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Molecular Genetics and Genomics: MGG

Qian Zhao, Dongna Ma, Yuping Huang, Weiyi He, Yiying Li, Liette Vasseur, Minsheng You
Transcription factors (TFs), which play a vital role in regulating gene expression, are prevalent in all organisms and characterization of them may provide important clues for understanding regulation in vivo. The present study reports a genome-wide investigation of TFs in the diamondback moth, Plutella xylostella (L.), a worldwide pest of crucifers. A total of 940 TFs distributed among 133 families were identified. Phylogenetic analysis of insect species showed that some of these families were found to have expanded during the evolution of P...
November 16, 2017: Molecular Genetics and Genomics: MGG
Ana Margarida Ferro, Patrícia Ramos, Ângela Guerra, Paula Parreira, Teresa Brás, Olinda Guerreiro, Eliana Jerónimo, Carmen Capel, Juan Capel, Fernando J Yuste-Lisbona, Maria F Duarte, Rafael Lozano, M Margarida Oliveira, Sónia Gonçalves
Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropicrin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from different origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities...
November 16, 2017: Molecular Genetics and Genomics: MGG
Liang Chen, Yuhong Zheng, Zhimin Dong, Fanfan Meng, Xingmiao Sun, Xuhong Fan, Yunfeng Zhang, Mingliang Wang, Shuming Wang
Soybean is the world's most important leguminous crop producing high-quality protein and oil. Elevating oil accumulation in soybean seed is always many researchers' goal. WRINKLED1 (WRI1) encodes a transcription factor of the APETALA2/ethylene responsive element-binding protein (AP2/EREBP) family that plays important roles during plant seed oil accumulation. In this study, we isolated and characterized three distinct orthologues of WRI1 in soybean (Glycine max) that display different organ-specific expression patterns, among which GmWRI1a was highly expressed in maturing soybean seed...
November 14, 2017: Molecular Genetics and Genomics: MGG
Xueyi Tian, Pu Zou, Mingzhi Miao, Zulin Ning, Jingping Liao
Proper establishment of adaxial-abaxial polarity is essential for the development of lateral organs, while former researches were mostly focused on the polarity regulation in leaves, and little is known in stamens, especially in the asymmetric ones. Canna indica (Zingiberales: Cannaceae) is a widely cultivated ornamental plant and the representative species to study the evolutionary development of Zingiberales. The androecium of Canna indica comprises 3-4 petaloid staminodes and a fertile stamen (FS), which consists of a one-theca anther and a petaloid appendage...
November 14, 2017: Molecular Genetics and Genomics: MGG
Khushwant Singh, Georgios Tzelepis, Miloslav Zouhar, Pavel Ryšánek, Christina Dixelius
Plasmodiophora brassicae is a soil-borne pathogen that belongs to Rhizaria, an almost unexplored eukaryotic organism group. This pathogen requires a living host for growth and multiplication, which makes molecular analysis further complicated. To broaden our understanding of a plasmodiophorid such as P. brassicae, we here chose to study immunophilins, a group of proteins known to have various cellular functions, including involvement in plant defense and pathogen virulence. Searches in the P. brassicae genome resulted in 20 putative immunophilins comprising of 11 cyclophilins (CYPs), 7 FK506-binding proteins (FKBPs) and 2 parvulin-like proteins...
November 11, 2017: Molecular Genetics and Genomics: MGG
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Chronic kidney disease and hyperuricemia are serious global health problems. Recent genome-wide association studies have identified various genetic variants related to these disorders. However, most studies have been conducted in a cross-sectional manner. To identify novel susceptibility loci for chronic kidney disease or hyperuricemia, we performed longitudinal exome-wide association studies (EWASs), using ~ 244,000 genetic variants and clinical data of Japanese individuals who had undergone annual health checkups for several years...
November 9, 2017: Molecular Genetics and Genomics: MGG
Xiangxiang Zhang, Rihui Li, Li Chen, Sailun Niu, Lei Chen, Jie Gao, Jing Wen, Bin Yi, Chaozhi Ma, Jingxing Tu, Tingdong Fu, Jinxiong Shen
Flower color in Brassica spp. is an important trait and considered a major visual signal for insect-pollinated plants. In previous study, we isolated and identified two genes (BjPC1 and BjPC2) that control the flower color in B. juncea, and mapped BjPC1 to a 0.13-cM region. In this study, we report the fine-mapping and candidate analysis of BjPC2. We conducted whole-genome resequencing, using bulked segregant analysis (BSA) to determine the BjPC2 candidate intervals. Crossing, allelism testing, and repeated full-sib mating were used to generate XG3, a near isogenic line (NIL) population that segregated on the BjPC2 locus...
November 8, 2017: Molecular Genetics and Genomics: MGG
Chong Tan, Zhiyong Liu, Shengnan Huang, Chengyu Li, Jie Ren, Xiaoyan Tang, Wenjie Liu, Shenling Peng, Hui Feng
Pectin-related genes play significant roles in pollen development and pollen tube growth, and their allelic variations are one of the major reasons for the abnormal development of male gametophyte. Currently, little is known about the role of the PMEI family in male sterility of plants. In this study, 97 putative PMEI genes were identified in Brassica rapa genome. By a phylogenetic analysis, the PMEI family was divided into 10 clades with highly conserved structural characteristics. The publically available RNA-seq data on different tissues of B...
November 8, 2017: Molecular Genetics and Genomics: MGG
Agnieszka Hara-Skrzypiec, J Śliwka, H Jakuczun, E Zimnoch-Guzowska
Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (B RD) and falling bolt (B FB) in combination with the evaluation of enzymatic discoloration...
October 27, 2017: Molecular Genetics and Genomics: MGG
Rubina Sharma, Kawaljit Matharoo, Rohit Kapoor, A J S Bhanwer
PGC-1α (Peroxisome proliferator-activated receptor gamma, coactivator 1 alpha) plays a key role in glucose homeostasis inside liver and muscle. The impact of six polymorphisms of PGC-1α with Type 2 Diabetes (T2D) susceptibility was evaluated on 1125 samples comprising of 554 T2D cases and 571 controls among three endogamous groups (Bania, Brahmin and Jat Sikh) of North-West India (Punjab). Single-locus analysis showed a significant differential pattern of genetic association of PGC-1α among studied groups emphasizing the role of ethnicity towards disease susceptibility...
October 24, 2017: Molecular Genetics and Genomics: MGG
Xin Liu, Rong Li, Yaqing Dai, Xuesen Chen, Xiaoyun Wang
The B-box proteins (BBXs) are a family of zinc finger proteins containing one/two B-box domain(s). Compared with intensive studies of animal BBXs, investigations of the plant BBX family are limited, though some specific plant BBXs have been demonstrated to act as transcription factors in the regulation of flowering and photomorphogenesis. In this study, using a global search of the apple (Malus domestica Borkh.) genome, a total of 64 members of BBX (MdBBX) were identified. All the MdBBXs were divided into five groups based on the phylogenetic relationship, numbers of B-boxes contained and whether there was with an additional CCT domain...
October 24, 2017: Molecular Genetics and Genomics: MGG
Guangzhi Mao, Qiang Ma, Hengling Wei, Junji Su, Hantao Wang, Qifeng Ma, Shuli Fan, Meizhen Song, Xianlong Zhang, Shuxun Yu
The young leaves of virescent mutants are yellowish and gradually turn green as the plants reach maturity. Understanding the genetic basis of virescent mutants can aid research of the regulatory mechanisms underlying chloroplast development and chlorophyll biosynthesis, as well as contribute to the application of virescent traits in crop breeding. In this study, fine mapping was employed, and a recessive gene (v 1) from a virescent mutant of Upland cotton was narrowed to an 84.1-Kb region containing ten candidate genes...
October 20, 2017: Molecular Genetics and Genomics: MGG
Hongyi Nie, Shupeng Xu, Cuiqin Xie, Haiyang Geng, Yazhou Zhao, Jianghong Li, Wei-Fone Huang, Yan Lin, Zhiguo Li, Songkun Su
Honey bee is a social insect. Its colony is mainly coordinated by the chemical signals such as pheromones produced by queen or brood. Correspondingly, the worker bee developed numerous complicated olfactory sensilla in antennae for detection of these colony chemical signals and nectar/pollen signals in foraging. With the normal development of new emerged workers, young adults (nurse bee) worked in colony at the first 2-3 weeks and then followed by the foraging activity outside of the hive, which give rise to great change of the surrounding chemical signals...
October 17, 2017: Molecular Genetics and Genomics: MGG
Hui-Min Liu, Jing-Yang He, Qiang Zhang, Wan-Qiang Lv, Xin Xia, Chang-Qing Sun, Wei-Dong Zhang, Hong-Wen Deng
Genome-wide association studies (GWAS) have been shown to have the potential of explaining more of the "missing heritability" of complex human phenotypes by improving statistical approaches. Here, we applied a genetic-pleiotropy-informed conditional false discovery rate (cFDR) to capture additional polygenic effects associated with estimated glomerular filtration rate (creatinine) (eGFRcrea) and type 2 diabetes (T2D). The cFDR analysis improves the identification of pleiotropic variants by incorporating potentially shared genetic mechanisms between two related traits...
October 16, 2017: Molecular Genetics and Genomics: MGG
Batool Hosseinpour, Sadegh Sepahvand, Kazem Kamali Aliabad, MohammadReza Bakhtiarizadeh, Ali Imani, Reza Assareh, Seyed Alireza Salami
In the original publication of the article, the affiliation of the third author has been incorrectly published as University of Yazd. However, the correct affiliation is Yazd University.
October 12, 2017: Molecular Genetics and Genomics: MGG
Tian Pu, Yang Liu, Rang Xu, Fen Li, Sun Chen, Kun Sun
Conotruncal heart defects (CTDs) are a group of cardiac malformations that involve outflow tract anomalies and the arterial pole of the heart. Recent reports have identified mutations in a number of genes associated with CTDs in human and animal models. ZFPM2 plays a role in cardiac development by acting as a transcriptional cofactor that interacts with GATA4. Because ZFPM2 was found to be important for cardiac development in a knockout mouse model, we screened for ZFPM2 mutations in 528 CTD patients. We identified six rare and nonsynonymous ZFPM2 variants, and this was the first time that five of these variants (R698Q, R736L, E1005K, T32A, and I488V) were reported in East Asians...
October 10, 2017: Molecular Genetics and Genomics: MGG
Yunyan He, Jianming Luo, Yang Chen, Xiaoheng Zhou, Shanjuan Yu, Ling Jin, Xuan Xiao, Siyuan Jia, Qiang Liu
Foetal haemoglobin (HbF) plays a dominant role in ameliorating the morbidity and mortality of β-thalassaemia. A better understanding of the loci and genes involved in HbF expression would be beneficial for the treatment of β-thalassaemia major. However, the genes associated with HbF expression remain largely unknown. In this study, we first explored large-scale data sets and examined the human genome for evidence of positive natural selection to screen out single nucleotide polymorphisms (SNPs). A genetic analysis of HbF levels was conducted in a Chinese cohort of patients with β-thalassaemia to confirm the bioinformatics results...
October 5, 2017: Molecular Genetics and Genomics: MGG
Yi-Hua Lu, Bing-Hua Wang, Wei Xia, Xing-Bo Mo, Long-Fei Wu, Xiao-Wei Zhu, Pei He, Fang-Fei Xie, Xin Lu, Fei-Yan Deng, Shu-Feng Lei
Extended homozygosity is a genomic region in which the copies inherited from parents are identical, and has obvious inter-individual differences in length and frequency. Runs of homozygosity (ROHs), regarded as a type of structure variations, may have potential capacity in regulating gene transcription. To learn more about the genome-wide distribution of ROH regions in humans and understand the potential roles, this study applied ROH-based approach to quantify and characterize ROHs in 41 Chinese Han female subjects, and test potential associations between ROHs and mRNA expressions by eQTL analysis to ascertain whether ROHs are relevant to gene transcription in peripheral blood mononuclear cells (PBMCs)...
October 4, 2017: Molecular Genetics and Genomics: MGG
Jae Hoon Lee, Youfu Zhao
The bacterial enhancer binding protein (bEBP) HrpS is essential for Erwinia amylovora virulence by activating the type III secretion system (T3SS). However, how the hrpS gene is regulated remains poorly understood in E. amylovora. In this study, 5' rapid amplification of cDNA ends and promoter deletion analyses showed that the hrpS gene contains two promoters driven by HrpX/HrpY and the Rcs phosphorelay system, respectively. Electrophoretic mobility shift and gene expression assays demonstrated that integration host factor IHF positively regulates hrpS expression through directly binding the hrpX promoter and positively regulating hrpX/hrpY expression...
September 30, 2017: Molecular Genetics and Genomics: MGG
Silvia Mrvová, Klára Frydrýšková, Martin Pospíšek, Václav Vopálenský, Tomáš Mašek
Alternative polyadenylation is an important and pervasive mechanism that generates heterogeneous 3'-termini of mRNA and is considered an important regulator of gene expression. We performed bioinformatics analyses of ESTs and the 3'-UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. This systematic analysis led to the prediction of new polyadenylation signals. All identified polyadenylation sites were subsequently verified by 3'RACE of transcripts isolated from human lymphoblastic cell lines...
September 23, 2017: Molecular Genetics and Genomics: MGG
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