Genome-wide Identification and Expression Analysis of NRAMP Transporter Genes in Cucumis sativus and Citrullus lanatus

2020 ◽  
Author(s):  
Huanxin Zhang ◽  
Guoquan Li ◽  
Na Cao ◽  
Huidong Yang ◽  
Fanghong Zhu
Keyword(s):  
Cucumis Sativus ◽  
Growth And Development ◽  
Citrullus Lanatus ◽  
Normal Growth ◽  
Comprehensive Analysis ◽  
Natural Resistance ◽  
Promoter Sequences ◽  
Genome Wide ◽  
Cd Transport ◽  
Heterologous Expression In Yeast

Natural resistance-associated macrophage proteins (NRAMPs) are able to transport various metal ions across cell membranes, which play an important role in plant normal growth and development. Here, a survey of cucumber (Cucumis sativus) and watermelon (Citrullus lanatus) genomes found a total of five CsNRAMPs and four ClNRAMPs, respectively. Based on the phylogenetic relationships, CsNRAMPs and ClNRAMPs were clustered into three groups (I, II and III). Five orthologous pairs were identified between cucumber and watermelon genome, and they were clustered on the same branch of the phylogenetic tree. The number of introns in CsNRAMPs and ClNRAMPs ranged from 3 to 13 and the genes from group Ι were more fragmented than those in group II. Subsequently, analysis of promoter sequences found that five putative transcription factors could act on NRAMPs. Moreover, CsNRAMPs and ClNRAMPs were differentially regulated by deficiencies of Fe, Mn, Cu or Zn, along with toxicities of Fe, Mn, Cu, Zn or Cd. Functional analysis by heterologous expression in yeast indicated that CsNRAMP4 and ClNRAMP3 participate in Cd transport. Overall, the comprehensive analysis of CsNRAMPs and ClNRAMPs reported herein may pave the way for further investigations examining the regulation and functions of this gene family in cucumber and watermelon.

scholarly journals Screening the USDA Watermelon Germplasm Collection for Drought Tolerance at the Seedling Stage

HortScience ◽  
2011 ◽  
Vol 46 (9) ◽  
pp. 1245-1248 ◽  
Author(s):  
Haiying Zhang ◽  
Guoyi Gong ◽  
Shaogui Guo ◽  
Yi Ren ◽  
Yong Xu ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Clustering Analysis ◽  
Growth And Development ◽  
Citrullus Lanatus ◽  
Germplasm Collection ◽  
Normal Growth ◽  
Seedling Stage ◽  
Breeding Lines ◽  
Germplasm Collections ◽  
Drought Tolerant

Because of the growing threat of global warming, drought stress could severely affect the normal growth and development of crop plants. To alleviate such an adverse effect, there is a need to screen watermelon germplasm collections to identify genetic sources for potential drought tolerance. In the present study, 820 accessions of USDA's Citrullus PIs and 246 watermelon breeding lines were evaluated for their drought tolerance at the seedling stage under extreme water stress conditions in a greenhouse. Significant variations in drought tolerance were observed in the Citrullus germplasm collections. Using fast clustering analysis, the tested watermelon materials could be assigned into four groups, including tolerant, intermediate tolerant, moderately sensitive, and sensitive, respectively. The most drought-tolerant Citrullus germplasm, including 13 Citrullus lanatus var. lanatus and 12 C. lanatus var. citroides accessions, were originated from Africa. These genetic materials could be used for rootstock breeding or for developing drought-tolerant watermelon cultivars.

scholarly journals Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nannan Qin ◽  
Yang Gao ◽  
Xiaojing Cheng ◽  
Yang Yang ◽  
Jiang Wu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plant Growth ◽  
Cucumis Sativus ◽  
Growth And Development ◽  
Upstream Region ◽  
Signal Pathways ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Genome Wide ◽  
Proliferation And Differentiation

Abstract Background Signal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues. The working system of CLE genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis of CLE genes in such plants. Results A total of 26 individual CLE genes were identified in Chinese long ‘9930’ cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes among Arabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of all CsCLEs genes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumber CLE genes indicates a possible relationship between CsCLE genes and certain functions of hormone response elements. Cucumber resulted closely related to Arabidopsis and melon, having seven and 15 orthologous CLE genes in Arabidopsis and melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process, CLE genes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber gene CLV3 was overexpressed in Arabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type. Conclusions In this study, 26 CLE genes were identified in Chinese long ‘9930’ cucumber genome. The CLE genes were mainly composed of alkaline hydrophilic unstable proteins. The genes of the CLE family were divided into seven classes, and shared close relationships with their homologs in Arabidopsis and melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, and CLV3, which the representative gene of the family, was overexpressed in Arabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

scholarly journals Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 413
Author(s):  
Qing Guo ◽  
Li Li ◽  
Kai Zhao ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Binding Protein ◽  
Gene Segment ◽  
Gene Expression Pattern ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization

2014 ◽  
Vol 289 (5) ◽  
pp. 855-872 ◽  
Author(s):  
Shengrui Liu ◽  
Muhammad Rehman Gul Khan ◽  
Yongping Li ◽  
Jinzhi Zhang ◽  
Chungen Hu
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Comprehensive Analysis ◽  
Zinc Finger Gene ◽  
Genome Wide

CONGENITAL SUCRASE-ISOMALTASE DEFICIENCY

PEDIATRICS ◽  
1972 ◽  
Vol 49 (6) ◽  
pp. 847-853
Author(s):  
I. Antonowicz ◽  
J. D. Lloyd-Still ◽  
K. T. Khaw ◽  
H. Shwachman
Keyword(s):  
Growth And Development ◽  
Clinical Presentation ◽  
Quantitative Estimation ◽  
Failure To Thrive ◽  
Normal Growth ◽  
Significant Rise ◽  
Small Intestinal Mucosa ◽  
Severe Diarrhea ◽  
Young Infants ◽  
Small Intestinal

Observations over a period of 6 years are reported on 10 children in whom the diagnosis of congenital sucrase isomaltase deficiency (SID) was confirmed by quantitative estimation of disaccharidase activity of the small intestinal mucosa. Repeat biopsies were performed on eight of the ten patients and showed no evidence that sucrase isomaltase activity is acquired. Sucrose tolerance tests (2 gm/kg) showed no significant rise in blood glucose in the seven patients in whom they were performed. This condition may appear in young infants with severe diarrhea resulting in a malabsorption syndrome and failure to thrive. It may also be manifest in a milder clinical presentation with bothersome diarrhea in spite of normal growth and development in the older infant or young child. The diagnosis in this latter group can be difficult, and is frequently missed.

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