Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism

We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69–86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.     

Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers

Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.     

太湖流域粳稻地方品种遗传多样性研究

太湖流域稻作历史悠久,是我国粳稻高产地区之一。但育成品种的遗传基础日趋狭窄,将会给农业生产带来潜在风险。为了有效利用地方水稻资源以扩大改良品种的遗传基础,作者通过调查19个农艺性状,对823个太湖流域粳稻地方品种的遗传多样性进行了研究。结果表明:15个数量性状的变异系数(CV)范围在4.6%(结实率)和33.7%(单株产量)之间。颖壳色、稃尖色、芒型和粒型4个质量性状分别有10、6、5、4种表现型。19个农艺性状的多样性指数(H′)变化范围在0.757(粒型)和1.930(每穗实粒数)之间,平均为1.540。9月10日以后抽穗的品种比9月10日及其以前抽穗的品种具有更丰富的表型变异。主成分分析表明,株高、单株有效穗、每穗总粒数、每穗实粒数、着粒密度、千粒重、单株产量和穗颈长等8个性状是解释太湖流域粳稻地方品种多样性的重要性状。     

Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers.

Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the Shannon-Weiner index of diversity. Genetic diversity was slightly higher in the modern cultivars than in the traditional cultivars from Tamil Nadu. Among the landraces from Jeypore, the lowland landraces showed the highest diversity. The present study showed that the process of breeding modern cultivars did not appear to cause significant genetic erosion in rice. Cluster analysis and the first component of principle component analysis (PCA) both showed a clear demarcation between the cultivars and landraces as separate groups, although the genetic distance between them was narrow. The modern cultivars were positioned between the landraces from Jeypore and the traditional cultivars from Tamil Nadu. The second component of PCA further separated medium and upland landraces from lowland landraces, with the lowland landraces found closest to the traditional and modern cultivars.     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czechia

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modem Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged overall possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

Genetic differentiation and geographical Relationship of Asian barley landraces using SSRs

Genetic diversity in 403 morphologically distinct landraces of barley (Hordeum vulgare L. subsp. vulgare) originating from seven geographical zones of Asia was studied using simple sequence repeat (SSR) markers from regions of medium to high recombination in the barley genome. The seven polymorphic SSR markers representing each of the chromosomes chosen for the study revealed a high level of allelic diversity among the landraces. Genetic richness was highest in those from India, followed by Pakistan while it was lowest for Uzbekistan and Turkmenistan. Out of the 50 alleles detected, 15 were unique to a geographic region. Genetic diversity was highest for landraces from Pakistan (0.70 ± 0.06) and lowest for those from Uzbekistan (0.18 ± 0.17). Likewise, polymorphic information content (PIC) was highest for Pakistan (0.67 ± 0.06) and lowest for Uzbekistan (0.15 ± 0.17). Diversity among groups was 40% compared to 60% within groups. Principal component analysis clustered the barley landraces into three groups to predict their domestication patterns. In total 51.58% of the variation was explained by the first two principal components of the barley germplasm. Pakistan landraces were clustered separately from those of India, Iran, Nepal and Iraq, whereas those from Turkmenistan and Uzbekistan were clustered together into a separate group.     

我国主栽皱环球盖菇菌株遗传多样性及栽培特性

对我国皱环球盖菇Stropharia rugosoannulata 20个主栽菌株进行了ISSR标记遗传多样性分析,使用的28个ISSR引物中22个具有多态性,UPGMA聚类分析显示遗传相似性水平在0.68-0.86之间,在0.72时可将菌株分为6个类群,类群间遗传差异较大.在PDA培养基上,除菌株Sr-03和Sr-0...     

Genetic diversity among Chinese landraces and cultivars of broomcorn millet (Panicum miliaceum) revealed by the polymerase chain reaction

Broomcorn millet is widely grown in Asia and Europe. This cereal is a very efficient user of soil water and is particularly adapted to sandy, dry soils and dry weather conditions. As one of the oldest crops in ancient China, it has played an important role in the formation and development of Chinese civilisation and culture. It is still one of the major grain crops in northern China where harsh climate conditions prevail. The genetic diversity and relationships among 32 accessions of broomcorn millet (Panicum miliaceum) from the major areas for broomcorn millet growing in China, in addition to six Indian landraces, were evaluated by PCR analysis with six introns splice junction or long random primers. A total of 56 DNA fragments across all materials were scored; among them, 42 (75%) were polymorphic as indicated by their absence in at least 1 of the 38 accessions tested, indicating a high variation at the DNA level among those accessions. Pair‐wise genetic dissimilarity (Dice’s coefficient) ranged from 0.0286 to 0.4737. The clustering largely corroborated with the geographical location of the origins of those accessions. The data indicated that the glutinous/non‐glutinous trait is also associated with the clustering. Majorities of the landraces from Yulin of Shaanxi were clustered into five groups, and majorities of the cultivars or breeding lines from Inner Mongolia were clustered into three groups. The results of this study suggest that the landraces from Yulin of Shaanxi were extensively utilised in the breeding programme of Shanxi, whereas this feature was not observed in the breeding programme of Inner Mongolia.     

河北省花生地方品种基于EST-SSR的遗传多样性及性状-标记相关分析

利用215对EST-SSR引物对70份河北省花生地方品种的遗传多样性进行扫描,结果表明,58对引物在不同材料间具有多态性,多态性引物比率为26.98%。共扩增出168个位点,其中156个为多态性位点;不同EST-SSR的多态性信息指数PIC变幅为0.063-0.9825,平均为0.5244。聚类分析结果表明,在阈值为8.00时,可以将各地方品种明显分为两大类,第Ⅰ类群为普通型,第Ⅱ类群为珍珠豆型和多粒型,与植物学分类一致。单标记－性状相关分析表明,同一标记位点可与多个性状相关,获得与5个农艺性状显著相关的标记12对。     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czech Republic

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modern Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged over all possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

Genetic diversity among cultivars of spring barley revealed by random amplified polymorphic DNA (RAPD)

RAPD (random amplified polymorphic DNA) polymorphism was studied in 23 malting and non-malting spring barley cultivars included in the official list of Polish cultivated varieties. Twenty-four 10-mer primers were tested in each cultivar, giving altogether 149 amplification products, 45% of which were polymorphic. The number of polymorphic bands revealed by one primer ranged from 1 to 6, with an average of 2.8. Genetic distance for all pairs of compared varieties was estimated and a dendrogram was constructed using unweighted pair group method of arithmetic means. The genetic distance between cultivars ranged from 0.11 for cvs. Apex and Bryl to 0.62 for cvs. Orthega and Madonna. Of the seven malting cultivars only two (Brenda and Stratus) formed one group at D = 0.25. The genetic distance between cvs. Brenda and Scarlett, especially recommended for brewery, was equal to 0.34. The detected polymorphism appeared to be sufficient for assessing genetic distances between cultivars, but on the basis of this polymorphism groups of malting and non-malting cultivars were not clearly distinguished.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.     

Genetic diversity in maize landraces from indigenous settlements of Northeastern Argentina

In South America, native maize germplasm has been extensively studied particularly for the Andean region. However, relatively few genetic diversity studies include materials from the eastern region of the continent. Herein we present a genetic diversity characterization of four Popcorn maize landraces, maintained in indigenous settlements, from Northeastern Argentina (NEA). In addition, one Popcorn landrace from Northwestern Argentina (NWA) was incorporated for comparison. We characterized these landraces using ten microsatellite markers. For the whole data set, a total of 65 alleles were found, with an average of 7.22 alleles per locus. The average gene diversity was 0.370. Global fit to Hardy–Weinberg proportions was observed in all landraces. Global estimates of F _ST revealed a significant differentiation among the populations. Individual Neighbor-joining clustering and Bayesian analyses allowed the recognition of most populations studied. Two main groups were distinguished by the Neighbor-joining clustering of populations. This grouping pattern would be consistent with a hypothesis of successive introductions of Popcorn in South America. The results presented will be useful to design strategies that maximize the utility of maize genetic resources.     

Genetic diversity assessment of summer squash landraces using molecular markers

Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash.     

Genetic diversity trends in twentieth century crop cultivars: a meta analysis

In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.     

Genetic control of the spring habit in old local cultivars and landraces of common wheat from Siberia

The inheritance of the spring habit was studied in 63 old local cultivars and landraces of common wheat from Eastern and Western Siberia and the Tyva Republic. Minimal polymorphism was observed for the dominant Vrn genes, controlling the spring habit in landraces of these regions. The control was digenic and involved the Vrnl and Vrn2 dominant genes in the majority (95%) of cultivars and was monogenic in three cultivars. None of the cultivars had the Vrn3 dominant gene, characteristic of the neighboring regions of China and Central Asia. Among 137 old local cultivars and landraces of Siberia, only one (cultivar Sibirskaya (k-23347) from Irkutsk oblast, was comparable in the response to the natural short day (photoperiod) to Chinese cultivars. Comparison of the results and the data reported for commercial cultivars revealed that the genotype frequencies of the dominant Vrn genes in Siberian landraces and commercial cultivars of common wheat remained essentially unchanged at least for the past 100 years. At the same time, Siberian landraces significantly differed in Vrn dominant gene frequencies from cultivars of the adjacent regions. It was assumed that the control of the spring habit by the two Vrn dominant genes is optimal for the climatic conditions of Siberia.     

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

The Chinese genebank contains 23,587 soybean landraces collected from 29 provinces. In this study, a representative collection of 1,863 landraces were assessed for genetic diversity and genetic differentiation in order to provide useful information for effective management and utilization. A total of 1,160 SSR alleles at 59 SSR loci were detected including 97 unique and 485 low-frequency alleles, which indicated great richness and uniqueness of genetic variation in this core collection. Seven clusters were inferred by STRUCTURE analysis, which is in good agreement with a neighbor-joining tree. The cluster subdivision was also supported by highly significant pairwise F _st values and was generally in accordance with differences in planting area and sowing season. The cluster HSuM, which contains accessions collected from the region between 32.0 and 40.5°N, 105.4 and 122.2°E along the central and downstream parts of the Yellow River, was the most genetically diverse of the seven clusters. This provides the first molecular evidence for the hypotheses that the origin of cultivated soybean is the Yellow River region. A high proportion (95.1%) of pairs of alleles from different loci was in LD in the complete dataset. This was mostly due to overall population structure, since the number of locus pairs in LD was reduced sharply within each of the clusters compared to the complete dataset. This shows that population structure needs to be accounted for in association studies conducted within this collection. The low value of LD within the clusters can be seen as evidence that much of the recombination events in the past have been maintained in soybean, fixed in homozygous self-fertilizing landraces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic diversity and population structure among cultivars of Saccharina japonica currently farmed in northern China

Close to 50% of the annual production of the brown alga Saccharina japonica, about 2 million tons (fresh weight), is produced through farming in Shandong province, China, principally around Rongcheng. Under artificial selection for phenotypic traits (e.g. color, blade length) cultivated strains (cultivars) face the problems of inbreeding depression, which can be caused by the close relationships of the parental plants. Hence, in an attempt to evaluate genetic variations and relationships among cultivars, 15 major farmed cultivars were selected and sampled from seven major hatcheries and analyzed using 15 microsatellite markers. A total of 94 alleles were found across all samples, with allele numbers ranging from three to 17 per locus. All of the cultivars exhibited relatively high levels of genetic diversity, with mean Nei's genetic diversity (H) and the Shannon's information index (I) of 0.466 and 0.862, respectively. A UPGMA dendrogram grouped all cultivars into three main clusters. However, two of the most commonly farmed cultivars (DB and BN) from different hatcheries failed to cluster together. Instead, differently named cultivars from the same hatchery tended to group together, implying that their high similarities is partly due to the presence of genetic mixing among cultivars within a hatchery or misuse of cultivar's names. Genetic analysis performed by Bayesian model‐based clustering revealed clear differentiation of three major subgroups (LJ‐202 and LJ‐205; LJ‐C033; XS‐2 and XS‐BN) and one admixed group (the remaining ten cultivars). Our results revealed ambiguous genetic relationships among certain cultivars of S. japonica farmed in northern China. A more stringent and prudent regulation should be applied during breeding and production process in the future.