Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs

Background

Peanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis.

Results

Two hundred ninety eight (298) loci were mapped in 21 linkage groups (LGs), spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC₁F₁ and then BC₂F₁ lines carrying the desirable donor segment with the best possible return to the background of the cultivated variety provided a set of lines offering an optimal distribution of the wild introgressions.

Conclusion

The genetic map developed, allowed the synteny analysis of the A and B genomes, the comparison with diploid and tetraploid maps and the analysis of the introgression segments from the wild synthetic into the background of a cultivated variety. The material we have produced in this study should facilitate the development of advanced backcross and CSSL breeding populations for the improvement of cultivated peanut.     

RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species.

Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.35-4.65) than for SSR primers (0.35-1.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.     

Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species

Polyploidy creates severe genetic bottlenecks, contributing to the genetic vulnerability of leading crops. Cultivated peanut is thought to be of monophyletic origin, harboring relatively little genetic diversity. To introduce variability from diploid wild species into tetraploid cultivated Arachis hypogaea, a synthetic amphidiploid [[A. batizocoi K9484 x (A. cardenasii GKP10017 x A. diogoi GKP10602)](4x)] was used as donor parent to generate a backcross population of 78 progeny. Three hundred seventy RFLP loci were mapped onto 23 linkage groups, spanning 2210 cM. Chromatin derived from the two A-genome diploid ancestors (A. cardenasii and A. diogoi) comprised mosaic chromosomes, reflecting crossing over in the diploid A-genome interspecific F(1) hybrid. Recombination between chromosomes in the tetraploid progeny was similar to chromosome pairing reported for A. hypogaea, with recombination generally between chromosomes of the same subgenomic affinity. Segregation distortion was observed for 25% of the markers, distributed over 20 linkage groups. Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed.     

野生花生种质的SSR遗传多样性

以花生属(Arachis)6个区组24种(包括栽培种)84份种质为材料,用SSR技术对其亲缘关系和遗传多样性进行了分析.从206对SSR引物中筛选到59对能扩增出稳定的多态性条带的引物,这些引物能在花生属基因组DNA中扩增出1～6个DNA片段.结果表明,84份种质的遗传距离为0.04～0.93,平均为0.64,其中匍匐区组的A.appressipila的2份种质(G4与G5)的遗传距离最小(0.04),匍匐区组的A.rigonii(G14)与根茎区组的A.glabrata(G28)的遗传距离最大(0.93).聚类分析结果与花生属的区组分类基本一致,栽培种花生被聚在花生区组中,而且7份栽培种被聚在同一亚亚组中,相同植物学类犁(相当于变种)的材料均被分别聚在一起.异形花区组与直立区组的亲缘关系最近,与花生区组的亲缘关系较近的是匍匐区组.花牛区组的二倍体野生种A.villosa、A.duranensis和A.benensis与栽培种化生关系较近,可以作为桥梁物种来转移其他野生花生的优良基因.     

Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp.

Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81.5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23.3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0.37 to 0.97. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9604-8) contains supplementary material, which is available to authorized users.     

Cloning and Characterization of Chromosomal Markers from a Cot-1 Library of Peanut ( Arachis hypogaea L.)

The cultivated peanut, Arachis hypogaea (AABB, 2n = 40), is an allotetraploid which was probably originated from a hybridization event between 2 ancestors, A. duranensis (A genome) and A. ipaensis (B genome) followed by chromosome doubling. The wild species in the Arachis section are useful genetic resources for genes that confer biotic and abiotic stress resistance for peanut breeding. However, the resource is not well exploited because little information on the genetic, cytogenetic, and phylogenetic relationships between cultivated peanut and its wild relatives is known. Characterization of its chromosome components will benefit the understanding of these issues. But the paucity of information on the DNA sequence and the presence of morphologically similar chromosomes impede the construction of a detailed karyotype for peanut chromosome identification. In our study, a peanut Cot-1 library was constructed to isolate highly and moderately repetitive sequences from the cultivated peanut, and the chromosomal distributions of these repeats were investigated. Both genome and chromosome specific markers were identified that allowed the distinguishing of A and B genomes in tetraploid peanut and a possible karyotyping of peanut chromosomes by FISH. In particular, a 115-bp tandem repetitive sequence was identified to be a possible centromere repetitive DNA, mainly localized in the centromeres of B chromosomes, and a partial retrotransposable element was also identified in the centromeres of B chromosomes. The cloning and characterization of various chromosomal markers is a major step for FISH-based karyotyping of peanut. The FISH markers are expected to provide a reference tool for sequence assembly, phylogenetic studies of peanut and its wild species, and breeding.     

A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae)

Cultivated peanut (Arachis hypogaea) is an important crop, widely grown in tropical and subtropical regions of the world. It is highly susceptible to several biotic and abiotic stresses to which wild species are resistant. As a first step towards the introgression of these resistance genes into cultivated peanut, a linkage map based on microsatellite markers was constructed, using an F₂ population obtained from a cross between two diploid wild species with AA genome (A. duranensis and A. stenosperma). A total of 271 new microsatellite markers were developed in the present study from SSR-enriched genomic libraries, expressed sequence tags (ESTs), and by “data-mining” sequences available in GenBank. Of these, 66 were polymorphic for cultivated peanut. The 271 new markers plus another 162 published for peanut were screened against both progenitors and 204 of these (47.1%) were polymorphic, with 170 codominant and 34 dominant markers. The 80 codominant markers segregating 1:2:1 (P<0.05) were initially used to establish the linkage groups. Distorted and dominant markers were subsequently included in the map. The resulting linkage map consists of 11 linkage groups covering 1,230.89 cM of total map distance, with an average distance of 7.24 cM between markers. This is the first microsatellite-based map published for Arachis, and the first map based on sequences that are all currently publicly available. Because most markers used were derived from ESTs and genomic libraries made using methylation-sensitive restriction enzymes, about one-third of the mapped markers are genic. Linkage group ordering is being validated in other mapping populations, with the aim of constructing a transferable reference map for Arachis.Electronic supplementary material is available for this at     

Physical mapping of the 5S and 18S-25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae)

The 5S and the 18S-25S rRNA genes were physically mapped by fluorescent in situ hybridization (FISH) in all botanical varieties of cultivated peanut Arachis hypogaea (2n = 4x = 40), in the wild tetraploid A. monticola, and in seven wild diploid species considered as putative ancestors of the tetraploids. A detailed karyotype analysis including the FISH signals and the heterochromatic bands was carried out. Molecular cytogenetic landmarks are provided for the construction of a FISH-based karyotype in Arachis species. The size, number, and chromosome position of FISH signals and heterochromatic bands are similar in all A. hypogaea varieties and A. monticola, but vary among the diploid species. Genome constitution of the species is discussed and several chromosome homeologies are established. The bulk of the chromosome markers mapped, together with data on geographical distribution of the taxa, suggest that peanut originated upon domestication of A. monticola and evidence that the diploids A. duranensis and A. ipaensis are the most probable ancestors of both tetraploid species. Allopolyploidy could have arisen by a single event or, if by multiple events, always from the same diploid species.     

High segregation distortion in maize B73 x teosinte crosses

Two genetic linkage maps of cultivated maize inbred lines and teosinte species were constructed. One population comprised 81 F(2) individuals derived from a cross between maize inbred line B73 and Zea mays ssp parviglumis, while the second consisted of 63 backcross individuals from a cross of maize inbred line B73 with Z. mays ssp diploperennis. In the B73 x Z. mays ssp parviglumis F(2) population, 172 simple sequence repeat (SSR) markers were mapped to 10 chromosomes, which covered 2210.8 cM. In the B73 x Z. mays ssp diploperennis backcross population, 258 SSR markers were mapped to 10 chromosomes, covering 1357.7 cM. Comparison of the two maps revealed that the total map length of Z. mays ssp diploperennis covers 1357.7 cM, which is about 61.4% of that of Z. mays ssp parviglumis (2210.8 cM). Extensive segregation distortion regions were found on chromosomes 1, 2, 3, 5, 6, 7, and 10 in the B73 x Z. mays ssp parviglumis F(2) population and on chromosomes 1-5 and 8-10 in the B73 x Z. mays ssp parviglumis backcross population. Segregation distortion analysis confirmed that the segregation distortion ratio in the interspecific population B73 x Z. mays ssp diploperennis was higher than in B73 x Z. mays ssp parviglumis. We found that the recombination distances are highly variable in these genetic crosses between cultivated and wild species of maize.     

Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome

Background  

The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives.     

Introgression of homeologous quantitative trait loci (QTLs) for resistance to the root-knot nematode [Meloidogyne arenaria (Neal) Chitwood] in an advanced backcross-QTL population of peanut (Arachis hypogaea L.)

Resistance to root-knot nematodes [Meloidogyne arenaria (Neal) Chitwood] is needed for cultivation of peanut in major peanut-growing areas, but significant resistance is lacking in the cultivated species (Arachis hypogaea L.). Markers to two closely-linked genes introgressed from wild relatives of peanut have been identified previously, but phenotypic evidence for the presence of additional genes in wild species and introgression lines has eluded quantitative trait locus (QTL) identification. Here, to improve sensitivity to small-effect QTLs, an advanced backcross population from a cross between a Florunner component line and the synthetic amphidiploid TxAG-6 [Arachis batizocoi × (A. cardenasii × A. diogoi)]^4× was screened for response to root-knot nematode infection. Composite interval mapping results suggested a total of seven QTLs plus three putative QTLs. These included the known major resistance gene plus a second QTL on LG1, and a potentially homeologous B-genome QTL on LG11. Additional potential homeologs were identified on linkage group (LG) 8 and LG18, plus a QTL on LG9.2 and putative QTLs on LG9.1 and 19. A QTL on LG15 had no inferred resistance-associated homeolog. Contrary to expectation, two introgressed QTLs were associated with susceptibility, and QTLs at some homeologous loci were found to confer opposite phenotypic responses. Long-term functional conservation accompanied by rapid generation of functionally divergent alleles may be a singular feature of NBS-LRR resistance gene clusters, contributing to the richness of resistance alleles available in wild relatives of crops. The significance for peanut evolution and breeding is discussed.     

The phylogenetic relationship of possible progenitors of the cultivated peanut

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid composed of A and B genomes. The phylogenetic relationship among the cultivated peanut, wild diploid, and tetraploid species in the section Arachis was studied based on sequence comparison of stearoyl-ACP desaturase and oleoyl-PC desaturase. The topology of the trees for both fatty acid desaturases displayed two clusters; one cluster with A genome diploid species and the other with B genome diploid species. The two homeologous genes obtained for each of the two fatty acid desaturases from the tetraploid species A. hypogaea and A. monticola were separated into the A and B genome clusters, respectively. The gene phylogenetic trees showed that A. hypogaea is more closely related to the diploid species A. duranensis and A. ipaensis than to the wild tetraploid species A. monticola, suggesting that A. monticola is not a progenitor of the cultivated peanut. In addition, for the stearoyl-ACP desaturase, the A. duranensis sequence was identical with one of the sequences of A. hypogaea and the A. ipaensis sequence was identical with the other. These results support the hypothesis that A. duranensis and A. ipaensis are the most likely diploid progenitors of the cultivated tetraploid A. hypogaea.     

Characterization of polymorphic microsatellite loci in cultivated and wildPanax ginseng

Ginseng (Panax ginseng) is one of the most important herbal remedies used in East Asia. The present study investigated six polymorphic microsatellite markers (PG29, PG281, PG287, PG668, PG1319, and PG1481) in samples of cultivated and wildP. ginseng collected in Korea. Total allelic number observed in this study was 27 (average allelic numbers per locus: 4.5). All examined loci exhibited deviation from the Hardy-Weinberg equilibrium and deficiency of heterozygosity in both cultivated and wild groups. Although the wild ginseng group exhibited slightly more polymorphic behavior (mean PIC=0.392, GD=0.454 and H_obs=0.129), compared with the cultivated group (mean PIC=0.383, GD=0.438 and H_obs=0.105), no significant differences of allele frequencies and genotype distributions were revealed. By combined analysis of six loci in 100 cultivated ginsengs, 71 different types were observed. The analyzed microsatellite loci in this study will be helpful for understanding genetic variation, QTL mapping and phylogenic studies inPanax species.     

An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations

Construction and improvement of a genetic map for peanut (Arachis hypogaea L.) continues to be an important task in order to facilitate quantitative trait locus (QTL) analysis and the development of tools for marker-assisted breeding. The objective of this study was to develop a comparative integrated map from two cultivated × cultivated recombinant inbred line (RIL) mapping populations and to apply in mapping Tomato spotted wilt virus (TSWV) resistance trait in peanut. A total of 4,576 simple sequence repeat (SSR) markers from three sources: published SSR markers, newly developed SSR markers from expressed sequence tags (EST) and from bacterial artificial chromosome end-sequences were used for screening polymorphisms. Two cleaved amplified polymorphic sequence markers were also included to differentiate ahFAD2A alleles and ahFAD2B alleles. A total of 324 markers were anchored on this integrated map covering 1,352.1 cM with 21 linkage groups (LGs). Combining information from duplicated loci between LGs and comparing with published diploid maps, seven homoeologous groups were defined and 17 LGs (A1-A10, B1-B4, B7, B8, and B9) were aligned to corresponding A-subgenome or B-subgenome of diploid progenitors. One reciprocal translocation was confirmed in the tetraploid-cultivated peanut genome. Several chromosomal rearrangements were observed by comparing with published cultivated peanut maps. High consistency with cultivated peanut maps derived from different populations may support this integrated map as a reliable reference map for peanut whole genome sequencing assembling. Further two major QTLs for TSWV resistance were identified for each RILs, which illustrated the application of this map.     

Random amplified polymorphic DNA (RAPD) analysis reveals genetic relationships among the annual Cicer species

 Random amplified polymorphic DNA markers were used to distinguish between nine different Cicer taxa representing the cultivated chickpea and eight other related annual wild species. Of the 75 random10-mer primers tested, only 8 amplified genomic DNA across all the species. A total of 115 reproducibly scorable RAPD markers were generated, all except 1 polymorphic, and these were utilized to deduce genetic relationships among the annual Cicer species. Four distinct clusters were observed and represented C. arietinum, C. reticulatum and C. echinospermum in first cluster followed by C. chorassanicum and C. yamashitae in the second cluster, while C. pinnatifidum, C. judaicum and C. bijugum formed the third cluster. Cicer cuneatum did not cluster with any of the species and was most distantly placed from the cultivated species. Except for the placement of C. chorassanicum and C. yamashitae, deduced species’ relationships agreed with previous studies. In addition, species-diagnostic amplification products specific to all the nine species were identified. The results clearly demonstrate a methodology based on random-primed DNA amplification that can be used for studying Cicer phylogeny and chickpea improvement. Received: 27 July 1998 / Accepted: 5 August 1998     

Putative genome donors ofArachis hypogaea (Fabaceae), evidence from crosses with synthetic amphidiploids

Chromosome pairing, pollen and pod fertility in hybrids between cultivated tetraploidArachis hypogaea and 15 synthetic amphidiploids from 8 diploid species (7 of the A genome and 1 of the B genome) of sect.Arachis have been utilized for the identification of putative genome donors in the evolution of cultivatedA. hypogaea. These results, in conjunction with evidence from morphological similarities, phytogeographical distribution and some phytochemical features, confirm the segmental amphidiploid origin ofA. hypogaea. A. batizocoi andA. duranensis are suggested as the donors of the B genome and the A genome respectively.     

Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis,Fabaceae)

This work reports the characterization of 11 polymorphic microsatellite loci in section Caulorrhizae. The primer pairs were designed from Arachis pintoi and showed full transferability to Arachis repens species. These new markers were used to evaluate the genetic diversity in germplasm (accessions and cultivars) of section Caulorrhizae. This new set of markers detected greater gene diversity than morphological and molecular markers such as AFLP (amplified fragment length polymorphism) and RAPD (rapid analysis of polymorphic DNA) previously used in this germplasm.     

Nuclear and chloroplast DNA differentiation in Andean potatoes.

Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T-type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry.     

Development and chromosomal localization of genome-specific markers by polymerase chain reaction in Brassica

Summary This paper reports the application of the RAPD (random amplification of polymorphic DNA sequence) markers in Brassica genetics. Forty-seven arbitrary decamer oligonucletides were used as primers to amplify genomic DNA by polymerase chain reaction. Some of the amplified products were genome specific and could be found in both diploid and derived amphidiploid species. Of a total of 65 such markers, 16 were A genome, 37 B genome, and 12 C genome specific. Of the 37 B-genome-specific markers, 11 were mapped on four independent chromosomes of B. nigra with the aid of existing B. napus-nigra disomic alien addition lines.