Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.)

The waxy gene, which encodes the granule bound starch synthase enzyme, is one of the key genes influencing starch synthesis in the rice endosperm. To investigate functional differences between GBSS alleles, we cloned and sequenced GBSS cDNA from a series of cultivars that differed substantially in apparent amylose content and starch viscosity characteristics. We found two single nucleotide polymorphisms in exons 6 and 10 that resulted in amino acid substitutions. These substitutions are associated with differences in apparent amylose content and viscosity characteristics. Subsequent sequencing of these regions from additional cultivars confirmed their association with particular rice quality characteristics. These point mutations could prove useful as molecular markers in the production of cultivars with superior eating, cooking and processing quality, and contribute to our understanding of the various structural and functional differences among granule bound starch synthase alleles.     

Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers.

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars 'Nipponbare' and 'Koshihikari' can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.     

单核苷酸多态性及其在鸡QTL定位上的应用

单核苷酸多态性是指DNA序列上的单个碱基变异,它具有分布广、多态信息含量大、易于检测和统计分析等优点,能较好用于基因图谱构建和数量性状QTL定位研究,被称为继RFLP和微卫星标记之后的第3代基因遗传标记。本文综述了单核苷酸多态性的性质及检测技术、利用候选基因SNP进行鸡QTL定位研究的现状,并对未来SNP的应用前景进行了展望。Abstract:Single nucleotide polymorphism (SNP) refers to the change of single nucleotide in DNA sequence.Because of its high density in genomes and easy in detection and analysis statistically,SNP can be used in genetic linkage map construction and QTL mapping.Here,the characters and detecting technology of SNP,as well as the status and foreground of the use of candidate gene SNP in chicken QTL mapping are introduced.     

单核苷酸多态性在作物遗传及改良中的应用

单核苷酸多态性（single nucleotide polymorphism,SNP）是等位基因间序列差异最为普遍的类型,可作为一种高通量的遗传标记。已建立了PCR扩增目标序列及其产物测序和电子SNP（eSNP）等多种发现和检测SNP的方法。玉米和大豆等作物也已开展了SNP分析。一些栽培作物种质的多样性不断减少,其结果使连锁不平衡（linkage disequilibrium,LD）增加,这有利于目的基因座上SNP单元型（haplotype）与表型的相关性分析。SNP已在作物基因作图及其整合、分子标记辅助育种和功能基因组学等领域展示了广泛的应用价值。Abstract:Single nucleotide polymorphism(SNP) is the most common type of sequence difference between alleles,which can be used as a kind of high-throughput genetic marker.Several different routes have been developed to discover and identify SNP.These include the direct sequencing of PCR amplicons,electronic SNP(eSNP) and so on.SNP assays have been made in many crop species such as maize and soybean.The elite germplasm of some crops have been narrowed in genetic diversity,increasing the amount of linkage disequilibrium(LD) present and facilitating the association of SNP haplotypes at candidate gene loci with phenotypes.SNP analysis has been broadly used in the field of plant gene mapping,integration of genetic and physical maps,DNA marker-assisted breeding and functional genomics.     

Polymorphism attribution of cSNPs in cancer-related genes located in loss regions with a high frequency of HCC between HBV and health groups

Cancer-related genes harbored in the loss regions containing a high frequency of hepatocellular carcinoma (HCC) were selected. Related information was gathered and the coding single nucleotide polymorphism (cSNP) sequences were obtained from the single nucleotide polymorphism (SNP) database. The appropriate primers and oligonucleotide probes were then designed in accordance with the SNP sites, and subsequently, the gene chips for detecting SNPs were constructed. Genomic DNA was extracted from blood samples of healthy controls and from patients with HBV infection. The sequences, including the SNPs, were amplified via polymerase chain reaction (PCR) and labeled using digoxigenin deoxyuridine tri-phosphate (Dig-dUTP). The labeled products were then hybridized with the SNP chips. Results confirmed that the differences in allele frequencies of three SNPs EGFL3 (rs947345), Caspase9 (rs2308950), and E2F2 (rs3218171) were distinct between HBV-infected patients and controls, suggesting that these SNPs ocuring in high frequency in HBV-infected individuals may be associated with susceptibility to HCC. Translated from Acta Scientiarum Naturalium Universitatis Nankaiensis, 2006, 39(3): 1–5 [译自: 南开大学学报(自然科学版)]     

Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis.

A rice semidwarfing gene, sd-1, known as the "green revolution gene," was isolated by positional cloning and revealed to encode gibberellin 20-oxidase, the key enzyme in the gibberellin biosynthesis pathway. Analysis of 3477 segregants using several PCR-based marker technologies, including cleaved amplified polymorphic sequence, derived-CAPS, and single nucleotide polymorphisms revealed 1 ORF in a 6-kb candidate interval. Normal-type rice cultivars have an identical sequence in this region, consisting of 3 exons (558, 318, and 291 bp) and 2 introns (105 and 1471 bp). Dee-Geo-Woo-Gen-type sd-1 mutants have a 383-bp deletion from the genome (278-bp deletion from the expressed sequence), from the middle of exon 1 to upstream of exon 2, including a 105-bp intron, resulting in a frame-shift that produces a termination codon after the deletion site. The radiation-induced sd-1 mutant Calrose 76 has a 1-bp substitution in exon 2, causing an amino acid substitution (Leu [CTC] to Phe [TTC]). Expression analysis suggests the existence of at least one more locus of gibberellin 20-oxidase which may prevent severe dwarfism from developing in sd-1 mutants.     

Polymorphisms in cytokine genes and risk of Helicobacter pylori infection among Jamaican children

Background: Infection by Helicobacter pylori is often acquired during childhood. Recent studies suggest that inflammatory cytokines may play a role in susceptibility to, and disease phenotype caused by, H. pylori infection, but the association of host genetic variability with risk of H. pylori infection has not been studied in children. Methods: We investigated the relationship between the risk of H. pylori antibody positivity and cytokine gene polymorphisms among 199 two‐year‐old Jamaicans. H. pylori seropositivity was determined by a validated research enzyme‐linked immunosorbent assay. Real‐time Taqman® polymerase chain reaction was used to determine variants at 17 loci in 11 cytokine genes (IL1A, IL1B, IL2, TNF, TLR4, IL4, IL6, IL10, IL10RA, IL12A and IL13). We estimated the odds ratio and the 95% confidence interval for the association of genetic polymorphisms with H. pylori seropositivity, using logistic regression. Results: Forty (20.1%) of 199 children were seropositive. Children's H. pylori seropositivity correlated highly with maternal H. pylori seropositivity (OR = 7.98, 95% CI = 1.05–60.60, p = .02). Children carrying IL1A?889T had a lower risk of H. pylori positivity, compared to those carrying ?889C, with each T allele associated with 43% risk reduction (OR = 0.57, 95% CI = 0.33–0.99, p‐trend = .05). No other loci we examined were associated with the risk of H. pylori seropositivity. Conclusions: The IL1A?889 T allele, known to express a higher level of cytokine IL‐1α, is associated with a lower risk of H. pylori infection among Jamaican children. Our finding supports the hypothesis that an upregulation of pro‐inflammatory cytokines may protect against persistent H. pylori colonization.     

Characterization of eight single nucleotide polymorphism markers in Aedes aegypti

Sequencing of part of seven genes from Aedes aegypti collected in 16 Brazilian cities revealed the existence of 53 single nucleotide polymorphisms (SNPs), representing one SNP every 52 base pairs. From these 53 SNPs, we selected eight that are independent and highly polymorphic. We describe the use of these markers for differentiation of Brazilian populations of A. aegypti. These are the first SNPs developed for delineating population structure in A. aegypti, and will be a useful complement to epidemiological studies.     

Large-scale identification and characterization of genetic variants in asthma candidate genes

Asthma is a chronic inflammatory disorder of the airways, and a number of genetic loci are associated with the disease. Candidate gene association studies have been regarded as effective tools to study complex traits. Knowledge of the sequence variation and structure of the candidate genes is required for association studies. Thus, we investigated the genetic variants of 32 asthma candidate genes selected by colocalization of positional and functional candidate genes. We screened all exons and promoter regions of those genes using 12 healthy individuals and 12 asthma patients and identified a total of 418 single nucleotide polymorphisms (SNPs), including 270 known SNPs and 148 novel SNPs. Levels of nucleotide diversity varied from gene to gene (0.72×10⁻⁴–14.53×10⁻⁴), but the average nucleotide diversity between coding SNPs (cSNPs) and noncoding SNPs was roughly equivalent (4.63×10⁻⁴ vs 4.69×10⁻⁴). However, nucleotide diversity of cSNPs was strongly correlated to codon degeneracy. Nucleotide diversity was much higher at fourfold degenerate sites than at nondegenerate sites (9.42×10⁻⁴ vs 3.14×10⁻⁴). Gene-based haplotype analysis of asthma-associated genes in this study revealed that common haplotypes (frequency >5%) represented 90.5% of chromosomes, and they could be uniquely identified with five or fewer haplotype-tagging SNPs per gene. Therefore, our results may have important implications for the selection of asthma candidate genes and SNP markers for comprehensive association studies using large sample populations.     

Polymorphism attribution of cSNPs in cancer-related genes located in loss regions with a high frequency of HCC between HBV and health groups

Cancer-related genes harbored in the loss regions containing a high frequency of hepatocellular carcinoma (HCC) were selected.Related information was gathered and the coding single nucleotide polymorphism (cSNP) sequences were obtained from the single nucleotide polymorphism (SNP) database.The appropriate primers and oligonucleotide probes were then designed in accordance with the SNP sites,and subsequently,the gene chips for detecting SNPs were constructed.Genomic DNA was extracted from blood samples of healthy controls and from patients with HBV infection.The sequences,including the SNPs,were amplified via polymerase chain reaction (PCR) and labeled using digoxigenin deoxyuridine tri-phosphate (Dig-dUTP).The labeled products were then hybridized with the SNP chips.Results confirmed that the differences in allele frequencies of three SNPs EGFL3 (rs947345),Caspase9 (rs2308950),and E2F2 (rs3218171) were distinct between HBV-infected patients and controls,suggesting that these SNPs ocuring in high frequency in HBV-infected individuals may be associated with susceptibility to HCC.     

Ethnic variations of a retinoblastoma susceptibility gene (RB1) polymorphism in eight Asian populations

An A → G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. TheRB1 SNP was present in all populations at an overall frequency of ≤0.18. Heterozygosity was higher in the Southeast Asian groups (0.14–0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04–0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. ThisRB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studyingRB1 inheritance by pedigree analysis.     

Linkage mapping of starch branching enzyme III in rice (Oryza sativa L.) and prediction of location of orthologous genes in other grasses

 The chromosomal position of Starch Branching Enzyme III (SBEIII) was determined via linkage to RFLP markers on an existing molecular map of rice (Oryza sativa L.). A cDNA of 890 bp was generated using specific PCR primers designed from available SBEIII sequence data and used as a probe in Southern analysis. The SBEIII cDNA hybridized to multiple restriction fragments, but these fragments mapped to a single locus on rice chromosome 2, flanked by CDO718 and RG157. The detection of a multiple-copy hybridization pattern suggested the possibility of a tandemly duplicated gene at this locus. The map location of orthologous SBE genes in maize, wheat, and oat were predicted based on previously published genetic studies and comparative maps of the grass family. Received : 5 August 1996 / Accepted : 13 September 1996     

Effect of high temperature on fine structure of amylopectin in rice endosperm by reducing the activity of the starch branching enzyme

Rice (Oryza sativa L.) grain quality is affected by the environmental temperature it experiences. To investigate the physiological molecular mechanisms of the effect of high temperatures on rice grain, a non-waxy indica rice was grown under two temperature conditions, (29/35 degrees C) and (22/28 degrees C), during the ripening stage in two phytotrons. The activities and gene expression of key enzymes for the biosynthesis of amylose and amylopectin were examined. The activity and expression levels of soluble endosperm starch synthase I were higher at 29/35 degrees C than that at 22/28 degrees C. In contrast, the activities and expression levels of the rice branching enzyme1, the branching enzyme3 and the granule bound starch synthase of the endosperm were lower at 29/35 degrees C than those at 22/28 degrees C. These results suggest that the decreased activity of starch branching enzyme reduces the branching frequency of the branches of amylopectin, which results in the increased amount of long chains of amylopectin of endosperm in rice grain at high temperature.     

Temperature induced changes in the starch components and biosynthetic enzymes of two rice varieties

The effects of temperature on starch and amylose accumulation, fine structure of amylopectin and activities of some enzymes related to starch synthesis in developing rice endosperms was examined. Two early indica rice varieties were used, differing in amylose concentration (AC, %), namely Jia 935 (low AC) and Jia 353 (high AC). The results showed that the effects of high temperature on AC and amylopectin fine structure were variety-dependent. High temperature caused a reduction in amylose concentration and an increase in the short chain (CL<22) proportion of amylopectin for Jia 935; while opposite was true for Jia 353. High temperature also reduced and increased the activity of granule-bound starch synthase (GBSS) in Jia 935 and in Jia 353, respectively. This suggests that a change in the ratio of amylose/starch due to temperature was attributable to a change in GBSS activity. Moreover, obvious differences between the two rice varieties were detected in the activities of sucrose synthase (SuSy), ADP-glucose pyrophosphorylase (ADPG-Ppase), soluble starch synthase (SSS), starch branching enzyme (SBE), starch de-branching enzyme (SDBE) and starch phosphorylase (SPase) to high temperature. Accumulation rate of amylose was significantly and positively correlated with GBSS for Jia 935, but not for Jia 353. Amylose accumulation was also significantly and positively correlated with the activities of SDBE, SBE, ADPG-Ppase and SuSy for both varieties. The results suggest that the ratio of amylose to starch in rice endosperm is not only related to GBSS, but also affected by the activities of SDBE, SBE, ADPG-Ppase and SuSy.     

First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome

A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (pi = 0.72 x 10(-3)) was lower when compared with diploid genotypes (pi = 2.31 x 10(-3)). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet.     

Biased distribution of single nucleotide polymorphisms (SNPs) in porcine Toll-like receptor 1 (TLR1), TLR2, TLR4, TLR5, and TLR6 genes

Toll-like receptors (TLRs) recognize various microbial components and induce immune responses. Polymorphisms in TLRs may influence their recognition of pathogen-derived molecules; swine TLRs are predicted to be associated with responses to infectious diseases such as pneumonia. In this study, we searched for single nucleotide polymorphisms (SNPs) in the coding sequences of porcine TLR1, TLR2, TLR4, TLR5, and TLR6 genes in 96 pigs from 11 breeds and elucidated 21, 11, 7, 13, and 11 SNPs, respectively, which caused amino acid substitutions in the respective TLRs. Distribution of these nonsynonymous SNPs was biased; many were located in the leucine-rich repeats, particularly in TLR1. These data demonstrated that the heterogeneity of TLR genes was preserved in various porcine breeds despite intensive breeding that was carried out for livestock improvement. It suggests that the heterogeneity in TLR genes is advantageous in increasing the possibility of survival in porcine populations.Electronic SupplementaryMaterial Supplementary material is available for this article at     

Cell-type specific,coordinate expression of two ADP-glucose pyrophosphorylase genes in relation to starch biosynthesis during seed development of Vicia faba L.

Several cDNA clones encoding two different ADP-glucose pyrophosphorylase (AGPase, EC 2.7.7.27) polypeptides denoted VfAGPC and VfAGPP were isolated from a cotyledonary library of Vicia faba L. Both sequences are closely related to AGPase small-subunit sequences from other plants. Whereas mRNA levels of VfAGPP were equally high in developing cotyledons and leaves, the mRNA of VfAGPC was present in considerable amounts only in cotyledons. During development of cotyledons, both mRNAs accumulated until the beginning of the desiccation phase and disappeared afterwards. The increase of AGPase activity in cotyledons during the phase of storage-product synthesis was closely followed by the accumulation of starch. The AGPase activity in crude extracts of cotyledons was insensitive to 3-phosphoglycerate whereas the activity from leaves could be activated more than five-fold. Inorganic phosphate inhibited the enzyme from both tissues but was slightly more effective on the leaf enzyme. There was a correlation at the cellular level between the distribution of VfAGPP and VfAGPC mRNAs and the accumulation of starch, as studied by in-situ hybridisation and by histochemical staining in parallel tissue sections of developing seeds, respectively. During the early phase of seed development (12–15 days after fertilization) VfAGPase mRNA and accumulation of starch were detected transiently in the hypodermal, chlorenchymal and outer parenchymal cell layers of the seed coat but not in the embryo. At 25 days after fertilization both synthesis of VfAGPase mRNA and biosynthesis of starch had started in parenchyma cells of the inner adaxial zone of the cotyledons. During later stages, the expression of VfAGPase and synthesis of starch extended over most of the cotyledons but were absent from peripheral cells of the abaxial zone, provascular and procalyptral cells.Abbreviations AGPase ADP-glucose pyrophosphorylase - DAF days after fertilization - Glc1P glucose-1-phosphate - 3-PGA 3-phosphoglycerate - VfAGPC AGPase subunit of Vicia faba mainly expressed in cotyledons - VfAGPP AGPase subunit of Vicia faba mainly expressed in leaves and cotyledons - pVfAGPC, pVfAGPP plasmids containing VfAGPC and VfAGPP, respectively This work was supported by the Bundesministerium für Forschung und Technologie BCT 0389, Molekular- und Zellbiologie von höheren Pflanzen und Pilzen. U.W acknowledges additional support by the Fonds der chemischen Industrie. We thank Elsa Fessel for excellent technical assistance.     

Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities

Apparent amylose content (AAC), gel consistency (GC), and gelatinization temperature (GT) are recognized as the most important determinants of rice eating and cooking qualities. The contributions of major starch-synthesis genes to these three traits have been investigated in the three consecutive experiments. In an initial QTL mapping with 130 doubled haploid (DH) lines, derived from an inter-subspecific cross of ‘Nanjing11’/‘Balilla’, the major QTLs responsible for AAC, GC, and GT coincided with the Wx (granule-bound starch synthase gene), Wx, and Sss IIa (soluble starch synthase gene) loci, respectively. In the second experiment, contributions of the major starch-synthesis genes to AAC, GC, and GT variations were estimated by using a multiple linear regression analysis. As shown, the Wx locus was a principal determinant for both AAC and GC, and could account for 58.5% and 38.9% of the phenotypic variations, respectively; while the Sss IIa locus was associated with GT, and could explain 25.5% of the observed variation. Eventually, a F₂ population consisting of 501 individuals, derived from an inter-subspecific cross of the two sticky rice varieties ‘Suyunuo’ and ‘Yangfunuo 4’, was examined with gene-tagged markers. In the absence of the Wx gene, none of the starch-synthesis genes investigated could dominate the GC variation, however, the Sss IIa locus could also explain 25.1% of the GT variation. In summary, the Wx locus dominates the AAC variation, and meanwhile plays a major role in the GC variation. The Sss IIa locus is a major factor in explaining the GT variation. Apart from the major genes, other genetic factors may also contribute to the GC/GT variations.     

Structure of rice starch and its relation to cooked-rice texture

Starch from seven varieties of rice, known to cook from very soft to very hard texture, was fractionated by gel-permeation chromatography on Sepharose CL-2B column. The high-molecular-weight fraction (Sepharose FRI) and the low-molecular-weight fraction (Sepharose FRII, further sub-divided into FRIIa, IIb and IIc) were debranched using isoamylase and fractionated on Biogel P-10. All the four fractions in all the different varieties of rice gave a similar trimodal chain profile, indicating the presence of branched molecules in all of them. Clearly, the branched component of starch (‘amylopectin’) is not necessarily big in size, but includes very small to very big molecules. The presence or absence of the largely linear, and relatively small molecule, ‘amylose’, could not be settled either way with the technique employed. However, based on certain assumptions, amylose content was calculated to be in the range of 7%–11% in the samples, much less than generally thought. The content of long-B chains of the branched molecule in the four Sepharose fractions individually and in aggregate, as well as the calculated amylose content, correlated well with the sensory tenderness of cooked rice. It was observed that the content of all long linear chains, including amylose if any, govern the texture of cooked rice.