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1. Characterization of invertase inhibitors (InvInhs) in tea plant, and their potential roles in participating in growth, development and cold response

Author:
Shan He; Bo Li; Huan Wang; Shicai Liang; Zhaotang Ding; Yu Wang; Kai Fan; Jianhui Hu; Xinchao Wang; Wenjun Qian
Source:
Scientia horticulturae 2023 v.308 pp. 111580
ISSN:
0304-4238
Subject:
acclimation; beta-fructofuranosidase; bioinformatics; chromosomes; cold; cold stress; cultivars; genome; tea; water stress
Abstract:
... Invertase inhibitor (InvInh) represses acid invertase (AI) activity though interacting with AI at post-translation level, which plays important roles in vegetative and reproductive processes and stress responses of plant. Our previous studies revealed that CsAI genes were involved in regulating cold response of tea plant, while the post-translation regulation mechanism of AI and the roles of InvIn ...
DOI:
10.1016/j.scienta.2022.111580

2. Comparative genomics analysis and genome assembly integration with the recombination landscape contribute to Takifugu bimaculatus assembly refinement

Author:
Yue Shi; Baohua Chen; Shengnan Kong; Qingmin Zeng; Leibin Li; Bo Liu; Fei Pu; Peng Xu
Source:
Gene 2023 v.849 pp. 146910
ISSN:
0378-1119
Subject:
Takifugu; chromosome mapping; chromosomes; economic valuation; genes; genetic recombination; genome assembly; genomics
Abstract:
... Takifugu genus has been brought to the fore in scientific and practical research due to its compact genome, explosive speciation progress and economic value. Here we updated the chromosome-level genome of Takifugu bimaculatus by an ultra-high-density linkage map, a classic and accurate way of chromosome assembly. The map constituted a robust assembly frame, with 92.2% (372.77 Mb) of the draft geno ...
DOI:
10.1016/j.gene.2022.146910

3. Comprehensive analysis of bZIP gene family and function of RcbZIP17 on Botrytis resistance in rose (Rosa chinensis)

Author:
Dandan Li; Xiaomei Li; Xintong Liu; Zhao Zhang
Source:
Gene 2023 v.849 pp. 146867
ISSN:
0378-1119
Subject:
Botrytis cinerea; Rosa chinensis; chromosomes; gene duplication; gene expression; genes; genome-wide association study; gray mold; ornamental plants; phylogeny; plant pathogens
Abstract:
... Rose is an important ornamental plant and a commercial source of natural fragrances and essential oils. However, gray mold is the most serious disease of rose during cultivation and post-harvest. In plants, the bZIP gene family is one of the important families of transcription factors that regulate many biological processes, including pathogen defense, light response, and stress signaling. Althoug ...
DOI:
10.1016/j.gene.2022.146867

4. Establishment and characterization of a cell line from the brain of the Japanese flounder (Paralichthys olivaceus) and its application in the study of viral infection

Author:
Zhaodi Sun; Yuqin Ren; Yitong Zhang; Yucong Yang; Guixing Wang; Zhongwei He; Yufeng Liu; Wei Cao; Yufen Wang; Yuanshuai Fu; Jilun Hou
Source:
Aquaculture 2023 v.562 pp. 738825
ISSN:
0044-8486
Subject:
Andrias davidianus; Hirame rhabdovirus; Iridovirus; Paralichthys olivaceus; actin; aquaculture; brain; cell lines; chromosome number; chromosomes; diploidy; fish; gene expression; genes; host-pathogen relationships; interleukin-8; karyotyping; neural stem cells; temperature; transfection; viruses
Abstract:
... Fish cell lines are important tools in many biological studies. Here, we established a new Japanese flounder brain (JFB) cell line from the brain tissue of the Japanese flounder (Paralichthys olivaceus), which was successfully sub-cultured for over 120 passages, and consisted predominantly of fibroblast-like cells. Sequencing of the actin gene confirmed that JFB cells were derived from the Japanes ...
DOI:
10.1016/j.aquaculture.2022.738825

5. Genetic diversity, population structure, linkage disequilibrium and GWAS for resistance to WSSV in Pacific white shrimp (Litopenaeus vannamei) using a 50K SNP chip

Author:
Thania Medrano-Mendoza; Baltasar F. García; Alejandra Caballero-Zamora; José M. Yáñez; Leobardo Montoya-Rodríguez; Juan C. Quintana-Casares; Marina Durán-Aguilar; Gabriel R. Campos-Montes
Source:
Aquaculture 2023 v.562 pp. 738835
ISSN:
0044-8486
Subject:
DNA-directed RNA polymerase; Litopenaeus vannamei; White spot syndrome virus; aquaculture; arylsulfatase; chromosomes; death; genetic variance; genetic variation; genome-wide association study; genotyping; hepatopancreas; humoral immunity; immune response; linkage disequilibrium; marker-assisted selection; necrotizing hepatopancreatitis; oxidoreductases; population structure; principal component analysis; quality control; Ecuador; Panama
Abstract:
... The objectives of this research were to assess the genetic diversity, population structure, linkage disequilibrium and perform a genome-wide association study (GWAS) to search for single nucleotide polymorphisms (SNPs) that associate with the resistance of Pacific white shrimp (Litopenaeus vannamei) to White Spot Syndrome Virus (WSSV). The line here analyzed was formerly founded with animals origi ...
DOI:
10.1016/j.aquaculture.2022.738835

6. Genome-wide identification of RNA editing sites in chloroplast transcripts and multiple organellar RNA editing factors in tea plant (Camellia sinensis L.): Insights into the albinism mechanism of tea leaves

Author:
Yuxin Zhao; Ruoshi Gao; Zhen Zhao; Shunkai Hu; Rui Han; Anburaj Jeyaraj; Emmanuel Arkorful; Xinghui Li; Xuan Chen
Source:
Gene 2023 v.848 pp. 146898
ISSN:
0378-1119
Subject:
Camellia sinensis; RNA; albino; chloroplast genome; chloroplasts; chromosomes; cultivars; genes; models; tea
Abstract:
... RNA editing is a post-transcriptional modification process, the chloroplast genes of which are involved in the process of chloroplast development in plant. However, the RNA editing sites of chloroplast genes remains unknown. In this study, we identified 39 RNA editing sites in 18 chloroplast genes from chloroplast genome of C. sinensis. Furthermore, the feature, structures and specificity of RNA e ...
DOI:
10.1016/j.gene.2022.146898

7. Physiological, biochemical, and genomic elucidation of the Ensifer adhaerens M8 strain with simultaneous arsenic oxidation and chromium reduction

Author:
Xianhong Li; Jingru Li; Qiancheng Zhao; Longkai Qiao; Limin Wang; Caihong Yu
Source:
Journal of hazardous materials 2023 v.441 pp. 129862
ISSN:
0304-3894
Subject:
DNA repair; Ensifer adhaerens; arsenic; chromium; chromosomes; genome; genomics; gold; metal tolerance; oxidation; plasmids; remediation
Abstract:
... This study reports the simultaneous oxidation of As(III) and reduction of the Cr(VI) strain Ensifer adhaerens M8 screened from soils around abandoned gold tailings contaminated with highly complex metals (loids). Physiological, biochemical, and genomic techniques were used to explore the mechanism. The strain M8 could simultaneously oxidize 1 mM As(III) and reduce 45.3 % 0.1 mM Cr(VI) in 16 h, and ...
DOI:
10.1016/j.jhazmat.2022.129862

8. 2-Mercaptoethanol promotes porcine oocyte maturation in vitro by maintaining autophagy homeostasis

Author:
Yaping Zhang; Qiqi Li; Wangchang Li; Ke Yan; Yaru Liu; Huiyan Xu; Mingsheng Jiang; Yangqing Lu; Xingwei Liang; Jianghua Shang; Xiaogan Yang
Source:
Theriogenology 2022 v.186 pp. 155-167
ISSN:
0093-691X
Subject:
animal reproduction; antioxidants; apoptosis; autophagy; beta-mercaptoethanol; chromosomes; extrusion; gene expression; homeostasis; mitochondria; oocytes; oxidative stress; rapamycin; swine
Abstract:
... 2-Mercaptoethanol (2-ME) is often used as an antioxidant to optimize culture systems for in vitro oocyte maturation in livestock. However, the relationship between 2-ME and autophagy has not yet been elucidated. In this study, we hypothesized that 2-ME can promote porcine oocyte maturation in vitro by maintaining autophagy homeostasis. To test this hypothesis, we explored the effects of 2-ME on th ...
DOI:
10.1016/j.theriogenology.2022.04.009

9. 63 K and 50 K SNP array based high-density genetic mapping and QTL analysis for productivity and fiber quality traits in cotton

Author:
S. Anjan Gowda; Ishwarappa S. Katageri; Rajesh S. Patil; P. Sharat Kumar; Gopal J. Tiwari; Satya N. Jena; Samir V. Sawant
Source:
Euphytica 2022 v.218 no.7 pp. 93
ISSN:
0014-2336
Subject:
Gossypium hirsutum; chromosome mapping; chromosomes; cotton; fiber quality; genome; normal distribution; principal component analysis; research institutions; single nucleotide polymorphism arrays
Abstract:
... The recombinant inbred lines of inter-specific cross, Gossypium hirsutum cv. DS-28 × G. barbadense cv. SBYF-425 was evaluated in three consecutive rainy seasons of 2017–18 (F₁₃), 2018–19 (F₁₄) and 2019–20 (F₁₅) in an augmented design. The preponderance of huge continuous variability for both productivity and fiber quality traits was recorded. The principal component analysis revealed that the mapp ...
DOI:
10.1007/s10681-022-03039-3

10. AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds

Author:
Xiaoyu Wang; Xiaowei Zhang; Daoran Fan; Juwu Gong; Shaoqi Li; Yujie Gao; Aiying Liu; Linjie Liu; Xiaoying Deng; Yuzhen Shi; Haihong Shang; Yuanming Zhang; Youlu Yuan
Source:
Theoretical and applied genetics 2022 v.135 no.9 pp. 3223-3235
ISSN:
0040-5752
Subject:
DNA; Gossypium hirsutum; chromosome mapping; chromosomes; gene expression; genetic background; genetic improvement; heterosis; heterozygosity; lint cotton; nucleotide sequences; phenotypic variation
Abstract:
... KEY MESSAGE : In this study, we present AAQSP as an extension of existing NGS-BSA applications for identifying stable QTLs at high resolution. GhPAP16 and GhIQD14 fine mapped on chromosome D09 of upland cotton are identified as important candidate genes for lint percentage (LP). Bulked segregant analysis combined with next generation sequencing (NGS-BSA) allows rapid identification of genome seque ...
DOI:
10.1007/s00122-022-04181-1

11. Abnormal Expression of microRNA-296-3p in Type 2 Diabetes Patients and its Role in Pancreatic β-Cells Function by Targeting Tensin Homolog Deleted on Chromosome Ten

Author:
Minggang Cheng; Yichen Guo; Weichuan Zhong; Xueyan Chen; Guangzhou Guo
Source:
Biochemical genetics 2022 v.60 no.1 pp. 39-53
ISSN:
0006-2928
Subject:
Western blotting; apoptosis; blood glucose; blood serum; cell proliferation; cell viability; chromosomes; flow cytometry; insulin; insulin secretion; noninsulin-dependent diabetes mellitus; protective effect; reverse transcriptase polymerase chain reaction; therapeutics; transfection; uric acid
Abstract:
... Diabetes mellitus (DM), a familiar disease, is characterized by high blood glucose levels owing to insulin deficiency. Researches have suggested that the incidence rate of diabetes is increasing and it has become an important global epidemic. The type 2 diabetes mellitus (T2DM) is featured with pancreatic β-cell loss and lack of insulin release. Nevertheless, the therapeutic methods that was helpf ...
DOI:
10.1007/s10528-021-10083-6

12. Abnormal overexpression of SoxD enhances melanin synthesis in the Ursa mutant of Bombyx mori

Author:
Niannian Wang; Yinxia Zhang; Wei Li; Zhangchuan Peng; Huan Pan; Shan Li; Tingcai Cheng; Chun Liu
Source:
Insect biochemistry and molecular biology 2022 v.149 pp. 103832
ISSN:
0965-1748
Subject:
Bombyx mori; chromosomes; color; dopamine; genomics; insect biochemistry; introns; larvae; melanin; melanization; metabolism; molecular biology; mutants; mutation; phenotype; phenotypic variation; silkworms; transcription factors; transposons; tyrosine
Abstract:
... The pigment and structural color of insects play crucial roles in body protection, ecological adaptation, and signal communication. Epidermal melanization is a common and main coloring pattern, which results in broad phenotypic diversity. Melanin is one of the compounds contributing to dark brown-black pigmentation, which is synthesized from dopamine and tyrosine by the melanin metabolism pathway. ...
DOI:
10.1016/j.ibmb.2022.103832

13. Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single‐cell level

Author:
Yuanyuan Zhou; Lu Fu; Kazufumi Mochizuki; Jie Xiong; Wei Miao; Guangying Wang
Source:
journal of eukaryotic microbiology 2022 v.69 no.4 pp. e12907
ISSN:
1066-5234
Subject:
DNA replication; Tetrahymena thermophila; chromosomes; cytokinesis; droplets; eukaryotic cells; interphase; microbiology; polyploidy
Abstract:
... Amitosis is widespread among eukaryotes, but the underlying mechanisms are poorly understood. The polyploid macronucleus (MAC) of unicellular ciliates divides by amitosis, making ciliates a potentially valuable model system to study this process. However, a method to accurately quantify the copy number of MAC chromosomes has not yet been established. Here, we used droplet digital PCR (ddPCR) to qu ...
DOI:
10.1111/jeu.12907

14. Activation of thermogenesis pathways in testis of diet-induced obesity mice

Author:
Hucheng Qing; Juan Hu; Huheng Fu; Zhikang Zhao; Weihua Nong; Junli Wang; Fenglian Yang; Sheng Zhao
Source:
Reproductive Biology 2022 v.22 no.3 pp. 100652
ISSN:
1642-431X
Subject:
blood glucose; chromosomes; heat production; high fat diet; male fertility; males; metabolism; obesity; quantitative polymerase chain reaction; sequence analysis; spermatogenesis; testes; thermic effect of food; transcription (genetics)
Abstract:
... High-fat diet (HFD) induced obesity (DIO) has been shown impacts on metabolism, hormonal profile, male fertility, and spermatogenesis. We employed genome-wide transcriptional analysis on the testis of diet induced obesity (DIO) and normal chow (NC) C57BL/6 J male mice to search genes regulated by obesity in testis. Both blood glucose and lipids contents significantly increased in DIO mice after 8 ...
DOI:
10.1016/j.repbio.2022.100652

15. Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae

Author:
Hosub Shin; Jeong Eun Park; Hye Rang Park; Woo Lee Choi; Seung Hwa Yu; Wonjun Koh; Seungill Kim; Hye Yeon Soh; Nomar Espinosa Waminal; Hadassah Roa Belandres; Joo Young Lim; Gibum Yi; Jong Hwa Ahn; June‐Sik Kim; Yong‐Min Kim; Namjin Koo; Kyunghee Kim; Sampath Perumal; Taegu Kang; Junghyo Kim; Hosung Jang; Dong Hyun Kang; Ye Seul Kim; Hyeon‐Min Jeong; Junwoo Yang; Somin Song; Suhyoung Park; Jin A. Kim; Yong Pyo Lim; Beom‐Seok Park; Tzung‐Fu Hsieh; Tae‐Jin Yang; Doil Choi; Hyun Hee Kim; Soo‐Seong Lee; Jin Hoe Huh
Source:
The new phytologist 2022 v.235 no.2 pp. 743-758
ISSN:
0028-646X
Subject:
Brassica rapa; DNA methylation; Raphanus sativus; allotetraploidy; asymmetry; chromosomes; cytogenetic analysis; epigenetics; epigenome; evolution; genome assembly; hybridization; hybrids; landscapes; meiosis; transcription (genetics); transcriptomics
Abstract:
... Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo g ...
DOI:
10.1111/nph.18155

16. Adult plant leaf rust resistance QTL derived from wheat line CI13227 maps to chromosomes 2AL, 4BS, and 7AL

Author:
James A. Kolmer; Matthew N. Rouse
Source:
The plant genome 2022 v.15 no.3 pp. e20215
ISSN:
1940-3372
Subject:
Puccinia recondita; Triticum aestivum; alleles; chromosome mapping; chromosomes; genotyping; inbred lines; leaf rust; leaves; mature plants; polymerase chain reaction; quantitative traits; single nucleotide polymorphism; spring wheat; winter wheat
Abstract:
... The winter wheat (Triticum aestivum L.) line CI13227 has been characterized as having adult plant resistance to leaf rust caused by Puccinia triticina Eriks (Pt). Line CI13227 was crossed with the susceptible spring wheat ‘Thatcher’ (Tc) and a Tc*2/CI13227 F₆ line with adult plant leaf rust resistance designated as 411A was derived. Line 411A was crossed with Tc to develop an F₆ recombinant inbred ...
DOI:
10.1002/tpg2.20215

17. Advances in Sugarcane Genomics and Genetics

Author:
Tianyou Wang; Jingping Fang; Jisen Zhang
Source:
Sugar tech 2022 v.24 no.1 pp. 354-368
ISSN:
0972-1525
Subject:
Saccharum officinarum; chromosomes; cultivars; genome; genomics; haploidy; sequence analysis; sugarcane; sugars; India; Indonesia
Abstract:
... Currently, genome analysis has become a routine component of molecular breeding of major crops. Today’s commercial sugarcane hybrids are the products of breeding over one hundred years with the starting clones produced by crossing two founding species (Saccharum officinarum and S. spontaneum) in India and Indonesia. Current sugarcane varieties have a highly complex and large genome with 100–130 ch ...
DOI:
10.1007/s12355-021-01065-4

18. Advances in the Molecular Cytogenetics of Bananas, Family Musaceae

Author:
Denisa Šimoníková; Jana Čížková; Veronika Zoulová; Pavla Christelová; Eva Hřibová
Source:
Plants 2022 v.11 no.4 pp. -
ISSN:
2223-7747
Subject:
Musa balbisiana; bananas; chromosome number; chromosomes; diploidy; evolution; fish; fluorescence; genome; genomics; hybridization; karyotyping; staple crops; trade; vegetative propagation
Abstract:
... The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata. It is worth mentioning that evolution and speciation in the Musaceae family were accompanied by large-scale ch ...
DOI:
10.3390/plants11040482

19. Agronomic assessment of the durum Rht18 dwarfing gene in bread wheat

Author:
G. J. Rebetzke; A. R. Rattey; W. D. Bovill; R. A. Richards; B. J. Brooks; M. Ellis
Source:
Crop & pasture science 2022 v.73 no.4 pp. 325-336
ISSN:
1836-0947
Subject:
Triticum aestivum; Triticum turgidum subsp. durum; agronomic traits; alleles; chromosomes; coleoptiles; durum wheat; genetic markers; harvest index; homozygosity; microsatellite repeats; pastures; phenotypic selection; plant height; seedling emergence
Abstract:
... The wheat Green Revolution Rht-B1b and Rht-D1b dwarfing alleles are associated with increased grain yields but also with reduced early growth and seedling emergence, especially if sowing conditions are unfavourable. The gibberellic acid-responsive, mutagen-derived Rht18 dwarfing gene was backcrossed from durum wheat (Triticum turgidum subsp. durum L.) cv. Icaro into tall bread wheat (Triticum aest ...
DOI:
10.1071/CP21645

20. Allele segregation analysis of F1 hybrids between independent Brassica allohexaploid lineages

Author:
Daniela Quezada-Martinez; Jun Zou; Wenshan Zhang; Jinling Meng; Jacqueline Batley; Annaliese S. Mason
Source:
Chromosoma 2022 v.131 no.3 pp. 147-161
ISSN:
0009-5915
Subject:
Brassica; allotetraploidy; chromosomes; diploidy; gene segregation; genome; genomics; genotyping; heterozygosity; hexaploidy; humans; hybridization; hybrids; karyotyping; meiosis; single nucleotide polymorphism arrays
Abstract:
... In the Brassica genus, we find both diploid species (one genome) and allotetraploid species (two different genomes) but no naturally occurring hexaploid species (three different genomes, AABBCC). Although hexaploids can be produced via human intervention, these neo-polyploids have quite unstable genomes and usually suffer from severe genome reshuffling. Whether these genome rearrangements continue ...
DOI:
10.1007/s00412-022-00774-3