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In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P over the 21 retained SSR loci close to 10. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H of 0.82 and observed heterozygosity H of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (F = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as 'King of Pippin' and 'Calville Rouge d'Hiver' as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity. [ABSTRACT FROM AUTHOR]

The common bean, an important source of protein and minerals for humans, complements cereals both nutritionally and as a rotation crop, supplying nitrogen and reducing soil pathogens. The aim of this study was to develop an operational SNP-based panel for common bean in order to facilitate SSR employment in genetic diversity and population structure analyses, and its use in breeding programs. A set of 88 diverse and important common bean cultivars/lines (53), landraces (33) and wild accessions (2) were genotyped. Overall, the 58 SSRs performed better at evaluating genetic diversity ( Ā = 7.38; He = 58.7 %; PI = 1.20E−45) than the 345 SNPs, of which the SSRs dinucleotides (SSR-di) were more informative ( Ā = 9.92; He = 72.5 %; PI = 3.40E−26) and a selected set of 13 SSRs ( Ā = 15.31/locus; He = 84.5 %; PI = 1.03E−19) allowed for the discrimination of all individuals. For the 345 high-quality scored SNPs a low combined PI (4.70E−119) and high PE (100 %) was obtained for the assessment of parentage and identity. The SNPs were very useful for linkage mapping in inter- (78.2 %) and intra-gene pool (17.7 %) crosses. Both markers afforded high resolution detection of inter-gene pool structure, with greater differentiation based on SNPs ( K = 2, F = 0.759). The SSRs-di differentiated cultivars/lines and landraces ( K = 3) of Mesoamerican origin. A set of 16 SSRs was selected to establish a routine and operational analysis of Genbank accessions allowing an efficient origin-based discrimination of common bean accessions. Operational genotyping panels based on SSRs and SNPs were derived, contributing to the growing integration of genomics with molecular breeding programs of the common bean. [ABSTRACT FROM AUTHOR]

Hazelnut ( Corylus avellana L.), a member of the family Betulaceae and the order Fagales, is native to Europe, Turkey, and the Caucasus. It has been cultivated for more than 5000 years. The majority of cultivars were selected from local wild populations over the past few centuries. Hazelnut is native to northern Portugal, with local production from landrace clonal selections. In recent years, hazelnut production has declined, and landraces are in danger of being lost. In this study, we used 16 microsatellite markers to investigate genetic diversity in wild populations, Portuguese landraces, and reference cultivars. A high level of polymorphism was found, as indicated by mean values for expected heterozygosity (0.74), observed heterozygosity (0.71), and polymorphism information content (0.78). A neighbor-joining dendrogram showed a clear separation of the wild genotypes from the landraces and reference cultivars. Bayesian analysis placed individuals in three groups, showing differentiation of wild populations, landraces, and reference cultivars. Our studies provide new insights on the origin of Portuguese landraces. [ABSTRACT FROM AUTHOR]

Assessment of genetic diversity is an essential component in germplasm characterization and utilization. Molecular markers serve as a valuable tool to assess the genetic variation and germplasm identification, which play a key role for faba ( Vicia faba L.) bean breeding. In this study, we analyzed the genetic diversity of faba bean accessions based on simple sequence repeats (SSRs) and morphological traits. Forty-six faba bean accessions, originating from different countries and from the ICARDA breeding program, were evaluated by using 15 morphological and agronomic traits and 17 simple sequence repeat (SSR) loci. Significant differences among accessions for the 15 morphological descriptors were observed. Analysis by SSR markers showed a high genetic diversity among the accessions: All SSRs showed polymorphism, and 101 alleles were revealed for all accessions. The number of alleles at each locus ranged from 2 to 10, with an average of 5.94 alleles per marker, and the polymorphic information content ( PIC) values ranged from 0.38 to 0.84 with a mean of 0.69. Expected heterozygosity ( He), observed heterozygosity ( Ho), unbiased expected heterozygosity ( UHe), and Shannon's information index ( I) showed existence of high genetic variation between accessions from different pedigree. Analyses of genetic distance of the accessions separated the accessions into two groups and seven and five subgroups according to morphological and SSR analysis, respectively. Principal component analysis (PCA) of the SSR markers showed that the first two principal components (PCs) explained a total of 43.90 % of the genetic variation and allowed to distinguish three groups of accessions. Regardless of the method of analysis, Tunisian cultivars are grouped together. For the rest of the accessions, the geographical origin did not seem to be the main factor for structuring the variability of the studied accessions. Elite accessions from the ICARDA faba bean program differed from others and clustered together. The results obtained suggested that the faba bean microsatellite markers can be used to efficiently distinguish faba bean genotypes and to estimate their genetic diversity. [ABSTRACT FROM AUTHOR]

Taxodium 'zhongshansa', an extremely flood-tolerant tree species, has been widely planted in eastern China due to its environmental attributes. Although much progress has been made in understanding its physiological response to flooding stress, as well as its rapid propagation and variety selection, little is known regarding its molecular genetics due primarily to a lack of reliable molecular markers. In this paper, 108,692 expressed sequence tags (ESTs) with a total size of 69.3 Mb derived from T. 'zhongshansa' were analyzed. And 10,038 simple sequence repeat (SSR) loci were identified from 8137 SSR-containing EST sequences. The average SSR frequency in the transcriptome was one in 6.90 kb of EST sequences. The most abundant repeat type was mononucleotide (6581, 65.56 %), followed by trinucleotide (2246, 22.37 %) and dinucleotide (1080, 10.76 %). After filtering unqualified SSR loci, loci with mononucleotide repeats and compound SSRs, 1958 EST-SSR loci were selected to design SSR makers. To validate this set of SSR markers, 503 primer pairs were randomly selected to amplify across 12 genomic DNA templates from three Taxodium species. Two hundred fifty-seven (51.09 %) out of 503 primer pairs amplified the expected products, of which 81 and 176 could amplify polymorphic and monomorphic bands, respectively. The functional categorization of EST sequences containing randomly selected markers revealed that 264 (52.49 %) had homology with known proteins. This set of EST-SSR markers will provide a valuable genetic and genomic tool for further genetic research in Taxodium, such as genetic map construction, quantitative trait loci mapping, and marker assisted selection. [ABSTRACT FROM AUTHOR]

Paphiopedilum orchids are evergreen perennials with distinct flowering behaviors; however, little genetic information hindered the understanding of these interesting flowering patterns. In this study, the floral transcriptomes of two Paphiopedilum species, Paphiopedilum concolor and Paphiopedilum hirsutissimum, and two popular cultivars were characterized. A total of 42.4-68.5 million clean reads were generated from these four Paphiopedilum orchid floral buds. De novo assembly yielded 73,201-79,086 unigenes with average lengths of 765-848 bp for these four floral transcriptomes, of which 42.5-43.1 % were annotated in public protein databases. With 8,019 unique protein-coding genes shared, similar function classifications were found among the four orchid floral transcriptomes, and 113 Paphiopedilum floral unigenes were found to be homologous to flowering genes in Arabidopsis. Of these flowering genes, many regulatory genes, namely, MIKC, NAC, MYB, WRKY, bZIP, bHLH transcription factors, and protein kinases and plant hormone signaling-related genes were identified. Notably, one gene, PIF4 may play vital roles for regulation flowering in warm seasons. A phylogeny clustering based on MIKC MADS-box gene family among Paphiopedilum, rice, and Arabidopsis classified the 61 Paphiopedilum members into 11 subfamilies, which provided some clues on floral organ specification and development in Paphiopedilum. Differentiation expression analysis among the four floral transcriptomes demonstrated that complicated molecular functions or biological processes, such as transmembrane transport, transcription regulation, signal transduction, defense response, etc., might be responsible for the differences among these orchid floral development processes, and partial of these expression genes were validated by qRT-PCR. Finally, 20,969 EST-SSRs were identified as potential molecular markers, and 15,137 SSRs were successful for primer designing. Of 62 candidate SSR primer pairs, 51 were successfully amplified with expected sizes and exhibited polymorphisms among 14 genotypes of Paphiopedilum orchids. Our data should not only provide valuable sequence resources for novel gene discovery and marker-assisted studies in Paphiopedilum but also give us some new insights into understanding of the molecular mechanisms of flowering and floral development in Paphiopedilum. [ABSTRACT FROM AUTHOR]

A segregating mapping population of 'Co-op 17' × 'Co-op 16' was used to identify quantitative trait loci (QTLs) associated with various fruit quality traits in apple. Phenotypic data were collected over 2 years for fruit circumference (in centimeter), diameter at midpoint (in centimeter), length (in centimeter), weight (in gram), total soluble solids (in degree Brix), and total titratable acids (in percent) for the segregating population. The phenotypic data along with a previously constructed genetic map, based on simple sequence repeat markers derived from expressed sequence tag and bacterial artificial chromosome end sequence databases, were used in marker-trait association analysis. Interval mapping identified two QTLs linked to fruit size components on linkage groups 03 and 05 with limit of detection scores of 3.27-4.06 and 3.29-4.02 along with phenotypic variation accounting for 15.4-46.4 and 18.3-21.9 %, respectively. [ABSTRACT FROM AUTHOR]

MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants, animals and fungi. To date, few citrus MADS-box genes and limited tissue expression profiling have been reported. In this study, 84 clementine mandarin and 52 sweet orange MADS-box genes have been identified using bioinformatics analysis. Subsequently, comparative analysis of these genes, including gene structures, phylogenetic relationships, conserved protein motifs, expression patterns, and simple sequence repeat (SSR) markers were identified in these citrus species. According to these analyses, these 136 MADS-box genes can be categorized into five (MIKC, MIKC, Mα, Mβ, and Mγ) groups, and the MIKC group was further divided into 13 subfamilies in two citrus species. In addition, gene duplication of MADS-box genes was also investigated in the clementine mandarin, sweet orange, rice and Arabidopsis genomes. A lower percentage of MADS-box gene duplication was found in the clementine mandarin and sweet orange genomes as compared with Arabidopsis. A survey of the two citrus species based on organ-specific expression profiling indicated that MADS-box genes exhibit various expression patterns, suggesting diverse and novel functions of MADS-box gene families in citrus. In addition, 128 new putative microsatellites with flanking sequences sufficient for primer design were also identified from 136 MADS genes. Sixteen SSRs were selected randomly for validation and transferability testing in 11 citrus species. Among 16 SSRs, 15 were identified as true-to-type SSR loci and were highly transferable among citrus species. These results provide a useful reference for the selection of candidate MADS-box genes for cloning and further functional analysis in citrus. [ABSTRACT FROM AUTHOR]

Pear is a fruit species with worldwide distribution belonging to the Rosaceae family. In this study, transcriptomes of 12 different tissues of pear were newly assembled, with a total of 17,353 SSR loci identified. Within these, repetitive sequences with dinucleotide and trinucleotide motifs were more abundant than other types. We developed 194 EST-SSR makers from the assembled sequences to test on seven pear varieties from different genetic backgrounds, on which 132 EST-SSR primers had amplicons. There were 108 primers with dinucleotide and trinucleotide motifs detecting a total of 311 alleles, with an average per primer of 2.88 and 2.86, respectively. These had better quality than primers with tetranucleotides, pentanucleotides, and hexanucleotides. Fifty polymorphic markers divided 36 pear genotypes into two groups with a similarity coefficient of 0.62. Results showed that Japanese pears had a comparatively close relationship with Chinese pears, indicating the great potential of the novel EST-SSR makers in future evaluations of pear germplasm. Furthermore, 54 EST-SSR markers were selected to test transferability to 96 other Rosaceae cultivars from eight species, including Japanese apricot, plum, apricot, peach, cherry, apple, strawberry, and loquat. Seventeen EST-SSR primers had PCR amplification products in at least one of the 96 accessions, with the highest transferability was from pear to apple at 29.63 %. Transferability from pear to Japanese apricot, plum, apricot, peach, cherry, strawberry, and loquat was 9.26, 14.81, 11.11, 12.96, 5.56, 3.7, and 12.96 %, respectively. Therefore, the newly developed EST-SSR markers can contribute to exploring the genetic relationship, evolution and comparative genomics, and gene introgressions in the Rosaceae family. [ABSTRACT FROM AUTHOR]

Genetic diversity of cherry species collected in Serbia has been investigated using 26 simple sequence repeat (SSR) markers developed in Prunus. This material consisted of 77 cherry accessions corresponding to the five following species, Prunus cerasus, Prunus avium, Prunus fruticosa, Prunus mahaleb, and Prunus serrulata. A total of 98 alleles were detected, with an average of 3.7 putative alleles per primer combination. Sixteen unique, species-specific, alleles were detected with nine primer pairs in four species, P. avium, P. cerasus, P. mahaleb, and P. serrulata. The highest number of unique alleles, 8, was observed in P. mahaleb and no species-specific alleles were detected in P. fruticosa. SSR markers generated unique fingerprints for all cherry accessions. Cluster analysis classified accessions into four groups according to their taxonomy, where P. avium and P. cerasus were grouped together, supporting P. avium as one of the progenitors of sour cherry. The highest genetic variability and potential value in rootstock breeding was observed in P. mahaleb and P. serrulata material. Principal component (PC) analysis explained more than 50 % of the total observed phenotypic variability using the first two components. The most important characteristics of PC1 were leaf length and width, fruit taste, color of leaf nectaries, fruit weight, leaf blade margin incisions, petiole length, size of vegetative buds, and length of internode. The most important characteristics of PC2 were shape of leaf blade at base, fruit skin color, and leaf blade length and tip angle. The investigated germplasm proved to be sufficiently genetically diverse for use in breeding programs and development of new cherry cultivars and rootstocks. [ABSTRACT FROM AUTHOR]

In this study, a population of 97 F seedlings from a cross between the interspecific hybrid (European × Chinese species) pear 'Bayuehong' (BYH) and the Chinese pear 'Dangshansuli' (DS) was used for establishing linkage maps and for quantitative trait loci (QTL) discovery. Using amplified length polymorphism (AFLP), simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers, along with the S locus for self-incompatibility, two parental linkage maps were constructed. The map of BYH consisted of 214 markers (143 AFLPs, 64 SRAPs, 6 SSRs, and S) mapped on all 17 linkage groups of the pear genome with a total length of 1,352.7 cM. The map of DS was comprised of 122 markers (83 AFLPs, 37 SRAPs, 1 SSR, and S) distributed along all 17 linkage groups and covering 1,044.3 cM. Based on phenotypic data from two successive years (2007 and 2008) for six fruit traits, including fruit weight (in grams), fruit diameter (in centimeters), fruit length (in centimeters), soluble solids content, fruit shape index, and maturity date, 19 QTLs were detected. These QTLs were mapped on LG 01, LG 02, LG 05, LG 07, LG 08, LG 10 of the BYH map and LG 02, LG 06, LG 15 of the DS map and accounting for 7.1 to 22.0 % of the observed phenotypic variance. Four QTLs, Pfi-8-1 for fruit shape index, Pfm-8-1 for fruit maturity date, Pfw-7-1 and Pfw-8-1 for fruit weight (in grams), with LOD scores ≥3.5, were deemed as major genes. QTLs Pfi-8-1, Pfm-8-1, and Pfw-8-1 were co-localized on LG 08 of the BYH map, along with Pfl-8-1 for fruit length. It was observed that on LG 07 of the BYH map, QTLs for fruit length, fruit shape index, and fruit weight were clustered. When QTL locations from both years were compared, Pfl-7-1 and Pfl-7-2 for fruit length, Pfi-2-1 and Pfi-2-2 for fruit shape index, and Pfm-8-1 and Pfm-8-2 for fruit maturity date were stably mapped onto the same linkage groups, respectively. Moreover, Pfm-8-1 and Pfm-8-2 were also located within the same region of LG 08 of the BYH map. [ABSTRACT FROM AUTHOR]

Armadillo (ARM) repeat proteins have tandem repeats of a degenerate sequence motif required for protein-protein interaction and are distributed widely in eukaryotes. In this study, we isolated and characterized a novel ARM repeat-like protein gene from the model legume Lotus japonicus that is differentially induced by abiotic stress. The gene, LjTDF- 5, encodes a hypothetical protein of 369 aa with a protein signature "ARM-type fold". Three-dimensional protein structure was predicted to consist of 23 α-helices and no β-sheets by homology modeling. The LjTDF- 5-homologous genes were distributed broadly in the plant kingdom and the C-terminal region, around 60 amino acids in length, was highly conserved in all of the homologs examined although any known functional domains or protein signatures in this region were not detected in silico analyses. Subcellular localization assays revealed that the sGFP-fused LjTDF-5 protein localized to the nuclei of onion epidermis cells, despite the protein not containing a typical nuclear localization signal. In quantitative real-time RT-PCR, the expression of LjTDF- 5 was highly induced by 100 mM NaCl in the roots and by dehydration in the shoot, but not by abscisic acid (ABA, 10 μM). These results suggest that the ARM repeat-like protein LjTDF-5 functions in or around the nucleus in response to high-salt stress and dehydration in L. japonicus. [ABSTRACT FROM AUTHOR]

Somatic hybridization in Cichorium species has already been extensively investigated. Hybrid or cybrid characterization requires an effective plasmotype screening method. We evaluated high resolution melting (HRM) analysis for the detection of specific mitochondrial (mt) and chloroplast (cp) markers to distinguish two industrial chicory ( Cichorium intybus var. sativum) plasmotypes from five wild type chicory ( C. intybus) and two endive ( C. endivia) plasmotypes. Three mt ( coxII-2, cob-1, and cob-2) and three cp HRM markers ( trnL-trnF, trnL-trnF-2, and ndhF-1) were successfully developed. Two markers ( coxII-2 and trnL-trnF) were additionally able to discriminate heterozygous plasmotypes containing at least 25 % of one parental plasmotype. Moreover, the technique was successfully used to characterize the cytoplasms of 50 simple sequence repeats (SSR) confirmed somatic hybrids of C. intybus var. sativum 'VL52' and C. endivia var. crispum 'Wallone Despa'. HRM enables a rapid (less than 2 h) and efficient high-throughput scanning of multiple fragments due to the 384-well plates and is cost efficient because of its small reaction volume of 10 μl. This is the first report on the use of HRM analysis on Cichorium species. The technique is a fast and simple alternative for laborious and costly sequencing in plasmotyping regenerants obtained after somatic fusion. [ABSTRACT FROM AUTHOR]

Nucleotide-binding site leucine-rich repeat (NB-LRR) genes play important roles in plant disease resistance. Due to its similarity to Rp1 in maize ( Zea mays), a novel NB-LRR gene was isolated from rice and designated as OsRP1L1 ( Oryza sativa Rp1-like 1). Analysis of expression of a super green fluorescent protein ( sGFP) fusion gene revealed that the OsRP1L1 protein localizes to the nucleolus. Expression patterns suggested that OsRP1L1 was involved in responses to several plant growth regulators (PGRs) and environmental stresses. To explore its function in bacterial blight (BB) resistance, OsRP1L1 was cloned and overexpressed in a susceptible japonica rice cultivar. Overexpression of OsRP1L1 moderately elevated the resistance of plants to Xanthomonas oryzae pv. oryzae strains PXO86 and PXO341. Transcriptome analysis showed that plants overexpressing OsRP1L1 had small changes in their transcriptome, with 26 genes showing statistically significant changes of more than two-fold. The most up-regulated transcripts-a DIN1-like gene and a terpene synthase ( TPS) gene-were up-regulated 7.9- and 7.6-fold, respectively. It was also noted that seven of the up-regulated genes have also reportedly been induced by overexpression of OsbZIP46, which has been identified recently as a player in ABA sensing. All these findings suggest that OsRP1L1 plays an important role in rice BB resistance, and may be useful as a genetic resource for engineering disease resistance in plants. [ABSTRACT FROM AUTHOR]