Agri Gene最新文献

Rice is a major cereal crop and serves as staple food for a large part of the human population. Rice blast is a very important disease that attacks rice and is found in every region where rice is grown. Here we identified differentially expressed genes during different time intervals of the blast infection. Our results show that at 24 hpi almost half of the identified genes (174 of 224) are under expressed, then at 36 hpi only 26 genes out of 278 identified genes were down regulated. Then for 2nd, 4th and 6th day mostly differentially expressed genes remained up regulated. Also, the most significant gene ontology terms identified for these genes were diterpenoid metabolic process, diterpene phytoalexin metabolic process and phytoalexin metabolic process, isoprenoid metabolic process, terpenoid metabolic process and lipid metabolic process. This study has led to a more comprehensive data for understanding rice defense response.

Ephedra gerardiana is commonly known as ‘Gerard's Joint fir’, used in the indigenous systems as well as in modern systems of medicine. Almost every part of the plant possesses innumerable medicinal properties. Here we examined the genetic diversity and population structure of E. gerardiana employing Direct Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR) methods. The cumulative (DAMD and ISSR) marker data revealed a high genetic diversity (P = 90.84%, H = 0.30, I = 0.45) at species level than at population levels (P = 62.43%, H = 0.22, I = 0.33), and moderate genetic differentiation (G_ST = 0.27) among populations. Unweighted pair group method for arithmetic mean (UPGMA), Principle coordinate analysis (PCoA) and Bayesian clustering analysis revealed a significant population structure, and are in congruence with geographic distribution of the accessions. Mantel test revealed a significant correlation between geographic and genetic distances (r = 0.86, P = 0.007). Comparatively, high genetic diversity at species level than the population levels showed that these populations have evolved in response to their respective environments, and geographical isolation have played an important role in genetic differentiation and population structuring. However, increasing anthropogenic pressure on natural habitats of E. gerardiana, warrants immediate in-situ and ex-situ conservation measures to preserve diverse genotypes available in western Himalayan region for long term sustainability of E. gerardiana. To the best of our knowledge, present study seems to be the first endeavour to analyse genetic diversity and population structure of E. gerardiana using molecular markers.

Leptin (LEP) plays a key role in the regulation of energy balance in mammals, with less well-defined roles in lower vertebrates. The existence of LEP orthologs in birds has been controversial and only recently have several avian LEP genes been reported. Still, LEP has been assumed to be missing from the chicken (Gallus gallus) genome. Here, we identify the chicken LEP (cLEP), which shares only 25% amino acid sequence identity with its human ortholog. However, it has considerably higher homology with avian LEPs, and phylogenetic analysis shows it as clustering with avian LEP sequences. The cLEP and the other known avian LEP sequences all have high GC content. We argue that this property is behind the technical difficulties impeding the identification of these avian genes. The identification of cLEP can be expected to help elucidate leptin signaling pathways in wild and domestic chickens.

To investigate the effects of alfalfa hay (AH) proportion, fish oil (FO) supplementation, and the length of FO supplementation on lipoprotein lipase (LPL), peroxisome proliferator activated receptorγ (PPARγ) and stearoyl-COA desaturase (SCD) gene expression in various adipose tissue depots, 36 Holstein bulls (initial body weight of 345 ± 61 kg) were randomly assigned to 6 dietary treatments in a 2 × 3 factorial arrangement, with 2 levels of AH (10 and 20% of dietary dry matter) and 3 levels of FO (0, 1.05 and 2.1% of dry matter). Samples of adipose tissue were collected at the middle and end of the period (day 90), after slaughtering. The RT-qPCR technique was used for gene expression analyses. The relative mRNA abundance of lipogenic genes was not correlated with AH proportion and FO interaction. Supplementation of FO increased LPL and SCD gene expression in visceral and subcutaneous adipose tissues regardless of AH proportion (P < 0.05). The gene expression of PPARγ was not affected by dietary treatments. Supplementation of FO increased the mRNA abundance of SCD1 gene more in subcutaneous than visceral adipose tissue (P < 0.01). Gene expression of PPARγ and SCD enzymes increased as a result of prolonged FO supplementation (P < 0.01), whereas LPL mRNA abundance was lower at the end of period comparing to the middle period (P < 0.01). The results demonstrate that FO supplementation increases the abundance of adipose tissue SCD mRNA, which in the case of enhancement in UFAs concentration as a result of higher mRNA abundance and enzyme activity, can benefit both human and animal health. Moreover, the duration of FO supplementation was found to be an important factor in regulating enzymes involved in adipose tissue metabolism.

In this study, the polymorphism of myostatin gene (MSTN-1) as a candidate gene for quantitative traits was analyzed in the rainbow trout (Oncorhynchus mykiss). The association between the MSTN-1 polymorphisms and growth traits were also studied. Forty broodstock parents of rainbow trout from two farms including Yasuj and Shahrkord were selected and tagged. These spawning were mated and then juveniles were raised at the ponds until 5 months post-hatching. Two single nucleotide polymorphisms (SNPs: g.660T > C and g.1904C > A) in intron 1 and 2 regions of the MSTN-1 gene in rainbow trout were determined by DNA sequencing and PCR-single stranded conformation polymorphism (PCR-SSCP) methods. The assessment results demonstrated that these two site mutations are synonymous mutations and therefore 6 haplotypes were revealed in these samples (n = 120). Moreover, One way ANOVA of the SNPs and growth traits revealed the genotypes of SNP g.1904C > A are associated with the length and body weight at 90 and 150 days of age (P < 0.05), whereas no significant association was found between the SNP g.660T > C and growth trait parameters. These results provide evidence that SNPs in MSTN-1 gene may be associated with length and body weight during the early stages of life (from hatching to 5 months of age), therefore MSTN-1 gene may be used for rainbow trout breeding program.

Grain shape is a determinate trait of rice quality and largely controlled by spikelet hull size. Although a series of genes controlling grain size have been cloned, the mechanism in epigenetic regulation remained largely unknown. Here, we report that knockdown of OsSET7, which encodes a putative H3K27 monomethyltransferase belonging to the SET-domain family in rice, results in enhanced cell proliferation of the spikelet hull, leading to a significant increase in grain length. The transcript of OsSET7 was accumulated both in vegetative and reproductive tissues, with stronger expression level in the young panicle, implying the crucial roles that OsSET7 plays in panicle development. The expression of cell cycle-related genes, such as E2Fs, CYCA2;2, CDKs, and MCMs was up-regulated in the osset7 mutant. In addition, both yeast two-hybrid system and bimolecular fluorescence complementation (BiFC) assay validated that OsSET7 could combine with proliferating cell nuclear antigen (PCNA). Taken together, our results demonstrate that OsSET7 plays an important role in rice spikelet hull elongation by regulating cell division, which provides a new insight into the functions of SET-domain genes in plants.

Yeast one- (Y1H) and two-hybrid (Y2H) assays are widely used to study transcription factors (TFs) and protein-protein interactions (PPIs), respectively. Here we combined the Y1H and Y2H into a yeast library-hybrid (YLH) assay, which can systematically screen transcription factors (TFs) and PPIs in one experimental pipeline. In typical TFs, the DNA-binding domain (DBD) and activation domain (AD) evolved separately, but were covalently linked. In the YLH assay, TFs are identified based on functionally conserved ADs, whereas in various Y1H assays TFs are identified based on DBDs. Using the YLH method, we isolated 51 pairs of maize-Rhizoctonia PPIs and 38 novel Rhizoctonia solani TFs. TFs and PPIs related to pathogen virulence and plant resistance responses were isolated by the YLH assay. Our results show that 57.75% of isolated TFs contain typical DBDs such as Zn2Cys6, nucleic acid-binding OB-fold, winged helix repressor DNA-binding, and zinc finger CCHC-type. Key PPI pairs related to major functional categories such as metabolism and cellular signalling were obtained. The percentage of verified PPIs is 69.39%. We proved that common TFs have nonspecific or broad-spectrum activities in the yeast plasmid gene expression system. YLH screening can be conducted on library scales to systematically reveal possible TFs and PPIs at the same time.

The identification of dairy cows with higher milk yield potential has been pursued for many years in different herds. Genomic studies have suggested that Single Nucleotide Polymorphisms (SNPs) within major genes may affect milk production and consequently result economic benefit to the farmers. Toll-like receptor 4 (TLR4) is an immunogenic gene activating innate and adaptive immune responses which is present in very close proximity to the quantitative trait loci (QTL) affecting milk production traits. The present research work was designed to explore the possible genetic variations in 5′ upstream region of TLR4 gene in Vrindavani cattle and their possible associations with milk production traits viz. total lactation milk yield, 305 days milk yield and lactation length. Nucleotide variability in 5′ upstream region of TLR4 gene was identified by PCR-RFLP and subsequent sequencing. The haplotypes were constructed using those SNPs. The association of these haplotypes with production traits was studied using SAS 9.3 software. Statistically significant association between these haplotypes and TLMY was observed. However, no significant association was found between haplotypes with MY305 and LL.

Plant under stress exercises a variety of changes at genetic and molecular level, including microRNA (miRNA) mediated post-transcriptional gene silencing. MicroRNA is a small endogenous non-coding RNA, which regulates the target genes post-transcriptionally. In the present study, 9 stress responsive miRNAs was successfully identified from available stress related EST libraries of Cajanus species applying computational approach. Six of them namely., miRNA156, miRNA2924, miRNA6214, miRNA5652, miRNA1862 and miRNA7982 are responsive to heat, drought and flood stresses and 3 miRNAs namely, miRNA395, miRNA417 and miRNA867 are disease responsive in Cajanus spp. Three out of 9 miRNAs namely, miRNA156, miRNA6214 and miRNA1862 identified in heat, drought and flood stress libraries, respectively belonged to Cajanus scarabaeoides, a close wild relative of C. cajan. miRNA156, miRNA1862, miRNA395 and miRNA417 target different transcription factors like wrky, cw-type zing finger protein, b3 domain containing protein and bsd domain-containing transcription factors. The target genes of identified miRNAs are playing crucial role in well defined molecular pathways like., cell division, translation machinery, epigenetic modification and ubiquitin proteasome pathway. The stress responsive miRNAs of Cajanus species identified in the present study provides a better understanding of the regulatory role of miRNAs in biotic and abiotic stresses.

Heavy metal pollution is an increasing environmental problem around the coastline. As a kind of sedentary mollusk, Venerupis philippinarum is an important sentinel to survey the environmental quality of coastal flat. Glutathione peroxidases are important anti-oxidant enzymes to alleviate oxidative stress caused by heavy metals. In the present study, a new cDNA sequence encoding a Se-containing glutathione peroxidase (VpSeGPx2) was isolated from V. philippinarum. The full-length cDNA of VpSeGPx2 was 963 bp with a conserved selenocysteine insertion sequence (SECIS) in its 3′-UTR, encoding a polypeptide of 242 amino acids with a signal peptide of 19-amino acids. Phylogenetic analysis revealed that VpSeGPx2 was clustered with Se-GPx proteins from marine mollusks. VpSeGPx2 was found to be significantly down-regulated by 10 μg/L of copper and up-regulated by 40 μg/L of copper. However, cadmium exposure seemed to have no significant effect on the expression of VpSeGPx2 transcripts. As for a previously cloned non-Se-containing VpGPx, both concentrations of copper exposure (10 and 40 μg/L) significantly increased its mRNA expression, and a higher concentration (40 μg/L) of cadmium significantly inhibited the expression of VpGPx transcript. These results suggested that VpSeGPx2 and VpGPx were both involved in the detoxification of copper pollution but seemed to play a different role in cadmium pollution.