Genetic diversity analysis of hulless barley from Shangri-la region revealed by SSR and AFLP markers

For adding the hulless barley resources of Shangri-la region to the global barley resource library, a basic work was done by us to assess their genetic diversity of this region. The genetic diversity of 60 hulless barley samples collected from three counties in Shangri-la region of Yunnan Province, were studied using SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) markers. A total of 70 alleles were detected for 19 pairs of SSR primers, and 525 band containing 464 polymorphic bands were revealed for 5 pairs of AFLP primers. The value of polymorphism information content (PIC) ranged from 0.03 to 0.86 for SSR primers. The total numbers of alleles were 51, 55, 43 in three populations and the polymorphic bands were 188, 205 and 141. The genetic distances and genetic identity among the three populations showed their close relationship. The gene diversity among populations relative to the total population diversity (Gst) was 0.13 for SSR markers and 0.02 for AFLP markers and indicated that just 13 and 2% variations were among populations, respectively. The UPGMA cluster analysis revealed that all of the samples grouped randomly rather than clustered into distinct groups corresponding to their populations, row types and spring/fall types. We concluded that there was high genetic diversity in the population of Shangri-la region and the formation of diversity was related to complex environment and inhabitants’ traditional practices.     

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.     

Genetic and phenotypic diversity in a germplasm working collection of cultivated tropical yams (Dioscorea spp.)

A working collection of yam (Dioscorea spp.) comprising 53 landraces and seven improved cultivars of four species (D. alata L., D. cayenensis Lam., D. dumetorum (Kunth) and D. rotundata Poir.) was evaluated for phenotypic and genetic diversity. The evaluation involved field assessment of 24 morphological traits and DNA analysis with 32 Simple sequence repeat (SSR) polymorphic markers. Diversity was greater between species than within species; highest in D. rotundata and lowest in D. alata and D. cayenensis. Analysis based on combined phenotypic and SSR marker data sets revealed a close relationship between D. rotundata and D. cayenensis, but D. alata and D. dumetorum remained as distinct species. D. alata was related genetically to D. rotundata and D. cayenensis, but phenotypically to D. dumetorum. The study showed that cultivars obtained from different farmers may bear the same name but be genetically different. Polymorphic SSR markers were identified that may be used for genetic analysis across yam species. The working collection assessed in this study represents a good gene pool for intra- and inter-specific hybridization in yam genetic improvement.     

Microsatellite-based analysis of genetic diversity in 91 commercial Brassica oleracea L. cultivars belonging to six varietal groups

Brassica oleracea L. includes various types of important vegetables that show extremely diverse phenotypes. To elucidate the genetic diversity and relationships among commercial cultivars derived by different companies throughout the world, we characterized the diversity and genetic structure of 91 commercial B. oleracea cultivars belonging to six varietal groups, including cabbage, broccoli, cauliflower, kohlrabi, kale and kai-lan. We used 69 polymorphic microsatellite markers showing a total of 359 alleles with an average number of 5.20 alleles per locus. Polymorphism information content (PIC) values ranged from 0.06 to 0.73, with an average of 0.40. Among the six varietal groups, kohlrabi cultivars exhibited the highest heterozygosity level, whereas kale cultivars showed the lowest. Based on genetic similarity values, an UPGMA clustering dendrogram and a two-dimensional scale diagram (PCoA) were generated to analyze genetic diversity. The cultivars were clearly separated into six different clusters with a tendency to cluster into varietal groups. Model-based structure analysis revealed six genetic groups, in which cabbage cultivars were divided into two subgroups that were differentiated by their head shape, whereas cauliflower and kai-lan cultivars clustered together into a single group. Furthermore, we identified 18 SSR markers showing 27 unique alleles specific to only one cultivar that can be used to discriminate 22 cultivars from the others. Our phylogenetic and population structure analysis presents new insights into the genetic structure and relationships among 91 B. oleracea cultivars and provides valuable information for breeding of B. oleracea species. In addition, we demonstrate the utility of SSR markers as a powerful tool for discriminating between the cultivars. The SSR markers described herein will also be helpful for Distinctness, Uniformity and Stability (DUS) test of new cultivars.     

Diversity and differentiation of <Emphasis Type="Italic">Oryza sativa</Emphasis> and <Emphasis Type="Italic">O. rufipogon</Emphasis> in Indonesia

Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F _ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.     

Genetic variability in Malacomeles denticulata (Rosaceae) from central Mexico revealed with SSR markers

Alternative berry crops belonging with the Rosaceae family currently have a great importance in the US and Canadian agribusiness, in this sense, the Mexican serviceberry (Malacomeles denticulata) is a fruit shrub mainly distributed in Mexico that has potential uses like horticultural crop; however, little information about its variability has been reported. That is why this research aims to determine the variability of M. denticulata by SSR markers. The apple SSR markers had a good transferability to Malacomeles (74 %); all transferable SSR are polymorphic and sixteen of them had high values of polymorphic information content, Nei’s expected heterozygosity (H_e), and Shannon’s information index (I), even the apple SSR loci were not previously proved in this species. Besides it was found high variability in the germplasm of central Mexico mainly within populations (72 %), where three different genetic pool were detected suggesting that a breeding program could be based in individual selection. That is why it is necessary select outstanding individual into population before to make hybridizations among these selected parents.     

Genetic analysis of wheat (Triticum aestivum L.) and related species with SSR markers

Genetic diversity among 19 Triticum aestivum accessions and 73 accessions of closely related species was analyzed using simple sequence repeat (SSR) markers. Forty-four out of 497 SSR markers were polymorphic. In total 274 alleles were detected (mean 6.32 alleles per locus). The polymorphic information content (PIC) of the loci ranged from 0.3589 to 0.8854 (mean 0.7538). The D genome contained the highest mean number of alleles (6.32) followed by the A and B genomes (6.13 and 5.94, respectively). The correlation between PIC and allele number was significant in all genome groups (0.7540, 0.7361 and 0.7482 for A, B and D genomes, respectively). Among the seven homologous chromosome groups, genetic diversity was lowest in group 7 and highest in group 5. In cluster and principal component analyses, all accessions grouped according to their genomes were consistent with their taxonomic classification. Accessions with the A and D genomes were clustered into two distinct groups, and AABB accessions showed abundant genetic diversity and a close relationship. Triticum durum and T. turgidum were clustered together, consistent with their morphological similarity. Cluster analysis indicated emmer is closely related to hexaploid wheat. Compared with common wheat, higher genetic variation was detected in spelt, T. aestivum subsp. yunnanense and subsp. tibetanum. In addition, a close genetic relationship between T. polonicum and T. macha was observed. The results of the clustering and principal component analyses were essentially consistent, but the latter method more explicitly displayed the relationships among wheat and closely related species.     

Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important traits. Despite these challenges, little molecular work has been done to explore genetic diversity and relationships in wild and cultivated black raspberry germplasm. Microsatellite, or simple sequence repeat (SSR), markers are highly polymorphic codominant markers useful for studying genetic diversity, population genetics, genetic fingerprinting and other applications. We examined genetic diversity in 148 wild and cultivated black raspberry accessions using 21 polymorphic SSR markers. Black raspberry cultivars clustered tightly and showed higher than expected heterozygosity while that of wild accessions was low. Relationships between wild black raspberry accessions were poorly resolved and regional clusters were mostly absent from our analysis. Our results indicated that wild black raspberry germplasm is a relatively untapped resource available for future breeding.     

Identification of 12 EST-derived SSR markers in Lumbricus rubellus

While many species of earthworms are globally distributed, very little is known about the genetic population dynamics of this diverse group. We present the characterization of novel simple sequence repeat (SSR) markers, including primer information, number of alleles, repeat motif, and approximate size ranges, to be used in population genetic analyses of the earthworm Lumbricus rubellus Hoffmeister 1843. Specifically, we designed and characterized 12 novel, polymorphic markers derived from published expressed sequence tags (EST) for amplification in L. rubellus. The mean number of alleles per locus was 6.25 ± 1.91, indicating these markers will be sufficiently polymorphic for population genetic studies of this species.     

Characterization of Seashore Paspalum (Paspalum vaginatum Swartz) Germplasm by Transferred SSRs from Wheat, Maize and Sorghum

One hundred and thirty SSR markers from wheat, maize and sorghum were screened for the transferability to Paspalum. The transfer rate was 67.5, 49.0 and 66.8% respectively. This would be a very efficient approach for DNA marker development for species which are not well studied molecularly. The polymorphism level for transferred SSR markers was 51.5% within species (Paspalum vaginatum) and 87.1% among Paspalum species. The high level of polymorphism is directly related to the high degree of heterozygosity maintained by its way of reproduction, i.e. self-incompatibility. Forty transferred polymorphic SSR markers were selected and used for characterization and evaluation of seventy-three Paspalum accessions. In total, 209 polymorphic bands were detected from these 40 SSR markers, with an average of five polymorphic bands per marker. The Paspalum accessions clustered into three major groups. Two very similar dendrograms can be generated from either 109 or 209 polymorphic bands. This led us to determine that 18 of the transferred SSR markers were sufficient for genetically differentiating the investigated germplasm accessions. The number of SSR markers required for germplasm characterization and evaluation is discussed. This is the first report of the transfer of SSR markers from major field crops to newly emerged environmental turfgrasses.     

Genetic diversity assessment of Ethiopian tetraploid wheat landraces and improved durum wheat varieties using microsatellites and markers linked with stem rust resistance

A set of 77 markers was used to describe the genetic diversity in a group of 58 tetraploid wheat accessions. Analysis was performed using 31 neutral SSR markers, 31 SSR/STS markers linked with reported major stem rust resistance genes and 15 SSR markers linked with QTL identified for resistance to Ethiopian stem rust races of Puccinia graminis Pers. f. sp. tritici Eriks. et E. Henn. (Pgt),including Ug99. The material consisted of 32 (Triticum durum s.l. incl. T. aethiopicum Jakubz., Triticum turgidum and Triticum polonicum) landraces and 22 registered T. durum varieties from Ethiopia that were released 1966–2009 and four T. durum varieties from ICARDA. A total of 720 alleles were detected. Considering the three marker sets, the mean number of alleles was higher for major stem rust resistance gene linked markers (9.9) followed by neutral SSR markers (9.2) and markers linked with QTL for stem rust resistance (8.5). Dendrograms derived from UPGMA analysis grouped the accessions into two major clusters. The principal component analysis based on the combination of the three marker sets formed three groups. The 1st group was composed of all the improved varieties, whereas the 2nd and the 3rd group contained the landraces. All the landraces that formed the 3rd group were susceptible to Ethiopian stem rust races of Pgt including Ug99. The information on the extent of the genetic diversity of the improved varieties obtained in this investigation will be helpful for developing appropriate breeding strategies to broadening the genetic base of durum wheat varieties in further breeding programmes.     

Cross-transferability of SSR markers in <Emphasis Type="Italic">Osmanthus</Emphasis>

Developing a molecular tool kit for hybrid breeding of Osmanthus species and related genera is an important step in creating a systematic breeding program for this species. To date, molecular resources have been aimed solely at Osmanthus fragrans with little work to develop markers for other species and cultivars. The objectives of this study were to (1) determine cross-transferability of O. fragrans and Chionanthus retusus derived SSRs in diverse Osmanthus taxa, (2) quantify the influence of locus-specific factors on cross-transferability, and (3) determine the genetic relationships between accessions. We tested 70 SSR markers derived from O. fragrans and C. retusus in 24 accessions of Osmanthus. Sixty-seven markers showed transfer to at least one other Osmanthus species with an overall transfer rate of 84% of loci across taxa. Genotyping with 42 microsatellite markers yielded a total of 367 loci. Number of alleles per locus ranged from 2 to 17 with a mean of 8.7 ± 4.8. Mean observed and expected heterozygosities were 0.560 ± 0.225 and 0.688 ± 0.230, respectively. Percent of polymorphic loci ranged from 40% in Osmanthus delavayi to 100% in O. fragrans. Osmanthus fragrans had the highest mean number of alleles per locus (4.2) while O. delavayi had the lowest (1.1). A reduced suite of eight-markers can distinguish between accessions with non-exclusion probabilities of identity from 3.91E?⁰⁴ to 2.90E?⁰⁷. The SSR markers described herein will be immediately useful to characterize germplasm, identify hybrids, and aid in understanding the level of genetic diversity and relationships within the cultivated germplasm.     

SSR和SRAP标记研究油菜杂交种骨干亲本的遗传多样性

用SSR和SRAP两种分子标记方法研究51份甘蓝型油菜杂交种亲本系的遗传多样性,并对两种分子标记研究结果进行比较。结果发现,在51份材料中,45对SSR引物共扩增出194条多态性条带,平均每对引物为4.3条,25对SRAP引物共扩增出197条多态性条带,平均每对引物为7.9条。UPGMA聚类分析表明,SSR和SRAP标记都可将51份亲本材料划分为五大类群,本所选育的玻里马细胞质雄性不育系（Polima CMS）的主要保持系和恢复系都聚在同一类群的不同亚群中。根据系谱资料分析发现,SRAP标记划分的类群与系谱资料更为接近,SRAP标记更适用于遗传关系较近材料的遗传多样性分析。SRAP标记揭示的亲本间遗传距离要大于SSR标记揭示的遗传距离。两种不同标记方法揭示出油菜亲本遗传多样性的差异主要是由不同的标记方法揭示的标记位点等位基因变异数不同造成的。     

Exploitation of <Emphasis Type="Italic">Malus</Emphasis> EST-SSRs and the utility in evaluation of genetic diversity in <Emphasis Type="Italic">Malus</Emphasis> and <Emphasis Type="Italic">Pyrus</Emphasis>

A total of 8117 suitable SSR-contaning ESTs were acquired by screening from a Malus EST database, among which dinudeotide SSRs were the most abundant repeat motif, within which, CT/TC followed by AG/GA were predominant. Based on the suitable sequences, we developed 147 SSR primer pairs, of which 94 pairs gave amplifications within the expected size range while 65 pairs were found to be polymorphic after a preliminary test. Eighteen primer pairs selected randomly were further used to assess genetic relationship among 20 Malus species or cultivars. As a result, these primers displayed high level of polymorphism with a mean of 6.94 alleles per locus and UPGMA cluster analysis grouped twenty Malus accessions into five groups at the similarity level of 0.6800 that were largely congruent to the traditional taxonomy. Subsequently, all of the 94 primer pairs were tested on four accessions of Pyrus to evaluate the transferability of the markers, and 40 of 72 functional SSRs produced polymorphic amplicons from which 8 SSR loci selected randomly were employed to analyze genetic diversity and relationship among a collection of Pyrus. The 8 primer pairs produced expected bands with the similar size in apples with an average of 7.375 alleles per locus. The observed heterozygosity of different loci ranged from 0.29 (MES₉₆) to 0.83 (MES₁₃₈), with a mean of 0.55 which is lower than 0.63 reported in genome-derived SSR marker analysis in Pyrus. The UPGMA dendrogram was similar to the previous results obtained by using RAPD and AFLP markers. Our results showed that these EST-SSR markers displayed reliable amplification and considerable polymorphism in both Malus and Pyrus, and will contribute to the knowledge of genetic study of Malus and genetically closed genera.     

Polymorphism of gliadins in <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss. local populations in two primary habitats in Dagestan

Polymorphism of gliadins was investigated in Aegilops tauschii from primary habitats “4”, near Hily, and “6”, near Rukel, in Dagestan, Russia 205 individual plants were analysed (53/50 and 54/48 plants of subsp. tauschii/subsp. strangulata from the habitats “4” and “6”, respectively) and 1/7 and 18/14 different haplotypes were found among the plants of subsp. tauschii/subsp. strangulata from the habitats “4” and “6”, respectively. No direct evidences of cross-pollination were pointed out, although gliadins electrophoretic phenotypes obtained allowed to suggest that it occur in Ae. tauschii with very low frequency. The data obtained revealed that during Ae. tauschii evolutionary history a local habitat could be populated many times by different phylogenetic lineages of the species. It was found that in Dagestan, at the very edge of the species area, several different lineages belonging to different subspecies could for a long time co-exist together in a local habit, and in such case a very high level of genetic variation in Ae. tauschii could be accumulated on a square of less than one hectare. The further studies of genetic variation in Ae. tauschii local populations, based on molecular genetic methods seems to be very prospective for understanding of peculiarities of the species evolution.     

Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution

Ethiopia is at the edge of the distribution for African wild rice, Oryza longistaminata. Here, chloroplast (cp) and simple sequence repeat (SSR) markers were applied to wild rice accessions in Ethiopia to evaluate how they differ from control O. longistaminata, O. barthii and O. glaberrima accessions which originated from African countries. Based on the cp genomes of African wild rice species, maternally inherited cpINDEL markers were developed. The cp indels helped to elucidate 20 plastid types. African cultivated rice shared a particular plastid type with one of annual O. barthii. Parts of northern wild rice in Ethiopia shared Type 6 with control O. longistaminata. The north group shared another type with parts of the south group. The 16 SSR markers amplified a total of 155 alleles in 215 rice accessions, with mean allelic richness of 9.688 per locus, observed heterozygosity of 0.241, expected heterozygosity of 0.724, polymorphic information content of 0.700, and a significant genetic differentiation of 0.215. Both cpINDEL and nuclear markers analyses suggested that wild rice in Ethiopia belongs to O. longistaminata. However, they carry both a unique plastid type and different population structure from control O. longistaminata collected from other areas in Africa. We concluded that the edge of its distribution maintains unique variation. These populations are regarded as valuable genetic resources for future rice breeding.

     

Comparison of genetic variation among accessions of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> using AFLP and SSR markers

Genetic diversity of 54 accessions of Aegilops tauschii from five countries was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphisms (AFLPs). In the case of AFLP analysis, a total of 256 amplification products obtained, 234 of them were polymorphic across all the 54 accessions. A total of 224 fragments were obtained from the 24 SSR primers and 219 of fragments were polymorphic across all the genotypes screened. Based on both AFLP and SSR markers, the highest percentage of polymorphisms were obtained in Iranian and accessions of unknown origin. The highest polymorphic information content (PIC) value was observed for SSRs (0.82) while the highest marker index (MI) value was for AFLPs (8.5) reflecting the hyper-variability of the first and the distinctive nature of the second system. Principal co-ordinate analysis (PCO) revealed congruent patterns of genetic relationships for both data sets, but did not group accessions strictly according to their geographical origins. Poor correlation was found between AFLP and SSR marker loci. This low association may be due to low number of AFLP and SSR markers. These results show that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Venetian olive (<Emphasis Type="Italic">Olea europaea</Emphasis>) germplasm: disclosing the genetic identity of locally grown cultivars suited for typical extra virgin oil productions

Olive (Olea europaea L.) is one of the most important tree crops of the Mediterranean regions. In spite of the increasing appreciation of typical extra virgin olive oils at world level, based on the use of local traditional varieties, very few studies have focused on the genetic characterisation of olive cultivars of regional interest, such as those grown in Veneto, a North-Eastern Italy region. A deep knowledge of the varieties cultivated in this territory is a key step to address the product quality, to increase market demand and to certify the origin of local olive oils. Here we have analyzed olive cultivars and cultivar groups within the olive cultivation area in Veneto, from the Garda Lake to the Euganean and Trevisan hills, by using discriminant SSR markers, in order to obtain a systematic genetic survey of the Veneto regional olive germplasm patrimony. A total of 203 previously uncharacterized olive samples were collected from ancient trees still grown by local farmers. The analyzed samples included also 36 olive reference cultivars from Veneto and neighbour Regions. We found 57 unique molecular profiles out of this set of olive accessions that were split into 15 cultivar groups corresponding to genetically distinct STRUCTURE clusters. Based on a common SSR database, our 239 Venetian accessions were compared with 280 olive reference genotypes representative of the Mediterranean cultivation area. From the genetic structure analysis, it has been observed that 80% of Venetian cultivars clustered in the central Mediterranean group, about 9% and 2% with the eastern and western varieties, respectively, and all the others resulted intermixed among two or three populations. We found that regionally the most common variety was “Casaliva”, corresponding to the widely diffused cultivar “Frantoio”, while others showed identity with known varieties grown in close regions, such as “Leccino”, “Miniol”, “Capolga” and “Bianchera”. Besides these genotypes, others were not matching any known reference and therefore they could be classified as true local varieties of indigenous origin, possibly deriving from the hybridization and selection made by farmers and from their adaptation to the local soil and climate conditions.     

Aegilops tauschii Coss.: allelic variation of enzyme-encoding genes and ecological differentiation of the species

Three hundred and seven accessions of Aegilops tauschii Coss., including 160 of subsp. tauschii and 147 of subsp. strangulata, representing all the species range—from Turkey to Kirgizstan, were analyzed electrophoretically. Twenty polymorphic enzyme-encoding loci were studied, 10 of which were essentially polymorphic in Ae. tauschii. Climatic data for each of the 307 Ae. tauschii habitats were taken from WORLDCLIM database of computer system ArcGIS. Forty-nine climatic parameters were considered: precipitation, minimum, mean and maximum temperatures for each month, and also the total annual level of precipitation. The data were analyzed with multivariate statistical methods, such as Principal Components Analysis (PCA), Multiple Correspondence Analysis (MCA) and Two-Block Partial Least Squares. Variability of climatic conditions among Ae. tauschii habitats is reflected by the two approximately orthogonal “vectors”. The “first vector” is mostly determined by negative impact of precipitation and minimum temperatures during winter. The “second vector” is mostly determined by negative impact of maximum temperatures during summer, and positive impact of precipitation during late spring and summer. Aegilops tauschii is essentially variable along the “second vector”, and especially high level of variation is characteristic for subsp. tauschii. This variation reflects that Ae. tauschii is very tolerable to the climatic variation during summer season. Aegilops tauschii subsp. strangulata is also characterized by the high level of variation along the “first vector”. Moreover, all the habitats of subsp. strangulata fall into the two distinct separate clusters: the habitats in Precaspian Iran, which have the highest minimum temperatures in winter,—and all the other habitats. In the plot of the first two factors of PCA, the “cluster of Precaspian Iran” can be further divided into “Western Precaspian Iran (WPI)”, having relatively higher level of annual rainfall, and relatively dryer “Eastern Precaspian Iran (EPI)”. This three groups of subsp. strangulata accessions, from WPI, EPI and other areas, are also distinctly differed in enzyme-encoding genes allelic variation, as revealed on the plot of the first two axes of MCA. In contrast to subsp. strangulata, the level of variation of subsp. tauschii along the “first vector” is rather low. It was pointed out that variation along “the first vector” reflects adaptive intraspecies divergence of Ae. tauschii: its subspecies strangulata “prefers” the habitats of seaside climate, with warm and moist winter; while subsp. tauschii mostly occupies the habitats with rather continental climate, with relatively cold and dry winter. Allelic variation of enzyme-encoding genes Acph1, Ak, Est2, Est5, Got1, Got2, and Got3 correlate with climate along “the first vector”. Apparently, polymorphism of these loci were involved into the process of Ae. tauschii intraspecies adaptive divergence. Allelic variation of Cat2 and Fdp loci correspond to climatic variation along “the second vector” in subsp. tauschii. Therefore Cat2 and Fdp are likely to be among the genes which polymorphism “helped” subsp. tauschii to succeed in vast geographical expansion far to the east from Caspian Sea.     

Analysis of genetic diversity in the tuber mustard (Brassica juncea var. tumida Tsen et Lee) in the Yangtze river basin of China

In the present study, analyses of SSR molecular markers were performed to investigate the genetic diversity of 133 tuber mustard cultivars. Eighty-one pairs of SSR primers from a total of 600 in Brassica produced stable amplified bands. In addition, 810 bands were detected among the cultivars, and 724 of those were polymorphic (89.38 %). The average number of bands per locus was 10.0 with a range from 5 to 16. Shannon’s information index for each SSR locus varied from 0.52 to 3.72, with an average of 2.74. The coefficients of genetic similarity in the SSR marker patterns among the 133 cultivars ranged from 0.77 to 0.91, with an average of 0.85. The cluster analysis showed that the cultivars could be classified into six clusters when the genetic similarity was 0.83, with 90.23 % of the cultivars included in Clusters 5 and 6. Principal component analysis was carried based on the SSR data. The results showed that the first three principal components could explain the genetic variation with 85.47, 0.67, and 0.61 %, and the 133 cultivars could be divided into six clusters according to the nearest phylogenetic relationship. It was indicated that the similarity was high and the genetic diversity was narrow among the 133 mustard tuber cultivars. 360 individuals from 24 cultivars were analyzed to reveal the genetic structure and genetic diversity within cultivars. A total of 925 alleles were detected in the 24 cultivars. Estimates of the mean number of alleles ‘A’, the effective allelic number ‘A_e’, the observed heterozygosity ‘H_o’, and expected heterozygosity ‘H_e’ were 6.0, 3.6, 0.64, and 0.37, respectively. An obvious genetic deviation from Hardy–Weinberg expectation was observed both among and within cultivars and a considerable genetic variation was revealed within rather than among cultivars. It is necessary to broaden the genetic basis of the breeding germplasm in tuber mustard. Based on their geographical distributions, the tuber mustard cultivars in this study can be divided into up-Yangtze river, mid-Yangtze river, and down-Yangtze river groups. Genetic diversity was highest in mid-Yangtze river group, followed by up-Yangtze river group, and then down-Yangtze river group. It was presumed that the origin center or genetic diversity center of tuber mustard was mid-Yangtze river, and the crop was transmitted along the Yangtze river in both directions.