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Bulked Segregant Analysis

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Maricelis Acevedo – One of the best experts on this subject based on the ideXlab platform.

  • inheritance and Bulked Segregant Analysis of leaf rust and stem rust resistance in durum wheat genotypes
    Phytopathology, 2017
    Co-Authors: Meriem Aoun, J A Kolmer, Matthew N Rouse, Shiaoman Chao, Worku Denbel Bulbula, Elias M Elias, Maricelis Acevedo


    Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and Bulked Segregant Analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized i…

Lining Zhao – One of the best experts on this subject based on the ideXlab platform.

  • identification and validation of single nucleotide polymorphism markers linked to first flower node in kenaf by using combined specific locus amplified fragment sequencing and Bulked Segregant Analysis
    Industrial Crops and Products, 2019
    Co-Authors: Hui Li, Defang Li, Lining Zhao


    Abstract It is important to develop DNA markers closely linked to the first flower node for molecular marker-assisted selection in kenaf breeding. Kenaf (Hibiscus cannabinus L.) is an annual, multipurpose industrial crop with a worldwide distribution. The higher the node of the first flower, the greater is the fiber yield. In this study, a population of 130 F2 individuals was constructed through the cross of K215(♀)×K89(♂). Twenty-five individuals with higher first flower node and twenty-five individuals with lower first flower node were chosen and their DNA were pooled to construct two Bulked DNA pools according to the phenotype. Specific-locus amplified fragment sequencing (SLAF-seq) combined with Bulked Segregant Analysis (BSA) was used to identify candidate DNA markers closely linked to the first flower node. Sixteen single-nucleotide polymorphism (SNP) loci were obtained from 11 related SLAF markers associated with the first flower node. SNP locus validation was performed using Sanger sequencing method. The SNP locus S961-2 in Sanger sequencing by using the primer M41961 was consistent with the SNP locus in the related SLAF-seq. The accuracy rate of the genotypes consistent with the first flower node was 91.2% (31/34). To our knowledge, S961-2 is the first SNP locus to be identified that is closely linked to the first flower node. This SNP locus may be useful for marker-assisted selection in breeding of high fiber yielding varieties of kenaf.

Lei Wang – One of the best experts on this subject based on the ideXlab platform.

  • quantitative trait loci detection of edwardsiella tarda resistance in japanese flounder paralichthys olivaceus using Bulked Segregant Analysis
    Chinese Journal of Oceanology and Limnology, 2016
    Co-Authors: Xiaoxia Wang, Wenteng Xu, Lei Wang, Songlin Chen


    In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese flounder (Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. olivaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association Analysis was initiated, combining Bulked Segregant Analysis (BSA) and quantitative trait loci (QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333 (♀: F0768 ×♂: F0915) (Nomenclature rule: F+year+family number) were used to detect simple sequence repeats (SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers (Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group (LG)-1 exhibited a significant difference between DNA, pooled/Bulked from the resistant and susceptible groups (P <0.001). Therefore, 106 individuals were genotyped using all the SSR markers in LG1 by single marker Analysis. Two different analytical models were then employed to detect SSR markers with different levels of significance in LG1, where 17 and 18 SSR markers were identified, respectively. Each model found three resistance-related QTLs by composite interval mapping (CIM). These six QTLs, designated qE1–6, explained 16.0%–89.5% of the phenotypic variance. Two of the QTLs, qE-2 and qE-4, were located at the 66.7 cM region, which was considered a major candidate region for E. tarda resistance. This study will provide valuable data for further investigations of E. tarda resistance genes and facilitate the selective breeding of disease-resistant Japanese flounder in the future.

  • a genome scan for quantitative trait loci associated with vibrio anguillarum infection resistance in japanese flounder paralichthys olivaceus by Bulked Segregant Analysis
    Marine Biotechnology, 2014
    Co-Authors: Lei Wang, Yingping Zhang, Han Deng, Ying Xu, Yongsheng Tian, Xiaolin Liao, Wenlong Li, Songlin Chen


    A recent genetic linkage map was employed to detect quantitative trait loci (QTLs) associated with Vibrio anguillarum resistance in Japanese flounder. An F1 family established and challenged with V. anguillarum in 2009 was used for QTL mapping. Of the 221 simple sequence repeat (SSR) markers used to detect polymorphisms in the parents of F1, 170 were confirmed to be polymorphic. The average distance between the markers was 10.6 cM. Equal amounts of genomic DNA from 15 fry that died early and from 15 survivors were pooled separately to constitute susceptible bulk and resistance bulk DNA. Bulked Segregant Analysis and QTL mapping were combined to detect candidate SSR markers and regions associated with the disease. A genome scan identified four polymorphic SSR markers, two of which were significantly different between susceptible and resistance bulk (P = 0.008). These two markers were located in linkage group (LG) 7; therefore, all the SSR markers in LG7 were genotyped in all the challenged fry by single marker Analysis. Using two different models, 11–17 SSR markers were detected with different levels of significance. To confirm the associations of these markers with the disease, composite interval mapping was employed to genotype all the challenged individuals. One and three QTLs, which explained more than 60 % of the phenotypic variance, were detected by the two models. Two of the QTLs were located at 48.6 cM. The common QTL may therefore be a major candidate region for disease resistance against V. anguillarum infection.