bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular linkage maps of thePopulusgenome
Authors: Yin Tongming , Zhang Xinye , Huang Minren , Wang Minxiu , Zhuge Qiang , Tu Shengming , Zhu Li-Huang , Wu Rongling
Published: November 2002

We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification.Key words: AFLP, Genetic map, poplar, RAPD, SSR.
An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus inPaspalum simplex
Authors: Labombarda Paola , Busti Alessandra , Caceres Maria Eugenia , Pupilli Fulvio , Arcioni Sergio
Published: November 2002

A mapping population of Paspalum simplex segregating for apomixis (asexual reproduction through seeds) was screened with AFLPs to find apomixis-linked markers. Four AFLPs linked to apomixis in coupling phase were found. Three of them did not show recombinants among the 87 individuals of the mapping population, whereas the other was more loosely linked. Integrating the AFLP data with those obtained previously with rice RFLP anchor markers, a map was drawn for the chromosome region of P. simplex encompassing apomixis. We cloned the three AFLPs tightly linked with apomixis into plasmid vectors and used them as probes to hybridize the restriction digested DNA of the mapping population. Two of them revealed RFLP bands linked to apomixis together with other alleles, whereas one was proven to belong to a hemizygous portion of the apomixis locus. The total picture resulting from AFLP and RFLP analyses was that a cluster of markers tightly linked with apomixis was detected in P. simplex together with two other markers that were more loosely linked. These two markers enclosed a relatively large chromosome segment characterized by strong repression of recombination. The block of recombination may have caused sequence divergence and, therefore, hemizygosity of some regions belonging to the apomixis-controlling chromosome segment of P. simplex. The potential of developing an apomixis-specific sequence for screening large-fragment libraries for the physical isolation of the locus encompassing apomixis is discussed.Key-words: AFLP, apomixis, hemizygosity.
Two-gene systems of vernalization requirement and narrow-sense earliness in einkorn wheat
Authors: Shindo Chikako , Sasakuma Tetsuo , Watanabe Naoko , Noda Kazuhiko
Published: November 2002

The genetic segregation of the heading trait was analyzed using a recombinant inbred line (RIL) of einkorn wheat, RILWA-1, derived from cultivated Triticum monococcum L., and wild-type T. boeoticum Boiss. The latency to heading was examined in 115 lines under controlled environmental conditions, as well as in the field, and the degrees of narrow-sense earliness and vernalization requirement were evaluated for quantitative trait locus (QTL) analysis. Single-marker analysis using 107 RFLP markers segregating in RILWA-1 detected 20 linking markers for heading factors. In all marker loci, the alleles for early heading were conferred by T. monococcum. In interval analysis of chromosome 5Am, two vernalization genes, Vrn-Am1 and Vrn-Am2, were precisely mapped to the Xcdo504Xpsr426 interval on the central region of the long arm and to the Xwg114Xwec87 interval on its distal region, respectively. Interval analysis also showed that two genes for narrow-sense earliness, designated Nse-3Amand Nse-5Am, were located on chromosome 3Amand 5Am, respectively. It was noticed that heading time in the field was determined mainly by Nse-3Am, suggesting that narrow-sense earliness is critical for heading in the field in einkorn wheat.Key words: QTL analysis, einkorn wheat, heading time, vernalization requirement, narrow-sense earliness.
Population structure of a lodgepole pine (Pinus contorta) and jack pine (P. banksiana) complex as revealed by random amplified polymorphic DNA
Authors: Ye Terrance Z , Yang Rong-Cai , Yeh Francis C
Published: November 2002

We studied the population structure of a lodgepole (Pinus contorta Dougl.) and jack pine (Pinus banksiana Lamb.) complex in west central Alberta and neighboring areas by assessing random amplified polymorphic DNA (RAPD) variability in 23 lodgepole pine, 9 jack pine, and 8 putative hybrid populations. Of 200 random primers screened, 10 that amplified 39 sharp and reproducible RAPDs were chosen for the study. None of the 39 RAPDs were unique to the parental species. RAPD diversity ranged from 0.085 to 0.190 among populations and averaged 0.143 for lodgepole pine, 0.156 for jack pine, 0.152 for hybrids, and 0.148 for all 40 populations. The estimated population differentiation based on GSTwas 0.168 for hybrids, 0.162 for lodgepole pine, 0.155 for jack pine, and 0.247 across all 40 populations. Cluster analysis of genetic distances generally separated jack pine from lodgepole pine and hybrids, but no division could be identified that further separated lodgepole pine from hybrids. The observed weak to mild trend of "introgression by distance" in the complex and neighbouring areas was consistent with the view that introgressive hybridization between lodgepole and jack pines within and outside the hybrid zone may have been through secondary contact and primary intergradation, respectively.Key words: introgression, lodgepolejack pine complex, natural hybridization, random amplified polymorphic DNA.
Evolution of 5S rDNA unit arrays in the plant genusNicotiana(Solanaceae)
Authors: Matyasek R , Fulnecek J , Lim K Y , Leitch A R , Kovarik A
Published: November 2002

Nicotiana tabacum (tobacco, Solanaceae) has two 5S ribosomal DNA (rDNA) families, one of unit length ~646 bp and the other ~430 bp, that differ in the length of the 5S rDNA non-transcribed spacer (NTS). The long 5S rDNA family, found on the T genome of tobacco and in Nicotiana tomentosiformis, contains a GC-rich subregion that is absent in the short family. We designed primers for this subregion and generated a probe that we used against a range of Nicotiana and related Solanaceous species. We demonstrated the presence of the GC-rich subregion in a range of Nicotiana species, but it was absent in Nicotiana sylvestris, Nicotiana longiflora, and two closely related genera, Petunia and Solanum. These data suggest that this subregion of the NTS is likely to have evolved with the genus Nicotiana. The absence of the subregion in N. sylvestris and N. longiflora is likely to have arisen by a deletion event in the evolution of section alatae. We demonstrate patterns of evolution in the 5S rDNA unit cluster in relation to a phylogenetic reconstruction of species relationships in section tomentosae. Nicotiana glutinosa diverged early from the section and contains a 5S rDNA family based on a 550-bp unit. After this divergence, 430- and 650-bp rDNA unit families evolved. The 650-bp family is found in all species of tomentosae (except N. glutinosa) and in tobacco. The 430-bp family within tomentosae includes the GC-rich subregion and is thus unrelated to the 430-bp family in N. sylvestris. Nicotiana setchellii is unusual in that it has three 5S rDNA loci, including one locus that is exceptionally large. This species, unique to tomentosae, has a very abundant 900-bp unit family. It is possible that this 900-bp family occurs on this one large locus. In N. tomentosa and N. kawakamii, the 650-bp family is predominant, whereas N. tomentosiformis and N. otophora have only the 650-bp family. There is no clear relationship between the number of 5S families and the number of 5S rDNA loci. Certainly the replacement of 5S rDNA units, perhaps by gene conversion, has occurred repeatedly in the evolution of genus Nicotiana.Key words: 5S rDNA, evolution, Nicotiana, Solanaceae, satellite homogenization.
A variable minisatellite sequence in the chloroplast genome ofSorbusL. (Rosaceae: Maloideae)
Authors: King R Andrew , Ferris Colin
Published: November 2002

The chloroplast genome is now known to be more variable than was once thought. Reports of RFLP (restriction fragment length polymorphism) and sequence variation, as well as variation in chloroplast microsatellites, are common. Here, data are presented on the variability of a minisatellite sequence in the chloroplast genome of Sorbus species. RFLP analysis of a PCR product comprising the region between the trnM and rbcL genes of nine Sorbus species identified seven size variants. Sequencing revealed the observed size polymorphism to be due to differences in the number of copies of an imperfect 9-bp motif. A more intensive survey of the variability of the minisatellite was undertaken in populations of Sorbus aucuparia. The potential uses of such regions in chloroplast DNA are discussed and a possible mechanism for the evolution of the minisatellite is presented.Key words: atpE, homoplasy, microsatellite, rowan, VNTR.
Molecular marker analysis of 24- and 25-chromosome plants obtained fromSolanum tuberosumL. subsp.andigena(2n= 4x= 48) pollinated with aSolanum phurejahaploid inducer
Authors: Samitsu Y , Hosaka K
Published: November 2002

Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.Key words: Solanum tuberosum subsp. andigena, RFLP, RAPD, haploid, trisomic.
Isolation, characterization, and localization of β-tubulin genomic clones of three Drosophila montium subgroup species
Authors: Drosopoulou Elena , Wiebauer Karin , Yiangou Minas , Mavragani-Tsipidou Penelope , Domdey Horst , Scouras Zacharias G
Published: November 2002

Genomic libraries were constructed from three Drosophila species, namely Drosophila auraria, Drosophila serrata, and Drosophila kikkawai, belonging to the Drosophila montium subgroup of the Drosophila melanogaster species group. Clones containing β-tubulin specific sequences were isolated, characterized by restriction endonuclease digestions and Southern hybridizations, and mapped by in situ hybridization on the polytene chromosomes of the species studied. The distribution of the β-tubulin loci was found to be similar in D. montium species and D. melanogaster.Key words: genomic clones, β-tubulin, gene family, evolution, Drosophila montium subgroup.
Linkage of AFLP markers tolhd 1, a recessive heterochronic gene in Italian ryegrass
Authors: Gao Zhen-Sheng , Sugita Shinichi , Ikeda Seishi , Cai Hong-Wei , Sasaki Tohru , Liang George H
Published: November 2002

A mutant, leafy head 1 (lhd 1), was discovered in Japan from the progeny of Italian ryegrass (Lolium multiflorum Lam.) 'Nioudachi' and local line 'Aichikei #3'. Compared with normal plants, the mutant plant is a dwarf with a larger number of internodes per stem, shorter internodes, and smaller leaves. The plants also head later in the season. Aerial roots are usually produced from the stem nodes during rainy seasons. In characterizing lhd 1, it was found to have many branches with small leaves and many small panicles on the upper part of the plant. Panicle development was severely disturbed in lhd 1 mutants, and the number of leaves produced in the vegetative phase was nearly twice that produced in the wild-type counterpart. The lhd 1 mutant appears to be a heterochronic mutation that is able to extend the vegetative period during development. The frequency of mutants in segregating populations indicated that lhd 1 is a recessive allele. To determine the linkage relationship between the lhd 1 gene and AFLP markers, 768 primer combinations were screened for polymorphisms using bulked segregant analyses in two populations with 316 and 30 plants, respectively. Five AFLP markers were linked to the lhd 1 locus. E3/M41-1 and E16/M14-2 cosegregated with lhd 1. E16/M14-1 and E30/M10-1 flanked the gene at a distance of 0.3 cM and E30/M14-2 was linked to lhd 1 at a distance of 0.6 cM.Key words: Lolium multiflorum, leafy head mutant, mapping.
Genomic organization and transcription of satellite DNA in the antAphaenogaster subterranea(Hymenoptera, Formicidae)
Authors: Lorite P , Renault S , Rouleux-Bonnin F , Bigot S , Periquet G , Palomeque T
Published: November 2002

A satellite DNA family (APSU) was isolated and characterized in the ant Aphaenogaster subterranea. This satellite DNA is organized in tandem repeats of 162 bp and is relatively AT rich (51.9%). Sequence analysis showed a high level of homogeneity between monomers. Loss of satellite DNA has been detected in queens in relation to workers, because the amount of satellite DNA in queens is about 25% of the amount found in workers. Restriction analysis of the total DNA with methylation-sensitive enzymes suggests that this DNA is not methylated. Analysis of the electrophoretic mobility of satellite DNA on non-denaturing polyacrylamide showed that this satellite DNA is only very lightly curved. Their possible transcription was analyzed using reverse transcription and polymerase chain reaction (RTPCR). The satellite DNA is transcribed on the two DNA strands at the same level in worker and queen pupae, as well as in worker adults.Key words: Formicidae, methylation, satellite DNA transcription.
Cytological and molecular analysis of centromere misdivision in maize
Authors: Kaszás Étienne , Kato Akio , Birchler James A
Published: November 2002

B chromosome derivatives suffering from breaks within their centromere were examined cytologically and molecularly. We showed by high resolution FISH that misdivision of the centromere of a univalent chromosome can occur during meiosis. The breaks divide the centromere repeat sequence cluster. A telocentric chromosome formed by misdivision was found to have the addition of telomeric repeats to the broken centromere. A ring chromosome formed after misdivision occurred by fusion of the broken centromere to the telomere. Pulsed-field electrophoresis analyses were performed on the telocentric and ring chromosomes to identify fragments that hybridize to both the telomeric repeat and the B-specific centromeric repeat. We conclude that healing of broken maize centromeres can be achieved through the mechanisms of addition or fusion of telomeric repeat sequences to the broken centromere.Key words: centromere, telomere, meiosis, chromosome healing, B chromosome, Zea mays.
Molecular and physical mapping of a barley gene on chromosome arm 1HL that causes sterility in hybrids with wheat
Authors: Taketa Shin , Choda Masayuki , Ohashi Ryoko , Ichii Masahiko , Takeda Kazuyoshi
Published: November 2002

Addition of the long arm of barley chromosome 1H (1HL) to wheat causes severe meiotic abnormalities and complete sterility of the plants. To map the barley gene responsible for the 1H-induced sterility of wheat, a series of addition lines of translocated 1H chromosomes were developed from the crosses between the wheat 'Shinchunaga' and five reciprocal translocation lines derived from the barley line St.13559. Examination of the seed fertility of the addition lines revealed that the sterility gene is located in the interstitial 25% region of the 1HL arm. The genetic location of the sterility gene was also estimated by physically mapping sequence-tagged site (STS) markers and simple-sequence repeat (SSR) markers with known map locations. The sterility gene is designated Shw (sterility in hybrids with wheat). Comparison of the present physical map of 1HL with two previously published genetic maps revealed a paucity of markers in the proximal 30% region and non-random distribution of SSR markers. Two inconsistencies in marker order were found between the present physical map and the consensus genetic map of group 1 chromosomes of Triticeae. On the basis of the effects on meiosis and chromosomal location, the relationship of the present sterility gene with other fertility-related genes of Triticeae is discussed.Key words: Hordeum vulgare, molecular markers, sterility, translocation, wheatbarley chromosome addition line.
Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower
Authors: Yu Ju-Kyung , Mangor Jodie , Thompson Lucy , Edwards Keith J , Slabaugh Mary B , Knapp Steven J
Published: November 2002

Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.Key words: microsatellites, Helianthus, Compositae, DNA polymorphisms.
LTR retrotransposons in the dioecious plantSilene latifolia
Authors: Matsunaga Sachihiro , Yagisawa Fumi , Yamamoto Maki , Uchida Wakana , Nakao Shunsuke , Kawano Shigeyuki
Published: November 2002

Conserved domains of two types of LTR retrotransposons, Ty1copia- and Ty3gypsy-like retrotransposons, were isolated from the dioecious plant Silene latifolia, whose sex is determined by X and Y chromosomes. Southern hybridization analyses using these retrotransposons as probes resulted in identical patterns from male and female genomes. Fluorescence in situ hybridization indicated that these retrotransposons do not accumulate specifically in the sex chromosomes. These results suggest that recombination between the sex chromosomes of S. latifolia has not been severely reduced. Conserved reverse transcriptase regions of Ty1copia-like retrotransposons were isolated from 13 different Silene species and classified into two major families. Their categorization suggests that parallel divergence of the Ty1copia-like retrotransposons occurred during the differentiation of Silene species. Most functional retrotransposons from three dioecious species, S. latifolia, S. dioica, and S. diclinis, fell into two clusters. The evolutionary dynamics of retrotransposons implies that, in the genus Silene, dioecious species evolved recently from gynodioecious species.Key words: retrotransposon, dioecious plant, sex chromosome.
Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G
Authors: Foster-Hartnett Dawn , Mudge Joann , Larsen Dana , Danesh Dariush , Yan Huihuang , Denny Roxanne , Peñuela Silvia , Young Nevin D
Published: November 2002

Eight DNA markers spanning an interval of approximately 10 centimorgans (cM) on soybean (Glycine max) molecular linkage group G (MLG-G) were used to identify bacterial artificial chromosome (BAC) clones. Twenty-eight BAC clones in eight distinct contiguous groups (contigs) were isolated from this genome region, along with 59 BAC clones on 17 contigs homoeologous to those on MLG-G. BAC clones in four of the MLG-G contigs were also digested to produce subclones and detailed physical maps. All of the BAC-ends were sequenced, as were the subclones, to estimate proportions in different sequence categories, compare similarities among homoeologs, and explore microsynteny with Arabidopsis. Homoeologous BAC contigs were enriched in repetitive sequences compared with those on MLG-G or the soybean genome as a whole. Fingerprint and cross-hybridization comparisons between MLG-G and homoeologous contigs revealed cases of highly similar physical organization between soybean duplicates, as did DNA sequence comparisons. Twenty-seven out of 78 total sequences on soybean MLG-G showed significant similarity to Arabidopsis. The homologs mapped to six compact genome segments in Arabidopsis, with the longest containing seven homologs spanning two million base pairs. These results extend previous observations of large-scale duplication and selective gene loss in Arabidopsis, suggesting that networks of conserved synteny between Arabidopsis and other angiosperm families can stretch over long physical distances.Key words: Arabidopsis thaliana, bacterial artificial chromosomes, Glycine max, microsynteny.
Assessment of genomic diversity among wheat genotypes as determined by simple sequence repeats
Authors: Ahmad M
Published: November 2002

Simple sequence repeats (SSRs) have been used to examine the genomic diversity of wheat (Triticum aestivum L.) germplasm. Thirteen wheat genotypes of diverse origin were analyzed with 43 selected SSRs to provide uniform and maximum genome coverage. A total of 156 allelic variants were detected at 43 SSR loci, ranging from two to eight per locus with an average of 3.6. The polymorphic information content (PIC) values of the loci ranged from 0.10 (Xgwm264) to 0.89 (Xgwm471 and Xgwm577). Genetic similarities calculated from SSR data ranged from 30.1 ('Era' and 'Klasic') to 90.1 ('Neepawa' and 'Thatcher') between genotypes. UPGMA analysis based on genetic distance estimates produced three loose groupings that were generally consistent with available pedigree information. Cultivars 'Neepawa' and 'Thatcher' are closely related. Their genetic relationship was confirmed by the facts that they share a common ancestor and are clustered together. There were two different 'Era' genotypes, one used in the 'Otane' pedigree and one used in this study. None of the other genotypes had a close common ancestor indicating any close genetic relationships. Principal coordinate analysis also confirmed this pattern of genetic diversity. A wide range of genomic diversity was observed among all the genotypes, proving them to be prime candidates for selective breeding for specific traits and broadening the genetic base.Key words: simple sequence repeats, genetic diversity, Triticum aestivum, genetic similarity estimates, cluster analysis.
Genomic structure and homoeologous relationship of the two α-subunit genes of a heterotrimeric GTP-binding protein in tobacco
Authors: Takumi Shigeo , Ida Makiko , Haisa Yoshiyuki , Ando Seiji , Nakamura Chiharu
Published: November 2002

A heterotrimeric GTP-binding protein (G protein) plays a number of important roles in the signal- transduction pathways of eukaryotic cells. The allotetraploid tobacco genome has two α-subunit genes, NtGA1 and NtGA2, of the heterotrimeric G protein. In this study, we determined the nucleotide sequences and the exon-intron structures of the NtGA loci in tobacco and its ancestral diploid species. The genomic sequences of the NtGA loci were interrupted by 13 introns. The sizes of most exons (12 of 14) were completely conserved among the NtGA genes and the Arabidopsis α-subunit gene (GPA1), but most introns (11 of 13) in the NtGA genes were longer than those in GPA1. In comparison with the genomic sequences of the NtGA orthologues of ancestral Nicotiana sylvestris and Nicotiana tomentosiformis, the tobacco NtGA1 and NtGA2 were concluded to be homoeologous and assigned to the S and T genomes, respectively. More than 300 mutations including insertionsdeletions (indels) and nucleotide substitutions were found in the intron regions between the NtGA1 and NtGA2 loci, whereas the exon sequences were highly conserved among these and GPA1. The structural comparison revealed larger divergence at the NtGA2 locus than at NtGA1.Key words: heterotrimeric G protein, homoeologous relationship, Nicotiana tabacum, SINE.
Molecular cloning, sequencing, and chromosome mapping of a 1A-encoded ω-type prolamin sequence from wheat
Authors: Masoudi-Nejad Ali , Nasuda Shuhei , Kawabe Akira , Endo Takashi R
Published: November 2002

Gliadins are the most abundant component of the seed storage proteins in cereals and, in combination with glutenins, are important for the bread-making quality of wheat. They are divided into four subfamilies, the α-, β-, γ-, and ω-gliadins, depending on their electrophoresis pattern, chromosomal location, and DNA and protein structures. Using a PCR-based strategy we isolated and sequenced an ω-gliadin sequence. We also determined the chromosomal subarm location of this sequence using wheat aneuploids and deletion lines. The gene is 1858 bp long and contains a coding sequence 1248 bp in length. Like all other gliadin gene families characterized in cereals, the ω-gliadin gene described here had characteristic features including two repeated sequences 300 bp upstream of the start codon. At the DNA level, the gene had a high degree of similarity to the ω-secalin and C-hordein genes of rye and barley, but exhibited much less homology to the α- and β-gliadin gene families. In terms of the deduced amino acid sequence, this gene has about 80 and 70% similarity to the ω-secalin and C-hordein genes, respectively, and possesses all the features reported for other gliadin gene families. The ω-gliadin gene has about 30 repeats of the core consensus sequences PQQPX and XQQPQQX, twice as many as other gliadin gene families. Southern blotting and PCR analysis with aneuploid and deletion lines for the short arm of chromosome 1A showed that the ω-gliadin was located on the distal 25% of the short arm of chromosome 1A. By comparison of PCR and A-PAGE profiles for deletion stocks, its genomic location must be at a different locus from gli-A1a in 'Chinese Spring'.Key words: glutenin, omega gliadin, storage protein, Triticum aestivum, secalin.
Molecular mapping of theClocus for presence of pungency inCapsicum
Authors: Blum Eyal , Liu Kede , Mazourek Michael , Yoo Eun Young , Jahn Molly , Paran Ilan
Published: November 2002

Pungency owing to the presence of capsaicinoids is a unique character of pepper (Capsicum spp.). Capsaicinoids are produced in the placenta and it has long been known that a single dominant gene, C, is required for pungent genotypes to produce capsaicinoids. We mapped C to pepper chromosome 2 in a cross between a pungent Capsicum frutescens wild accession and a non-pungent Capsicum annuum bell pepper. This position confirmed results from earlier studies. The RFLP marker TG 205 cosegregated with C and two additional RFLP markers were also located within 1 cM. The recessive allele at the C locus is used in breeding programs around the world focused on very diverse germplasm, hence any of these tightly linked markers may be of value as potential sources of useful markers for marker-assisted selection. To demonstrate this point, we developed a PCR-based CAPS (cleaved amplified polymorphic sequence) marker linked to C using the sequence of the Capsicum fibrillin gene located 0.4 cM from C. The use of molecular markers for high-throughput screening for the c allele in pepper breeding programs is discussed.Key words: pepper, pungency, marker-assisted selection.
Identification, structure, and differential expression of members of a BURP domain containing protein family in soybean
Authors: Granger Cheryl , Coryell Virginia , Khanna Anupama , Keim Paul , Vodkin Lila , Shoemaker Randy C
Published: November 2002

Expressed sequence tags (ESTs) exhibiting homology to a BURP domain containing gene family were identified from the Glycine max (L.) Merr. EST database. These ESTs were assembled into 16 contigs of variable sizes and lengths. Consistent with the structure of known BURP domain containing proteins, the translation products exhibit a modular structure consisting of a C-terminal BURP domain, an N-terminal signal sequence, and a variable internal region. The soybean family members exhibit 3598% similarity in a ~100-amino-acid C-terminal region, and a phylogenetic tree constructed using this region shows that some soybean family members group together in closely related pairs, triplets, and quartets, whereas others remain as singletons. The structure of these groups suggests that multiple gene duplication events occurred during the evolutionary history of this family. The depth and diversity of G. max EST libraries allowed tissue-specific expression patterns of the putative soybean BURPs to be examined. Consistent with known BURP proteins, the newly identified soybean BURPs have diverse expression patterns. Furthermore, putative paralogs can have both spatially and quantitatively distinct expression patterns. We discuss the functional and evolutionary implications of these findings, as well as the utility of EST-based analyses for identifying and characterizing gene families.Key words: BURP domain, expressed sequence tag, gene duplication, Glycine max.
Ascertaining maternal and paternal lineage withinMusaby chloroplast and mitochondrial DNA RFLP analyses
Authors: Carreel F , de Leon D Gonzalez , Lagoda P , Lanaud C , Jenny C , Horry J P , du Montcel H Tezenas
Published: November 2002

In banana, the maternal transmission of chloroplast DNA and paternal transmission of the mitochondrial DNA provides an exceptional opportunity for studying the maternal and paternal lineage of clones. In the present study, RFLP combined with hybridization of heterologous mitochondrial and chloroplastic probes have been used to characterize 71 wild accessions and 131 diploid and 103 triploid cultivated clones. In additon to Musa acuminata and Musa balbisiana, other species from the four Musa sections were studied to investigate their contribution to the origin of cultivated bananas. These molecular analyses enable the classification of the Musa complex to be discussed. Results ascertain relationships among and between the wild accessions and the mono- and interspecific diploid and triploid bananas, particularly for the acuminata genome. Parthenocarpic varieties are shown to be linked to M. acuminata banksii and M. acuminata errans, thus suggesting that the first center of domestication was in the Philippines  New Guinea area.Key words: Musa, RFLP, cpDNA, mtDNA, lineage.
Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers
Authors: Zhou Wenchun , Kolb Frederic L , Bai Guihua , Shaner Gregory , Domier Leslie L
Published: November 2002

Three chromosomal regions associated with scab resistance were detected in a common cultivar, Ning7840, by microsatellite and AFLP analysis. Six microsatellites on chromosome 3BS, Xgwm389, Xgwm533, Xbarc147, Xgwm493, Xbarc102, and Xbarc131, were integrated into an amplified fragment length polymorphism (AFLP) linkage group containing a major quantitative trait locus (QTL) for scab resistance in a mapping population of 133 recombinant inbred lines (RILs) derived from 'Ning7840' × 'Clark'. Based on single-factor analysis of variance of scab infection data from four experiments, Xgwm533 and Xbarc147 were the two microsatellite markers most tightly associated with the major scab resistance QTL. Interval analysis based on the integrated map of AFLP and microsatellite markers showed that the major QTL was located in a chromosome region about 8 cM in length around Xgwm533 and Xbarc147. Based on mapping of six microsatellite markers on eight 3BS deletion lines, the major QTL was located distal to breakage point 3BS-8. In total, 18 microsatellites were physically located on different subarm regions on 3BS. Two microsatellites, Xgwm120 and Xgwm614, were significantly associated with QTL for scab resistance on chromosome 2BL and 2AS, respectively. The resistance alleles on 3BS, 2BL, and 2AS were all derived from 'Ning7840'. Significant interaction between the major QTL on 3BS and the QTL on 2BL was detected based on microsatellite markers linked to them. Using these microsatellite markers would facilitate marker-assisted selection to improve scab resistance in wheat.Key words: Fusarium head blight, quantitative trait locus, physical mapping, Triticum aestivum L.
RAPD-based genetic linkage maps of yellow passion fruit (Passiflora edulisSims. f.flavicarpaDeg.)
Authors: Carneiro Monalisa Sampaio , Camargo Luis Eduardo Aranha , Coelho Alexandre Siqueira Guedes , Vencovsky Roland , Júnior Rui Pereira Leite , Stenzel Neusa Maria Colauto , Vieira Maria Lucia Carneiro
Published: November 2002

A single cross between two clones of passion fruit (Passiflora edulis Sims. f. flavicarpa Deg., 2n = 18) was selected for genetic mapping. The mapping population was composed of 90 F1plants derived from a cross between 'IAPAR 123' (female parent) and 'IAPAR 06' (male parent). A total of 380 RAPD primers were analyzed according to two-way pseudo-testcross mapping design. The linkage analysis was performed using Mapmaker version 3.0 with LOD 4.0 and a maximum recombination fraction (θ) of 0.30. Map distances were estimated using the Kosambi mapping function. Linkage maps were constructed with 269 loci (2.38 markers/primer), of which 255 segregated 1:1, corresponding to a heterozygous state in one parent and null in the other. The linkage map for 'IAPAR123' consisted of 135 markers. A total of nine linkage groups were assembled covering 727.7 cM, with an average distance of 11.20 cM between framework loci. The sizes of the linkage groups ranged from 56 to 144.6 cM. The linkage map for 'IAPAR 06' consisted of 96 markers, covering 783.5 cM. The average distance between framework loci was 12.2 cM. The length of the nine linkage groups ranged from 20.6 to 144.2 cM. On average, both maps provided 61% genome coverage. Twenty-four loci (8.9%) remained unlinked. Among their many applications, these maps are a starting point for the identification of quantitative trait loci for resistance to the main bacterial disease affecting passion fruit orchards in Brazil, caused by Xanthomonas campestris pv. passiflorae, because parental genotypes exhibit diverse responses to bacterial inoculation.Key words: Passiflora, genetic mapping, molecular markers, pseudo-testcross mapping strategy.
Genomic targeting and high-resolution mapping of the domestication geneQin wheat
Authors: Faris Justin D , Gill Bikram S
Published: November 2002

The Q locus is largely responsible for the domestication of bread wheat. Q confers the free-threshing character of the spike and influences other important agronomic traits. Using chromosome deletion lines, Q was placed on the physical map within a submicroscopic segment of the long arm of chromosome 5A. We targeted markers to the segment by comparative mapping of anonymous RFLP clones, AFLP, and mRNA differential display analysis of deletion lines 5AL-7 and -23, which have deletion breakpoints that flank the Q locus. Differentially expressed sequences detected fragments at various loci on group 5 chromosomes suggesting that Q may be a regulatory gene. We identified 18 markers within the Q gene deletion interval and used them to construct a genetic linkage map of the region in F2populations derived from chromosome 5A disomic substitution lines. The genetic map corresponding to the deletion segment was 20-cM long, and we identified markers as close as 0.7 cM to the Q gene. An estimate of base pairs per centimorgan within the region is 250 kb/cM, an 18-fold increase in recombination compared with the genomic average. Genomic targeting and high-density mapping provide a basis for the map-based cloning of the Q gene.Key words: Triticum aestivum, positional cloning, physical mapping.
A molecular marker tightly linked toP, a gene required for flower and seedcoat color in common bean (Phaseolus vulgarisL.), contains the Ty3-gypsyretrotransposonTpv3g
Authors: Erdmann Paula M , Lee Rian K , Bassett Mark J , McClean Phillip E
Published: November 2002

In common bean (Phaseolus vulgaris L.), the expression of color in flower and seedcoat tissues requires the dominant allele of the P gene. The fully recessive p allele completely suppresses color expression in these tissues, whereas in specific genetic backgrounds, the pgriallele potentiates a grayish-white seedcoat and pale violet (nearly white) flowers with two violet dots on the banner petals. As a first step to gaining a better understanding of this important gene, we phenotypically scored an F2population segregating for P and pgriand subsequently screened contrasting bulk DNA samples with oligonucleotide primers to uncover random amplified polymorphic DNA (RAPD) fragments. OU32300, an RAPD marker linked in coupling phase to the dominant allele, mapped 1.3 cM from P. The core 'BAT93' × 'Jalo EEP558' recombinant inbred population was scored, and the marker mapped to linkage group B7. The segregating fragment was cloned, sequenced, and shown to possess significant homology to the Ty3gypsy class of retrotransposons. We have named the element Tpv3g. It is estimated that about 100 copies of the element are present in the common bean genome. Phylogenetic analysis placed Tpv3g in the class A group of plant retrotransposons.Key words: common bean, molecular markers, Phaseolus vulgaris L., seedcoat color, Ty3gypsy retrotransposon.
Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome
Authors: Jiang Zhihua , Melville Jenna S , Cao Honghe , Kumar Sudhir , Filipski Alan , Verrinder Gibbins Ann M
Published: November 2002

Based on published information, we have identified 991 genes and gene-family clusters for cattle and 764 for pigs that have orthologues in the human genome. The relative linear locations of these genes on human sequence maps were used as "rulers" to annotate bovine and porcine genomes based on a CSAM (contiguous sets of autosomal markers) approach. A CSAM is an uninterrupted set of markers in one genome (primary genome; the human genome in this study) that is syntenic in the other genome (secondary genome; the bovine and porcine genomes in this study). The analysis revealed 81 conserved syntenies and 161 CSAMs between human and bovine autosomes and 50 conserved syntenies and 95 CSAMs between human and porcine autosomes. Using the human sequence map as a reference, these 991 and 764 markers could correlate 72 and 74% of the human genome with the bovine and porcine genomes, respectively. Based on the number of contiguous markers in each CSAM, we classified these CSAMs into five size groups as follows: singletons (one marker only), small (24 markers), medium (510 markers), large (1120 markers), and very large (>20 markers). Several bovine and porcine chromosomes appear to be represented as di-CSAM repeats in a tandem or dispersed way on human chromosomes. The number of potential CSAMs for which no markers are currently available were estimated to be 63 between human and bovine genomes and 18 between human and porcine genomes. These results provide basic guidelines for further gene and QTL mapping of the bovine and porcine genomes, as well as insight into the evolution of mammalian genomes.Key words: Human, cattle, pig, orthologous genes, CSAM, comparative mapping.
Genetic mapping of theLr20Pm1resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat
Authors: Neu Christina , Stein Nils , Keller Beat
Published: November 2002

The Lr20Sr15Pm1 resistance locus in hexaploid wheat confers resistance to three different fungal wheat pathogens (leaf rust, stem rust, and powdery mildew). It was previously localized in the distal region of chromosome arm 7AL. As a first step towards the isolation of this complex locus, we performed molecular mapping of the Lr20 and Pm1 genes in three F2populations. In two populations, a cluster of 8 and 12 markers, respectively, cosegregated with the resistance genes. In a third population based on a cross between a susceptible lr20 mutant and a resistant cultivar, all clustered markers were monomorphic. However, in this population the recombination frequency proximal to the Lr20 gene was up to 60 times higher, indicating that the complete genetic linkage of the clustered markers is not due to a close physical linkage of the probes but is caused by suppressed recombination. This was supported by the analysis of Triticum monococcum BAC clones where no physical linkage between cosegregating probes was observed. Suppressed recombination at the Lr20Pm1 locus is likely the result of an alien introgression of chromatin from an unidentified wild relative species or is due to chromosomal rearrangements.Key words: wheat, leaf rust, powdery mildew, resistance, suppressed recombination.
Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae
Authors: Hizume Masahiro , Shibata Fukashi , Matsumoto Ayako , Maruyama Yukie , Hayashi Eiji , Kondo Teiji , Kondo Katsuhiko , Zhang Shozo , Hong Deyuan
Published: November 2002

Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.03.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.Key words: AT-rich tandem repetitive DNA, fluorescence in situ hybridization, Larix, proximal DAPI band.
Effects of an intense ice storm on the structure of a northern hardwood forest
Authors: Rhoads Anne G , Hamburg Steven P , Fahey Timothy J , Siccama Thomas G , Hane Elizabeth N , Battles John , Cogbill Charles , Randall Jesse , Wilson Geoff
Published: November 2002

A major ice storm in January 1998 provided an opportunity to study the effects of a rare, intense disturbance on the structure of the northern hardwood forest canopy. Canopy damage was assessed using visual damage classes within watersheds of different ages at the Hubbard Brook Experimental Forest (HBEF) and changes in leaf area index in two of these watersheds. Ice thickness was measured, and ice loads of trees were estimated using regression equations. In the 60- to 120-year-old forests (mean basal area 26 m2·ha1), damage was greatest in trees >30 cm diameter at breast height and at elevations above 600 m. Of the dominant tree species, beech (Fagus grandifolia Ehrh.) was the most damaged, sugar maple (Acer saccharum Marsh.) was the most resistant, and yellow birch (Betula alleghaniensis Britt.) was intermediate. Trees with advanced beech bark disease experienced heavier ice damage. Little damage occurred in the 14-year-old forest, while the 24- to 28-year-old forest experienced intense damage. In the young stands of this forest, damage was greatest between 600 and 750 m, in trees on steep slopes and near streams, and among pin cherry (Prunus pensylvanica L.). Recovery of the canopy was tracked over three growing seasons, and root growth was monitored 1 year after the storm. Because of the high density of advance regeneration from beech bark disease and root sprouting potential in ice-damaged beech, HBEF will likely see an increase in beech abundance in older forests as a result of the storm. There will also be a more rapid change from pioneer species to mature northern hardwoods in the younger forests. These predictions illustrate the ability of rare disturbances to increase heterogeneity of forest structure and composition in this ecosystem, especially through interactions with other disturbances.