Structural and functional analysis of new plant promoter pro-SmAMP1 from <Emphasis Type="Italic">Stellaria media</Emphasis>

The nucleotide sequence of a fragment of the promoter region of pro-SmAMP1 gene, having a length of 1257 bp and encoding antifungal peptides, was determined in chickweed (Stellaria media (L.) Vill.). Computer analysis of the nucleotide sequence revealed a number of cis-elements that are typical strong plant promoters. Five 5′-deletion variants were created taking into account the distribution of cis-elements:–1235,–771,–714,–603, and–481 bp of pro-SmAMP1 gene promoter, which were fused to the coding region of the uidA reporter gene in pCambia1381Z plant expression vector. The efficacy of pro-SmAMP1 promoter deletion variants was determined by transient expression in plants of Nicotiana benthamiana and using sequential generations of transgenic Nicotiana tabacum plants. It was found that the levels of GUS reporter protein activity in the extracts from transgenic and agroinfiltrated plants using all deletion variants of pro-SmAMP1 gene promoter were 3–5 times higher than those of 35S CaMV viral promoter. The highest activity of GUS protein was observed in the leaves of transgenic tobacco plants and closely correlated with the mRNA level of encoding gene. The levels of GUS activity did not differ significantly among 11 independent homozygous lines of T₂ generation of N. tabacum plants with different deletion variants of pro-SmAMP1 promoter. The results give reason to assume that all deletion variants of pro-SmAMP1 promoter provide stable and high level of expression of controlled genes. The shortest deletion variant–481 bp of pro-SmAMP1 promoter should be viewed as a potentially strong plant promoter for the genetic engineering of plants.     

Genomic structure,expression and association study of the porcine <Emphasis Type="Italic">FSD2</Emphasis>

The fibronectin type III and SPRY domain containing 2 (FSD2) on porcine chromosome 7 is considered a candidate gene for pork quality, since its two domains, which were present in fibronectin and ryanodine receptor. The fibronectin type III and SPRY domains were first identified in fibronectin and ryanodine receptor, respectively, which are candidate genes for meat quality. The aim of this study was to elucidate the genomic structure of FSD2 and functions of single nucleotide polymorphisms (SNPs) within FSD2 that are related to meat quality in pigs. Using a bacterial artificial chromosome clone sequence, we revealed that porcine FSD2 consisted of 13 exons encoding 750 amino acids. In addition, FSD2 was expressed in heart, longissimus dorsi muscle, psoas muscle, and tendon among 23 kinds of porcine tissues tested. A total of ten SNPs, including four missense mutations, were identified in the exonic region of FSD2, and two major haplotypes were obtained based on the SNP genotypes of 633 Berkshire pigs. Both haplotypes were associated significantly with intramuscular fat content (IMF, P < 0.020) and moisture percentage (MP, P < 0.002). Moreover, haplotype 2 was associated with meat color, affecting yellowness (P = 0.002). These haplotype effects were further supported by the alteration of putative protein structures with amino acid substitutions. Taken together, our results suggest that FSD2 haplotypes are involved in regulating meat quality including IMF, MP, and meat color in pigs, and may be used as meaningful molecular makers to identify pigs with preferable pork quality.     

Sequence polymorphisms in <Emphasis Type="Italic">Zmisa2</Emphasis> gene are significantly associated with starch pasting and gelatinization properties in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Researches on the genetic basis of starch pasting and gelatinization properties will provide foundation of maize improvement for quality, feed and industrial applications. Maize gene Zmisa2, encoding an isoamylase-type starch debranching enzyme, plays important roles in starch biosynthesis. In this study, the genomic sequences of the gene Zmisa2 in 72 elite maize inbred lines were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. In addition, seven pasting and four gelatinization properties of maize were measured for the tested inbred lines using rapid visco analyzer and differential scanning calorimeter, respectively. A total of 99 sequence variants, including 91 SNPs and 8 indels, were identified at the promoter and coding regions of this gene. Although the frequency of polymorphism in promoter region is much higher than that of coding region, the SNPs in the coding region of maize gene Zmisa2 classified this gene into 21 haplotypes, which encode 11 different ISA2 proteins. Furthermore, the association of the variants of Zmisa2 gene with maize starch pasting and gelatinization properties was estimated, and the results revealed that seven SNPs in coding region, including four nonsynonymous sites, were significantly associated with phenotypic variations of pasting time and enthalpy of transition (ΔH). These results suggested that the polymorphism in maize Zmisa2 locus could be used in molecular marker-assisted selection for improvement of quality in maize breeding programs.     

Distribution and linkage disequilibrium analysis of polymorphisms of <Emphasis Type="Italic">GH1</Emphasis> gene in different populations of pigs associated with body size

Growth hormone (GH) has been considered as a candidate gene for growth and body size in pigs. In this study, polymorphisms of the GH1 gene were evaluated for associations with body size traits in 190 pig individuals. Seventeen single-nucleotide polymorphisms (SNPs) were identified in GH1 gene of the large pig breeds and miniature pig breeds using direct sequencing and genotyped by allele-specific PCR approach. Notably, six (g.237A>G, g.283T>C, g.309A>G, g.318A>G, g.540A>G and g.544A>G) of them were significantly associated with body size, of which three loci (g.283T>C, g.309A>G, g.318A>G) located in the signal-peptide coding region of GH1 gene compose a CGG haplotype for large pigs and TAA haplotype for miniature pigs (P< 0.001), two loci (g.540A>G and g.544A>G) located in the second intron of GH1 gene compose a GG haplotype for large pigs and AA haplotype for miniature pigs (P< 0.001). Our results demonstrate that these SNPs in GH1 gene are associated with the body size of pigs providing genetic basis for pig breeding with the improved economic benefits.     

The First Report on Single Nucleotide Polymorphisms of the <Emphasis Type="Italic">HSPA13</Emphasis> Gene in Koreans

Heat shock proteins (HSPs) are known as molecular chaperones, and they function in response to cell stress. HSPA13, also called STCH, is a member of the HSP70 family. In general, HSP70 family may play a protective role in prion diseases. In a recent study, the overexpression of HSPA13 was shown to shorten the incubation time of prion diseases. Although the exact role of HSPA13 in the pathogenesis of prion diseases remains unknown, the expression level of HSPA13 is significantly associated with the latent phase of prion diseases. It has been known that single nucleotide polymorphisms (SNPs) in promoter and open reading frame (ORF) region of genes can affect either gene expression or gene function. The purpose of this study was to investigate genotype and allele frequencies of SNPs found in the promoter and ORF of HSPA13 in healthy Korean population to obtain the information for subsequent population genetics and prion diseases studies. We observed four SNPs in the promoter region of HSPA13, of which two have previous identified (c.-608C>G; rs2242662 and c.-381G>A; rs2242661) and two are novel (c.-321C>T and c.-300A>G). Interestingly, we did not observe any polymorphisms in the ORF of this gene. To our knowledge, this is the first study of polymorphisms in the human HSPA13 gene.     

Expression Profiles of <Emphasis Type="Italic">IGF</Emphasis>-<Emphasis Type="Italic">1R</Emphasis> Gene and Polymorphisms of its Regulatory Regions in Different Pig Breeds

Insulin like growth factor 1 receptor (IGF-1R) is a candidate gene for growth and carcass traits in regulating animal growth, metabolism and endocrine. It is widely expressed in liver, muscle, bone tissues where the IGF-1R functions as a factor that promotes cell growth. In this study, the protein expression level of IGF-1R gene in liver and muscle tissues of three periods (birth, weaning and adult) of three pig breeds (BamaXiang pigs (BM), Tibetan pigs (TM) and Junmu No.1 pigs (JM)) were tested by western blot. SNPs within the regulatory region of pig IGF-1R gene were detected using direct sequencing and then the genotypes were identified through AS-PCR approach. Results showed expression profiles of IGF-1R gene between liver and muscle tissues were different and significant differences were also found among pig breeds. In the same time, four SNPs were detected in the regulatory region of IGF-1R gene, among which the genotype frequency of three (g.?1468G > C, g.?1192 C > T and g.330,424 C > T) were significantly different among the pig breeds. BM tended to heterozygous (GC/CT) of the anterior two loci, while TM and JM preferred the other two homozygotes respectively. For the g.330,424 C > T, all pig breeds were tended to be the heterozygous. In conclusion, the SNPs with different genotype distribution among the three pig breeds may explain the gene expression difference between the different pig breeds.     

Genetic polymorphisms in the 5'-flanking region of the melanocortin 1 receptor (<Emphasis Type="Italic">MC1R</Emphasis>) gene in foxes

The one of the key pigment genes, the melanocortin 1 receptor (MC1R) gene, plays a fundamental role in the determination of coat color in a variety of mammals. However, so far there has been no report regarding the genetic variants of the MC1R promoter region and the potential association of its mutations with coat color in foxes. This work aimed to characterize 5'-flanking region of the MC1R gene and its mutations associated with coat color variations in foxes. A total of 76 individuals including 64 red foxes (Vulpes vulpes), representing 11 color morphs, and 12 arctic foxes (Vulpes lagopus), representing 2 color morphs were studied. To explore the potential cause of coat color variation in foxes, an 1105 bp region located upstream of the MC1R gene coding region was sequenced in 76 foxes. In the present study, a 1267 bp 5'-flanking region of fox MC1R gene was obtained using a PCR-mediated chromosome-walking technique and a 1105 bp segment was sequenced. A total of 8 novel SNPs and an insertion/deletion of 4 nucleotides were detected. The results of mutations analysis indicated that SNPs g.-52G>A, g.-266A>G, g.-297T>C, g.-300G>A and the insertion/deletion spaning positions g.-382~-379 were important in distinguishing V. vulpes and V. lagopus. This work, for the first time, described and confirmed the different variants existed in the 5'-flanking region of MC1R gene between red foxes and arctic foxes. These findings may be extremely helpful for further exploring the alternative splicings or promoter activity of MC1R gene for different coat-colored foxes.