Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers

Genetic variation and relationships among 47 mango germplasm and 3 relative species from Guangxi province in China, were analyzed using Start Codon Targeted (SCoT) markers. Using 33 selected SCoT primers 273 bands were generated with an average of 8.27 bands per primer among the 50 accessions, of which 208 (76.19%) were polymorphic. Genetic relationships estimated using the SM similarity coefficient generated values between different pairs of accessions that varied from 0.531 to 0.923 with an average of 0.782. These coefficients were utilized to construct a dendrogram using the UPGMA. All 50 accessions were basically classified into six clusters and correspond well with their recorded pedigrees. The results will provide much more useful information for the management of germplasm and will also be useful to improve the current breeding strategies. The results also demonstrate that the SCoT marker system is useful for identification and genetic diversity analysis of mango cultivars.     

Characterization of genetic diversity in chickpea using SSR markers,Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP)

Physiology and Molecular Biology of Plants - To evaluate the genetic diversity among 48 genotypes of chickpea comprising cultivars, landraces and internationally developed improved lines genetic...     

不同龙眼资源遗传多样性的SCoT和ISSR 比较分析

应用SCoT和ISSR标记对36份龙眼资源和1份近缘种龙荔的遗传多样性进行分析。结果表明:12对SCoT引物共扩增出127条带,平均每条引物扩增10.58条带;15条ISSR引物共扩增出117个条带,平均扩增7.8条带。UPGMA聚类结果表明:SCoT标记和ISSR标记分别在相似系数0.672和0.685水平上,均可将37份材料分成6大类群,SCoT和ISSR标记均适用于龙眼材料的遗传多样性分析,如果将两种标记的数据进行综合分析,可以缩小单一标记的误差。研究结果为龙眼种质资源的保存和利用提供了重要的依据。     

Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance.     

Genetic diversity of Hemarthria altissima and its related species by EST-SSR and SCoT markers

There is a need for an appropriate evaluation of Hemarthria germplasm resources using genetic analysis. Understanding their genetic background will promote effective development and utilization of its germplasm resources in plant breeding. We examined the genetic diversity and relationships among 46 Hemarthria germplasm resources from four continents. Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) and Start Codon Targeted (SCoT) markers were used to investigate species Hemarthria altissima (36), Hemarthria compressa (8) and Hemarthria uncinata (2). We selected 19 EST-SSR primers and generated 550 polymorphic (94.7%). Twenty one SCoT primers were selected and amplified to produce 597 bands with 89.4% of polymorphic bands. The Mantel test between EST-SSR and SCoT matrices revealed significant correlations (r = 0.854) and the data from both markers were combined for cluster analysis. The 46 materials were clustered into two main groups by UPGMA clustering with a similarity coefficient ranging from 0.573 to 0.940 and the dendrogram was basically concordant with geographical origins and species. Among the three Hemarthria species, H. altissima was genetically closest to H. compressa while it was not close to H. uncinata. When the utility of the two markers were compared, we found EST-SSR to be more efficient than SCoT in determining the genetic diversity study of Hemarthria species.     

Wild Panax vietnamensis and Panax stipuleanatus markedly increase the genetic diversity of Panax notoginseng (Araliaceae) revealed by start codon targeted (SCoT) markers and ITS DNA barcode

In order to evaluate whether the two wild species, Panax vietnamensis (from Vietnam) and Panax stipuleanatus (from primeval forest, Yunan Province) could markedly increase the genetic diversity of cultivated Panax notoginseng (Wenshan, Yunnan Province), both start codon targeted (SCoT) markers and internal transcribed spacer (ITS) DNA barcode were firstly employed in this genus. A total of 173 amplification bands were generated by 16 selected SCoT primers, in which 153 (89.5%) were polymorphic. Nei's gene-diversity indicated that the genetic diversity of three species (h = 0.16 and I = 0.27) was obviously higher than that of P. notoginseng (h = 0.09). Similarly, 38 different ITS sites out of 639 (5.9%) were detected among three species, but only one was different within 22 samples of P. notoginseng. Analysis of molecular variance (AMOVA) showed a greater proportion of genetic diversity existed within (61.3%) rather than among (38.7%) groups at genus level. In addition, P. vietnamensis had a closer relationship with P. notoginseng than P. stipuleanatus. These results would be significant for increasing the genetic diversity of P. notoginseng population by hybridization with P. vietnamensis and P. stipuleanatus, thus obtaining more varieties for future cultivar breeding and germplasm resources management.     

Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker

Genetic diversity and relationship of Lycoris species were investigated using SCoT marker analysis. Of 57 SCoT primers screened, 23 SCoT primers were identified to be high polymorphism. A total of 154 DNA bands with size varied from 0.2 kb to 2.5 kb were amplified, and 131 (82.5%) of them were polymorphic. The average number of polymorphic DNA band per primer was 5.7. Based on Nei's similarity coefficients and genetic distances, total of 43 accessions from 14 species of the genus Lycoris tested were clustered into four groups. Group I consisting of 17 accessions was further divided into two subgroup (Ia and Ib). Subgroup Ia included four species with red flower and 22 (2n) chromosomes. Subgroup Ib contained Lycoris haywardii and Lycoris albiflora which were natural hybrids with oyster white flower. Group II consisted of three species with yellow flower and 16 (2n) chromosomes. Group III was composed of Lycoris Squamigera, Lycoris incarnata and all of hybrids whose flower color was variegated. Group IV only has one species (Lycoris sprengeri) whose petal was a mixture of pink and blue. Notably, the polymorphism generated by SCoT was associated with flower color and chromosome number in this genus plants. The present data provide high-valued information for the management of germplasm, genetic improvement, and conservation of the genetic resources of Lycoris species, important horticulture and medical plants.     

Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species,as genome progenitors of bread wheat,using SCoT markers

We assessed the molecular genetic diversity and relationships among some Aegilops and Triticum species using 15 start codon-targeted (SCoT) polymorphism markers. A total of 166 bands amplified, of which 164 (98.79%) were polymorphic. Analysis of molecular variance and inter-population differentiation (Gst) indicated high genetic variation within the studied populations. Our analyses revealed high genetic diversity in T. boeoticum, Ae. cylindrica, T. durum and Ae. umbellulata, low diversity in Ae. crassa, Ae. caudata and Ae. speltoides, and a close relationship among Ae. tauschii, T. aestivum, T. durum, T. urartu, and T. boeoticum. Cluster analysis indicated 180 individuals divided into 8 genome homogeneous clades and 11 sub-groups. T. aestivum and T. durum accessions were grouped together, and accessions with the C and U genomes were grouped into the same clade. Our results support the hypothesis that T. urartu and Ae. tauschii are two diploid ancestors of T. aestivum, and also that Ae. caudata and Ae. umbellulata are putative donors of C and U genomes for other Aegilops species that possess these genomes. Our results also revealed that the SCoT technique is informative and can be used to assess genetic relationships among wheat germplasm.     

Genetic diversity and taxonomic studies of date plum (Diospyros lotus L.) using morphological traits and SCoT markers

Date plum persimmon (Diospyros lotus L.) is an important fruit crop in China due to its better compatibility as a major root stock for Diospyros kaki Thunb. The objective of this study was to reveal the diversity and taxonomic status based on morphological and molecular markers for 26 date plum persimmon accessions from different ecogeographical areas. Significant variability was observed in the 26 date plum persimmon accessions using the analysis of 5 quantitative and 16 qualitative morphological characters of branches, fruits and seeds. Molecular diversity was analyzed using start codon targeted (SCoT) markers. A total of 118 bands were produced with 11 SCoT primers; genetic similarity was ranged from 0.42 to 0.83, which indicating higher genetic variation among accessions. Based on the cluster results of morphological and molecular data, the results showed that date plum persimmon may be divided into five taxonomic types which including male date plum persimmon, rounded seedless date plum persimmon, rounded seedy date plum persimmon, obround seedless date plum persimmon, and oblate seedy date plum persimmon.     

三年桐EST-SSR标记的开发与种质遗传多样性分析

以三年桐品种对年桐发育中的种子为材料,构建c DNA文库,获得3202个原始EST序列,经过去除冗余和低质量序列后,获得1047条非冗余单一序列,利用MISA软件从其中的173个非冗余EST序列中搜索得到212个SSR位点。其中,二核苷酸重复类型为主导(68.39%),其次是三核苷酸重复类型(25.94%),其优势基元为AG/CT(43.87%)、AT/AT(19.34%)和AGC/GCT(5.66%)。针对可设计引物的68个序列进行EST-SSR引物设计,结合PCR扩增和数据分析,鉴定出14对多态性标记,用该14对引物对169份三年桐种质资源进行遗传多样性检测,共得到41个等位基因(Na),平均每对引物扩增出2.93个等位基因,期望杂合度(He)变幅为0.08~0.63,平均值为0.33,多态性信息含量(PIC)变幅为0.08~0.56,平均值为0.3,表明14对EST-SSR标记多态性较高,能较好地反映三年桐种质的遗传多样性。三年桐种质资源按群体进行非加权配对算术平均法(UPGMA)聚类分析,群体间的相似度变幅为0.9604~0.9986,遗传距离变幅为0.0022~0.0404,表明三年桐群体间的遗传多样性相对较低,亲缘关系较近。对169份三年桐种质资源个体进行聚类分析,结果显示不同地理种源的遗传关系缺乏明显的地理结构。     

Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents

Hexaploid tritordeum (H^chH^chAABB; 2n?=?42) results from the cross between Hordeum chilense (H^chH^ch; 2n?=?14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n?=?28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70 % of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop.     

Insight into genetic relation and diversity of cultivated and semi-domesticated under-utilized Crotalaria species gained using start codon targeted (SCoT) markers

To augment conventional crop improvement approaches in cultivated sunnhemp (Crotalaria juncea L.) and other under-utilized Crotalaria species, genetic diversity of 94 genotypes from seven Crotalaria species was studied using 20 Start Codon Targeted (SCoT) markers. High allele number (1.32), polymorphism information content (0.37) and resolving power (6.59) established SCoT as a reliable marker system for genetic analysis in Crotalaria. All the species except Crotalaria retusa L. exhibited high number of SCoT amplicons. Analysis of molecular variance revealed significant variability between (24.0%) the species as well as within species (76.0%). A cluster analysis identified distinct groups corresponding to the seven species and also identified sub-groups within the species. The sunnhemp cultivars were distant from the landraces, suggesting the need of population improvement using distantly related genotypes. Species relationship identified Crotalaria pallida Aiton to be a close relative of C. juncea. The results of principal coordinate analysis were comparable to that of cluster analysis, revealing high genetic variability in sunnhemp and other semi-domesticated Crotalaria species. The study further suggests some measure for conservation of genetic resources and genetic improvement of these species based on the results of diversity analysis.     

Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace chickpea (Cicer arietinum L.) genotypes collected from north-west of Iran

Morphological traits and three molecular markers techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and directly amplified minisatellite DNA (DAMD) markers were compared for fingerprinting of 40 landraces chickpea genotypes collected from different geographical locations of north-west of Iran. Variance analysis of ten measured morphological traits showed significant differences existed between genotypes. Cluster analysis based on morphological traits, divided genotypes in three distinct clusters. Average polymorphism information content (PIC) for ISSR, DAMD and SCoT markers was 0.216, 0.232 and 0.232, respectively, and this revealed that SCoT markers were more informative, followed by ISSRs marker, than other markers for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. Accessions from same geographical regions mostly showed more genetic similarities than those from origins far isolated apart. These results suggest that efficiency of SCOT, DAMD and ISSR markers was relatively the same in fingerprinting of genotypes but SCOT and DAMD analysis are more effective in fingerprinting of chickpea genotypes. To our knowledge, this is the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and DAMD) and the ISSR technique on a set of samples of chickpea. Overall, our results indicate that SCOT, ISSR and DAMD fingerprinting could be used to detect polymorphism for genotypes of chickpea.     

Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens)

In order to assess the applicability of bovine microsatellite markers for population genetic studies in Swiss yak, 131 bovine microsatellite markers were tested on a panel of 10 animals. Efficient amplification was observed for 124 markers (94.6%) with a total of 476 alleles, of which 117 markers (94.3%) were polymorphic. The number of alleles per locus among the polymorphic markers ranged from two to nine. Seven loci (ILSTS005, BMS424B, BMS1825, BMS672, BM1314, ETH123 and BM6017) failed to amplify yak genomic DNA. Two cattle Y-chromosome specific microsatellite markers (INRA126 and BM861) amplified genomic DNA from both male and female yaks. However, two additional markers on cattle Y-chromosome (INRA124 and INRA189) amplified DNA from only males. Of the polymorphic markers, 24 microsatellites proposed by CaDBase for within- and cross-species comparisons and two additional highly polymorphic markers (MHCII and TGLA73) were used to investigate the genetic variability and the population structure of a Swiss yak herd that included 51 additional animals. The polymorphic information content ranged from 0.355 to 0.752, while observed heterozygosity (HO) ranged from 0.348 to 0.823. Furthermore, a set of 13 markers, organized into three multiplex polymerase chain reactions, was evaluated for routine parentage testing. This set provided an exclusion probability in a family of four yaks (both parents and two offspring) of 0.995. These microsatellites serve as useful tools for genetic characterization of the yak, which continues to be an important domestic livestock species.     

Genetic diversity and the population structure at two ploidy levels of Lycoris radiata as revealed by SCoT analysis

Ploidy differences can occur between and within species. To decipher the genetic structure of a species with different ploidy levels, we investigated an area of China where diploid and triploid individuals of Lycoris radiata co-occur. Twenty-six populations of L. radiata were sampled across its natural range, and SCoT markers were used to assess the genetic diversity and population structure. Chromosome counts revealed that 10 populations were diploid and 16 were triploid, each population showed a single cytotype. SCoT analysis revealed high genetic diversity at the species level (PPB = 93.1%; H = 0.258; I = 0.396). However, compared to the triploid strains of Lycoris, the diploid strains had a relatively higher genetic diversity. One possible interpretation for these results is that the triploid strains only propagated using bulb division, while the diploid strains reproduced using sexual propagation and bulb division. Our investigation of the genetic structure, based on UPGMA and PCoA cluster analyses, revealed that populations of L. radiata are divided into three genetic groups. In addition, our results indicate that Yangtze River can affect population diffusion, which played an important role in the genetic differentiation of L. radiata. Lastly, our results suggest that the triploid sterile species of L. radiata might possess two origins.     

Museum samples provide novel insights into the taxonomy and genetic diversity of Irish red grouse

The taxonomic status of red grouse in Ireland has been the subject of considerable debate over the past century. Irish red grouse are usually classified as Lagopus lagopus scoticus, which is the same subspecies as that found in Britain, but some ornithologists believe that native Irish red grouse constitute an endemic subspecies, namely L. lagopus hibernicus. The considerable decline of Irish red grouse over the past century, along with possible hybridization with introduced grouse from Britain, have highlighted the need to resolve their taxonomic status as part of a biodiversity management plan. However, genetic analysis of samples from a single point in time will provide limited insight into potentially confounding historical events such as hybridization and introgression. We therefore compared mtDNA sequences from both current and historical samples of the two putative subspecies, scoticus and hibernicus, to see if they are or were genetically distinct. Red grouse from Britain and Ireland shared mitochondrial haplotypes, and our historical data suggest that this is unlikely to be the result of recent hybridization and introgression. These findings, combined with a general lack of documented differences in behaviour and ecology, suggest that Irish red grouse should remain classified as L. lagopus scoticus. At the same time, we found evidence that a significant amount of genetic diversity has been lost from Irish red grouse over the past century, presumably as a result of diminishing population sizes and fragmentation of extant populations. A loss of habitat, combined with the declining numbers and genetic diversity of Irish red grouse, justify their designation as an All-Ireland Priority (Red List) species and a Northern Ireland Priority Species for conservation.     

中国龙虾微卫星标记的筛选及遗传多样性分析

文章以M13通用引物和重复序列(CT)₁₅、(AT)₁₅引物, 利用PCR法对中国龙虾(Panulirus stimpsoni Hoehuis)部分基因组DNA文库进行筛选。共获得78个微卫星序列, 分别分布于55个阳性重组克隆中, 其中完美型(perfect)共50个, 占64%; 非完美型(imperfect)3个, 占3.8%; 混合完美型(compound perfect)6个, 占7.7%; 混合非完美型(compound imperfect)19个, 占24.5%。根据微卫星序列, 设计并筛选出15对微卫星多态性引物, 对中国龙虾的群体进行了遗传多样性分析。获得3~12个等位基因, 等位基因大小在78~425 bp之间, 基本符合引物设计的理论长度。期望杂合度范围为0.48~0.87, 平均值为0.71, 表明中国龙虾基因组微卫星具有较高的杂合度与遗传多样性。15个微卫星位点的PIC值从0.44到0.84, 平均值为0.60, 说明这些微卫星位点在中国龙虾基因组中包含丰富的遗传信息, 合适用于中国龙虾的各种分子标记及遗传学分析和应用。     

Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection

Past breeding strategies for dairy cattle have been very effective in producing rapid genetic gain to achieve industry targets and raise profitability. Such gains have been largely facilitated by intense selection of sires combined with the use of artificial insemination. However, this practice can potentially limit the level of genetic diversity through inbreeding and selection plateaus. The rate of inbreeding in Australia is increasing, primarily as a result of semen importation from a small number of prominent bulls from the USA. The effect of this genetic influx in the Australian dairy cattle population is poorly understood both in terms of diversity and local adaptation/divergence. This study uses 845 genome-wide SNP genetic markers and 431 bulls to characterize the level of genetic diversity and genetic divergence within the Australian and international Holstein Friesian dairy population. No significant differences in genetic diversity (as measured by heterozygosity [H(o)] and allelic richness [A]) were observed over the 25-year time period (1975-1999) for bulls used in Australia. The importation of foreign semen into Australia has increased the effective population size until it was in effect a sub-sample of the global population. Our data indicate that most individuals are equally closely related to one another, regardless of country of origin and year of birth. In effect, the global population can be considered as one single population unit. These results indicate that inbreeding, genetic drift and selection has had little effect at reducing genetic diversity and differentiating the Australian Holstein Friesian population at a genome-wide level.     

Analysis of the genetic diversity and relationships among and within species of Hippophae (Elaeagnaceae) based on RAPD markers

RAPD markers were used to assess the genetic diversity and inter- and intra-specific relationships of the genus Hippophae L. and to study the correlation between genetic distances and geographic distances among populations of H. rhamnoides ssp. sinensis. The results analyzed by the percentage of polymorphic loci and Shannon information index indicated that a high level of genetic diversity existed both among and within species of the genus Hippophae. In the UPGMA dendrogram, the species or subspecies were clustered into two main groups but not strictly grouped according to sect. Hippophae and sect. Gyantsensis Lian. The multiple regression analysis and Mantel test both indicated a significant correlation between genetic distance and altitude distance among populations of H. rhamnoides ssp. sinensis, and the cluster analysis suggested that the genetic variation among populations of H. rhamnoides ssp. sinensis was linked to their monophyletic origin. Moreover, some degree of genetic differentiation was found among samples collected at different times.