A population analysis of Robertsonian and Ag-NOR polymorphisms in brown trout (Salmo trutta)

An analysis of Robertsonian polymorphism and variation in the number of active NORs has been carried out in several populations of brown trout (Salmo trutta) from Northwestern Spain. The karyotype of this species appears to be soundly established, and essentially no variation has been found in chromosome number. Interindividual and interpopulation variation in arm number was detected, with figures ranging between 100 and 102 among individuals, and between 100.10 and 100.80 among populations. This variation in arm number is solely attributable to the polymorphism of the short arm of the main NOR-bearing pair 11, which can appear from acrocentric to metacentric in different individuals. Most populations analyzed showed the standard distribution of active NORs previously observed in this species. The Miño drainage basin, and specially the Chamoso population, showed a multi-chromosomal distribution of active NORs, with several new locations, always telomeric. In most cases no concordance was observed between previously detected rDNA sites in S. trutta and the new Ag-NOR locations. This fact suggests a transposition mechanism rather than an activation of silent rDNA sites to explain this multichromosomal NOR pattern.     

AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [ Triticum turgidum L. subsp. durum (Desf.) Husn.

A substantial amount of between and within cultivar genetic variation was detected in all the 13 registered modern Canadian durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husn.) cultivars based upon amplified restriction fragment polymorphism (AFLP). Of the approximately 950 detected AFLP markers, only 89 were polymorphic, with 41 between cultivars whereas the remaining 48 showed polymorphism within at least one cultivar. The ancestry of Canadian durum wheat cultivars was traced back to 125 cultivars, selections, and breeding lines including 17 landraces. Mean pair-wise genetic distance based on the kinship coefficient was 0.76. On the other hand, AFLP-based mean pair-wise genetic distance was 0.40. Even though there was a large difference between the means of the two diversity measures, a moderate positive correlation (r=0.457, p<0.002) was detected between the two distance matrices. Cluster analysis with the entire AFLP data divided all cultivars into three major groups reflecting their breeding origins. One group contained ’Pelissier’ alone, which was a selection from a landrace introduced into the US from Algeria. On the other hand such groupings among cultivars were not evident when KIN was used for genetic diversity measures instead. The level of genetic variation among individuals within a cultivar at the breeders’ seed level was estimated based on an inter-haplotypic distance matrix derived from the AFLP data. We found that the level of genetic variation within the most-developed cultivars is fairly substantial despite rigorous selection pressure aimed at cultivar purity in breeding programs. Comparison of AFLP and pedigree-based genetic diversity estimates in crop species such as durum wheat can provide important information for plant improvement. Received: 26 January 2001 / Accepted: 31 May 2001     

枇杷属内栽培种和部分野生种ITS序列分析

对不同栽培区的25种普通枇杷品种以及7种枇杷属野生种的ITS序列进行扩增并测序,采用邻接法和最大简约法进行系统发育树的构建并对枇杷属内不同种间的遗传关系进行了分析。结果表明:枇杷属植物ITS序列ITS1+5.8S rDNA+ITS2总长度为592 bp或594 bp,长度变化发生在ITS2。所有样本的ITS1和5.8S rDNA长度一样,都是223 bp和168 bp;而ITS2为201 bp或203 bp。5种枇杷属野生种的ITS序列长度为594 bp,包括栎叶枇杷、大渡河枇杷、南亚枇杷、南亚枇杷窄叶变种和大瑶山枇杷;其余2种枇杷属野生种(麻栗坡枇杷、小叶枇杷)和普通枇杷栽培种的ITS序列长度都为592 bp。所有样本ITS序列的GC含量为64.2%~64.5%,其中ITS1为64.1%~65.5%,ITS2为68.1%~72.6%。对所有样本的ITS序列比对产生44个可变位点,其中38个为简约信息位点,其中11个位于ITS1,5个位于5.8S rDNA,22个位于ITS2。最大的种间序列差异为7.7%,最小的种间差异发生在麻栗坡枇杷和小叶枇杷之间,仅为0.2%。普通枇杷种内的ITS序列差异很低,25种普通枇杷栽培种之间的序列差异为0~1.5%。所研究的枇杷属植物可分为3个分支。分支Ⅰ包括所有普通枇杷品种,分支Ⅱ包含5种野生枇杷种,包括栎叶枇杷、大渡河枇杷、南亚枇杷、南亚枇杷窄叶变种和大瑶山枇杷;分支Ⅲ由2个野生枇杷种(麻栗坡枇杷、小叶枇杷)组成。该研究结果表明ITS序列对枇杷种间鉴定和系统发育分析具有一定意义,但对普通枇杷栽培种间的鉴定作用不大。     

Ribosomal RNA genes in Scots pine (Pinus sylvestris L.): Chromosomal organization and structure

The nuclear 18S, 5.8S and 25S rRNA genes exist as thousands of rDNA repeats in the Scots pine genome. The number and location of rDNA loci (nucleolus organizers, NORs) were studied by cytological methods, and a restriction map from the coding region of the Scots pine rDNA repeat was constructed using digoxigenin-labeled flax rDNA as a probe. Based on the maximum number of nucleoli and chromosomal secondary constrictions, Scots pine has at least eight NORs in its haploid genome. The size of the Scots pine rDNA repeat unit is approximately 27 kb, two- or threefold larger than the typical angiosperm rDNA unit, but similar in size to other characterized conifer rDNA repeats. The intergenic spacer region (IGS) of the rDNA repeat unit in Scots pine is longer than 20 kb, and the transcribed spacer regions surrounding the 5.8S gene (ITS1 and ITS2) span a region of 2.9 kb. Restriction analysis revealed that although the coding regions of rDNA repeats are homogeneous, heterogeneity exists in the intergenic spacer region between individuals, as well as among the rDNA repeats within individuals.     

不同产地瓠瓜品种ITS序列的遗传多样性分析

对国产29个瓠瓜也Lagenariasiceraria（Molina）Standl.页品种的ITS序列进行了扩增及测序,并结合引自GenBank的国产9个瓠瓜品种以及国外6个瓠瓜品种和3个同属种类的ITS序列,对它们的ITS序列长度和GC含量以及变异位点进行比较,在此基础上构建系统发育树并对47个样本间的遗传关系进行研究。结果显示：供试47个样本的ITS序列均由ITS1、5.8SrDNA及ITS2组成,各样本间的ITS序列长度、GC含量以及变异位点差异明显。国产38个瓠瓜品种的ITS序列（包括ITS1、5.8SrDNA及ITS2）长度为619-627bp、GC含量为58.00%-63.32%;国外9个样本的ITS序列长度为591-626bp,GC含量为54.17%-63.26%。序列比对结果显示：国产38个瓠瓜品种的ITS序列同源率为84.6%-100.0%,包含221个变异位点;其中,来源于山东的品种‘砧木2’（‘ZhenmuNo.2’）的ITS序列包含的变异位点最多,与其他品种间的同源率也最低。在系统发育树上,国产38个瓠瓜品种可分为3个分支,来源于山东的品种‘砧木2’和来源于河南的品种‘西瓜砧木1’（‘XiguazhenmuNo.1’）各自聚为第1和第2分支;其余36个品种聚为第3分支。而供试的47个样本则可分为2个分支和5个亚组,第1分支可分为2个亚组,包括国产品种‘砧木2’和产自日本的2个品种;第2分支包含的44个样本则进一步分为3个亚组,国产品种‘西瓜砧木1’和产自法国的品种‘白花瓠瓜’（‘White-floweredgourd’）各自聚为第1和第2亚组,其余的42个样本聚为第3亚组。研究结果表明：供试的不同产地瓠瓜品种间存在丰富的遗传变异和地理分化现象,其ITS序列差异与地理分布有一定关系。     

Intra-isolate heterogeneity of the ITS region of rDNA in Pythium helicoides

Heterogeneity of the rDNA ITS region in Pythium helicoides and the phylogenetic relationship between P. helicoides and closely related species were investigated. In PCR-RFLP analysis of the rDNA ITS region of six P. helicoides isolates investigated, including the type culture, intraspecific variation was found at the HhaI site. The total length of fragments was longer than before cutting, indicating sequence heterogeneity within isolates. Digestion of the cloned rDNA ITS region derived from seven isolates with HhaI revealed polymorphisms among and within single zoospore isolates, and variability of the region was also present among the clones derived from the same isolate. To test whether the rDNA ITS region of closely related species and other regions in the genome of P. helicoides are also variable, the rDNA ITS region of P. ultimum and the cytochrome oxydase II (cox II) gene encoded in mitochondria were sequenced. P. ultimum had little variation in the rDNA ITS region. The cox II gene sequences of both species revealed only a low intraspecific variability and no intra-isolate variation. In the phylogenic tree based on the rDNA ITS sequences, all clones of P. helicoides formed one large clade that was distinct from the clades comprising morphologically similar species, such as P. oedochilum and P. ostracodes, and was closely related to P. chamaehyphon rather than the other species.     

Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution

The ITS sequences of Acropora spp. are the shortest so far identified in any metazoan and are among the shortest seen in eukaryotes; ITS1 was 70-80 bases, and ITS2 was 100-112 bases. The ITS sequences were also highly variable, but base composition and secondary structure prediction indicate that divergent sequence variants are unlikely to be pseudogenes. The pattern of variation was unusual in several other respects: (1) two distinct ITS2 types were detected in both A. hyacinthus and A. cytherea, species known to hybridize in vitro with high success rates, and a putative intermediate ITS2 form was also detected in A. cytherea; (2) A. valida was found to contain highly (29%) diverged ITS1 variants; and (3) A. longicyathus contained two distinct 5.8S rDNA types. These data are consistent with a reticulate evolutionary history for the genus Acropora.      

Structure and inheritance of ribosomal DNA variants in cultivated and wild hop, Humulus lupulus L.

Genetic variation was assessed among cultivated and wild hop, Humulus lupulus, by restriction fragment length polymorphisms (RFLPs) of the ribosomal RNA genes (rDNA). Two rDNA length variants of 10.3 and 9.3 kbp represented by three phenotypes designated A, B and C were detected with XhoI. Restriction-site mapping showed that hop rDNA is structurally similar to those of most higher plants. A high level of homogeneity existed in rDNA repeat lengths among the diverse hop genotypes. Generally, phenotype A was predominant in wild and cultivated European and Asian genotypes; phenotype B in North American cultivars; while phenotype C was present only in native North American hop, providing a potential molecular marker for the identification of this germ plasm. The rDNA data provided genetic evidence for the separation of native and cultivated American genotypes and supports the hypothesis that North American hop cultivars are of hybrid origin from European and native American genotypes. The segregation of rDNA phenotypes in four F₁ families suggests that a single locus with two co-dominant alleles controls genetic variability for rDNA variants in hop.     

Variation in the nuclear ribosomal DNA internal transcribed spacer (ITS) region of Pinus rzedowskii revealed by PCR-RFLP

 In the genus Pinus the internal transcribed spacers (ITS1 and ITS2) and the 5.8s region of the nuclear ribosomal DNA are approximately 3000 bp in length. ITS1 is considerably longer than ITS2 and partial sequences of ITS1 indicate that this region is evolving rapidly and exhibits intraspecific variation. The ITS2 and 5.8s regions are relatively conserved. We surveyed restriction fragment length variability of PCR-amplified fragments (PCR-RFLP) of the ITS region in four populations (86 individuals) of Pinus rzedowskii, a pine endemic to western Michoacán, Mexico. Five of the restriction endonucleases assayed revealed variation, with a total of 13 variants, most of which were length mutations of 300–900 bp. A moderate degree of population differentiation was detected. The average diversity (Shannon’s index) of ITS fragment size patterns was 1.19, with 34% of the variation due to differences among populations and 66% due to differences among individuals within populations. The same individuals were assayed for nine polymorphic isozymes, which gave diversity measures similar to those of each restriction endonuclease. Received: 25 August 1997 / Accepted: 19 September 1997     

Arbitrarily primed-PCR based diversity assessment reflects hierarchical groupings of Indian tetraploid wheat genotypes

Genetic diversity analysis using PCR with arbitrary decamer primers (RAPD — random amplified polymorphic DNA) was carried out in a set of 63 tetraploid wheat genotypes which comprised 24 durum landraces, 18 durum cultivars, nine dicoccum cultivars, ten less commonly cultivated species and two wild tetraploid species. The durum and dicoccum wheat genotypes are a part of the germplasm used in Indian tetraploid wheat breeding programs. A total of 206 amplification products were obtained with 21 informative primers, of which 162 were polymorphic. The highest degree of polymorphism was seen in the wild and less commonly cultivated species (68.9%). Durum released cultivars showed greater polymorphism (50.6%) than landraces (44.8%), while dicoccum cultivars showed a considerably low level of polymorphism (23.6%). Cluster analysis led to the separation of wild and cultivated genotypes, and among cultivated emmer wheat distinct groups were formed by the durum cultivars, durum landraces and dicoccum cultivars. The subgroupings of landraces had no relation to their geographical distribution. The durum cultivars formed subgroups based on common parentage in their pedigree. Among species, wild timopheevi wheat (T. araraticum) and its cultivated form (T. timopheevi) formed a distinct group distant from all other genotypes. The present study is a first attempt at determining the genetic variation in Indian tetraploid wheats at the molecular level. Received: 10 January 1999 / Accepted: 30 January 1999     

Variation in fructooligosaccharide contents during plant development and in different cultivars of durum wheat

Abstract

Fructooligosaccharides (FOS) have received a great deal of attention for their properties as prebiotic components. Several plants store FOS in their tissues as carbohydrate source or as osmoregulators. In comparison with the other natural FOS sources, cereals, in particular durum wheat, store a significant amount of these oligosaccharides during their growth. To gain a deeper insight on the relationships between FOS and plant/kernel development, FOS levels were analysed in the grains and stems of a widely cultivated durum wheat cultivar (Simeto), during the whole period of grain filling. In addition, a broad analysis of FOS contents was carried out by comparing their levels in the stems and grains of 45 cultivars of durum wheat harvested at two development stages. Results show a large variation among cultivars in their capability to metabolise FOS.     

Quantifying relationships between rooting traits and water uptake under drought in Mediterranean barley and durum wheat

In Mediterranean regions drought is the major factor limiting spring barley and durum wheat grain yields. This study aimed to compare spring barley and durum wheat root and shoot responses to drought and quantify relationships between root traits and water uptake under terminal drought.One spring barley（Hordeum vulgare L. cv. Rum） and two durum wheat Mediterranean cultivars（Triticum turgidum L. var durum cvs Hourani and Karim） were examined in soil‐column experiments under well watered and drought conditions. Root system architecture traits, water uptake, and plant growth were measured. Barley aerial biomass and grain yields were higher than for durum wheat cultivars in well watered conditions. Drought decreased grain yield more for barley（47%） than durum wheat（30%, Hourani）. Root‐to‐shoot dry matter ratio increased for durum wheat under drought but not for barley, and root weight increased for wheat in response todrought but decreased for barley. The critical root length density（RLD） and root volume density（RVD） for 90% available water capture for wheat were similar to（cv. Hourani） or lower than（cv. Karim） for barley depending on wheat cultivar. For both species, RVD accounted for a slightly higher proportion of phenotypic variation in water uptake under drought than RLD.     

Domesticated emmer wheat [T. turgidum L. subsp. dicoccon (Schrank) Thell.] as a source for improvement of zinc efficiency in durum wheat

Modern durum wheat (AABB) is more sensitive to zinc (Zn) deficiency than bread wheat (AABBDD). One strategy to increase productivity and expansion of durum wheat industry in Zn-deficient soils is to improve its ability to grow and yield in such soils. This ability is termed Zn efficiency. In a growth room experiment using soil culture, we assessed the potential of Triticum turgidum L. subsp. dicoccon (Shrank) Thell. (domesticated emmer wheat, AABB) as a genetic resource for further improvement of Zn efficiency in modern durum wheat. Twenty four accessions of domesticated emmer wheat, four durum landraces/cultivars, and two bread wheat cultivars/ advanced breeders lines of known Zn efficiency were tested under Zn deficiency and Zn sufficiency. Significant variation was observed among genotypes in Zn deficiency symptoms, dry matter production, shoot Zn concentration, shoot Zn content and Zn utilisation efficiency (physiological efficiency). We identified domesticated emmer wheat accessions with greater Zn efficiency than modern durum wheat and even bread wheat genotypes. These accessions could be used in breeding programs to improve Zn efficiency of durum wheat. The results suggest that Zn efficiency of durum or bread wheat is likely to be determined collectively by its progenitors.     

RIBOSOMAL DNA AND RAPD VARIATION IN THE RARE PLANT FAMILY LACTORIDACEAE

Lactoris fernandeziana, endemic to the island of Masatierra in the Juan Fernandez Archipelago, is the only living member of the primitive angiosperm family, Lactoridaceae. The species was surveyed for ribosomal DNA (rDNA) and RAPD (Random Amplified Polymorphic DNA) variation. Previous analyses of allozymes had revealed no variation within the species. Variation was found for length in the intergenic spacer and for restriction sites in the 18S–25S genes of rDNA, and for the presence of amplified bands using 16 primers. Different rDNA repeat lengths and restriction site variants were detected within individuals as well as within and among populations. The level of variation in RAPDs is low relative to other Juan Fernandez endemic species surveyed, and nearly all variants were restricted to single populations. The rDNA length variants were distributed throughout the island, whereas the rDNA restriction site variants and RAPD markers indicated minor genetic differences among the populations.     

Catalogue of alleles of gliadin-coding loci in durum wheat (Triticum durum Desf.)

Gliadins are seed storage proteins which are characterized by high intervarietal polymorphism and can be used as genetic markers. As a result of our work, a considerably extended catalogue of allelic variants of gliadin component blocks was compiled for durum wheat; 74 allelic variants for four gliadin-coding loci were identified for the first time. The extended catalogue includes a total of 131 allelic variants: 16 for locus Gli-A1(d), 19 for locus Gli-B1(d), 41 for locus Gli-A2(d), and 55 for locus Gli-B2(d). The electrophoretic pattern of the standard cultivar and a diagram are provided for every block identified. The number of alleles per family is quite small for loci Gli-A1(d) and Gli-B1(d) of durum wheat, as contrasted to loci Gli-A2(d) and Gli-B2(d) that are characterized by large families including many alleles. The presence of large block families determines a higher diversity of durum wheat for loci Gli-A2(d) and Gli-B2(d) as compared to Gli-A1(d) and Gli-B1(d). The catalogue of allelic variants of gliadin component blocks can be used by seed farmers to identify durum wheat cultivars and evaluate their purity; by breeders, to obtain homogenous cultivars and control the initial stages of selection; by gene bank experts, to preserve native varieties and the original biotypic composition of cultivars.     

Length variation in the internal transcribed spacers of ribosomal DNA in Picea abies and related species

The structure and variation of nuclear ribosomal DNA (rDNA) units of Picea abies, (L.) Karst. was studied by restriction mapping and Southern hybridization. Conspicuous length variation was found in the internal transcribed spacer (ITS) region of P. abies, although the length of this region is highly conserved both within and among most of the plant species. Two types of ITS variants (A and B), displaying a size difference of 0.5 kb in the ITS2 region, were present within individuals of P. abies from Sweden, Central Europe and Siberia. A preliminary survey of 14 additional Eurasian and North American species of Picea suggested that length variation in the ITS region is widespread in this genus. Alltogether three length variants (A, B and C) were identified. Within individuals of eight Picea species, two length variants were present within the genome (combinations of A and B variants in P. glehnii, P. maximowiczii, P. omorika, P. polita and P. sitchensis and variants B and C in P. jezoensis, P. likiangensis and P. spinulosa). Within individuals from five species, however only one rDNA variant was present in their genome (variant A in P. aurantiaca, P. engelmannii, P. glauca, P. koraiensis and P. koyamai; variant B in P. bicolor). The ITS length variation will be useful as a molecular marker in evolutionary studies of the Picea species complex, whose phylogeny is controversial. The presence of intraindividual variation in, and shared polymorphism of the, ITS length variants raises questions about the occurrence of interspecific hybridization during the evolutionary history of Picea.     

Nucleolar behavior during meiosis in four species of phyllostomid bats (Chiroptera, Mammalia)

We analyzed the behavior of the nucleolus, nucleolar structures and nucleolus organizer regions (NORs) during meiotic division in four species of phyllostomid bats that have different numbers and locations of NORs. Nucleoli began disassembly at leptotene, and the subcomponents released from the nucleolus were dispersed in the nucleoplasm, associated with perichromosomal regions, or they remained associated with NORs throughout division. In Phyllostomus discolor, a delay in nucleolus disassembly was observed; it disassembled by the end of pachytene. The RNA complexes identified by acridine orange staining were observed dispersed in the nucleoplasm and associated with perichromosomal regions. FISH with rDNA probe revealed the number of NORs of the species: one NOR in Carollia perspicillata, one pair in Platyrrhinus lineatus and P. discolor, and three pairs in Artibeus lituratus. During pachytene, there was a temporary dissociation of the homologous NORs, which returned to pairing at diplotene. The variation in the number (from one to three pairs) and location of NORs (in sex or autosomal chromosomes, at terminal or interstitial regions) did not seem to interfere with the nucleolar behavior of the different species because no variation in nucleolar behavior that could be correlated with the variation in the number and chromosomal location of NORs was detected.     

Molecular characterisation of the Wx-B1 allelic variants identified in cultivated emmer wheat and comparison with those of durum wheat

Emmer wheat is a neglected crop that could be used in the breeding of modern durum wheat for quality, one important aspect of which is the starch composition that is related to the waxy proteins. A collection of 87 accessions of Spanish emmer wheat was analysed for waxy protein composition by SDS?CPAGE. No polymorphism was found for the Wx-A1 gene. However, for the Wx-B1 gene, three alleles were detected, two of them new. The whole gene sequence of these alleles was amplified by PCR in three fragments, which were digested with several endonucleases to determine internal differences in the sequence. These variants were also compared with the Wx alleles present in durum wheat. Differences in size and restriction sites were detected. DNA sequence analysis confirmed that the alleles found in emmer wheat are different from those in durum wheat. The first data suggested that these alleles showed a different influence on the amylose content of these lines. The variation found could be used to enlarge the gene pool of durum and emmer wheat, and design new materials with different amylose content.     

Genetic diversity of durum wheat as determined by AFLP in fluorescence

The DNA of fifteen Italian cultivars of durum wheat (Triticum turgidum L. ssp. durum) were analyzed by in fluorescence amplified fragment length polymorphism (fAFLP) in order to obtain the characteristic fingerprintings of genotypes and assess their genetic relatedness. Among 64 combinations of fluorescence labelled primers, three different combinations were chosen as producing a total of 6630 AFLP fragments, 2277 (34.3 %) of them being polymorphic. By using this fAFLP methodology a DNA fingerprinting of each durum wheat cultivar was generated for genotype identification. Analysis of the genetic relationships show the low variability among durum wheat cultivars.