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8. Fingerprint construction through genotyping by sequencing for applied breeding in Brassica rapa

Author

Li, Guoliang, Yue, Lixin, Cai, Xu, Li, Fei, Zhang, Hui, Zhang, Shujiang, Zhang, Shifan, and Sun, Rifei

Subjects
Nucleotide sequencing -- Methods, Rape (Plant) -- Genetic aspects, DNA sequencing -- Methods, Genotype -- Observations, Biological sciences
Abstract

This study evaluated the genotyping by sequencing (GBS) protocol for fingerprinting Brassica rapa, and the data derived were more reliable than the re-sequencing data of B. rapa. Of the 10 enzyme solutions used to analyze the numbers of genotypes and single-nucleotide polymorphisms (SNPs) in B. rapa, five solutions showed better results, namely, A (HaeIII, 450-500 bp), E (RsaI+HaeIII, 500-550 bp), F (RsaI+HaeIII, 500-600 bp), G(RsaI+HaeIII, 'All' fragment), and J (RsaI+EcaRV-HF ([R]), 'All' fragment). The five enzyme solutions showed less than 40% similarity in different individuals from various samples, and 90% similarity between two individuals from one sample. The E enzyme solution was the most suitable for fingerprinting B. rapa, revealing well-distributed SNPs in the whole genome. Of the 82 highly inbred lines and 18 [F.sub.1] lines of B. rapa sequenced by GBS in the E enzyme solution, known parents of 10 [F.sub.1] lines were verified, and male parents were discovered for 8 [F.sub.1] lines that had only known female parents. This study provides a valuable method for screening parents for [F.sub.1] lines in B. rapa for the efficient evaluation of GBS with varied library construction strategies. Key wards: Brassica rapa, genotyping by sequencing, single-nucleotide polymorphisms, fingerprinting, [F.sub.1] lines, applied breeding. Cette etude a cherche a evaluer le potentiel du protocole de genotypage par sequencage (GBS) pour dresser des empreintes genetiques chez le Brassica rapa. Les donnees obtenues se sont averees plus fiables que celles derivees du re-sequencage de B. rapa. Des dix protocoles enzymatiques employes pour analyser le nombre de genotypes et de polymorphismes mono-nucleotidiques (SNP), cinq ont montre de meilleurs resultats: les protocoles A(HaeIII, 450-500 pb), E (RsaI + HaeIII, 500-550 pb), F (RsaI + HaeIII, 500-600 pb), G (RsaI + HaeIII, [much less than] Tous [much greater than]les fragments) et J (RsaI + EcoRV-HF*, [much less than] Tous [much greater than]les fragments). Les cinq protocoles enzymatiques offraient moins de 40 % de simi-larite entre individus differents et plus de 90 % de similarite entre deux individus de la meme accession. Le proto-cole E s'est avere le meilleur pour produire des empreintes genetiques chez le B. rapa, produisant des SNP bien distribues sur l'ensemble du genome. Les auteurs ont analyse 82 lignees hautement fixees et 18 [F.sub.1] du B. rapa au moyen du GBS avec le protocole E. Ils ont pu confirmer les parents connus pour 10 [F.sub.1] et les parents males ont ete identifies pour 8 [F.sub.1] dont seul le parent femelle etait connu. Cette etude fournit, au terme d'une evaluation effi-ciente de plusieurs protocoles de preparation de librairies GBS, une methode utile pour identifier les parents de [F.sub.1] chez le B. rapa dans le contexte de l'amelioration genetique. [Traduit par la Redaction] Mots-cles: Brassica rapa, genotypage par sequen^age, polymorphismes mono-nucleotidiques, [F.sub.1], selection appliquee., Introduction In the past, reference genome sequences of many crops have provided a mass of information for understanding acrop's genomic variation and genome evolution. Owing to the genome-wide abundance of [...]

Published
2022
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16. Identification of Clubroot (Plasmodiophora brassicae) Resistance Loci in Chinese Cabbage (Brassica rapa ssp. pekinensis) with Recessive Character

Author

Zhang, Hui, primary, Liu, Xitong, additional, Zhou, Jinyan, additional, Strelkov, Stephen E., additional, Fredua-Agyeman, Rudolph, additional, Zhang, Shifan, additional, Li, Fei, additional, Li, Guoliang, additional, Wu, Jian, additional, Sun, Rifei, additional, Hwang, Sheau-Fang, additional, and Zhang, Shujiang, additional

Published
2024
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32. Mapping and Validation of BrGOLDEN: A Dominant Gene Regulating Carotenoid Accumulation in Brassica rapa

Author

Zhang, Lei, primary, Zhang, Shifan, additional, Dai, Yun, additional, Wang, Shaoxing, additional, Wang, Chenggang, additional, Li, Fei, additional, Zhang, Hui, additional, Chen, Guohu, additional, Yuan, Lingyun, additional, Hou, Jinfeng, additional, Tang, Xiaoyan, additional, Zhu, Shidong, additional, Sun, Rifei, additional, Li, Guoliang, additional, and Zhang, Shujiang, additional

Published
2022
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36. Clinical Characteristics of Anti-N-Methyl-d-Aspartate Receptor Encephalitis Overlapping with Demyelinating Diseases: A Review

Author

Zhang, Shujiang, Yang, Yuan, Liu, Wenyu, Li, Zuoxiao, Li, Jinmei, and Zhou, Dong

Subjects
Immunology, Immunology and Allergy
Abstract

Anti-N-methyl-d-aspartate receptor encephalitis (NMDARe), a common autoimmune encephalitis, can be accompanied by demyelinating disorders, including multiple sclerosis (MS), neuromyelitis optica spectrum disorder (NMOSD), and myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD). To compare the clinical characteristics of patients with different overlapping syndromes, we searched the PubMed database and performed a systematic review. Of the 79 patients with overlapping syndromes, 15 had MS, 18 had aquaporin-4-antibody-positive NMOSD (AQP4-Ab-positive NMOSD), and 46 had MOGAD. Compared with classical NMDARe, overlapping syndromes showed atypical symptoms, such as limb weakness, sensory disturbance, and visual impairments in addition to the main symptoms of NMDARe and a lower ratio of ovarian teratoma. Patients with MOGAD overlap were the youngest, while patients with MS and AQP4-Ab-positive NMOSD overlap tended to be older than patients with classical NMDARe. A majority of patients with NMDARe who overlapped with MS or AQP4-Ab-positive NMOSD were female, but this was not the case for patients overlapped with MOGAD. When NMDARe and demyelinating diseases occurred sequentially, the interval was the longest in patients with NMDARe overlapped with MS. A favorable outcome was observed in patients overlapping with MOGAD, but no robust comparison can be drawn with the patients overlapping with AQP4-Ab-positive NMOSD and MS regarding the small number of available data. The long-term prognosis of overlapping syndromes needs further investigation.

Published
2022
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39. Benefits of Endovascular Treatment in Late Window for Acute Ischemic Stroke Selected without CT Perfusion: A Real-World Study

Author

Yang,Yuan, Cui,Ting, Li,Zuoxiao, Li,Jinglun, Duan,Ting, Yuan,Zhengzhou, Wang,Changyi, Wan,Jincheng, Li,Cao, Zhang,Shujiang, Li,Ling, Hu,Fayun, Wu,Bo, Yang,Yuan, Cui,Ting, Li,Zuoxiao, Li,Jinglun, Duan,Ting, Yuan,Zhengzhou, Wang,Changyi, Wan,Jincheng, Li,Cao, Zhang,Shujiang, Li,Ling, Hu,Fayun, and Wu,Bo

Abstract

Yuan Yang,1,2 Ting Cui,1 Zuoxiao Li,2 Jinglun Li,2 Ting Duan,3 Zhengzhou Yuan,2 Changyi Wang,1 Jincheng Wan,1 Cao Li,4 Shujiang Zhang,2 Ling Li,2 Fayun Hu,1 Bo Wu1 1Center of Cerebrovascular Diseases, Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China; 2Department of Neurology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 3Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China; 4Department of Radiology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of ChinaCorrespondence: Bo Wu; Fayun Hu, Center of Cerebrovascular Diseases, Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China, Tel +86-18980602142 ; +86-15902861270, Email dr.bowu@hotmail.com; hufayun2006@163.comObjective: This study examined the functional outcomes and safety of endovascular treatment (EVT) in acute ischemic stroke (AIS) patients owing to large vessel occlusion of the anterior circulation, presented during a late-time window (6– 24 hours after last seen well (LSW)) in a real-world practice.Methods: This was a retrospective analysis from a bi-center prospective cohort. According to the stroke treatment, patients with continuous Alberta Stroke Plan Early Aspect score (ASPECTS) ≥ 6 on non-contrast CT (NCCT) and moderate to good collateral state on CT angiography (CTA) were divided into EVT group and standard medical treatment (SMT) group. The primary outcome was the rate of functional independence (90-day mRS ≤ 2). Safety outcomes were the occurrence of symptomatic intracranial hemorrhage (sICH) and the 90-day mortality.Results: Among the 288 enrolled patients (53.5% male, median age 64 years), there were 167 patients in the EVT group and 121 in the SMT group. After multivariable adjustments for potential confounders, EVT w

Published
2022

40. Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis

Author

Zhang, Lei, primary, Dai, Yun, additional, Yue, Lixin, additional, Chen, Guohu, additional, Yuan, Lingyun, additional, Zhang, Shifan, additional, Li, Fei, additional, Zhang, Hui, additional, Li, Guoliang, additional, Zhu, Shidong, additional, Hou, Jinfeng, additional, Tang, Xiaoyan, additional, Zhang, Shujiang, additional, and Wang, Chenggang, additional

Published
2022
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