Characterization and distribution of novel alleles of the vernalization gene Vrn-A1 in Chinese wheat(Triticum aestivum L.) cultivars

The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement.Vrn-1 is a major regulator of this requirement.In this study,two novel alleles of Vrn-A1 were discovered in Chinese cultivars:vrn-A1n was identified in two landraces,Jiunong 2 and Ganchun 16,and Vrn-A1o was detected in Duanhongmangmai.Both novel alleles showed a linked duplication in the promoter region.The common copy of these two alleles was identical to the recessive allele vrn-A1.Compared with the recessive allele vrn-A1,the other copy of vrn-A1n contained a 54-bp deletion in the promoter region and the distinct copy of Vrn-A1o contained an11-bp deletion in the promoter region.In segregating populations in the greenhouse under nonvernalizing(20–25°C)and long-day(16 h light)conditions,plants with the novel vrn-A1n allele did not head earlier than those with the recessive vrn-A1 allele.However,plants that were either homozygous or heterozygous for the novel Vrn-A1o allele headed earlier than those with the recessive vrn-A1 allele.To identify the novel allele with the small-sized product and facilitate screening,a DNA marker for the novel dominant allele Vrn-A1o was designed.Analysis of the novel-allele distribution showed that two cultivars carrying the vrn-A1n allele were dispersed in the northwestern spring wheat zone,and 12 cultivars carrying the dominant Vrn-A1o allele were widely distributed in the northwestern spring wheat zone,Xinjiang winter and spring wheat zone,Yellow and Huai River valley winter wheat zone,and QinghaiTibetan Plateau spring and winter wheat zone.Our study identifies useful germplasm and a DNA marker for wheat breeding.

Relationship between autoimmune hepatitis and HLA-DR4 and DRβ allelic sequences in the third hypervariable region in Chinese

AIM To analyze the association of HLA-DRBl with autoimmune hepatitis (AIH) in patients from China.``METHODS In .32 patients and 45 healthy controls,polymerase chain reaction amplification with sequencespecific primers (PCR-SSP) was performed to examine the association of certain alleles or polymorphic sequences of HLA-DRB1 with AIH.``RESULTS HLA-DRB1 typing by PCFLSSP showed that DR4had a significantly increased frequency among patients with AIH versus healthy control (46.9% versus 20.8%;relative risk 3.35, P=0.014). In subtypes of DR4, there was a trend of increase in the gene frequency of DRB10405 in patients with AIH versus healthy controls (21.9%vs 6.3%, P=0.04, but Pc 0.08). In addition, asignificant increase was found in the alleles frequency encoding QRRAA from the third hyperpolymorphic region of DR4 in the patients with AIH (86.7% of DR4 positive patients vs 40.0% in DR4 positive controls, P 0.016, Pc =0.028. RR 9.75).``CONCLUSION AIH in Chinese is associated with HLADR4. There is a relationship between QRRAA sequence within the third hyperpolymorphic region of the DRB allele and AIH in Chinese.

Association of HLA-B Alleles With Human Immunodeficiency Virus Type 1 Infection in the Yi Ethnic Group in Sichuan Province

Objective To determine the distribution of HLA-B alleles in the Chinese Yi ethnic group and its association with HIV infection. Methods One hundred and six unrelated healthy HIV negative and 73 HIV positive Chinese Yi ethnic individuals were typed by PCR-SSP. Results The frequency of alleles B*07, B*35, and B*46 were increased in HTV-1 -positive subjects, whereas the alleles B*55, B*44 and B*78 were absent in the HIV-infected persons studied. The B*46 allele was present in a significantly higher gene frequency among HIV-1-positive individuals (P=0.02, OR=3.32, 95% CI=1.13-9.78) compared with control subjects. Conclusion HLA-B*46 may be associated with its susceptibility to HIV-1 infections.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress,and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding.To understand the genetic basis of waterlogging tolerance(WT)in chrysanthemums,we performed a genome-wide association study(GWAS)using 92,811 single nucleotide polymorphisms(SNPs)in a panel of 88 chrysanthemum accessions,including 64 spray cut and 24 disbud chrysanthemums.The results showed that the average MFVW(membership function value of waterlogging)of the disbud type(0.65)was significantly higher than that of the spray type(0.55)at P<0.05,and the MFVW of the Asian accessions(0.65)was significantly higher than that of the European accessions(0.48)at P<0.01.The GWAS performed using the general linear model(GLM)and mixed linear model(MLM)identified 137 and 14 SNP loci related to WT,respectively,and 11 associations were commonly predicted.By calculating the phenotypic effect values for 11 common SNP loci,six highly favorable SNP alleles that explained 12.85—21.85%of the phenotypic variations were identified.Furthermore,the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified(r2=0.45;P<0.01).A major SNP locus(Marker6619-75)was converted into a derived cleaved amplified polymorphic sequence(dCAPS)marker that cosegregated with WT with an average efficiency of 78.9%.Finally,four putative candidate genes in the WT were identified via quantitative real-time PCR(qRT-PCR).The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection(MAS)in chrysanthemum WT breeding programs.

Detection of Allelic Variation in Chinese Wheat (Triticum aestivum L.) Germplasm with Drought ToleranceUsing SSR Markers

Allelic variation in two domestic wheat landraces, Pingyaobaimai and Mazhamai, two cornerstone breeding materials and their derived cultivars with drought tolerance was detected by SSR (simple sequence repeat) markers. The clustering of 25 accessions showed that the similarity between Pingyaobaimai and Yandal817, the latter was developed from the former, was 0.71, the highest one of all accessions, but the similarities were very low between these two accessions and other accessions including their derived cultivars. A similar situation was revealed between Mazhamai and its derived cultivars. Pingyaobaimai and its three derived cultivars shared three alleles at loci Xgwm526, Xgwm538 and Xgwm126 on chromosome arms 2BL, 4BL and 5AL, respectively. There were six shared alleles in Mazhamai and its derived cultivars, in order of Xgwm157, Xgwm126, Xgwm212, Xgwm626, Xgwm471 and Xgwm44 on chromosome arms 2DL, 5AL, 5DL, 6BL, 7AS and 7DC, respectively. Only one shared allele was detected between the pedigrees of Pingyaobaimai and Mazhamai. The difference of shared alleles in two cornerstone breeding materials and their derived cultivars revealed the diversity in Chinese wheat germplasm with drought tolerance and the complication in genetic basis of drought tolerance in wheat.

Identification of Multiple Alleles at the Wx Locus and Development of Single Segment Substitution Lines for the Alleles in Rice

The microsatellite markers 484/485 and 484/W2R were used to identify the multiple alleles at the Wx locus in rice germplasm. Fifteen alleles were identified in 278 accessions by using microsatellite class and G-T polymorphism. Among these alleles, （CT）12-G, （CT）15-G, （CT）16-G, （CT）17-G, （CT）18-G and （CT）21-G have not been reported. Seventy-two single-segment substitution lines （SSSLs） carrying different alleles at the Wx locus were developed by using Huajingxian 74 with the （CT）11-G allele as a recipient and 20 accessions containing 12 different alleles at the Wx locus as donors. The estimated length of the substituted segments ranged from 2.2 to 77.3 cM with an average of 17.4 cM.

Variation in allelic frequencies at loci associated with kernel weight and their effects on kernel weight-related traits in winter wheat

Knowledge of allelic frequencies at loci associated with kernel weight and effects on kernel weight-related traits is crucial for yield improvement in wheat. Kernel weight-related traits were evaluated in 200 Chinese winter wheat cultivars(lines) grown at the Xinxiang Experimental Station, Chinese Academy of Agricultural Sciences, Xinxiang in Henan Province, for three consecutive years from 2014 to 2016. Alleles associated with kernel weight at nine loci, TaCKX6-D1, TaCwi-A1, TaCWI-4A, TaGS1a, TaGS5-A1, TaGS3-3A, TaGW2-6A, TaSus2-2B, and TaTGW6-A1, were determined for all cultivars(lines). ANOVA showed that genotypes, years and their interactions had significant effects on thousand-kernel weight(TKW), kernel length(KL) and kernel width(KW). The overall mean frequencies of alleles conferring high and low TKW at the nine loci were 65.9% and 33.4%, with the ranges of 37.0%–85.0% and 13.5%–63.0% for single loci. The frequencies of high-TKW alleles were over 50.0% at eight of the loci. Genotypes at each locus with the high-TKW allele had higher TKW than those with the low-TKW allele. The high-TKW allele Hap-H at the TaSus2-2B locus can be preferably used to increase grain yield due to its high TKW(49.32 g). A total of 18 main allelic combinations(ACs) at nine loci were detected. Three ACs(AC1–AC3) had significantly higher TKW than AC6 with high-TKW alleles at all nine loci even though they contained some low-TKW alleles. This indicated that other loci controlling kernel weight were present in the high-TKW cultivars. This work provides important information for parental selection and marker-assisted selection for breeding.

Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids

Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.

Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers

A collection of 167 Thai and exotic rice accessions was subjected for evaluation of genetic diversity and assessment of relationship by simple sequence repeat (SSR) markers. Among a total of 49 SSR markers, 13 markers distributing over 12 rice chromosomes showed clear polymorphic band patterns, and they were selected for genetic assessment. A total of 110 alleles were detected with an average of 8.46 alleles per locus. The averages of gene diversity, heterozygosity and polymorphic information content were 0.59, 0.02 and 0.56, respectively. The unweighted-pair group method with arithmetic averages (UPGMA) clustering analysis was performed for genetic distance, and phylogenetic tree was constructed. The result showed that this rice collection was divided into two major groups, classified as japonica and indica subspecies. Within the japonica group, temperate japonica and tropical japonica subgroups can be clearly separated. Three-dimensional principal component analysis projection and model-based population structure analysis showed consistent clustering results with two major groups of UPGMA analysis, supporting the classification of japonica and indica subspecies. The indica allelic frequency was also investigated to provide an indicative guide for breeders to overcome the practical problems on sterility of inter-subspecies hybrid offspring. This rice collection and information obtained in this study will be useful for rice breeding programs.

Allelic Variation in Loci for Adaptive Response and Its Effect on Agronomical Traits in Chinese Wheat(Triticum aestivum L.)

Heading date was an important trait that decided the adaptation of wheat to environments. It was modiifed by genes involved in vernalization response, photoperiod response and development rate. In this study, four loci Xgwm261, Xgwm219, Xbarc23 and Ppd-D1 which were previously reported related to heading time were analyzed based on three groups of wheat including landraces （L）, varieties bred before 1983 （B82） and after 1983 （A83） collected from Chinese wheat growing areas. Generally, heading date of landrace was longer than that of varieties. Signiifcant differences in the heading time existed within the groups, which implied that diversiifcation selection was much helpful for adaptation in each wheat zone. Photoperiod insensitive allele Ppd-D1a was the ifrst choice for both landrace and modern varieties, which promoted the heading date about four days earlier than that of sensitive allele Ppd-D1b. The three SSR loci had different characters in the three groups. Predominant allele combination for each zone was predicted for wheat group L and A83, which made great contribution to advantageous traits. Xgwm219 was found to be signiifcantly associated with heading date in Yellow and Huai River Winter Wheat Zone （Zone II） and spike length in Middle and lower Yangtze Valley Winter Wheat Zone （Zone III）, which implied functional diversiifcation for adaption. Variation for earliness genes provided here will be helpful for whet breeding in future climatic change.

HLA class Ⅱ alleles and risk for peripheral neuropathy in type 2 diabetes patients

The potential impact of human leukocyte antigen （HLA） genotype variations on development of diabetic peripheral neuropathy （DPN） is not well determined. This study aimed to identify the association of HLA class II alleles with DPN in type 2 diabetes （T2D） patients. Totally 106 T2D patients, 49 with DPN and 57 without DPN, and 100 ethnic-matched healthy controls were analyzed. Both groups of the patients were matched based on sex, age, body mass index （BMI） and duration of T2D. Polyneuropathy was diagnosed using electrodiagnostic methods. HLA-DRB1 and DQB1 genotyping was performed in all subjects by the polymerase chain reaction with sequence-specific primers （PCR-SSP） method. T2D patients with DPN showed higher frequencies of HLA-DRB1＊10 and DRB1＊12 alleles compared to control group （P = 0.04）. HLA-DQB1＊02 allele and HLA-DRB1＊07-DQB1＊02 haplotype were associated with a decreased risk for developing DPN in T2D patients （P = 0.02 and P = 0.05 respectively）. Also, patients with severe neuropathy showed higher frequencies of DRB1＊07 （P = 0.003） and DQB1＊02 （P = 0.02） alleles than those with mild-to-moderate form of neuropathy. The distribution of DRB 1 and DQB 1 alleles and haplotypes were not statistically different between all patients and healthy controls. Our findings implicate a possible protective role of HLA-DQB1＊02 allele and HLA-DRB1＊07-DQB1＊02 haplotype against development of peripheral neuropathy in T2D patients. Therefore, variations in HLA genotypes might be used as genetic markers for prediction and potentially management of neuropathy in T2D patients.

The distribution of HLA-A,-B,and-DRB1 alleles and haplotypes in inhabitants of Guizhou Province of China

The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence spe- cific oligonucleotide probe （PCR-rSSOP） method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A＊1 1（30.72%） and A＊02（30.65%）, B＊40（16.27%） and B＊46（16.27%）, and DRBl＊09（15.91%） and DRBl＊15（13.51%）, respectively. The most common haplotype was A＊02-B＊46- DRBl＊09（5.59%） in A-B-DRB1, A＊02-B＊46（I 1.73%） in A-B, B＊46-DRBl＊09（7.49%） in B-DRB1, and A＊02- DRBl＊09（8.08%） in A-DRB1. Some baplotypes with strong linkage disequilibrium （LD） were found not only in the common haplotypes, such as A＊33-B＊58, B＊30-DRB1＊07, and B＊33-DRB1＊03, but also in the rare haplotypes, such as A＊01-B＊37, B＊37-DRB1＊10, and A＊01-DRB1＊10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.

Effects of marker density and minor allele frequency on genomic prediction for growth traits in Chinese Simmental beef cattle

Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding. However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values （GEBVs）. To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms （SNPs） based on varying markers densities and minor allele frequency （MAF） for average daily gain （ADG）, live weight （LW） and carcass weight （CW） in 1 059 Chinese Simmental beef cattle. Two strategies were proposed for SNP selection to construct different marker densities： 1） select evenly-spaced SNPs （Strategy 1 ）, and 2） select SNPs with large effects estimated from BayesB （Strategy 2）. Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation. Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13＋0.002, 0.21＋0.003 and 0.25＋0.003, respectively. In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1. Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K （3% of 770K） SNPs with large effects was equal to the predictive ability of using all SNPs. For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01-0.1. Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.

The allelic distribution and variation analysis of the NAM-B1 gene in Chinese wheat cultivars

The NAM-B1 gene is a member of the NAC（NAM,ATAF,and CUC）transcription factor family and plays an important role in regulating wheat grain protein content（GPC）.The ancestral NAM-B1 allele has been discovered in many tetraploid wild emmer（Triticum turgidum ssp.dicoccoides）accessions and few domesticated emmer accessions（T.turgidum ssp.dicoccum）,however,it is rarely found in hexaploid bread wheat（Triticum aestivum L.）.There are no systematic reports on the distribution of NAM-B1 alleles in Chinese wheat cultivars.In this study,the NAM-B1 alleles in 218 Chinese cultivars were investigated.The cultivars were collected from five major wheat regions（12 provinces）,covering most of the winter wheat growing regions in China.The results showed that the NAM-B1 gene is present in 53（24.3%）cultivars and absent in the remaining 165（75.7%）cultivars.Further analysis revealed that in contrast to the wild-type allele,the NAM-B1 gene in Chinese wheat cultivars contained a 1-bp insertion in the coding region.This caused a frame-shift mutation and introduced a stop codon in the middle of the gene,rendering it non-functional.Polymorphisms were detected in DNA sequences of 21cultivars among these 53 cultivars.However,cD NA sequence analysis suggested that these variations in the exon region were not able to restore NAM-B1 gene（1-bp insertion）function.Thus,exploring the distribution of NAM-B1 gene variations（1-bp insertion and deletion）can provide some information for improving the quality of winter wheat in China and other countries.

Studies of Multi-Allelic Polymorphism of Dominant Dwarfing Genes in Wheat

Dwarfing breeding of wheat in the world is confined to the exploitation of recessive dwarfing sources. None of the dominant dwarfing sources discovered in common wheat (Triticum aestivum L.) has found wide exploitation in wheat breeding due to the extreme dwarfness of their plants (2055 cm). We found in our work that some stable mutant lines with their plant height enhanced to different extents could be obtained in large populations derived from the stock seeds of the dominant dwarfing sources Aibian1 carrying Rht10 on 4DS and being 2055 cm tall and Aisu2 carrying Rht3 on 4BS and being 55 cm tall, or from their descendants of induced mutation treatments, or from the segregating descendants of their crosses with mid- or tall-statured genotypes. Subsequently, we studied these mutation-derived lines differing in plant height with near isogenic lines and observed that the character of their enhanced plant height bred true, each carrying a semi-dominant dwarfing gene for a definite height and that as the plant height of the mutation-derived lines increased, the yield-contributing characters of their near isogenic lines were significantly improved. When test crosses with marker genes and physiological and biochemical genetic marker tests were performed to re-localize the semi-dominant dwarfing genes carried by the mutation-derived lines, it was confirmed that they shared common loci with Rht10 and Rht3 and that they were all mutation-derived multiple alleles. It is thus speculated that dominant dwarfing genes are of 'multi-allelic polymorphism'. In other words, dominant dwarfing genes, which are ultra-dwarfing, are liable to develop by mutation into a group of multiple alleles with plant height enhanced to different extents and some may have a height close to the ideal plant height for wheat breeding. Therefore, these results offer a fundamentally new approach for the exploitation of dominant dwarfing sources in wheat breeding.

Self-compatibility in peach[Prunus persica(L.)Batsch]:patterns of diversity surrounding the S-locus and analysis of SFB alleles

Self-incompatibility(SI)to self-compatibility(SC)transition is one of the most frequent and prevalent evolutionary shifts in flowering plants.Prunus L.(Rosaceae)is a genus of over 200 species most of which exhibit a Gametophytic SI system.Peach[Prunus persica(L.)Batsch;2n=16]is one of the few exceptions in the genus known to be a fully selfcompatible species.However,the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and,in order to fill that gap,in this study 24 peach accessions were analyzed.Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes.The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant(P>0.05),except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus.Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additionalα-helices at the C-termini.Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2,while the SFB1 seemed to evolve neutrally.Thus,our results show that the SFB2 allele diversified after P.persica and P.dulcis(almond)divergence,a period which is characterized by an important bottleneck,while SFB1 diversified at a transition time between the bottleneck and population expansion.

Determination of the Number of SSR Alleles Necessary for the Analysis of Genetic Relationships Between Maize Inbred Lines

The amount of molecular marker information has considerable impact on the results of studies of crop germplasm genetic relationships in crop. The number of alleles required to reveal genetic relationship in maize inbred lines is a theoretical issue that needs to be addressed. In this study, 112 pairs of SSR （simple sequence repeat） primers and 97 maize inbred lines were selected to study the relationship between the number of inbred lines and the number of SSR primers and alleles required for a stable cluster. The results showed that the number of SSR primers is not tightly associated with the stability of the cluster analysis results, while an increase in the number of alleles can significantly improve the stability of cluster analysis results. The number of inbred lines （X） is significantly associated with the number of alleles required for stable cluster analysis （Y）, and the regression equation is Y- 600.8xe（-15.9/x）. This equation can be used to calculate the number of SSR alleles required for a genetic relationship study of maize inbred lines. These results provide a reference for determining of SSR alleles number in genetic relationship analysis of maize inbred line and other crop germplasm.

Two novel gene-specific markers at the Pik locus facilitate the application of rice blast resistant alleles in breeding

Blast,a disease caused by Magnaporthe oryzae,is a major constraint for rice production worldwide.Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to control the disease.The blast resistance Pik locus,located on chromosome 11,contains at least six important resistance genes,but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs due to their limited scope of application.In this study,two PCR-based markers,Pikp-Del and Pi1-In,were developed to target the specific In Del(insertion/deletion)of the Pik-p and Pi-1 genes,respectively.The two markers precisely distinguished Pik-p,Pi-1,and the K-type alleles at the Pik locus,which is a necessary element for functional genes from rice varieties.Results also revealed that only several old varieties contain the two genes,of which nearly half carry the K-type alleles.Therefore,these identified varieties can serve as new gene sources for developing blast resistant rice.The two newly developed markers will be highly useful for the use of Pik-p,Pi-1 and other resistance genes at the Pik locus in markerassisted selection(MAS)breeding programs.

Differential expressions among five Waxy alleles and their effects on the eating and cooking qualities in specialty rice cultivars

Eating and cooking qualities（ECQs） of rice are important attributes due to its major influence on consumer acceptability. To better understand the molecular mechanism of the variation in ECQs, we investigated and compared the expressions among different alleles of the Waxy（Wx） gene and its effect on ECQs in specialty rice cultivars. The results showed that the accumulation of amylose was positively and significantly correlated to the level of mature Wx m RNA and granule-bound starch synthase I（GBSS I） in developing rice grain at 12 days after flowering. The amount of GBSS I and its activity together are the main factors controlling amylose synthesis. Differences in ECQs among five Wx allele types were investigated in samples from 15 rice varieties. The apparent amylose content（AAC） and gel consistency（GC） were similar in each type of Wx allele. The AAC followed the order, Wx^a type〉Wx^in type〉Wx^b type〉Wx^mq type〉wx. Contrary to this, the GC showed an opposite trend compared to AAC. There was a wide variation in rapid visco analyzer（RVA） profile among five Wx allele types, while varieties sharing a specified Wx allele had basically the similar RVA profile, although there was a slight difference in some RVA parameters, peak, hot paste and cool paste viscosities.

Ethnic differences in gastric cancer genetic susceptibility:Allele flips of interleukin gene

Polymorphisms in promoter regions of inflammatory cytokines have been widely studied,and potentially functional polymorphisms have been discovered.Conflicting results from meta-analyses of interleukin(IL)-1B and IL-10 polymorphisms show differences in gastric cancer susceptibilities between Caucasian and Asian populations.In particular,we note the suggestion of an allele flip in IL-1B and IL-10 gene polymorphisms.In Asian populations,the IL-1B-1464G/-511C/-31T haplotype indicates risk for gastric cancer,while the opposite haplotype,IL-1B-1464C/-511T/-31C is the risk-related allele in Caucasians.Furthermore,while IL-10-1082G/-819C/-592C is associated with gastric cancer in Asians,IL-10-1082A/-819T/-592T is linked to gastric cancer risk in Caucasians.These seemingly contradictory results may be attributed to distinct carcinogenic mechanisms underlying the different gastric cancer subtypes.The allele flip observed in IL-10 and gastric cancer appears to reflect allelic heterogeneity,similar to that observed in IL-1B.In this review,we focus on the allele flip phenomenon observed between different ethnic groups in an effort to resolve certain controversial results from recent studies on interleukin polymorphism.In addition,we re-emphasize the importance of stratifying gastric cancer subtypes based on anatomical site and Lauren classification to prevent false associations arising through dilution of true ones.