Genealogical use of chloroplast DNA variation for intraspecific studies of Aegilops tauschii Coss.

Intraspecific patterns of chloroplast DNA variation was studied in Aegilops tauschii Coss., the D-genome progenitor of bread wheat. Nucleotide sequences of ten chloroplast microsatellite loci were analyzed for 63 accessions that cover the central part of the species distribution. As is often the case with nuclear microsatellites, those of chloroplasts of Ae. tauschii bear complex mutations. Several types of mutations other than change in the microsatellite repeat number were found, including base substitutions and length mutations in flanking regions. In total, eight mutations were present in the flanking regions of four loci. Most mutations in the flanking regions of microsatellite repeats are associated with biallelic polymorphisms. Phylogeographic analyses showed that such biallelic polymorphisms are useful to investigate intraspecific patterns of monophyletic lineage divergence. In contrast, most microsatellite repeat sites are multiallelic, variable within intraspecific lineages, and useful to compare degrees of genetic diversity between lineages. These findings show that the chloroplast genome harbors evolutionary variations informative for intraspecific studies of Ae. tauschii and can be analyzed by genealogical approaches.Electronic Supplementary Material Supplementary material is available for this article at     

Flowering time diversification and dispersal in central Eurasian wild wheat Aegilops tauschii Coss.: genealogical and ecological framework

Timing of flowering is a reproductive trait that has significant impact on fitness in plants. In contrast to recent advances in understanding the molecular basis of floral transition, few empirical studies have addressed questions concerning population processes of flowering time diversification within species. We analyzed chloroplast DNA genealogical structure of flowering time variation in central Eurasian wild wheat Aegilops tauschii Coss. using 200 accessions that represent the entire species range. Flowering time measured as days from germination to flowering varied from 144.0 to 190.0 days (average 161.3 days) among accessions in a common garden/greenhouse experiment. Subsequent genealogical and statistical analyses showed that (1) there exist significant longitudinal and latitudinal clines in flowering time at the species level, (2) the early-flowering phenotype evolved in two intraspecific lineages, (3) in Asia, winter temperature was an environmental factor that affected the longitudinal clinal pattern of flowering time variation, and (4) in Transcaucasus-Middle East, some latitudinal factors affected the geographic pattern of flowering time variation. On the basis of palaeoclimatic, biogeographic, and genetic evidence, the northern part of current species' range [which was within the temperate desert vegetation (TDV) zone at the Last Glacial Maximum] is hypothesized to have harbored species refugia. Postglacial southward dispersal from the TDV zone seems to have been driven by lineages that evolved short-flowering-time phenotypes through different genetic mechanisms in Transcaucasus-Middle East and Asia.     

基于穗形特征与分子标记进行中国节节麦核心种质的创建

节节麦是普通小麦D基因组供体,遗传多样性丰富,而我国节节麦资源是有别于中东节节麦资源的重要基因源。为了合理高效地管理、评价、保护和利用我国节节麦资源,本研究将野生采集的762份中国节节麦资源作为试验材料,基于SSR标记分组状况,利用小穗长、护颖长、护颖宽、外稃长、外稃宽、内稃长、内稃宽、穗宽、粒长和粒宽等10个穗形性状指标,在欧氏距离、马氏距离和4种取样比例下构建节节麦核心种质候选集。进而采用均值差异百分率、极差符合率、方差差异百分率及变异系数变化率4个指标对不同方法构建的核心种质候选集的可行性和有效性进行评价,并利用原种质和核心种质的主成分分析法进行验证,最终确定基于欧氏距离、10%取样比例下、采用最小距离逐步取样法构建的包含76个样品的节节麦核心种质能够以最小的资源份数、最大限度地代表我国节节麦的遗传多样性。     

Genetic diversity of Iranian <Emphasis Type="Italic">Aegilops tauschii</Emphasis> Coss. using microsatellite molecular markers and morphological traits

Aegilops tauschii Coss. is a diploid (2n = 2x = 14,DD) goat grass species which has contributed the D genome in common wheat. Genetic variations in 28 accessions of Aegilops tauschii belonged to different provinces of Iran, were evaluated using 16 morphological traits and 19 SSR markers. In number of spikelet per spike and plant height, there was a high variation in ssp. tauschii and ssp. strangulata respectively and for days to mature a low variation in both subspecies was found. Discriminant function analysis showed that 67.9% of original grouped cases correctly classified. Factor analysis indicated that three factor explain 66.49% of total variation. The three clusters revealed by the cluster analysis were not consistent with their geographical distributions. We determined 208 alleles using 19 microsatellites. Average of alleles for every locus was 10.94. The total average of PIC was 0.267. 2261 bands produced for total of genotypes and Chinese Spring had the highest bands (95 alleles). The range of similarity coefficients was between 0.23 and 0.73. Genotypes were clustered using UPGMA method. The accessions did not match according to morphological cluster and geographical regions. 51.2% of total variations were related to 9 principle components.     

Population structure of wild wheat D‐genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat

Aegilops tauschii Coss. is the D‐genome progenitor of hexaploid wheat. Aegilops tauschii, a wild diploid species, has a wide natural species range in central Eurasia, spreading from Turkey to western China. Amplified fragment length polymorphism (AFLP) analysis using a total of 122 accessions of Ae. tauschii was conducted to clarify the population structure of this widespread wild wheat species. Phylogenetic and principal component analyses revealed two major lineages in Ae. tauschii. Bayesian population structure analyses based on the AFLP data showed that lineages one (L1) and two (L2) were respectively significantly divided into six and three sublineages. Only four out of the six L1 sublineages were diverged from those of western habitats in the Transcaucasia and northern Iran region to eastern habitats such as Pakistan and Afghanistan. Other sublineages including L2 were distributed to a limited extent in the western region. Subspecies strangulata seemed to be differentiated in one sublineage of L2. Among three major haplogroups (HG7, HG9 and HG16) previously identified in the Ae. tauschii population based on chloroplast variation, HG7 accessions were widely distributed to both L1 and L2, HG9 accessions were restricted to L2, and HG16 accessions belonged to L1, suggesting that HG9 and HG16 were formed from HG7 after divergence of the first two lineages of the nuclear genome. These results on the population structure of Ae. tauschii and the genealogical relationship among Ae. tauschii accessions should provide important agricultural and evolutionary knowledge on genetic resources and conservation of natural genetic diversity.     

Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.)

Powdery mildew is a major fungal disease in wheat growing areas worldwide. A novel source of resistance to wheat powdery mildew present in the germplasm line NC97BGTD7 was genetically characterized as a monogenic trait in greenhouse and field trials using F₂ derived lines from a NC97BGTD7 X Saluda cross. Microsatellite markers were used to map and tag this resistance gene, now designated Pm34. Three co-dominant microsatellite markers linked to Pm34 were identified and their most likely order was established as: Xbarc177-5D, 5.4cM, Pm34, 2.6cM, Xbarc144-5D, 14cM, Xgwm272-5D. These microsatellite markers were previously mapped to the long arm of the 5D chromosome and their positions were confirmed using Chinese Spring nullitetrasomic Nulli5D-tetra5A and ditelosomic Dt5DL lines. Pm2, the only other known Pm gene on chromosome 5D, has been mapped to the short arm and its specificity is different from that of Pm34.     

A high-density genetic linkage map of Aegilops tauschii, the D-genome progenitor of bread wheat

 Aegilops tauschii is the diploid D-genome progenitor of bread wheat (Triticum aestivum L. em Thell, 2n=6x=42, AABBDD). A genetic linkage map of the Ae. tauschii genome was constructed, composed of 546 loci. One hundred and thirty two loci (24%) gave distorted segregation ratios. Sixty nine probes (13%) detected multiple copies in the genome. One hundred and twenty three of the 157 markers shared between the Ae. tauschii genetic and T. aestivum physical maps were colinear. The discrepancy in the order of five markers on the Ae. tauschii 3DS genetic map versus the T. aestivum 3D physical map indicated a possible inversion. Further work is needed to verify the discrepancies in the order of markers on the 4D, 5D and 7D Ae. tauschii genetic maps versus the physical and genetic maps of T. aestivum. Using common markers, 164 agronomically important genes were assigned to specific regions on Ae. tauschii linkage, and T. aestivum physical, maps. This information may be useful for map-based cloning and marker-assisted plant breeding. Received: 23 March 1998 / Accepted: 27 October 1998     

Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers

Asparagus officinalis L. is a dioecious perennial plant globally known for its fine flavor and high nutritional value. An evaluation of genetic diversity in 46 asparagus accessions was carried out based on morphological and inter-simple sequence repeat (ISSR) markers. The result show that the coefficient of variation for 20 morphological characteristics is between 12.45 and 62.22%. Factor analysis revealed that nine factors explained 83.37% of the total variance. At Euclidean distance of 135.7, 46 accessions were divided into two clusters. Genetic similarity coefficient (GSC) based on ISSR data ranged from 0.60 to 0.97, suggesting a relatively abundant genetic base. Furthermore, the 46 asparagus accessions could also be grouped into three major clusters at a GSC of 0.74. And there is no significant relation between the two marker systems using the Mantel test. Clustering based on morphological traits compared with that based on ISSR data was not consistent, however, some common groupings were observed between two dendrograms. Therefore the results elucidated asparagus germplasm genetic background and determined hybrid parents, which will facilitate optimal application of asparagus germplasm resources and provide additional data for genetic improvement.

     

Evaluation of bamboo genetic diversity using morphological and SRAP analyses

Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections.     

Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r = 0.78) was better than that of the RAPD marker system (r = 0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.     

Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran

Background and Aims: The diploid goat grass Aegilops tauschii (2n = 2x = 14) is nativeto the Middle East and is the D-genome donor to hexaploid breadwheat. The aim of this study was to measure the diversity ofdifferent subspecies and varieties of wild Ae. tauschii collectedacross the major areas where it grows in Iran and to examinepatterns of diversity related to the taxa and geography. Methods: Inter-retroelement amplified polymorphism (IRAP) markers wereused to analyse the biodiversity of DNA from 57 accessions ofAe. tauschii from northern and central Iran, and two hexaploidwheats. Key Results: Eight IRAP primer combinations amplified a total of 171 distinctDNA fragments between 180 and 3200 bp long from the accessions,of which 169 were polymorphic. On average, about eight fragmentswere amplified with each primer combination, with more bandsbeing amplified from accessions from the north-west of the countrythan from other accessions. Conclusions: The IRAP markers showed high levels of genetic diversity. Analysisof all accessions together did not allow the allocation of individualsto taxa based on morphology, but showed a tendency to put accessionsfrom the north-west apart from others regions. It is speculatedthat this could be due to different activity of retroelementsin the different regions. Within the two taxa with most accessions,there was a range of IRAP genotypes that could be correlatedclosely with geographical origin. This supports suggestionsthat the centre of origin of the species is towards the south-eastof the Caspian Sea. IRAP is an appropriate marker system toevaluate genetic diversity and evolutionary relationships withinthe taxa, but it is too variable to define the taxa themselves,where more slowly evolving morphological, DNA sequence or chromosomalmakers may be more appropriate.     

Assessment of genetic diversity and relatedness among Tunisian almond germplasm using SSR markers

Genetic diversity of 50 Tunisian almond (Prunus dulcis Mill.) genotypes and their relationships to European and American cultivars were studied. In total 82 genotypes were analyzed using ten genomic SSRs. A total of 159 alleles were scored and their sizes ranged from 116 to 227 bp. The number of alleles per locus varied from 12 to 23 with an average of 15.9 alleles per locus. Mean expected and observed heterozygosities were 0.86 and 0.68, respectively. The total value for the probability of identity was 4 × 10(-13) . All SSRs were polymorphic and they were able all together to distinguish unambiguously the 82 genotypes. The Dice similarity coefficient was calculated for all pair wise and was used to construct an UPGMA dendrogram. The results demonstrated that the genetic diversity within local almond cultivars was important, with clear geographic divergence between the northern and the southern Tunisian cultivars. The usefulness of SSR markers for almond fingerprinting, detection of synonyms and homonyms and evaluation of the genetic diversity in the Tunisian almond germplasm was also discussed. The results confirm the potential value of genetic diversity preservation for future breeding programs.     

高大山羊草(Aegilops longissima Schweinf.and Muschl.)遗传多样性的RAPD分析

通过70个 RAPD 引物对高大山羊草15份材料进行扩增,共扩增出766条带,其中无多态性(即相同带)的带115条,占总带数的15%,有多态性的带651条,占总带数的85%。通过分析,发现高大山羊草的 Y315、Y316、Y317与其它12份材料差异很大,这3份材料的特异带有253条,占整个多态性带数的38.9%。经 NTSYS 系统聚类表明,高大山羊草 Y315、Y316、Y317这3份材料为一个类群,而其余12份材料为另一类群;这2个类群中任何一份山羊草与另一类群中任何一份山羊草的遗传距离均很大,变幅为1.38～1.58,是它们各自类群内遗传距离的3倍以上。鉴于这两类材料在分子水平的 RAPD 扩增产物上差异很大,并考虑到这两个类群在形态上也确实存在明显差异,因而建议将高大山羊草分为两个亚种,当然这一观点还有待收集更多的材料做进一步的研究。     

Deciphering the genetic diversity and population structure of Turkish bread wheat germplasm using iPBS-retrotransposons markers

Molecular Biology Reports - Research activities aiming to investigate the genetic diversity are very crucial because they provide information for the breeding and germplasm conservation activities....     

Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely ‘underutilized’ due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still ‘lagging’ cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11–12% of SSR loci pairs revealed a significant LD. At the significance threshold (r² ≥ 0.1), a genome-wide average of LD declines within the genetic distance at < 10 cM in the landrace stocks germplasm and > 30 cM in variety germplasm. Genome wide LD at r² ≥ 0.2 was reduced on average to  1–2 cM in the landrace stock germplasm and 6–8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historical meiotic events, should be useful to effectively exploit potentially new genetic variation by using MAS programs.     

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.