Analysis of the Genetic Relationships in Chinese Ziziphus with SRAP Markers

The phylogenic and genetic relationships in germplasm resources of Chinese Ziziphus were studied at molecular levels, for providing new molecular evidences of classification, protection, and utilization of germplasm resources of Ziziphus. The sequence-related amplified polymorphism （SRAP） was assessed to analyse the genetic relationships among 14 species of Ziziphus, 11 cultivars of Z. jujuba Mill., and one outgroup. A total of 580 DNA bands were amplified by 19 selective primers, 570 of which （98.28%） were polymorphic. The average number of polymorphic DNA bands amplified by each primer was 30. The genetic similarities of 26 sample materials were between 0.22 and 0.99. UPGMA method cluster analysis showed that 26 sample materials were classified into six cluster groups with the genetic similarity of 0.28. The results showed that SRAP technique is efficient in studying genetic relationships among Ziziphus, Z. jujuba Mill. and Z. acidojujuba C. Y. Cheng et M. J. Liu which should be treated as one species, and further infraspecific classification of Z. jujuba Mill. should be classified into two subspecies; the scientific names of new taxa, Chinese jujube, and wild jujube were Ziziphus jujuba Mill. subsp, jujuba and Ziziphus jujuba Mill. subsp, spinosa （Bunge） J. Y. Peng, X. Y. Li et L. Li, respectively. Z. xiangchengensis Y. L.Chen et P. K. Chou, Z. montana W.W. Smith and Z. mairei Dode might be originated from same ancestry. Z xiangchengensis Y. L. Chen et P. K. Chou and Z. montana W.W. Smith should be treated as one species. The infrasubspecific taxon of Z. jujuba Mill. was not suitable to set up varieties.

Analysis of genetic relationships between grain milling quality traits and plant agronomic traits of rice

Since seed and maternal plant are in different generations,the grain milling traits and plant agronomic traits of rice are based on differentgenetic models.Using the genetic modelswhich could estimate covariance componentsbetween two traits with unequal design matri-ces,we analyzed the gentic relationships be-

Analysis of the Germplasm Resources and Genetic Relationships Among Hybrid Cymbidium Cultivars and Native Species with RAPD Markers

The random amplified polymorphic DNA （RAPD） marker was assessed to detect the genetic relationships among 48 hybrid Cymbidium cultivars from Japan, Korea, China, and USA, and 2 species of native Cymbidium. Twenty primers were screened from 100 random decamer primers, and a total of 258 DNA bands were amplified, 253 of which （98.1%） were polymorphic. The average number of polymorphic DNA bands amplified by each primer was 12.6. All cultivars were distinguishable when a number of primers were considered. Genetic similarities among the cultivars and species were estimated based on the amount of band sharing ranging from 0.364-0.817 with an average of 0.581. According to the data, a dendrogram of genetic relationship, which was constructed using the UPGMA method, showed that all the tested cultivars and native species were classified into five cluster groups with the similarity coefficient of 0.592. It revealed that the genetic relationships among tested accessions were to some extent related with their origin, flower colour, branch type, and genealogy. It further indicated that the RAPD technique is a useful tool for studying the genetic relationships among hybrid Cymbidium cultivars.

Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill,native to China

China is a center of diversity for Malus Mill,with 27 native species including 21 wild species and six domesticated species.We applied a set of 19 simple sequence repeat markers to genotype 798 accessions of 17 species(12 wild species and five cultivated species)of Malus originating from 14 provinces in China.A total of 500 alleles were detected.Diversity statistics indicated a high level of genetic variation as quantified by the average values of the effective allele number(N_(e)).expected heterozygosity(H_(e)),and Shannon's Information Index(I)(10.309,0.886,and 2.545,respectively).Malus sieversii(MSR;H_(e)=0.814,I=2.041,N_(e)=6.054),M.baccata(MBB;H_(e)=0.848,/=2.350,N_(e)=8.652),M.toringoides(MTH;He=0.663,I=1.355,N_(e)=3.332),and M.hupehensis(MHR;H_(e)=0.539,I=0.912,N_(e)=0.579)showed a higher level of genetic diversity in this study than the previous studies.MSR and MBB contributed to the origin and evolution of some accessions of M.domestica subsp.chinensis(MDC).However,other accessions of MDC showed a closer genetic distance with MBB and cultivated species,especially M.robusta(MRB),M.asiatica(MAN),and M.prunifolia(MPB).Not all accessions of MDC were descended from MSR in Xinjiang Uygur Autonomous Region of China.This research provides novel insights into the genetic relationships of Malus native to China,which will be useful for genetic association studies,germplasm conservation,and breeding programs.

Genetic Relationships among Prunus mume var. pendula Using AFLP Markers

Genetic relationships among Prunus mume var. pendula were studied by using AFLP markers. 18 accessions representing 14 cultivars of Prunus mume var. pendula were selected from the germplasm collection at the Research Center of China Mei Flower. Seven Mse I-EcoR I AFLP primer combinations revealed 450 legible bands, and 269 of which were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity and Neis (72) distance coefficient. A UPGMA dendrogram demonstrated the genetic relationships of the cultivars. The information given by AFLP markers was basically consistent with the morphological classification and the evolutionary history of the morphotypes, and roughly supported the new revised classification system for Chinese Mei Cultivars. But there were still several exceptions: 1) the Guhong Chuizhi inserted between the Tiaoxue Chuizhi and the Danfen Chuizhi; 2) the Wufu Chuizhi kept off the Pink Pendant Form, and the Moshan Chuizhi was removed from Viridiflora Pendant Form; 3) the Danbi Chuizhi and the Shuangbi Chuizhi of Viridiflora Pendant Form got together well but fell within the Pink Pendant Form.

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.

Analysis on Genetic Diversity of 40 Flowering Cherry Cultivars and Construction of Molecular ID Based on SSR Markers

Studying on the genetic diversity and genetic relationship of flowering cherry cultivars is extremely important for germplasm conservation, cultivar identification and breeding. Flowering cherry is widely cultivated as an important woody ornamental plant in worldwide, especially Japan, China. However, owning to the morphological similarity, many cultivars are distinguished hardly in non-flowering season. Here, we evaluated the genetic diversity and genetic relationship of 40 flowering cherry cultivars, which are mainly cultivated in China. We selected 13 polymorphicprimers to amplify to allele fragments with fluorescent-labeled capillary electrophoresis technology. The population structure analysis results show that these cultivars could be divided into 4 subpopulations. At the population level, Na and Ne were 6.062, 4.326, respectively. Ho and He were 0.458 and 0.670, respectively. The Shannon’s information index (I) was 1.417. The Pop3, which originated from P. serrulata, had the highest Ho, He, and I among the 4 subpopulations. AMOVA showed that only 4% of genetic variation came from populations, the 39% variation came from individuals and 57% (p < 0.05) came from intra-individuals. 5 polymorphic SSR primers were selected to construct molecular ID code system of these cultivars. This analysis on the genetic diversity and relationship of the 40 flowering cherry cultivars will help to insight into the genetic background, relationship of these flowering cherry cultivars and promote to identify similar cultivars.

Analysis of Genetic Diversity and Relationships of Seven Chinese Indigenous Pig Breeds and Three Exotic Pig Breeds Using the DNA Differential Display Technique

The genetic diversity and relationships of seven Chinese indigenous pig breeds （Meishan, Erhualian, Hezuo, Bamei, Qingping, Tongcheng, and Huainan） and three exotic pig breeds （Large White, Landrace, and Duroc） were analyzed using the DNA differential display technique by means of eight primer combinations. A total of 123 reproducible bands were used to calculate mean Nei＇s gene diversity, and mean Shannon＇s information index for each pig population. Based on these the Nei＇s standard genetic identity and distance were estimated, which was used to construct a dendrogram tree for the 10 pig breeds. The experimental results obtained and the method used in this study for evaluating the genetic diversity and relationships of pigs were also discussed.

Genetic relationship and pedigree of Chinese watermelon varieties based on diversity of perfect SNPs

Watermelon(Citrullus lanatus)is one of the world’s most important fruit crops,and China produces the most watermelons in the world.Recently,a watermelon variome consisting of 414 key resequenced accessions was reported.However,the genetic relationships and pedigree of Chinese watermelon varieties in the seed market remain unclear.In this study,241 evenly distributed perfect single nucleotide polymorphisms(SNPs)derived from the watermelon variome were selected for variety identification.The diversity of 247 Chinese watermelon varieties was identified based on their SNP genotypes.The 247 watermelon varieties were clustered into five subpopulations:the East Asian ecotype,intermediate ecotype,small fruit with red flesh ecotype,small fruit with yellow flesh ecotype,and American ecotype.We further established the pedigree of four subpopulations,of which JingXinNo.1,ZaoChunHongYu,HuangXiaoYu and XiaoLan,and Sugarlee were the main doner of the East Asian ecotype,small fruit with red flesh ecotype,small fruit with yellow flesh ecotype,and American ecotype,respectively.Thirty-two core SNPs were selected and applied in watermelon variety identification.They were also validated by the Kompetitive allele-specific PCR(KASPar)platform.The present study furthered our understanding of the genetic relationships and pedigree of watermelon varieties in China,and will help to manage the plant variety protection in watermelon.

Assessment of the Genetic Relationship and Diversity of Mango and Its Relatives by cplSSR Marker

Chloroplast inter-simple sequence repeat markers in mango were developed and used to analyze the genetic relationship and diversity of mango and its relatives. Thirty-six mango cultivars （Mangifera indica L.） and its relative species collected from the fruit germplasm collection in the Guangxi Academy of Agricultural Sciences, China, were examined by ISSR-PCR with chloroplast DNA （cpDNA）. Eight better primers for chloroplast DNA that provided reproducible, polymorphic DNA amplification patterns were screened from 50 ISSR primers and used for UPGMA analysis. According to the band patterns with 8 primers for chloroplast DNA, all cultivars tested were distinguished from each other and these showed ample genetic diversity; the average percentage of polymorphism was 77.2%. The 36 samples could be clustered into four groups by UPGMA analysis at the coefficient 0.74. The results indicated that the cplSSR marker was a new powerful tool for the identification of mango cultivars or its relative species, and their genetic relationship analysis and diversity evaluation.

Study of Yield Combining Ability and Genetic Relationship Among Exotic Tropical,Subtropical Maize(Zea mays L.) Inbreds and Temperate Maize Inbreds in China

Information on the genetic relationship between tropical maize (Zea mays L), germplasm and temperate maize germplasm is of great value to maize breeding. The objective of this study was to determine the combining ability and genetic relationship of 25 inbreds extracted from five tropical maize populations and a land race, with four temperate maize inbreds (Huangzaosi, Mol7, B73 and Dan 340). The 25 tropical inbreds were crossed with the four temperate inbreds and evaluated. Lines from Suwanl and POP28 had high general combining ability (GCA) for grain yield. The lines from POP32 (ETO) had the highest special combining ability (SCA) with B73; the average SCA value of the 5 lines was 879 kg/ha. The lines from Suwanl had the second-highest SCA (584 kg/ha) with Huangzaosi. The lines from Suwanl had the greatest relative heterosis (20%) with B73, followed by the lines from POP32 (ETO) with B73 (19%). Five heterotic patterns have been identified from this study: Suwanl × Reid, ETO × Reid, POP28× Reid, POP28× Ludahong-gu, and Suwan1× Lancaster.

Genetic Diversity Analysis of Wild Tea Plants in Yunnan Province Using EST-SSR Markers

In this study, 27 pairs of EST-SSR primers were employed to analyze the genetic diversity and genetic relationship of 100 wild tea plant germplasm re- sources and 22 cultivars, according to the results, a total of 88 polymorphic bands were amplified with 27 pairs of primers; the variation of effective alleles accounted for 69.01% ; a total of 183 genotypes were detected, with a variation range of 4 -11 ; averagely 6.78 genotypes were amplified with each primer pair; Shannon index （I） of 27 primer pairs ranged from 0.32 to I. 35, with an average of 0.88 ; the observed heterozygosity （0.52） was basically consistent with the expected het- erozygosity （0.52） ; the average polymorphism heterozygosity was 0.48, which was very close to 0.50 ; the average Nei＇s index was 0.51, which was higher than 0. 50 ; the average polymorphism information content （PIC） was 0.52, which was higher than 0.50, indicating high genetic diversity among wild tea germplasm resources in Yuunan Province. According to the clustering results, based on geographical origins and genetic backgrounds, 122 materials were clustered into 14 categories. Dendrogram based on Nei＇s genetic distance revealed complex genetic relationships among wild tea germplasm resources in Yunnan Province. This study provided certain reference for subsequent preservation, development and research of wild tea germplasm resources in China.

Genetic architecture of embryo size and related traits in maize

The embryo in maize has a critical role in controlling kernel nutrition components and grain yield.We measured five embryo weight and size traits,six kernel weight and size traits,and five embryo-tokernel ratio traits in a nested association mapping(NAM)population of 611 recombinant inbred lines(RILs)derived from four inbred lines including the high-oil,giant-embryo line BY815 as the common parent.Using three statistical methods,we identified 5–22 quantitative trait loci(QTL)for each trait,explaining 4.7%–46.7%of the phenotypic variation.The genetic architecture of maize embryo size and its related traits appeared to be dominated by multiple small-effect loci with little epistasis,and the genetic control underlying embryo size appeared to be distinct from that underlying kernel size.A trait–QTL association network included 205 nodes and 439 edges and revealed 28 key loci associated with at least three traits.Cloned maize genes including Zm Urb2,Emp12 and Zm BAM1 d,maize orthologs of known rice genes that control seed size including BG1,XIAO and GS9,and 11 maize orthologs of Arabidopsis EMBRYO-DEFECTIVE(EMB)genes were identified as underlying these key loci.Further,the phenotypic and genetic relationships between embryo size and kernel size were evaluated,and genetic patterns for identified loci that control embryo size and its related traits were proposed.Our findings reveal distinct genetic architectures for embryo size,kernel size,and embryo-to-kernel ratio traits and establish a foundation for the improvement of embryo-size-mediated kernel nutrition and grain yield.

Analysis on Genetic Relationship of Oxya chinensis and Oxya japonica from Xuzhou and Pingshan, China

Genetic relationship among Oxya chinensis populations and Oxya japonica populations collected from Xuzhou City, Jiangsu Province and Pingshan County, Hebei Province, China were analyzed by random amplified polymorphic DNA （RAPD） markers. A total of 125 DNA bands ranging from 200 to 2 200 bp were amplified by 10 random primers in DNA samples from 43 grasshopper individuals. One hundred and twenty-three （99%） of these bands were polymorphic. Shannon＇s index showed that the genetic, diversity within O. chinensis （0.3432） was higher than that of O. japonica （0.2781）. Nei＇s genetic distance between O. chinensis population and O. japonica population from the same area was less than that between populations from two different areas. The dendrogram based on Nei＇s genetic distance of RAPD markers was constructed using the unweighted pair group method with the arithmetic average （UPGMA） and Neighbor-Joining （NJ） methods. Cluster analysis indicated that all the individuals were grouped into two main clusters. O. chinensis populations from Xuzhou and Pingshan formed one cluster, and O. japonica populations from the two regions belonged to another cluster. The results demonstrated that RAPD can detect within species, and among closely related species. polymorphisms to distinguish minor difference among individuals

High gene flows promote close genetic relationship among finewool sheep populations(Ovis aries) in China

The aim of our present study was to construct genetic structure and relationships among Chinese fine-wool sheep breeds. 46 individuals from 25 breeds or strains were genotyped based on the Illumina Ovine 50K SNP array. Meanwhile, genetic variations among 482 individuals from 9 populations were genotyped with 10 microsatellites. In this study, we found high genetic polymorphisms for the microsatellites, while 7 loci in the Chinese superfine Merino strain （Xinjiang types） （CMS） and 5 loci in Gansu alpine superfine-wool sheep strain （GSS） groups were found deviated from Hardy-Weinberg equilibrium （HWE）. Genetic drift FsT=0.019 （P〈0.001） and high gene flows were detected in all the 7 fine-wool sheep populations. Phylogenetic analysis showed fine-wool sheep populations were clustered in a group independent from the Chinese indigenous breeds such that the 7 fine-wool sheep clustered distinct from Liangshan semifine-wool sheep （LS） and Hu sheep （HY） reflected by different population differentiation analyses. Overall, our findings suggested that all fine-wool sheep populations have close genetic relationship, which is consistent with their breeding progress. These populations, therefore, can be regarded as open-breeding populations with high levels of gene flows. Furthermore, the two superfine-wool strains, viz., CMS and GSS, might be formed by strong artificial selection and with frequent introduction of Australian Merino. Our results can assist in breeding of superfine-wool sheep and provide guidance for the cultivation of new fine-wool sheep breeds with different breeding objectives.

Genetic relationship between parasitized and non-parasitized Haloxylon ammodendron in the Alxa Desert

Haloxylon ammodendron （C. A. Mey.） Bunge is a host for the holoparasitic plant Cistanche deserticola Y. C. Ma, the original source of medicinal material known as Herba Cistanchis. The inter-simple sequence repeat marker was used to assess the genetic variations and relationships among six accessions ofH. ammodendron with a total of 120 individuals collected from three localities in the Alxa Desert, Inner Mongolia, China. At each locality, individuals both parasitized （PP） by C. deserticola and non-parasitized （NP） were sampled. The results showed that Nei＇s gene diversity and Shannon＇s index of PP accessions were higher, but were not significantly different, from those of NP accessions. An unweighted pair-group method arithmetic average dendrogram showed two clusters, one that included all PP accessions, and the other the NP accessions. Genetic differentiation therefore existed between PP and NP accessions, which might be attributed to low gene flow between the NP and PP groups （Nm〈 1）. However, the relationship between genetic distance and geographic distance within each group, although not statistically significant in this study, might be associated with high gene flow in both the NP and PP groups.

Genetic Relationship of the 1780-1760 Ma Dykes and the Coeval Volcanics in the Lvliang Area, North China

The 1780-1760 Ma Taihang dyke swarm and the coeval Xiong’er volcanic province are the most widespread magmatic events occurring post the amalgamation of the two North China cratons.It has been debated whether

Analysis of Genetic Relationship among Celery Germplasms by RAPD

In this study, forty celery cultivars introduced from different regions of China were used as experimental materials to verify and analyze the practicability of RAPD technology in the identification of celery cuhivars. The results showed that RAPD technology could distinguish accurately the genetic relationship among various celery cultivars as a simple and ideal DNA molecular marker technology suitable for genetic relationship analysis. To be specific, 13 RAPD primers with clear amplified bands and significantly different number of amplified bands were screened, which provided basis for the identification of genetic relationship among different celery cultivars.

rbcL Gene Sequencing of Several Species Belonging to Morus and Their Genetic Relationship

[Objective] The paper was to sequence the rbcL gene of several species belonging to Morus, and to explore the genetic relationship of Morus plants. [Method] Through DNA extraction, PCR amplification, sequencing, splicing and correction, a total of 56 rbcL gene sequences were obtained. [Result] Alignment results showed that there were 1 279 permutation sites in rbcL sequence of Morus plants; variable sites accounted for 6.8% of the total sequence length, and the ratio of transition pairs to transversion pairs （R= si/sv） was 1.2. The rbcL sequence of Broussonetia papyrifera was selected as the outgroup, which was downloaded from GenBank. Genetic analysis results showed that M. alba, M. notabilis, M. rubra and Kuisang （the sample of this study） had distant relationship, and the other Morus plants had relatively close relationship. [Conclusion] The results lay a foundation for selection, identification and classification of Morus plants.

Analysis of Genetic Relationship among Boehmeria Varieties Using cpSSR Markers

By using cpSSR （chloroplast microsatellites） markers, the genetic relationship among Boehmeria varieties was analyzed. Five pairs of cpSSR primers with excellent amplification result, clear amplification band and good repeatability were screened from 22 pairs of cpSSR primers, and the polymorphism rate was 22.73%. By using these five pairs of cpSSR primers, 16 polymorphic loci were amplified from eight experimental materials, with an average of 3.2 loci. According to the results of duster analysis, these experimental materials were divided into three categories. The clustering results were consistent with the classification results based on chloroplast gene sequences.