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https://www.readbyqxmd.com/read/29666883/snp-based-pool-genotyping-and-haplotype-analysis-accelerate-fine-mapping-of-the-wheat-genomic-region-containing-stripe-rust-resistance-gene-yr26
#1
Jianhui Wu, Qingdong Zeng, Qilin Wang, Shengjie Liu, Shizhou Yu, Jingmei Mu, Shuo Huang, Hanan Sela, Assaf Distelfeld, Lili Huang, Dejun Han, Zhensheng Kang
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China...
April 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29665794/mapping-a-male-fertility-restoration-locus-for-the-a-4-cytoplasmic-genic-male-sterility-system-in-pearl-millet-using-a-genotyping-by-sequencing-based-linkage-map
#2
Anna Pucher, C Tom Hash, Jason G Wallace, Sen Han, Willmar L Leiser, Bettina I G Haussmann
BACKGROUND: Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A4 CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf)...
April 17, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29659569/targeted-next-generation-sequencing-identifies-functionally-deleterious-germline-mutations-in-novel-genes-in-early-onset-familial-prostate-cancer
#3
Paula Paulo, Sofia Maia, Carla Pinto, Pedro Pinto, Augusta Monteiro, Ana Peixoto, Manuel R Teixeira
Considering that mutations in known prostate cancer (PrCa) predisposition genes, including those responsible for hereditary breast/ovarian cancer and Lynch syndromes, explain less than 5% of early-onset/familial PrCa, we have sequenced 94 genes associated with cancer predisposition using next generation sequencing (NGS) in a series of 121 PrCa patients. We found monoallelic truncating/functionally deleterious mutations in seven genes, including ATM and CHEK2, which have previously been associated with PrCa predisposition, and five new candidate PrCa associated genes involved in cancer predisposing recessive disorders, namely RAD51C, FANCD2, FANCI, CEP57 and RECQL4...
April 16, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29610576/comparison-of-three-pcr-based-assays-for-snp-genotyping-in-plants
#4
Chiara Broccanello, Claudia Chiodi, Andrew Funk, J Mitchell McGrath, Lee Panella, Piergiorgio Stevanato
Background: PCR allelic discrimination technologies have broad applications in the detection of single nucleotide polymorphisms (SNPs) in genetics and genomics. The use of fluorescence-tagged probes is the leading method for targeted SNP detection, but assay costs and error rates could be improved to increase genotyping efficiency. A new assay, rhAmp, based on RNase H2-dependent PCR (rhPCR) combined with a universal reporter system attempts to reduce error rates from primer/primer and primer/probe dimers while lowering costs compared to existing technologies...
2018: Plant Methods
https://www.readbyqxmd.com/read/29593764/genetic-dissection-and-simultaneous-improvement-of-drought-and-low-nitrogen-tolerances-by-designed-qtl-pyramiding-in-rice
#5
Bo Feng, Kai Chen, Yanru Cui, Zhichao Wu, Tianqing Zheng, Yajun Zhu, Jauhar Ali, Bingbing Wang, Jianlong Xu, Wenzhong Zhang, Zhikang Li
Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29584564/association-between-mica-gene-variants-and-the-risk-of-hepatitis-c-virus-induced-hepatocellular-cancer-in-a-sicilian-population-sample
#6
Giuseppa Augello, Daniele Balasus, Caterina Fusilli, Tommaso Mazza, Maria Rita Emma, Lydia Giannitrapani, Rosalia Agliastro, Melchiorre Cervello, Giuseppe Montalto
There are currently no biomarkers that predict hepatocellular carcinoma (HCC) risk in patients with hepatitis C virus (HCV)-related cirrhosis. We investigated the relationships among major histocompatibility complex (MHC) class I chain-related gene A (MICA) polymorphisms, plasma levels of soluble MICA (sMICA), and HCC risk in patients with HCV-related HCC. One hundred fifty-four HCV-related HCC patients, 93 HCV-related liver cirrhosis (LC) cases, and 244 healthy controls, all sampled from the native Sicilian population, were genotyped using the KASP™ single-nucleotide polymorphism genotyping method...
March 27, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29563850/accelerating-public-sector-rice-breeding-with-high-density-kasp-markers-derived-from-whole-genome-sequencing-of-indica-rice
#7
Katherine A Steele, Mark J Quinton-Tulloch, Resham B Amgai, Rajeev Dhakal, Shambhu P Khatiwada, Darshna Vyas, Martin Heine, John R Witcombe
Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci...
2018: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/29560515/characterisation-and-mapping-of-adult-plant-stripe-rust-resistance-in-wheat-accession-aus27284
#8
Vallence Nsabiyera, Harbans S Bariana, Naeela Qureshi, Debbie Wong, Matthew J Hayden, Urmil K Bansal
A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S...
March 20, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29560514/identification-and-rapid-mapping-of-a-gene-conferring-broad-spectrum-late-blight-resistance-in-the-diploid-potato-species-solanum-verrucosum-through-dna-capture-technologies
#9
Xinwei Chen, Dominika Lewandowska, Miles R Armstrong, Katie Baker, Tze-Yin Lim, Micha Bayer, Brian Harrower, Karen McLean, Florian Jupe, Kamil Witek, Alison K Lees, Jonathan D Jones, Glenn J Bryan, Ingo Hein
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes. We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis...
March 20, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29511035/the-association-of-polymorphisms-in-lncrna-h19-with-hepatocellular-cancer-risk-and-prognosis
#10
Ming-Li Yang, Zhe Huang, Qian Wang, Huan-Huan Chen, Sai-Nan Ma, Rong Wu, Wei-Song Cai
Background: Hepatocellular cancer (HCC) is one of the major causes of cancer related mortality. Genetic polymorphisms may affect the susceptibility and clinical outcome of cancers. We aim to manifest the association of single nucleotide polymorphisms (SNPs) of lncRNA- H19 gene with the risk and prognosis of HCC. Methods: A total of 944 samples composed of 472 HCC patients and 472 matched controls were included in the risk analysis and among them 350 HCC samples were investigated in the prognosis analysis. KASP method was conducted for the SNP genotyping...
March 6, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29492347/kompetitive-allele-specific-pcr-kasp%C3%A2-genotyping-of-48-polymorphisms-at-different-caprine-loci-in-french-alpine-and-saanen-goat-breeds-and-their-association-with-milk-composition
#11
Szilvia Kusza, Ludovic Toma Cziszter, Daniela Elena Ilie, Maria Sauer, Ioan Padeanu, Dinu Gavojdian
Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine ( n  = 24) and Saanen ( n  = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13 ...
2018: PeerJ
https://www.readbyqxmd.com/read/29449853/targeted-haplotype-comparisons-between-south-african-wheat-cultivars-appear-predictive-of-pre-harvest-sprouting-tolerance
#12
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
https://www.readbyqxmd.com/read/29396589/a-new-leaf-rust-resistance-gene-lr79-mapped-in-chromosome-3bl-from-the-durum-wheat-landrace-aus26582
#13
Naeela Qureshi, Harbans Bariana, Vikas Venu Kumran, Sivasamy Muruga, Kerrie L Forrest, Mathew J Hayden, Urmil Bansal
A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection. Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3...
February 2, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29297326/advantages-of-amplifluor-like-snp-markers-over-kasp-in-plant-genotyping
#14
Satyvaldy Jatayev, Akhylbek Kurishbayev, Lyudmila Zotova, Gulmira Khasanova, Dauren Serikbay, Askar Zhubatkanov, Makpal Botayeva, Aibek Zhumalin, Arysgul Turbekova, Kathleen Soole, Peter Langridge, Yuri Shavrukov
BACKGROUND: KASP (KBioscience Competitive Allele Specific PCR) and Amplifluor (Amplification with fluorescence) SNP markers are two prominent technologies based upon a shared identical Allele-specific PCR platform. METHODS: Amplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs). RESULTS: Advantages of the Amplifluor-like system over KASP include the significantly lower costs and much greater flexibility in the adjustment and development of 'self-designed' dual fluorescently-labelled UPs and regular GSPs...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29285885/a-mutation-in-the-progesterone-receptor-predisposes-to-hev-infection-in-hiv-positive-patients
#15
Jose D Debes, Suzan D Pas, Zwier M A Groothuismink, Marchina E van der Ende, Robert A de Man, Andre Boonstra
BACKGROUND AND AIMS: Infection with Hepatitis E virus (HEV) can cause chronic liver disease in immunocompromised hosts. In transplant recipients, the use of certain immunosuppressants and food habits has been proposed as risk factors for HEV. In individuals infected with the human immunodeficiency virus (HIV), risk factors for HEV infection are less clear. We aimed to study the association between a mutation in the progesterone receptor (PR) named PROGINS and HEV-infected in HIV-positive individuals...
December 28, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/29224884/a-genome-wide-association-study-for-left-sided-displacement-of-the-abomasum-using-a-high-density-single-nucleotide-polymorphism-array
#16
S Lehner, I Zerbin, K Doll, J Rehage, O Distl
Left-sided displacement of the abomasum (LDA) is a frequent disease in dairy cattle causing significant financial losses for dairy farmers. Heritability (h2 ) of this complex disease was estimated at up to 0.5 in German Holstein (GH) cattle. Using the Bovine High Density BeadChip (Illumina Inc., San Diego, CA) comprising 588,753 single nucleotide polymorphisms (SNP) after quality control for 126 LDA cases and 280 population-based controls, we used a mixed linear model analysis in a genome-wide association study (GWAS)...
February 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29224171/genetic-mapping-and-validation-of-the-loci-controlling-7s-%C3%AE-and-11s-a-type-storage-protein-subunits-in-soybean-glycine-max-l-merr
#17
Jeffrey D Boehm, Vi Nguyen, Rebecca M Tashiro, Dale Anderson, Chun Shi, Xiaoguang Wu, Lorna Woodrow, Kangfu Yu, Yuhai Cui, Zenglu Li
Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F2 population, which were validated with an F5 RIL population. The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs...
March 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29222636/identification-introgression-and-molecular-marker-genetic-analysis-and-selection-of-a-highly-effective-novel-oat-crown-rust-resistance-from-diploid-oat-avena-strigosa
#18
Howard W Rines, Marisa E Miller, Martin Carson, Shiaoman Chao, Tyler Tiede, Jochum Wiersma, Shahryar F Kianian
Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs. A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing...
March 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29163598/an-rna-sequencing-transcriptome-analysis-of-grasspea-lathyrus-sativus-l-and-development-of-ssr-and-kasp-markers
#19
Xiaopeng Hao, Tao Yang, Rong Liu, Jinguo Hu, Yang Yao, Marina Burlyaeva, Yan Wang, Guixing Ren, Hongyan Zhang, Dong Wang, Jianwu Chang, Xuxiao Zong
Grasspea ( Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeqTM 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29118424/methods-for-scarless-selection-free-generation-of-human-cells-and-allele-specific-functional-analysis-of-disease-associated-snps-and-variants-of-uncertain-significance
#20
Nicole B Coggins, Jacob Stultz, Henriette O'Geen, Luis G Carvajal-Carmona, David J Segal
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants...
November 8, 2017: Scientific Reports
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