lentil accessions. A set of 138 cultivated lentil accessions from 34 countries were evaluated in four environments (2 sites × 2 yr) in Saskatchewan, Canada...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#7
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28719638/combination-of-twelve-alleles-at-six-quantitative-trait-loci-determines-grain-weight-in-rice
#8
Yuxiang Zeng, Junsheng Shi, Zhijuan Ji, Zhihua Wen, Yan Liang, Changdeng Yang
Grain weight, which is controlled by quantitative trait loci (QTLs), is one of the most important determinants of rice yield. Although many QTLs for grain weight have been identified, little is known about how different alleles in different QTLs coordinate to determine grain weight. In the present study, six grain-weight-QTLs were detected in seven mapping populations (two F2, one F3, and four recombinant inbred lines) developed by crossing 'Lemont', a United States japonica variety, with 'Yangdao 4', a Chinese indica variety...
2017: PloS One
https://www.readbyqxmd.com/read/28713401/genome-wide-association-study-reveals-natural-variations-contributing-to-drought-resistance-in-crops
#9
REVIEW
Hongwei Wang, Feng Qin
Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712062/genome-editing-and-genetic-engineering-in-livestock-for-advancing-agricultural-and-biomedical-applications
#10
Bhanu P Telugu, Ki-Eun Park, Chi-Hun Park
Genetic modification of livestock has a longstanding and successful history, starting with domestication several thousand years ago. Modern animal breeding strategies predominantly based on marker-assisted and genomic selection, artificial insemination, and embryo transfer have led to significant improvement in the performance of domestic animals, and are the basis for regular supply of high quality animal derived food. However, the current strategy of breeding animals over multiple generations to introduce novel traits is not realistic in responding to the unprecedented challenges such as changing climate, pandemic diseases, and feeding an anticipated 3 billion increase in global population in the next three decades...
July 15, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28711956/mapping-stripe-rust-resistance-gene-yrzh22-in-chinese-wheat-cultivar-zhoumai-22-by-bulked-segregant-rna-seq-bsr-seq-and-comparative-genomics-analyses
#11
Yong Wang, Jingzhong Xie, Huaizhi Zhang, Bingmin Guo, Shunzong Ning, Yongxing Chen, Ping Lu, Qiuhong Wu, Miaomiao Li, Deyun Zhang, Guanghao Guo, Yan Zhang, Dengcai Liu, Shaokui Zou, Jianwei Tang, Hong Zhao, Xicheng Wang, Jun Li, Wuyun Yang, Tingjie Cao, Guihong Yin, Zhiyong Liu
A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F5:6 and F6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22...
July 15, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28711251/association-of-candidate-gene-polymorphisms-with-milk-technological-traits-yield-composition-and-somatic-cell-score-in-italian-holstein-friesian-sires
#12
E Viale, F Tiezzi, F Maretto, M De Marchi, M Penasa, M Cassandro
Advances in DNA-based marker technology have enabled the identification of genomic regions underlying complex phenotypic traits in livestock species. The incorporation of detected quantitative trait loci into genetic evaluation provides great potential to enhance selection accuracies, hence expediting the genetic improvement of economically important traits. The objective of the present study was to investigate 96 single nucleotide polymorphisms (SNP) located in 53 candidate genes previously reported to have effects on milk production and quality traits in a population of highly selected Holstein-Friesian bulls...
July 12, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28710536/resistance-to-tomato-leaf-curl-new-delhi-virus-in-melon-is-controlled-by-a-major-qtl-located-in-chromosome-11
#13
Cristina Sáez, Cristina Esteras, Cecilia Martínez, María Ferriol, Narinder P S Dhillon, Carmelo López, Belén Picó
Identification of three genomic regions and underlying candidate genes controlling the high level of resistance to ToLCNDV derived from a wild melon. SNP markers appropriated for MAS management of resistance. Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite begomovirus that severely affects melon crop (Cucumis melo) in the main production areas of Spain since 2012. In this work, we evaluated the degree of resistance of four accessions (two belonging to the subsp. agrestis var. momordica and two to the wild agrestis group) and their corresponding hybrids with a susceptible commercial melon belonging to the subsp...
July 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28710433/high-density-genetic-linkage-map-construction-and-quantitative-trait-locus-mapping-for-hawthorn-crataegus-pinnatifida-bunge
#14
Yuhui Zhao, Kai Su, Gang Wang, Liping Zhang, Jijun Zhang, Junpeng Li, Yinshan Guo
Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706525/functional-marker-assisted-improvement-of-stable-cytoplasmic-male-sterile-lines-of-rice-for-bacterial-blight-resistance
#15
Jegadeesan Ramalingam, Palanisamy Savitha, Ganesh Alagarasan, Ramasamy Saraswathi, Ranganathan Chandrababu
Bacterial blight (BB), caused by Xanthomonas oryzae pv.oryzae is one among the major diseases in rice, which in severe condition cause losses up to 60% in total yield. Marker assisted pyramiding of three broad spectrum BB resistance genes (xa5, xa13, and Xa21) in prominent rice varieties is the most economical and effective strategy for the management of the BB disease. We report here the pyramiding of three genes (xa5, xa13, and Xa21) in maintainer lines (CO 2B, CO 23B, and CO 24B) of three promising wild abortive cytoplasmic male sterile lines (CO 2A, CO 23A, and CO 24A) through functional markers assisted back cross breeding...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28703042/genome-wide-association-mapping-of-fusarium-head-blight-resistance-in-spring-wheat-lines-developed-in-the-pacific-northwest-and-cimmyt
#16
Rui Wang, Jianli Chen, James A Anderson, Junli Zhang, Weidong Zhao, Justin Wheeler, Natalie Klassen, Deven R See, Yanhong Dong
Fusarium head blight is a destructive disease of wheat in humid and semi-humid areas of the world. It has emerged in the Pacific Northwest (PNW) in recent years because of changing climate and crop rotation practices. Our objectives in the present study were to identify and characterize QTL associated with FHB resistance in spring wheat lines developed in the PNW and the International Maize and Wheat Improvement Center (CIMMYT). A total of 170 spring wheat lines were evaluated in field and greenhouse trials in 2015 and 2016...
July 13, 2017: Phytopathology
https://www.readbyqxmd.com/read/28702191/regularized-quantile-regression-for-snp-marker-estimation-of-pig-growth-curves
#17
L M A Barroso, M Nascimento, A C C Nascimento, F F Silva, N V L Serão, C D Cruz, M D V Resende, F L Silva, C F Azevedo, P S Lopes, S E F Guimarães
BACKGROUND: Genomic growth curves are generally defined only in terms of population mean; an alternative approach that has not yet been exploited in genomic analyses of growth curves is the Quantile Regression (QR). This methodology allows for the estimation of marker effects at different levels of the variable of interest. We aimed to propose and evaluate a regularized quantile regression for SNP marker effect estimation of pig growth curves, as well as to identify the chromosome regions of the most relevant markers and to estimate the genetic individual weight trajectory over time (genomic growth curve) under different quantiles (levels)...
2017: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/28698960/genome-wide-qtl-analysis-identified-significant-associations-between-hypoxia-tolerance-and-mutations-in-the-gpr132-and-abcg4-genes-in-nile-tilapia
#18
Hong Lian Li, Xiao Hui Gu, Bi Jun Li, Chao Hao Chen, Hao Ran Lin, Jun Hong Xia
Exposure to hypoxia induces both acute and chronic stress responses, which plays an important role in health of cultured organisms including growth, reproduction, immunity, and other energy demanding activities. Application of advanced genomic technologies allows rapid identification of hypoxia trait-associated genes and precise selection of superior brood stocks with high tolerance in tilapia. By applying QTL-seq and double-digest restriction-site associated DNA sequencing (ddRAD-seq) techniques, we identified four genome-wide significant quantitative trait loci (QTLs) for hypoxia tolerance and many suggestive QTLs in Nile tilapia...
July 11, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28685541/application-values-of-detection-of-serum-ca199-ca242-and-ca50-in-the-diagnosis-of-pancreatic-cancer
#19
X F Lei, S Z Jia, J Ye, Y L Qiao, G M Zhao, X H Li, H Chang
Pancreatic cancer is characterized by rapid onset, high malignancy and high mortality, thus its early diagnosis is effective for improving the survival rate of patients. To discuss the values of detection of carbohydrate antigen (CA) 50, CA242 and CA199 in the diagnosis of pancreatic cancer, this study randomly selected 112 patients who were confirmed as having stage Ia~IIb pancreatic ductal adenocarcinoma (PDAC) in the Shandong Provincial Hospital, China, from May 2012 to May 2013 as a malignant group. One hundred patients with benign pancreatic lesions and 90 healthy people were selected in the same period as a benign group and a healthy control group, respectively...
April 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28674662/bmi-prediction-within-a-korean-population
#20
Jin Sol Lee, Hyun Sub Cheong, Hyoung-Doo Shin
BACKGROUND: Body Mass Index (BMI) is widely regarded as an important clinical trait for obesity and other diseases such as Type 2 diabetes, coronary heart disease, and osteoarthritis. METHODS: This study uses 6,011 samples of genotype data from ethnic Korean subjects. The data was retrieved from the Korea Association Resource. To identify the BMI-related markers within the Korean population, we collected genome-wide association study (GWAS) markers using a GWAS catalog and also obtained other markers from nearby regions...
2017: PeerJ
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