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.

Genetic Diversity of Gli-1, Gli-2 and Glu-1 Alleles in Sichuan Wheat Landraces

Genetic diversity at Gli_1, Gli_2 and Glu_1 loci was investigated in 89 Sichuan wheat (Triticum aestivum L.) landraces by using acid polyacrylamide gel electrophoresis (APAGE) and SDS_PAGE. In these landraces, a total of 32 gliadin and 3 high_molecular_weight (HMW) glutenin patterns were observed. In total, 14, 15 and 5 alleles were identified at Gli_1, Gli_2 and Glu_1, respectively. At each locus, the alleles in higher frequency were Gli_A1a (89%), Gli_B1h (46%), Gli_D1a (65%), Gli_A2a (64%), Gli_B2j (45%), Gli_D2a (48%), Glu_A1c (99%), Glu_B1b (99%) and Glu_D1a (100%). The Nei's genetic variation index (H) of Sichuan wheat landraces was 0.370?6, varying from 0 to 0.708?7. The highest genetic diversity was found at Gli_B2 locus, while the lowest was found at Glu_D1. The genetic diversity at Gli loci was higher than that of Glu_1 loci among these landraces, but it was much lower than that of modern wheat cultivars. These results indicated a narrow genetic base of Sichuan wheat landraces. In this study, “Chengdu_guangtou” had the identical gliadin and HMW_glutenin patterns with “Chinese Spring”, further supporting the proposal that “Chinese Spring” is a strain of “Chengdu_guangtou”.

Genetic Diversity of Gli-1,Gli-2 and Glu-1 Alleles Among Chinese Endemic Wheats

Genetic diversity at Gli_1, Gli_2 and Glu_1 loci was investigated in 32 accessions of Chinese endemic wheat by using acid polyacrylamide gel electrophoresis (APAGE) and sodium dodecyl sulfate (SDS)_PAGE. There were 8 gliadin and 3 high_molecular_weight (HMW)_glutenin patterns in 14 Yunnan hulled wheat ( Triticum aestivum ssp. yunnanese King) accessions, 9 gliadin and 4 HMW_glutenin patterns in 9 Tibetan weedrace ( T. aestivum ssp. tibetanum Shao ) accessions, and 9 gliadin and 5 HMW_glutenin patterns in 9 Xinjiang rice wheat ( T. petropavlovskyi Udacz. et Migusch.) accessions. One accession (i.e. Daomai 2) carried new subunits 2.1+10.1 encoded by Glu_D1. Among the three Chinese endemic wheat groups, a total of 10, 14 and 11 alleles at Gli_1 locus; 11, 14 and 12 alleles at Gli_2 locus; and 5, 6 and 8 alleles at Glu_1 locus were identified, respectively. Among Yunnan hulled wheat, Tibetan weedrace and Xinjiang rice wheat, the Nei's genetic variation indexes were 0.3798, 0.5625 and 0.5693, respectively. These results suggested that Tibetan weedrace and Xinjiang rice wheat had higher genetic diversity than Yunnan hulled wheat.

Characterization of Genetic Polymorphism of Novel MHC B-LBⅡ Alleles in Chinese Indigenous Chickens

Genetic polymorphism of the major histocompatibility complex （MHC） B-LBⅡ gene was studied by amplification of exon 2 using PCR, followed by cloning and DNA sequencing in eight indigenous Chinese chicken populations. To reveal the genetic variation of the B-LB Ⅱ gene, 37 types of patterns detected by PCR-SSCP were investigated first, which would be used to screen novel B-LB Ⅱsequences within the breeds. The types of PCR-SSCP patterns and final sequencing allowed for the identification of 31 novel MHC B-LBⅡ alleles from 30 unrelated individuals of Chinese chickens that were sampled. These are the first designators for the alleles of chicken MHC B-LBⅡ gene based on the rule of assignment for novel mammalian alleles. Sequence alignment of the 31 B-LB Ⅱ alleles revealed a total of 68 variable sites in the fragment of exon 2, of which 51 parsimony informative and 17 singleton variable sites were observed. Among the polymorphic sites, the nucleotide substitutions in the first and second positions of the codons accounted for 36.76% and 35.29%, respectively. The sequence similarities between the alleles were estimated to be 90.6%-99.5%. The relative frequencies of synonymous and nonsynonymous nucleotide substitutions within the region were 2.92%±0.94% and 14.64%±2.67%, respectively. These results indicated that the genetic variation within exon 2 appeared to have largely arisen by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of the β1 domain coded by exon 2 revealed 6 synonymous mutations and 27 nonsynonymous substitutions at the 33 disparate sites. In particular, the nonsynonymous substitutions at the putative peptide-binding sites are considered to be associated with immunological specificity of MHC B-LB Ⅱ molecule in Chinese native chickens. These results can provide a molecular biological basis for the study of disease resistance in chicken breeding.

A Recursive Algorithm for Offspring's Genotype Frequency of Selfing Population on Multiple Alleles with Limited Loci

This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous gene of limited loci increases by generations.Relative increment reduces by generations and the genotype frequency tends to a definite value finally.The genotype frequency of limited loci with hybrid gene tends to 0 finally.But it is possibility that the genotype frequency increases in previous generations then reduces later.It is found that the number of the hybrid gene are more,the speeds tending to 0 are quicker.

Influence of HLA-DRB1 alleles and HBV genotypes on interferon-α therapy for chronic hepatitis B

AIM. To investigate the influence of HLA-DRB1 alleles and HBV genotypes on inberferon-α therapy for chronic hepatitis B. METHODS： HLA-DRBI＊03, ＊07, ＊09,＊12, ＊15 alleles were determined using polymerase chain reaction/sequence specific primer （PCR/SSP） technique in 126 patients with chronic hepatitis B and 76 normal control subjects in Shandong Province, and HBV genotypes were determined by nested-PCR analysis using type-specific primers in 126 patients. RESULTS： The positivity of HLA-DRB1＊07 allele in chronic hepatitis B group was significantly higher than that in normal control group （X^2 = 6.33, P〈0.025, RR = 2.37）. Among the 126 patients, genotype B was found in 38 （30.2%）, genotype C in 69 （54.8%）, and mixed genotype （B＋C） in 19 （15.0%）, genotypes D-F were not found. Among the 46 DRB1＊07（＋） patients, 7 were responders and 39 were non-responders among them （X^2 = 6.71, P〈0.05）. The positivity of HLADRB1＊07 and prevalence of HBV genotype C were significantly higher in non-responders than in responders. CONCLUSION： High positivities of HLA-DRB1 ＊07 allele and HBV genotype C are closely associated with the lower response to interferon-α therapy for chronic hepatitis B.

Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas:segregation and null allele identification for linkage analysis

Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

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.

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.

Specific HLA-DQB1 alleles associated with risk for development of hepatocellular carcinoma:A meta-analysis

AIM:To evaluate the association of human leukocyte antigen(HLA)-DQB1 alleles with hepatocellular carcinoma(HCC) through meta-analysis of published data.METHODS:Case-control studies on HLA-DQB1 allele association with HCC published up to January 2010 were included in the analyses.The odds ratios(ORs) of HLADQB1 allele distributions in HCC patients were analyzed and compared with healthy controls.The meta-analysis software REVMAN 5.0 was applied for investigating heterogeneity among individual studies and for summarizing all the studies.A meta-analysis was performed using fixed-effect or random-effect methods,depending on the absence or presence of significant heterogeneity.Seven case-control studies containing 398 cases and 594 controls were included in the final analysis.RESULTS:Among the five family alleles,two(DQB1*02 and DQB1*03) were found to be significantly associated with the risk of HCC.The combined OR for the association of DQB1*02 and DQB1*03 allele with the risk for HCC was 1.78(95% CI:1.05-3.03,P = 0.03) and 0.65(95% CI:0.48-0.89,P = 0.007),respectively.Among the 13 specific alleles,two(DQB1*0502 and DQB1*0602) were significantly associated with risk of HCC.The combined OR for the association of DQB1*0502 and DQB1*0602 allele with the risk for HCC was 1.82(95% CI:1.14-2.92,P = 0.01) and 0.58(95% CI:0.36-0.95,P = 0.03),respectively.No significant association was established for other HLA-DQB1 family alleles and specific alleles.CONCLUSION:Our results support the hypothesis that specific HLA-DQB1 allele families and alleles might influence the susceptibility or resistance to HCC,although it needs further investigations.

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.

Characterization of a Novel Weak Allele of RGA1/D1 and Its Potential Application in Rice Breeding

Semi-dwarfing improves the lodging resistance and yield of rice,and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height,resulting in reduced genetic diversity and negative agronomic traits.Thus,exploring alternative sources of dwarfism is imperative for rice breeding.Here,we identified a novel RGA1 allele,d1-w,from a local indica variety Xiaolixiang(XLX)using a map-based cloning approach.Compared with other rice varieties,RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level.The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding.Compared with transgenic XLX plants(XLX^(D1)),XLX exhibited reduced plant height,increased stem strength,lower reactive oxygen species accumulation,delayed senescence,stronger photosynthesis,higher grain yield and quality(including external,milling and nutritional qualities),and enhanced resistance to drought and Rhizoctonia solani.Therefore,we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

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 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.

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.

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.

Molecular characteristics of S-RNase alleles as the determ inant of self-i ncompatibility in the style of Fragaria viridi

Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the genetic mechanism underlying SI control in strawberry remains unclear.Two candidate S-RNases(S a-and S^-RNase)identi fi ed in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were con fi rmed to be SI determinants at the S locus following genotype identi fi cation and intraspeci fi c hybridization using sel fi ng progenies.Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria;however,none of the compatible species contained S-RNase.Although the results of interspeci fi c hybridization experiments showed that F.viridis(SI)styles could accept pollen from F.mandshurica(self-compatible),the reciprocal cross was incompatible.S a and S b-RNase contain large introns,and their noncoding sequences(promotors and introns)can be transcribed into long noncoding RNAs(lncRNAs).Overall,the genus Fragaria exhibits S-RNase-based gametophytic SI,and S-RNase loss occurs at the S locus of compatible germplasms.In addition,a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species.Furthermore,the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.

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.

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.

Elite sd1 alleles in japonica rice and their breeding applications in northeast China

The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified,and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources.Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice.Two new sd1 alleles were identified in indica rice.In 295 japonica accessions from northeast Asia,except for the weak functional allele SD1-EQ,sd1-r was the major allele,reducing plant height in comparison with SD1-EQ.Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search,genealogical analysis,and d Caps markers.Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan,and sd1-j is commonly used in east China and Kyushu in Japan.Dongnong-and Xiushui-series cultivars carrying sd1-r and sd1-j,respectively,are essential branches of the backbone parents of Chinese japonica rice,Akihikari and Ce21,with the largest number of descendants and derived generations.In semi-dwarf japonica rice breeding,sd1-d was introgressed into Daohuaxiang 2(DHX2).Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280,respectively,after withstanding typhoon-induced strong winds and heavy rains in 2020,and are anticipated to become useful intermediate materials for future genetic research and breeding.This work will facilitate the introduction,parental selection,and marker-assisted breeding,and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.