Plant Gene最新文献_第8页

Mapping and identification of QTL for agro-physiological traits in rice (Oryza sativa L.) under drought stress 干旱胁迫下水稻农业生理性状QTL定位与鉴定

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100397

Rizky Dwi Satrio , Miftahul Huda Fendiyanto , Ence Darmo Jaya Supena , S. Suharsono , M. Miftahudin

{"title":"Mapping and identification of QTL for agro-physiological traits in rice (Oryza sativa L.) under drought stress","authors":"Rizky Dwi Satrio , Miftahul Huda Fendiyanto , Ence Darmo Jaya Supena , S. Suharsono , M. Miftahudin","doi":"10.1016/j.plgene.2022.100397","DOIUrl":"10.1016/j.plgene.2022.100397","url":null,"abstract":"<div>Exploring novel QTLs for drought tolerance traits using a new rice genetic resource would be valuable to dissect the mechanisms underlying the complexity of the trait. Here, we used a recombinant inbred line population to detect the QTL associated with agro-physiological traits under drought stress, in particular incorporating the SNPs and 147 phenotype data, analyzed the transcript expression of genes within QTL using differential gene expression meta-analysis and qRT-PCR technique. Composite interval mapping analysis allowed the detection of 154 QTLs distributed into 66 regions, which included a large QTL cluster called ‘hotspot QTL’ that strongly associated with drought tolerance on rice chromosome 8. We found several genes within the QTL-containing regions that were highly expressed based on the meta-analysis approach. In the future, the QTL reported here may be utilized for marker-assisted breeding and the candidate drought-responsive genes could be characterized for dissecting a comprehensive molecular mechanism of drought tolerance in rice.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100397"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44128375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Molecular mapping of Chilli veinal mottle virus (ChiVMV) resistance in hot pepper (Capsicum annuum L.) 辣椒对辣椒脉斑病毒（ChiVMV）抗性的分子定位

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100396

Naresh Ponnam , Madhavi Reddy K , Krishna Reddy M , Lakshamana Reddy D.C , Anand C. Reddy , Hemachandra Reddy P

{"title":"Molecular mapping of Chilli veinal mottle virus (ChiVMV) resistance in hot pepper (Capsicum annuum L.)","authors":"Naresh Ponnam , Madhavi Reddy K , Krishna Reddy M , Lakshamana Reddy D.C , Anand C. Reddy , Hemachandra Reddy P","doi":"10.1016/j.plgene.2022.100396","DOIUrl":"10.1016/j.plgene.2022.100396","url":null,"abstract":"<div>Chilli veinal mottle virus (ChiVMV) is a serious potyvirus affecting chilli cultivation in India causing economic yield losses. Breeding resistant varieties/ hybrids is best advocated strategy for viral management. Molecular mapping and markers development greatly facilitates accelerated breeding. Genotyping-by-sequencing was employed for marker discovery and simultaneous genotyping of F2 population developed using contrast parents. Total 6628 single nucleotide polymorphisms (SNP) and 18,125 silicoDArT markers were determined. The SNPs and silicoDArT markers ranged from 280 on chromosome 8 to 625 on chromosome 3 and 857 on chromosome 8 to 1753 on chromosome 3, respectively. Genome wide association study (GWAS) detected 17 SNPs and 21 silicoDArT markers associated with ChiVMV resistance. A major genomic region on chromosome 9 was identified as major candidate loci for ChiVMV resistance. A cluster of defense related genes and elongation translation factors (eIFLE) responsible for disease resistance were predicted within the GWAS regions. A cleaved amplified polymorphic sequence ChiVMVR9_2 CAPS marker was developed for the major resistant locus which was physically mapped at 2,458,715 bp on chromosome 9. This marker can be used in marker-assisted breeding and genomic selection. Further fine mapping of the identified region will facilitate precise marker assisted selection for resistance.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100396"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46016815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Squalene synthase in plants – Functional intricacy and evolutionary divergence while retaining a core catalytic structure 植物中的角鲨烯合酶——功能复杂性和进化差异，同时保留核心催化结构

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2023.100403

Anjan Hazra, Madhurima Dutta, Rajashree Dutta, Ekta Bhattacharya, Rahul Bose, Suparna Mandal Biswas

{"title":"Squalene synthase in plants – Functional intricacy and evolutionary divergence while retaining a core catalytic structure","authors":"Anjan Hazra, Madhurima Dutta, Rajashree Dutta, Ekta Bhattacharya, Rahul Bose, Suparna Mandal Biswas","doi":"10.1016/j.plgene.2023.100403","DOIUrl":"10.1016/j.plgene.2023.100403","url":null,"abstract":"<div>Squalene is the crucial intermediate for the biosynthesis of many bioactive triterpenoids, such as phytosterol in plants or cholesterol in animals. Squalene synthase (SQS) is the essential gene of the squalene biosynthetic pathway, which catalyzes the head-to-head condensation of two farnesyl pyrophosphate or farnesyl diphosphate (FPP) molecules in a two-step reaction and formation of linear C30 squalene. SQS ubiquitously occurs in all eukaryotic organisms. However, the activity of this gene varies significantly, leading to diverse squalene content in plants. The present study focused on the variation in the expression landscape of SQS gene copies with varying evolutionary backgrounds. Afterward, a reflection of the sequence divergence on the catalytic structure of the protein was examined. The genome-scale mining of the SQS homologs revealed varying degrees of duplication events, sequence evolution of the gene sequence itself, and the adjoining regulatory architecture. Contrasting expressional patterns and the regulatory modules pinpoint the importance of transcriptional regulation of this essential gene. Three-dimensional organizations of SQS from diverse evolutionary taxa and their consensus structures enlightened the conservation of critical catalytic domains, nonetheless divergence in the majority of the protein. As a whole, the outputs of this study provide some valuable insights for understanding the functional regulation of SQS under different tissues and environments.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100403"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47649755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Erratum to “The complete chloroplast genome of Chinese medicine (Psoralea corylifolia): Molecular structures, barcoding and phylogenetic analysis” [Plant Gene 21C (2020) 100216] “中药补骨脂(Psoralea corylifolia)叶绿体全基因组:分子结构、条形码和系统发育分析”[植物基因21C (2020) 100216]

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100402

Wei Tan , Han Gao , Huanyu Zhang , Xiaolei Yu , Xiaoxuan Tian , Weiling Jiang , Kun Zhou

引用次数: 0

Genome-wide identification of the bHLH transcription factor family and analysis of bHLH genes related to puerarin biosynthesis in Pueraria lobata var. thomsonii (Benth.) 葛根bHLH转录因子家族的全基因组鉴定及葛根素生物合成相关基因分析

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100390

Liang Xiao , Ding Huang , Zhengdan Wu , Xiaohong Shang , Sheng Cao , Wendan Zeng , Liuying Lu , Pingli Shi , Huabing Yan

{"title":"Genome-wide identification of the bHLH transcription factor family and analysis of bHLH genes related to puerarin biosynthesis in Pueraria lobata var. thomsonii (Benth.)","authors":"Liang Xiao , Ding Huang , Zhengdan Wu , Xiaohong Shang , Sheng Cao , Wendan Zeng , Liuying Lu , Pingli Shi , Huabing Yan","doi":"10.1016/j.plgene.2022.100390","DOIUrl":"10.1016/j.plgene.2022.100390","url":null,"abstract":"<div>Plant basic helix-loop-helix (bHLH) transcription factors are involved in diverse biological process. So far, there has been no report to systematically carry out comprehensive identification of bHLH members in Pueraria lobata var. thomsonii (Benth.) (P. thomsonii), a traditional Chinese herb that is an excellent source of puerarin. Phylogenetic analysis showed that 219 bHLH genes were identified in the P. thomsonii and classified into 13 subfamilies. All the PlbHLH genes were distributed on the 11 chromosomes unevenly and the number of PlbHLH genes on each chromosome varied from 12 to 44. Both of tandem and segmental duplications were key factors driving bHLH gene family expansion in P. thomsonii. A total of 20 conserved motifs were found in PlbHLH gene family, 185 PlbHLH members contain more than two introns, and genes within the same subfamily appeared to share similar intron-exon gene structures. The Ka/Ks analysis indicated PlbHLH gene family undergo purifying selection during evolution. Combined the RNA-seq data with the qRT-PCR detection results, PlbHLH79/148/149 were found to be the most probably candidate genes which were involved in puerarin biosynthesis pathway. Together, our study provided a good foundation for further research into the regulatory mechanism of the candidate PlbHLH proteins for puerarin biosynthesis in P. thomsonii.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100390"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41909005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene expression differences related to pre-harvest sprouting uncovered in related wheat varieties by RNAseq analysis RNAseq分析发现相关小麦品种收获前发芽相关基因表达差异

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2023.100404

Bryan W. Penning

引用次数: 1

Erratum to “Identification of miRNAs and evaluation of candidate genes expression profile associated with drought stress in barley” [Plant Gene 20C (2019) 100205] “与大麦干旱胁迫相关的miRNA鉴定和候选基因表达谱评估”勘误表[Plant Gene 20C（2019）100205]

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100392

Sajjad Zare , Farhad Nazarian-Firouzabadi , Ahmad Ismaili , Hassan Pakniyat

引用次数: 0

Erratum to “Dual transcriptional analysis of Ocimum basilicum and Peronospora belbahrii in susceptible interactions” [Plant Gene 29C (2022) 100350] “basilicum和Peronospora belbahrii在敏感互作中的双转录分析”[Plant Gene 29C (2022) 100350]

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100398

Eric T. Johnson , Hye-Seon Kim , Miaoying Tian , Nativ Dudai , Ofir Tal , Itay Gonda