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Marker assisted selection

Haichao Jiang, Jie Hu, Zhi Li, Jia Liu, Guanjun Gao, Qinglu Zhang, Jinghua Xiao, Yuqing He
BACKGROUND: The brown planthopper (BPH), an insect species that feeds on rice plants (Oryza sativa L.), is one of the most destructive insect pests of rice. BPH can be controlled with chemical pesticides, but they are expensive in terms of the cost and environmental hazards. Hence, utilization of resistance genes in resistant varieties is considered as a more economical and eco-friendly effective method for control. RESULTS: In this study, six dominant BPH-resistance genes (Bph3, Bph14, Bph15, Bph18, Bph20 and Bph21) were introduced into an elite indica rice cultivar Jin 23B using the marker-assisted selection (MAS) method of breeding...
April 11, 2018: Rice
Lifei Luo, Rong Huang, Aidi Zhang, Cheng Yang, Liangming Chen, Denghui Zhu, Yongming Li, Libo He, Lanjie Liao, Zuoyan Zhu, Yaping Wang
Transgenic Yellow River carp is characterized by rapid growth rate and high feed-conversion efficiency and exhibits a great application prospect. However, there is still a significant separation of growth traits in the transgenic Yellow River carp family; as such, growth-related genotypes must be screened for molecular marker-assisted selection. In this study, 23 growth-related candidate genes containing 48 SNP markers were screened through bulked segregant analysis (BSA) among transgenic Yellow River carp family members showing significant separation of growth traits...
April 5, 2018: Functional & Integrative Genomics
Yang Cui, Hailong Yan, Ke Wang, Han Xu, Xuelian Zhang, Haijing Zhu, Jinwang Liu, Lei Qu, Xianyong Lan, Chuanying Pan
A previous whole-genome association analysis identified lysine demethylase 6A ( KDM6A ), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats...
2018: Frontiers in Genetics
Diego Cerrudo, Shiliang Cao, Yibing Yuan, Carlos Martinez, Edgar Antonio Suarez, Raman Babu, Xuecai Zhang, Samuel Trachsel
To increase genetic gain for tolerance to drought, we aimed to identify environmentally stable QTL in per se and testcross combination under well-watered (WW) and drought stressed (DS) conditions and evaluate the possible deployment of QTL using marker assisted and/or genomic selection (QTL/GS-MAS). A total of 169 doubled haploid lines derived from the cross between CML495 and LPSC7F64 and 190 testcrosses (tester CML494) were evaluated in a total of 11 treatment-by-population combinations under WW and DS conditions...
2018: Frontiers in Plant Science
Xiping Yang, Md S Islam, Sushma Sood, Stephanie Maya, Erik A Hanson, Jack Comstock, Jianping Wang
Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control...
2018: Frontiers in Plant Science
Xiu Feng, Xiaomu Yu, Beide Fu, Xinhua Wang, Haiyang Liu, Meixia Pang, Jingou Tong
BACKGROUND: A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain. RESULTS: A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C...
April 2, 2018: BMC Genomics
Kittipat Ukoskit, Ganlayarat Posudsavang, Nattapat Pongsiripat, Prasert Chatwachirawong, Peeraya Klomsa-Ard, Patthinun Poomipant, Somvong Tragoonrung
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis...
March 31, 2018: Genomics
Daniela Torello Marinoni, Nadia Valentini, Ezio Portis, Alberto Acquadro, Chiara Beltramo, Shawn A Mehlenbacher, Todd C Mockler, Erik R Rowley, Roberto Botta
The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection...
2018: PloS One
Dominique D A Pincot, Thomas J Poorten, Michael A Hardigan, Julia M Harshman, Charlotte B Acharya, Glenn S Cole, Thomas R Gordon, Michelle Stueven, Patrick P Edger, Steven J Knapp
Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae , threatens strawberry ( Fragaria × ananassa ) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance...
March 30, 2018: G3: Genes—Genomes—Genetics
Hongyan Zhu, Ning Qin, Thobela Louis Tyasi, Yang Jing, Dehui Liu, Shuguo Yuan, Rifu Xu
Transcription factors (TFs) encoded by SALL1 and SALL3 genes play central roles in the regulation of ovarian development in hens. The present study aimed to examine polymorphisms of these two genes in Chinese Dagu chickens, and to identify the effects of TFs on the laying performance. Among the population, two novel single-nucleotide polymorphisms (SNPs) were identified by single-strand conformation polymorphism (SSCP) in the amplicons of the candidate genes. The effect of the SNP (729C > A) in exon 2 of SALL1 gene on egg production at 43, 57, and 66 weeks and EW at 30 and 43 weeks were the most significant in the 360 samples (P < 0...
March 30, 2018: Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology
Tianheng Ren, Yangshan Hu, Yingzi Tang, Chunsheng Li, Benju Yan, Zhenglong Ren, Feiquan Tan, Zongxiang Tang, Shulan Fu, Zhi Li
Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513...
2018: Frontiers in Plant Science
Stephanie Meller Kochav, Raul J Flores, Lauren K Truby, Veli K Topkara
BACKGROUND: The pulmonary artery pulsatility index (PAPi) - defined as the ratio of pulmonary artery pulse pressure to right atrial pressure -emerged as a powerful predictor of right ventricular (RV) failure in patients with acute inferior myocardial infarction and those undergoing left ventricular assist device placement, however, its prognostic utility in the advanced heart failure population remains largely unknown. METHODS AND RESULTS: We comparatively analyzed PAPi with traditional indices of RV function including RV stroke work index (RVSWI) and right atrial /pulmonary capillary wedge pressure ratio (RAP/PCWP) in the ESCAPE trial...
March 26, 2018: Journal of Cardiac Failure
Gioconda Garcia-Santamaria, Duc Hua, Clay Sneller
Information on the genetic control of the quality traits of soft wheat ( Triticum aestivum ) is essential for breeding. Our objective was to identify QTL associated with end-use quality. We developed 150 F4-derived lines from a cross of Pioneer 26R46 × SS550 and tested them in four environments. We measured flour yield (FY), softness equivalent (SE), test weight (TW), flour protein content (FP), alkaline water retention capacity (AWRC), and solvent retention capacity (SRC) of water (WA), lactic acid (LA), sucrose (SU), sodium carbonate (SO)...
2018: PeerJ
Andrew Smith, Manuel Galli, Isabella Piga, Vanna Denti, Martina Stella, Clizia Chinello, Nicola Fusco, Davide Leni, Marco Manzoni, Gaia Roversi, Mattia Garancini, Angela Ida Pincelli, Vincenzo Cimino, Giulia Capitoli, Fulvio Magni, Fabio Pagni
The main aim of the study was to assess the feasibility of matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) in the pathological investigation of Medullary Thyroid Carcinoma (MTC). Formalin-fixed paraffin-embedded (FFPE) samples from seven MTC patients were analysed by MALDI-MSI in order to detect proteomic alterations within tumour lesions and to define the molecular profiles of specific findings, such as amyloid deposition and C cell hyperplasia (CCH). nLC-ESI MS/MS was employed for the identification of amyloid components and to select alternative proteomic markers of MTC pathogenesis...
March 24, 2018: Journal of Proteomics
Ibrahim S Elbasyoni, A J Lorenz, M Guttieri, K Frels, P S Baenziger, J Poland, E Akhunov
The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms...
May 2018: Plant Science: An International Journal of Experimental Plant Biology
Eitaro Sawayama, Daiki Noguchi, Kei Nakayama, Motohiro Takagi
We previously reported a body color deformity in juvenile red sea bream, which shows transparency in the juvenile stage because of delayed chromatophore development compared with normal individuals, and this finding suggested a genetic cause based on parentage assessments. To conduct marker-assisted selection to eliminate broodstock inheriting the causative gene, developing DNA markers associated with the phenotype was needed. We first conducted SNP mining based on AFLP analysis using bulked-DNA from normal and transparent individuals...
March 23, 2018: Marine Biotechnology
Yin Zhang, Guidong Miao, Hanafiah Fazhan, Khor Waiho, Huaiping Zheng, Shengkang Li, Mhd Ikhwanuddin, Hongyu Ma
The crucifix crab, Charybdis feriatus, which mainly inhabits Indo-Pacific region, is regarded as one of the most high-potential species for domestication and incorporation into the aquaculture sector. However, the regulatory mechanisms of sex determination and differentiation of this species remain unclear. To identify candidate genes involved in sex determination and differentiation, high throughput sequencing of transcriptome from the testis and ovary of C. feriatus was performed by Illumina platform. After removing adaptor primers, low-quality sequences and very short (<50 nt) reads, 80...
March 23, 2018: Physiological Genomics
G J Ma, Q J Song, S G Markell, L L Qi
A novel rust resistance gene, R15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance...
March 21, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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
Mingxia Zhao, Guomei Wang, Yueqiang Leng, Humphrey Wanjugi, Pinggen Xi, Mike Grosz, Mohamed Mergoum, Shaobin Zhong
ND2710 is a hard red spring wheat line with a very high level of resistance to Fusarium head blight (FHB). It was selected from the progeny of a cross between ND2603 (an advanced breeding line derived from the Sumai 3/Wheaton cross) and Grandin (a spring wheat cultivar). The FHB resistance of ND2710 is presumably derived from Sumai 3 since the other parents Grandin and Wheaton are very susceptible to FHB. To identify and map the quantitative trait loci (QTL) for FHB resistance in ND2710, we developed a mapping population consisting of 233 recombinant inbred lines (RILs) from the cross between ND2710 and the spring wheat cultivar 'Bobwhite'...
March 21, 2018: Phytopathology
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