Genetic diversity of different apricot geographical groups determined by SSR markers.

Forty apricot cultivars with different geographic origins belonging to the germplasm collections of St. Istvan University (Budapest, Hungary) and the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were studied by means of SSR markers. The aim of the study was to determine the genetic relationships among genotypes from different eco-geographical groups. Sixteen primer pairs flanking microsatellite sequences in the peach genome were assayed. Eleven of them were polymorphic in the set of cultivars studied and allowed every genotype to be unambiguously distinguished. Genetic diversity in the population studied was analyzed using several variability parameters. A total of 34 alleles were detected with a mean value of 3.1 alleles/locus. The expected heterozygosity mean was 0.46 and the observed heterozygosity was 32% on an average leading to a high value of the Wright's fixation index (0.32). Additionally, UPGMA cluster analysis based on Nei's genetic distance grouped genotypes according to their geographic origins and pedigrees. SSR markers have proved to be an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in apricot.     

Population structure and genetic diversity in bottle gourd [Lagenaria siceraria (Mol.) Standl.] germplasm from India assessed by ISSR markers

Genetic diversity analysis was undertaken in 42 geographically distant genotypes accessions of bottle gourd (Lagenaria siceraria) from India northeastern (14) and northern region (28) using inter-simple sequence repeat (ISSR) markers. A total of 209 amplified bands were obtained from 20 ISSR primers used in this study, of which 186 were polymorphic with 89.00 % band polymorphism. Various parameters namely, observed number of alleles, effective number of alleles, Nei’s gene diversity/heterozygosity, resolving power, Shannon’s information index and gene flow were estimated under experiment. Jaccard’s similarity coefficient matrix was generated for pairwise comparisons between individual ISSR profiles and UPGMA cluster analysis based on this matrix showed clustering into six groups. Jaccard’s coefficient of similarity values ranged from 0.409 to 0.847, with a mean of 0.628 revealing a moderate level of genetic diversity. The Bayesian model-based approach to infer hidden genetic population structures using the multilocus ISSR markers revealed two populations among the 42 genotypes. This is the first report on the assessment of genetic variation using ISSR markers in this medicinal vegetable plant, and this study of diversity analysis will be helpful in analyzing future hybrid breeding strategy and devising effective germplasm exploration and conservation strategy.     

德宏水牛微卫星标记分析的群体遗传变异

德宏水牛是云南省地方水牛的优良品种之一,为了进一步阐明其群体遗传变异和遗传结构,筛选了分别位于水牛14条染色体上的15对微卫星引物,对德宏水牛81个个体进行了检测分析.共检测到62个等位基因,每个座位等位基因数目从2到6个不等,平均等位基因数为4.13,该水牛群体期望杂合度和多态信息含量分别为0.6520±0.1526和0.5863±0.1789,各座位的遗传分化系数在0～0.0919之间,平均值为0.0202.每个座位的基因流较大,平均12.1502.研究结果表明德宏水牛群体遗传多样性较丰富,亚群间的遗传分化程度低,基因流较大,且很少发生近交.     

野生杏和栽培杏的遗传多样性和遗传结构分析

利用SSR分子标记结合荧光毛细管电泳检测技术,研究了野生杏和栽培杏的遗传多样性和遗传结构,结果显示:27个SSR位点,平均每个位点检测到17.82个等位基因(Na)和7.44个有效等位基因(Ne),平均Shannon's信息指数(I)为2.23,平均期望杂合度(He)和观察杂合度(Ho)分别为0.70和0.52。基于SSR位点,群体水平上平均等位基因数、有效等位基因数、期望杂合度、观察杂合度和Shannon's信息指数分别为6.59、4.15、0.70、0.53和1.50,说明我国杏种质资源遗传多样性丰富,其中野生杏资源遗传多样性明显高于栽培杏资源,野生杏中西伯利亚杏种质遗传多样性最高且具有较多的特异等位基因,而栽培杏中仁用杏遗传多样性最低,特有等位基因较少。聚类分析将供试159份种质分为4组。群体遗传结构分析将159份种质划分为5个类群,分类情况与传统形态指标划分基本一致。通过本研究可知,我国杏资源遗传多样性丰富,遗传结构较为复杂;西伯利亚杏与栽培杏亲缘关系较远;野生普通杏与栽培杏具有类似的遗传结构,推测野生普通杏为栽培杏原始种;仁用杏遗传多样性较低,遗传背景狭窄。本研究结果可为杏资源新品种选育及持续利用提供重要的理论依据。     

Genetic diversity changes in Indian lentils over the times

The genetic diversity of 96 genotypes of lentil comprising 34 cultivars, 46 advanced breeding lines, and 16 germplasm lines were studied using 260 SSR markers. These markers generated a total of 749 alleles. The alleles/locus ranged from 2 to 16 with an average value of 2.87. Polymorphic information content varied from 0.02 to 0.91 with a mean of 0.30. Major allelic frequency ranged from 0.14 to 0.99 with a mean of 0.77. Studied genotypes were clustered into two groups according to their breeding history. Advanced breeding lines derived from exotic lines were clustered in one group, while another group accommodated most of the cultivars and advanced breeding lines with common cultivars in parentage. The germplasm lines were sub-clustered within first group. Cumulatively, first three principal components contributed 21.2% to the total variability. Advanced breeding lines showed higher number of alleles/locus and gene diversity (He) than other sets of genetic materials. In present study, no significant differences were observed between cultivars developed in different decadal groups for both NA and He. Moreover, genetic diversity changes between small and large seeded lentil cultivars were also found non-significant in this study. These findings showed that the use of alien genes can help to diversify active gene pool for developing improved new cultivars in lentil.     

Assessment of genetic diversity and population structure in gladiolus (<Emphasis Type="Italic">Gladiolus hybridus</Emphasis> Hort.) by ISSR markers

ISSR (Inter simple sequence repeat) markers were used to assess the genetic diversity and population structure in 53 indigenous and exotic genotypes of gladiolus (Gladiolus hybridus Hort.). Molecular markers analysis showed PIC ranges from 0.42 (ISSR 861) to 0.99 (ISSR 855, ISSR 856 and ISSR 889) with an average 0.812, marker index ranged from 0.99 (ISSR 889) to 9.26 (ISSR 851) with an average 4.66 and resolving power of the primers ranged from 0.03 (ISSR 889) to 11.58 (ISSR 861) with an average value 3.80. The dendrogram based UPGMA clustering showed that all the 53 genotypes grouped into three main clusters. Nei’s gene diversity (Na) varied from 0.929 to 1.717, effective number of alleles (Ne) varied from 1.262 to 1.369, Shannon’s information index (I) ranged from 0.251 to 0.359 and gene diversity (He) was in the range from 0.167 to 0.229. Population structure analysis revealed three groups in which 32 genotypes were admixture types.     

Assessment of genetic variation and differentiation of hop genotypes by microsatellite and AFLP markers.

Microsatellites have many desirable marker properties and have been increasingly used in crop plants in genetic diversity studies. Here we report on the characterisation of microsatellite markers and on their use for the determination of genetic identities and the assessment of genetic variability among accessions from a germplasm collection of hop. Thirty-two polymorphic alleles were found in the 55 diploid genotypes, with an average number of eight alleles (3.4 effective alleles) for four microsatellite loci. Calculated polymorphic information content values classified three loci as informative markers and two loci as suitable for mapping. The average observed heterozygosity was 0.7 and the common probability of identical genotypes was 3.271 x 10(-4). An additional locus, amplified by one primer pair, was confirmed by segregation analysis of two crosses. The locus discovered was heterozygous, with a null allele in the segregating population. The same range of alleles was detected in nine triploid and five tetraploid hop genotypes. Cultivar heterozygosity varied among all 69 accessions, with only one cultivar being homozygous at four loci. Microsatellite allele polymorphisms distinguished 81% of all genotypes; the same allelic profile was found mainly in clonally selected cultivars. Cultivar-specific alleles were found in some genotypes, as well as a specific distribution of alleles in geographically distinct hop germplasms. The genetic relationship among 41 hop accessions was compared on the basis of microsatellite and AFLP polymorphisms. Genetic similarity dendrograms showed low correlation between the two marker systems. The microsatellite dendrogram grouped genetically related accessions reasonably well, while the AFLP dendrogram showed good clustering of closely related accessions and, additionally, separated two geographically distinct hop germplasms. The results of microsatellite and AFLP analysis are discussed from the point of view of the applicability of the two marker systems for different aspects of germplasm evaluation.     

Assessment of genetic diversity and DNA profiling of linseed (<Emphasis Type="Italic">Linum usitatissimum</Emphasis> subsp. <Emphasis Type="Italic">usitatissimum</Emphasis> L.) germplasm using SSR markers

Access to genetic diversity is essential for any progress in adapting linseed (Linum usitatissimum subsp. usitatissimum L.) cultivation to changing environmental conditions or to the changing market needs. An attempt has been made in the present study to assess genetic diversity in 96 genotypes of linseed including varieties, landraces and exotic material. A total of 38 SSR primers amplified 153 alleles with 4.0 alleles per marker locus. The number of alleles ranged from 2 to 15 and the observed polymorphism ranged from 50 to 100%. Average genetic dissimilarity ranged from 2 to 50%. In order to analyze the efficiency for unambiguous identification of linseed germplasm, various statistical measures, viz., number of genotyping patterns, polymorphism information content, resolving power, discrimination power, probability of identity and probability of random identity, identified a set comprising of primers LU7, LU27, LU25, LU20 and LU31 (or LU637) for DNA fingerprinting of linseed germplasm. UPGMA cluster analysis showed that all genotypes could be grouped into four main clusters. Cluster 2 was the largest consisting of mainly landraces, whereas, Cluster 4 was the smallest. Cluster 1 consisted of mainly the released cultivars. Cluster 3 and Cluster 4 were smaller clusters and consisted of exotic genotypes. Principal co-ordinate analysis further substantiated the UPGMA clustering patterns of the observed genetic relationship. To explain 70–80% variability, 17–23 PCOs were needed, whereas 70 components were needed to explain the whole variability in the linseed material under study. Analysis of molecular variance indicated that most of the genetic variation is owing to the individuals within single population, whereas grouping of linseed material into varieties, landraces and exotics accounted for nearly 10% of the total genetic variation. The utility of SSR markers in diversity assessment and cultivar identification is discussed.     

Cost‐effective development of highly polymorphic microsatellite in Japanese quail facilitated by next‐generation sequencing

Next‐generation sequencing technologies permit rapid and cost‐effective identification of numerous putative microsatellite loci. Here, from the genome sequences of Japanese quail, we developed microsatellite markers containing dinucleotide repeats and employed these for characterisation of genetic diversity and population structure. A total of 385 individuals from 12 experimental and one wild‐derived Japanese quail lines were genotyped with newly developed autosomal markers. The maximum number of alleles, expected heterozygosity and polymorphic information content (PIC) per locus were 10, 0.80 and 0.77 respectively. Approximately half of the markers were highly informative (PIC ≥ 0.50). The mean number of alleles per locus and observed heterozygosity within a line were in the range of 1.3–4.1 and 0.11–0.53 respectively. Compared with the wild‐derived line, genetic diversity levels were low in the experimental lines. Genetic differentiation (F_ST) between all pairs of the lines ranged from 0.13 to 0.83. Genetic clustering analyses based on multilocus genotypes of individuals showed that most individuals formed clearly defined clusters corresponding to the origins of the lines. These results suggest that Japanese quail experimental lines are highly structured. Microsatellite markers developed in this study may be effective for future genetic studies of Japanese quail.     

Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers

We assessed the molecular genetic diversity and population structure of Amaranthus species accessions using 11 simple sequence repeat markers. A total of 122 alleles were detected, and the number of alleles per marker (N_A) ranged from 6 to 21 with an average of 11.1 alleles. The frequency of major alleles per locus ranged from 0.148 to 0.695, with an average value of 0.496 per marker. The overall polymorphic information content values were 0.436–0.898, with an average value of 0.657. The observed heterozygosity (H_O) and expected heterozygosity (H_E) ranged from 0.056 to 0.876 and from 0.480 to 0.907, with average values of 0.287 and 0.698, respectively. The average H_O (0.240) was lower than the H_E and gene flow (Nm), and showed substantial genetic variability among all populations of amaranth accessions. The sample groupings did not strictly follow the geographic affiliations of the accessions. A similar pattern was obtained using model-based structure analysis without grouping by species type. Knowledge of the genetic diversity and population structure of amaranth can be used to select representative genotypes and manage Amaranthus germplasm breeding programs.     

两个镜鲤半同胞家系的遗传多样性及经济性状分析

在两个镜鲤半同胞家系中,各随机选取47尾作为实验鱼,测量体重、体长、全长等数量性状,利用24个微卫星分子标记对其进行遗传检测,共检测到57个等位基因,每个基因座的等位基因数为1－6个不等,平均等位基因3.21个,片段长度在134－371bp之间,有效等位基因数Ne为1.00－2.89, 平均观察杂合度Ho为0.00－0.83,平均期望杂合度He为0.00－0.66,平均多态信息含量PIC为0.00－0.58。结果表明：2个家系的遗传多样性处于中度水平,但连锁不平衡分析表明这两个家系在较大的选择压力下,已严重偏离Hardy-Wenberg平衡。利用SPSS程序下的GLM过程对24个微卫星位点与主要经济性状的相关性进行分析,结果发现：HLJ519,HLJ848、HLJ855、HLJE8 4个微卫星位点对镜鲤体重显著影响(p<0.05),其中,位点HLJ519,HLJ848、HLJ855还对体长和全长存在显著影响(p<0.05)。对这些位点基因型所对应的表型均值进行了多重比较,找到了一些对主要经济性状有利的基因型。     

引进美洲红点鲑群体遗传多样性微卫星的分析

为了解引进种美洲红点鲑种群遗传结构和种质资源现状,本研究利用15个微卫星标记对其养殖群体遗传多样性进行了分析。结果表明:在30个个体中,15对微卫星引物除1对扩增产物为单态外,其余14对在美洲红点鲑群体内扩增均出现了多态,14个多态性位点等位基因数目为3～7不等,共检测到等位基因数为69个,平均有效等位基因数为3.03;期望杂合度在0.540～0.809之间,平均期望杂合度为0.664;多态信息含量在0.360～0.719之间,平均多态信息含量为0.578,表明引进的美洲红点鲑遗传多样性水平较高,具有良好的选育潜力,可以作为良好的育种材料。     

Diversification of indigenous gene- pool by using exotic germplasm in lentil (Lens culinaris Medikus subsp. culinaris)

Genetic diversity was studied among 21 accessions of lentil using SSR markers and morphological traits in order to assess the diversification of Indian gene-pool of lentil through introgression of exotic genes and introduction of germplasm. Among these , 16 genotypes either had ‘Precoz’ gene, an Argentine line in their pedigree or genes from introduced lines from ICARDA. Sixty five SSR markers and eight phenotypic traits were used to analyse the level of genetic diversity in these genotypes. Forty three SSR markers (66 %) were polymorphic and generated a total of 177 alleles with an average of 4.1 alleles per SSR marker. Alleles per marker ranged from 2 to 6. The polymorphic information content ranged 0.33 to 0.80 with an average of 0.57, suggesting that SSR markers are highly polymorphic among the studied genotypes. Genetic dissimilarity based a dendrogram grouped these accessions into two main clusters (cluster I and cluster II) and it ranged 33 % to 71 %, suggesting high level of genetic diversity among the genotypes. First three components of PCA based morphological traits explained higher variance (95.6 %) compared to PCA components based on SSR markers (42.7 %) of total genetic variance. Thus, more diversity was observed for morphological traits and genotypes in each cluster and sub-cluster showed a range of variability for seed size, earliness, pods/plant and plant height. Molecular and phenotypic diversity analysis thus suggested that use of germplasm of exotic lines have diversified the genetic base of lentil germplasm in India. This diversified gene-pool will be very useful in the development of improved varieties of lentil in order to address the effect of climate change, to adapt in new cropping systems niches such as mixed cropping, relay cropping, etc. and to meet consumers’ preference.     

Genetic diversity and population structure of common bean (Phaseolus vulgaris) landraces from China revealed by a new set of EST-SSR markers

A new set of EST-SSR markers were developed and employed to analyze the genetic diversity and population structure of Phaseolus vulgaris in China. A total of 2452 microsatellites were identified in 2144 unigenes assembled from P. vulgaris ESTs, indicating that merely 6.9% of the 30,952 unigene sequences contained SSRs. Seventeen of 153 randomly designed EST-SSR primer pairs successfully amplified polymorphic products in 31 landraces from six major production provinces of China, with the mean number of alleles per locus of 2.700 and polymorphism information content of 0.378. The observed and expected heterozygosity ranged from 0.100 to 0.954 and 0.081 to 0.558, respectively. Using these markers, both an unrooted neighbor-joining tree and principal coordinates analysis showed that almost all of the landraces were separated according with their regional distribution. Moreover, population structure analysis revealed that all genotypes formed into three distinct clusters (k = 3), suggesting that geographic and climatic factors could provide diverse degrees of selection pressure. Accordingly, germplasm collection and cross breeding among different regions are suggested to accelerate the process of diverse germplasm creation and broaden germplasm resources of Chinese common bean.     

Characterization of hawthorn (<Emphasis Type="Italic">Crataegus</Emphasis> spp.) genotypes by SSR markers

Hawthorn (Crataegus spp.) is an edible wild fruit that is used in traditional medicine, landscape studies, and food and beverage industries in many countries. It is an important wild plant species in Turkey and is numerous in the Yozgat Province. Genetic and breeding studies on hawthorn are very limited. Therefore, we aimed to characterize 91 hawthorn genotypes using simple sequence repeat (SSR) markers. The SSRs were developed from apple and pear and were screened in hawthorn for amplification and polymorphisms. A total of 265 alleles were detected from thirty-two SSR primer pairs, and those were used to identify genetic relationships. The number of alleles ranged from 2 to 21 alleles per locus with a mean value of 8.28. The Hi05b09 locus showed the highest allele number (Na?=?21). The polymorphism information content (PIC) values ranged from 0.16 (CH03d10) to 0.89 (C6554) with a mean value of 0.60. An Unweighted Pair Group Method with Arithmetic Average method was used to cluster the genotypes, and four major clusters were obtained from the amplification of the SSRs. STRUCTURE software identified four populations (ΔK?=?4) and eight sub-populations (ΔK?=?8), and four major clusters similar results to UPGMA analysis. Our study showed that the SSR markers could be utilized as a reliable tool for the determination of genetic variations and relationships of hawthorn genotypes. A basic molecular analysis on the hawthorn genotypes identified in this study will promote the collection of germplasm collection and the selection of parents’ in future cross-breeding studies.     

Deciphering allelic variability and population structure in buckwheat: An analogy between the efficiency of ISSR and SSR markers

Food and nutritional security continue to be the issues of concern in developing countries like ours. Exploring the reservoir of high potential unexplored genetic resources could address the world’s food and nutritional insecurity. The availability of diverse data and the population structure of any crop germplasm is a valuable genetic resource for discovering genes that can help achieve food and nutritional stability. We used seven ISSR and seven SSR markers to investigate diversity among 63 buckwheat genotypes, including landraces from India''s northwestern Himalayas. Various parameters such as percent polymorphism, PIC, resolving power, and marker index was used to evaluate the inequitable efficacy of these markers. We foundthat both marker systems are effective in detecting polymorphism in buckwheat germplasm. Seven ISSRs produced 55 polymorphic bands, while seven SSRs produced 32bands. When compared to ISSRs, SSRs had a greater average PIC value (0.43) than that of (0.36). ISSRs, on the other hand, had a resolving power of (4.38) compared to (1.42) for SSRs. The hierarchical cluster analysis dendrogram divided genotypes into three major clusters. We found that both marker systems were equally accurate in grouping buckwheat genotypes according to their geographical origins. Using 7 ISSR and 7 SSR markers, the model-based STRUCTURE analysis established a population with two sub-populations that correspond to species-based groupings. Within the population, there was a high level of genetic diversity. These results have consequences for both buckwheat breeding and conservation efforts.Keyword: Buckwheat, SSR, ISSR, Genetic diversity, Population structure     

Development of EST‐SSRs in Cucumis sativus from sequence database

Simple sequence repeat markers derived from expressed sequence tags (EST‐SSR) are potentially valuable tools for plant breeding and germplasm collection conservation, and increasingly, efforts have been made for developing this type of marker. We have identified 20 polymorphic SSR markers from cucumber ESTs deposited in public sequence database. The average allele number was 3.3 per locus, ranging from two to six alleles during screening 20 cucumber genotypes with the mean expected heterozygosity of 0.477. Amplification products were also detected by 13 pairs of primer in Cucumis melo. These informative EST‐SSR markers can be used in cucumber genetic improvement projects.     

Establishment of paternity testing system using microsatellite markers in Chinese Holstein

To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.     

Isolation and characterization of polymorphic microsatellite loci from the water mite Hygrobates fluviatilis (Acari: Hydrachnidia: Hygrobatidae)

We developed and characterized 13 microsatellite markers from the water mite Hygrobates fluviatilis. The genotypes of 32 diploid females were assessed, and all of the loci were polymorphic. The number of alleles per locus ranged from two to 21, and the observed heterozygosity ranged from 0.063 to 0.813. These microsatellite markers are the first published for water mites and will contribute to research on the population structure of this widespread species.