Intrachromosomal mapping of the nucleolar organiser region relative to three marker loci on chromosome 1B of wheat (Triticum aestivum)

Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses

Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.

Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them. In this paper, chromosome 1 linkage maps of Triticum aestivum, T. tauschii, and T. monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe. The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones. There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps. A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species. Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat. The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae.

Glu-B2, a storage protein locus controlling the D group of LMW glutenin subunits in bread wheat (Triticum aestivum)

Genes controlling the synthesis of the D group of low-molecular-weight (LMW) subunits of glutenin occur on the short arms of chromosomes 1B and 1 D. Their position on chromosome 1 B, relative to the storage protein lociGlu-B1(long arm) andGli-B1(short arm), was estimated by analysing the backcross-one progeny of two different crosses. To estimate recombination between the D subunit genes andGli-B1, half grains were analysed by two-dimensional electrophoresis. TheGli-B1locus contains genes for the B group of LMW glutenin subunits, γ-gliadins and ω-gliadins although only the latter were made use of in this study to distinguish the parental alleles. Additionally, the complementary half grains were analysed by sodium dodecyl sulphate, polyacrylamide-gel electrophoresis to estimate recombination betweenGli-B1andGlu B1, coding for high-molecular-weight (HMW) glutenin subunits. The D subunit genes occur at a new locus, provisionally defined asGlu-B2, which lies in betweenGlu-B1andGli-B1, 17 cM from the former and 22 cM from the latter. On the basis of previous mapping data involvingGli-B1, it was concluded that the D subunit genes occur close to the nucleolar organizing region and probably on the short-arm satellite, likeGli-B1.

Genetic linkage map of the nucleolus organizer region in the soybean

Simple polymorphisms in ribosomal DNA repeats in the nucleolus organizer region (NOR) permitted the development of markers for the genetic mapping of the soybean NOR. The markers map to the top end of soybean linkage group F, one of either telomeric end predicted in the cytogenetic and primary trisomic studies.

Comparative analyses between lolium/festuca introgression lines and rice reveal the major fraction of functionally annotated gene models is located in recombination-poor/very recombination-poor regions of the genome

Publication of the rice genome sequence has allowed an in-depth analysis of genome organization in a model monocot plant species. This has provided a powerful tool for genome analysis in large-genome unsequenced agriculturally important monocot species such as wheat, barley, rye, Lolium, etc. Previous data have indicated that the majority of genes in large-genome monocots are located toward the ends of chromosomes in gene-rich regions that undergo high frequencies of recombination. Here we demonstrate that a substantial component of the coding sequences in monocots is localized proximally in regions of very low and even negligible recombination frequencies. The implications of our findings are that during domestication of monocot plant species selection has concentrated on genes located in the terminal regions of chromosomes within areas of high recombination frequency. Thus a large proportion of the genetic variation available for selection of superior plant genotypes has not been exploited. In addition our findings raise the possibility of the evolutionary development of large supergene complexes that confer a selective advantage to the individual.

Introgression mapping in the grasses

The unique properties of Lolium/Festuca hybrids and their derivatives provide an ideal system for intergeneric introgression. At IGER a focus on the Lolium perenne/Festuca pratensis system is being exploited to elucidate genome organization in the grasses, determination of the genetic control of target traits and the isolation of markers for marker-assisted selection in breeding programmes.

In-situ comparative mapping (ISCM) of Glu-1 loci in Triticum and Hordeum

The ability to detect small low- or single-copy DNA sequences by fluorescence in-situ hybridization (FISH) is an important step towards physical mapping of plant genomes. In this study, the FISH technique was used to physically map the Glu-1 loci controlling high-molecular weight (HMW) glutenin in common wheat (Triticum aestivum cv. 'Chinese Spring') and tritordeum (an amphiploid between T. turgidum cv. durum and Hordeum chilense). The probe used was the single-copy Glu-D1-1d gene coding the 1Dx5 HMW glutenin subunit. Three loci were mapped on chromosomes of wheat homoeologous group 1 (arm 1AL, 1BL and 1DL). The Glu-1 loci were mapped (fraction of the distance from the centromere) at positions 0.76 +/- 0.01, 0.69 +/- 0.01 and 0.76 +/- 0.01, on arms 1AL, 1BL and 1DL, respectively. The Glu-1 loci were also mapped on chromosomes of homoeologous group 1 of tritordeum at positions 0.75 +/- 0.01, 0.70 +/- 0.01 and 0.60 +/- 0.01, on arms 1AL, 1BL and 1HchL, respectively. Chromosomes with positive signals were identified by reprobing chromosome preparations using both the GAA-satellite and pAs1 sequences simultaneously. The application of the FISH technique to study homoeology among different genomes is discussed.

Physical and genetic mapping in the grasses Lolium perenne and Festuca pratensis

A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1.

QTL analysis of fertility-restoration against cytoplasmic male sterility in wheat

The cytoplasm of Triticum timopheevi causes cytoplasmic male sterility (CMS) in common wheat (T. aestivum) cv. 'Chinese Spring' (CS), and that of Aegilops kotschyi causes CMS in spelt wheat (T. spelta) var. duhamelianum (Sp). CS has fertility-restoring (Rf) genes against the latter cytoplasm and Sp has the ones against the former. To know the genetic system concerning to CMS, we crossed 66 F8 recombinant inbred lines (RILs) derived from a cross between CS and Sp as males to the alloplasmic lines of CS and Sp having the cytoplasms of T. timopheevi and Ae. kotschyi, respectively. The fertilities of respective F1 plants derived from the crosses were examined for QTL analysis. The major QTLs detected in both systems were located on the short arm of chromosome 1B. One minor QTL on chromosome 2B was also commonly detected in both of the systems, while other minor QTLs against T timopheevi cytoplasm were distributed on the chromosomes 2A, 4B, and 6A.

CEREAL CHROMOSOME STRUCTURE, EVOLUTION, AND PAIRING

▪ Abstract  The determination of the order of genes along cereal chromosomes indicates that the cereals can be described as a single genetic system. Such a framework provides an opportunity to combine data generated from the studies on different cereals, enables chromosome evolution to be traced, and sheds light on key structures involved in cereal chromosome pairing. Centromeric and telomeric regions have been highlighted as important in these processes.

Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes

The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy. Key words: wheat, rice, comparative mapping, deletion lines.

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (</=1 Mb/cM) correspond to only 4.9% of the total barley genome and harbor 47.3% of the 429 markers of the studied RFLP map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning.

Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) is a powerful means by which single- and low-copy DNA sequences can be localized on chromosomes. Compared to the mitotic metaphase chromosomes that are normally used in FISH, synaptonemal complex (SC) spreads (hypotonically spread pachytene chromosomes) have several advantages. SC spreads (1) are comparatively free of debris that can interfere with probe penetration, (2) have relatively decondensed chromatin that is highly accessible to probes, and (3) are about ten times longer than their metaphase counterparts, which permits FISH mapping at higher resolution. To investigate the use of plant SC spreads as substrates for single-copy FISH, we probed spreads of tomato SCs with two single-copy sequences and one low-copy sequence (ca. 14 kb each) that are associated with restriction fragment length polymorphism (RFLP) markers on SC 11. Individual SCs were identified on the basis of relative length, arm ratio, and differential staining patterns after combined propidium iodide (PI) and 4', 6-diamidino-2-phenylindole (DAPI) staining. In this first report of single-copy FISH to SC spreads, the probe sequences were unambiguously mapped on the long arm of tomato SC 11. Coupled with data from earlier studies, we determined the distance in micrometers, the number of base pairs, and the rates of crossing over between these three FISH markers. We also observed that the order of two of the FISH markers is reversed in relation to their order on the molecular linkage map. SC-FISH mapping permits superimposition of markers from molecular linkage maps directly on pachytene chromosomes and thereby contributes to our understanding of the relationship between chromosome structure, gene activity, and recombination.

Comparative RFLP mapping of the chlorotoluron resistance gene (Su1) in cultivated wheat (Triticum aestivum) and wild wheat (Triticum dicoccoides)

Chlorotoluron is a selective phenylurea herbicide widely used for broad-leaved and annual grass weed control in cereals. Variation in the response to chlorotoluron (CT) was found in both hexaploid bread wheat (Triticum aestivum L.) and wild tetraploid wheat (Triticum dicoccoides KöRN.). Here, we describe the comparative mapping of the CT resistance gene (Su1) on chromosome 6B in bread and wild wheat using RFLP markers. In bread wheat, mapping was based on 58 F(4) single-seed descent (SSD) plants of the cross between a genotype sensitive to chlorotoluron, 'Chinese Spring' (CS), and a resistant derivative, the single chromosome substitution line, CS ('Cappele-Desprez' 6B) [CS (CAP6B). In T dicoccoides, mapping was based on 37 F(2) plants obtained from the cross between the CT-susceptible accession B-7 and the resistant accession B-35. Nine RFLP probes spanning the centromere were chosen for mapping. In bread wheat Su1 was found to be linked to alpha-Amy-1 (9.84 cM) and Xpsr371 (5.2 cM), both on the long arm of 6B, and Nor2 (2.74 cM) on the short arm. In wild wheat the most probable linkage map was Nor2-Xpsr312-Su1-Pgk2, and the genetic distances between the genes were 24.8cM, 5.3cM, and 6.8cM, respectively. These results along with other published map data indicate that the linear order of the genes is similar to that found in T. aestivum. The results of this study also show that the Su1 gene for differential response to chlorotoluron has evolved prior to the domestication of cultivated wheat and not in response to the development and use of chemicals.

Detection of a highly heterozygous locus in recombinant inbred lines of rice and its possible involvement in heterosis

Forty-seven recombinant inbred (RI) lines derived from a cross between two indica rices, cv 'Phalguna' and the Assam land race ARC 6650, were subjected to restriction fragment length polymorphism (RFLP) analysis using cloned probes defining 150 single-copy loci uniformly dispersed on the 12 chromosomes of rice. Of the probes tested, 47 detected polymorphism between the parents. Heterozygosity was calculated for each line and for each of the polymorphic loci. Average heterozygosity per line was 9.6% but was excessive (>20%) in the 5 lines that seemed to have undergone outcrossing immediately prior to harvest. Average heterozygosity detected by each probe across the 47 RI lines was 9.7%. The majority of probes revealed the low level of heterozygosity (<8%) expected for F5-F6 lines in a species showing about 5% outbreeding. On the other hand, 7 probes exhibited heterozygosity in excess of 15%, while with a eighth probe (RG2 from chromosome 11) heterozygosity varied according to the restriction enzyme employed, ranging from 2% with SaII to 72% with EcoRV. The presence of 34 recombination sites in a segment of the genome as short as 24 kb indicates a strong selection for recombination between two neighbouring loci, one required as homozygous for the 'Phalguna' allele, and the other heterozygous. Since selection was principally for yield advantage over that of the high-yielding parent, 'Phalguna', one or both of these loci may be important for heterosis in this cross. The results also indicate that heterozygosity as measured by RFLP can depend on the particular restriction endonuclease employed.

Refined physical mapping of theSec-1locus on the satellite of chromosome 1R of rye (Secale cereale)

The Sec-1 locus (ω-secalin) of rye (Secale cereale L.) was mapped in the satellite of the short arm of chromosome 1R using fluorescence in situ hybridization and a genomic probe called pSec2B. Sec-1 is located in the middle of the satellite at the junction of the proximal euchromatic and the distal heterochromatic regions. Double hybridization experiments using rDNA and pSec2B showed that the NOR spans over the secondary constriction of the short arm of chromosome 1R and that there is a clearly visible gap between the NOR and Sec-1. Heterologous hybridization of pSec2B to barley visualized the B-hordein locus on chromosome 1H.Key words: fluorescence in situ hybridization, physical mapping, genetic mapping, secalin, rye, B-hordein, rDNA.

A genetic map of rye chromosome 1R integrating RFLP and cytogenetic loci

A genetic map of rye, Secale cereale L., chromosome 1R covering 247 cM was constructed utilizing 27 RFLP and four C-band markers, including terminal C-bands. Genetic mapping of C-bands and the centromere, and in situ hybridization of three RFLP clones, allowed for the integration of the genetic and cytological maps. Eight contact points between the genetic and cytological maps revealed variation in the recombination distance to cytological distance ratio ranging between 0.25 and 1.95, a 7.8-fold difference. Recombination was found to be highest in the satellite region of 1RS and lowest in the most distal region of 1RL.

Cytogenetic and molecular mapping of the wheat-Aegilops longissima chromatin breakpoints in powdery mildew-resistant introgression lines

The amount of alien chromatin introgressed in eight wheat/Ae. longissima Pm13 recombinant lines, involving breakpoints on the short arms of wheat chromosomes 3B and 3D, was evaluated by cytogenetic and molecular approaches. For each line the residual homologous synaptic ability of the recombinant chromosome in its proximal wheat and distal alien portion was estimated through meiotic analyses. Subsequently, telocentric and RFLP mapping were used to assess the genetic distance from the wheat centromere to the wheat/Ae. longissima breakpoints. One 3B recombinant line was distinguished from the other four by the chromosome pairing and telocentric mapping analyses. RFLP analysis succeeded in differentiating the remaining four lines into two groups. Chromosome pairing and telocentric mapping of the three 3D recombinant lines suggested that all had distinct breakpoints. However, the RFLP data could not discriminate between the two more proximal translocations. Physical locations for some RFLP loci were determined by a comparison of genotypes and C-banding karyotypes. This showed a considerable expansion of the genetic map compared to its physical length.

Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination

The construction of comparative genetic maps of chromosomes 4A(m) and 5A(m) of Triticum monococcum and chromosomes of homoeologous groups 4, 5 and 7 of T. aestivum has provided insight into the evolution of these chromosomes. The structures of chromosomes 4A, 5A and 7B of modern-day hexaploid bread wheat can be explained by a 4AL/5AL translocation that occurred at the diploid level and is present both in T. monococcum and T. aestivum. Three further rearrangements, a 4AL/7BS translocation, a pericentric inversion and a paracentric inversion, have taken place in the tetraploid progenitor of hexaploid wheat. These structural rearrangements and the evolution of chromosomes 4A, 5A and 7B of bread wheat are discussed. The presence of the 4AL/5AL translocation in several Triticeae genomes raises two questions - which state is the more primitive, and is the translocation of mono- or poly-phylogenetic origin?The rearrangements that have occurred in chromosome 4A resulted in segments of both arms having different positions relative to the telomere, compared to 4A(m) and to 4B and 4D. Comparisons of map length in these regions indicate that genetic length is a function of distance from the telomere, with the distal regions showing the highest recombination.

Physical distribution of translocation breakpoints in homoeologous recombinants induced by the absence of the Ph1 gene in wheat and triticale

The physical distribution of translocation breakpoints was analyzed in homoeologous recombinants involving chromosomes 1A, 1B, 1D of wheat and 1R of rye, and the long arms of chromosome 7S of Aegilops speltoides and 7A of wheat. Recombination between homoeologues was induced by removal of the Ph1 gene. In all instances, translocation breakpoints were concentrated in the distal ends of the chromosome arms and were absent in the proximal halves of the arms. The relationship between the relative distance from the centromere and the relative homoeologous recombination frequency was best explained by the function f(x)=0.0091e(0.0592x). The pattern of recombination in homoeologous chromosomes was essentially the same as in homologues except that there were practically no double exchanges. Among 313 recombinant chromosomes, only one resulted from a double crossing-over. The distribution of translocation breakpoints in translocated arms indicated that positive chiasma interference operated in homoeologous recombination. This implies that the reduction of the length of alien chromosome segments present in translocations with wheat chromosomes may be more difficult than the production of the original recombinants.

The physical location of fourteen RFLP markers in rice (Oryza sativa L.)

A biotin-labeled in situ hybridization technique was used in order to physically map RFLP markers to the chromosomes of rice (Oryza sativa L.). Fourteen RFLP markers, associated with the ends of the linkage groups on rice chromosomes 7, 8, 11, 12, were physically mapped onto specific regions of the chromosomes. The average detection rate of in situ hybridization was 5.91%. The markers were located on seven different chromosome arms. Ten of the fourteen markers were distributed near the chromosome ends. This demonstrated that the RFLP linkage groups involved covered a wide physical distance and that the centromeric region was bisected by all but one linkage group. Two markers covered a short genetic distance but were physically distant, while two covering a longer genetic distance were physically closer together. This indicates that considerable variation can, and does, exist between genetic and physical maps.This paper is a contribution of the U.S. Department of Agriculture, Agricultural Research Service, and Missouri Agricultural Experiment Station, Journal Series No. 11 882All programs and services of the U.S. Department of Agriculture are offered on a nondiscriminatory basis without regard to race, color, national origin, religion, sex, age, marital status, or handicap.

Localization of translocation breakpoints in somatic metaphase chromosomes of barley

Karyotype analyses based on staining by acetocarmine followed by Giemsa N-banding of somatic metaphase chromosomes of Hordeum vulgare L. were carried out on 61 reciprocal translocations induced by X-irradiation. By means of computer-based karyotype analyses all of the 122 breakpoints could be localized to defined sites or segments distributed over the seven barley chromosomes. The pre-definition of translocations with respect to their rearranged chromosome arms from other studies rendered it possible to define the break positions even in translocations having exchanged segments equal in size and the breakpoints located distally to any Giemsa band or other cytological marker. The breakpoints were found to be non-randomly spaced along the chromosomes and their arms. All breaks but one occurred in interband regions of the chromosomes, and none of the breaks was located directly within a centromere. However, short and long chromosome arms recombined at random. An improved tester set of translocations depicting the known break positions of most distal location is presented.

An RFLP-based genetic map of pearl millet (Pennisetum glaucum)

Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F2 population, derived from a single F1 plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.

Linkage relationships between prolamin genes on chromosomes 1A and 1B of durum wheat

Gliadin and glutenin electrophoresis of F2 progeny from four crosses of durum wheat was used to analyse the linkage relationships between prolamin genes on chromosomes 1A and 1B. The results showed that these genes are located at the homoeoallelic lociGlu-1,Gli-3,Glu-3 andGli-1. The genetic distances between these loci were calculated more precisely than had been done previously for chromosome 1B, and the genetic distances betweenGli-A3,Glu-A3 andGli-A1 on chromosome 1A were also determined. Genes atGli-B3 were found to control someω-gliadins and one B-LMW glutenin, indicating that it could be a complex locus.

The distribution of RFLP markers on chromosome 2(2H) of barley in relation to the physical and genetic location of 5S rDNA

The 5S rDNA locus on the long arm of barley chromosome 2(2H) was genetically mapped in two crosses in relation to 30 other RFLP loci. Comparison of the genetic maps with the previously published physical position of the 5S rDNA, determined by in-situ hybridization, showed that there was a marked discrepancy between physical and genetic distance in both crosses, with recombination being less frequent in the proximal part of the arm. Pooled information from the present study and other published genetic maps showed that at least 26 of the 44 (59%) RFLPs that have been mapped on 2(2H)L lie distal to the 5S rDNA locus even though this region is only 27% of the physical length of the arm. The distribution of RFLP markers is significantly different from expected (P < 0.01), implying that the low-copy sequences used for RFLP analysis occur more frequently in distal regions of the arm and, or, that sequences in distal regions are more polymorphic.

Physical distribution of recombination in B-genome chromosomes of tetraploid wheat

Several studies have indicated a noncorrespondence between genetic and physical distances in wheat chromosomes. To study the physical distribution of recombination, polymorphism for C-banding patterns was used to monitor recombination in 67 segments in 11 B-genome chromosome arms of Triticum turgidum. Recombination was absent in proximal regions of all chromosome arms; its frequency increased exponentially with distance from the centromere. A significant difference was observed between the distribution of recombination in physically short and physically long arms. In physically short arms, recombination was almost exclusively concentrated in distal segments and only those regions were represented in their genetic maps. In physically long arms, while a majority of the genetic distance was again based upon recombination in distal chromosome segments, some interstitial recombination was observed. Consequently, these regions also contributed to the genetic maps. Such a pattern of recombination, skewed toward terminal segments of chromosomes, is probably a result of telomeric pairing initiation and strong positive chiasma interference. Interference averaged 0.81 in 35 pairs of adjacent segments and 0.57 across the entire recombining portions of chromosome arms. The total genetic map lengths of the arms corresponded closely to those expected on the basis of their metaphase-I chiasma frequencies. As a consequence of this uneven distribution of recombination there can be a 153-fold difference (or more) in the number of DNA base pairs per unit (centiMorgan) of genetic length.

A cytogenetic map on the entire length of rye chromosome 1R, including one translocation breakpoint, three isozyme loci and four C-bands

A cytogenetic map of the whole 1 R chromosome of rye has been made, with distances between adjacent markers shorter than 50% recombination. Included in the map are isozyme loci Gpi-R1, Mdh-R1 and Pgd2, the telomere C-bands of the short arm (ts1) and the long arm (tl1), two interstitial C-bands in the short arm proximal to the nuclear organizing region (NOR) (is1) and in the middle of the long arm (il1), respectively, and translocation T273W (Wageningen tester set). By means of electron microscope analysis of spread pachytene synaptonemal complexes, the breakpoint of this translocation was physically mapped in the short arm of 1R, proximal to NOR, and in the long arm of 5R (contrary to previous assumptions). The data indicated the marker order: ts1 - Gpi-R1 - is1 - T273W/Mdh-R1 - il1 - Pgd2 - tl1. A comparison between genetic and physical maps revealed that recombination is mainly restricted to the distal regions of both arms. For the translocation T273W, in heterozygotes no recombinants were observed between the translocation breakpoint and its two adjacently located markers (is1 and Mdh-R1), but recombination was not reduced in the distal regions of the chromosome. The segregations of several other isozyme and C-band markers also analyzed in the investigation presented here were consistent with observations of earlier authors concerning chromosome asignment and linkage relationships.

RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye

Genetic maps of chromosomes 3A, 3B and 3D of wheat and 3R of rye were developed using 22 DNA probes and two isozyme marker systems. Analysis of the 49 loci mapped showed extreme clustering around the centromere in all four maps, with large 'gaps' in the distal chromosome regions, which is interpreted as being due to strong localisation of recombination towards the ends of the wheat and rye chromosomes. In the centromeric regions gene orders are highly conserved between the three wheat genomes and the rye genome. However, the unpredictable behaviour of the DNA clones that map in distal chromosome locations may indicate that the genomes are diverging most rapidly in the regions of higher recombination. A comparison of cDNA and genomic probes showed the latter to be much more efficient for revealing RFLP. Some classes of gDNA clones, i.e. chromosome-specific sequences and those hybridizing in a non-homoeologous manner, were seen to be most polymorphic. Correlations between map locations and RFLP levels showed no clear relationship. In addition to anonymous DNA clones, the locations of known function clones, sedoheptulose-1,7-bisphosphatase (XSbp), carboxypeptidase I (XCxp1) and a bZIP protein (XEmbp), were ascertained along with those for two isozyme loci, Mal-1 and Est-5.

Genetic linkage between C-bands and storage protein genes in chromosome 1B of tetraploid wheat

Genetic mapping of polymorphic C-bands allows direct comparisons between genetic and physical maps. Eleven C-bands and two seed storage protein genes on chromosome 1B, polymorphic between Langdon durum and four accessions of T. dicoccoides, were used to study the distribution of recombination along the entire length of the chromosome. Recombination in the short arm was almost completely restricted to the satellite, two-thirds of the arm's length from the centromere; the Gli-B1 gene was found to be tightly linked to the telomeric C-band. In the long arm, the distal 51.4% of the arm accounted for 88% of recombination; the proximal half of the arm accounted for the remaining 12%. While the amount of crossing-over differed significantly between the four T. dicoccoides 1B chromosomes, there were no significant differences in the relative distributions of crossing-over along the chromosome. Consequently, the genetic maps obtained from the four individual T. dicoccoides chromosomes were combined to yield a consensus map of 14 markers (including the centromere) for the chromosome.

Genetic mapping between Gli-B1 locus and a telomeric C-heterochromatin band in wheat

Using C-banding it has been possible to prove that the bread wheat varieties 'Holdfast' and 'CapelleDesprez' shows an intense band of telomeric heterochromatin on the short arm of chromosome 1B, while the variety 'Pané-247' presents a very thin band. Gliadin study using pH-acid electrophoresis revealed the existence of differences in the Gli-B1 locus in the three varieties. Analysis of the progeny of the (P x H) x CD hybrid revealed recombination between the heterochromatin C-band and locus Gli-B1, and allowed the genetic distance between the two markers to be calculated as 6.55±3.16 cMorgan. This is the first time the genetic distance from a locus to the chromosome telomere has been directly obtained in wheat. The heterochromatin C-band studied here gives us a cytological marker on chromosome 1B that can be used as a reference point in the localization of other genes.

Linkage and cytogenetic maps of genes controlling endosperm storage proteins and isozymes in rye (Secale cereale L.)

An F1 plant fromSecale cereale ssp.ancestrale xtelocentric substitution lines3R of the cultivated rye "Petkus spring" was used as female in a cross with the inbred line Riodeva (I28), which has the standard chromosome arrangement. Single plants from this backcross progeny were analyzed for chromosome constitution, storage protein, and isozymic patterns. The seed protein loci were identified asSec-1a andSec-1b loci controlling 40-Kγ-secalins andω-secalins, respectively. These loci are located on the short arm of chromosome1R. TheSec-3 locus controlling high-molecular-weight secalins is located on the long arm of chromosome1R. A further seed protein locus,Pr-3 (55-K protein), was located on the short arm of chromosome1R. A linkage was found between the6Pgd-2 isozyme locus controlling 6-phosphogluconate dehydrogenase isozymes located on the long arm of chromosome1R and the four seed protein loci. The results favor the gene order:6Pgd-2 ...Sec-3 ... [centromere] ...Pr-3 ...Sec-1b ...Sec-1a. Other linkages detected werePer-3a andPer-3b (0.33±0.33 cM),Est-8 andEst-12 (0.33±0.33 cM), andGot-3 and centromere (20.57±2.42 cM). The proxidase (Per), glutamate oxaloacetate transaminase (Got), and esterase (Est) loci were located on chromosome arms2RS,3RL, and6RL, respectively. The distances and the maps obtained are compared with data available in the literature.

RFLP-based genetic maps of wheat homoeologous group 7 chromosomes

Restriction fragment length polymorphism (RFLP) mapping was attempted using 18 cDNA clones, 14 anonymous and 4 of known function, which had been shown to have homologous DNA sequences on the group 7 chromosomes of wheat. The loci identified by these probes have been mapped on one or more chromosomes in this homoeologous group using linkage data derived from various F2, random inbred, doubled haploid and single chromosome recombinant populations. The maps also include three isozyme loci, five disease resistance loci, two anthocyanin pigment loci and a vernalisation response locus. The mapping data have been used to determine the extent of map co-linearity over the A, B and D genomes, the degree of RFLP variability in the three genomes and the relative efficiency of various restriction enzymes in detecting RFLPs in wheat. The strategy for future mapping in wheat, particularly the use of "alien" genomes or segments, such as that from Aegilops ventricosa used here, is discussed.

Isozyme variation and RFLPs at the β-amylase loci in wheat

Forty-one hexaploid wheat genotypes have been examined for RFLPs detected by a β-amylase probe using three restriction enzymes, and for mature grain β-amylase isozyme polymorphism following IEF. The two homoeoallelic series assayed for RFLPs differed: little variation was found at group 2 chromosome homoeoloci, while the group 4/5 chromosome homoeoloci displayed considerable variation. Varieties that displayed a RFLP with one RE almost always did likewise with the other two REs, suggesting that most of the polymorphisms observed were due to large DNA rearrangements. Comparison of the variation in grain β-amylase isozymes with the RFLP results indicated strong associations between particular RFLP and isozyme alleles.

The detection and estimation of linkage using doubled haploid or single seed descent populations

In many plant species, particularly those of agricultural importance, there is now much effort being devoted to developing comprehensive genetic maps using biochemical and molecular markers. Because these techniques often involve destructive sampling of individual plants the use is increasingly made of homozygous or near-homozygous recombinant lines for linkage studies in preference to F2 or backcross generations. The present paper describes methods for the detection and estimation of linkage using such generations for commonly encountered genetic situations.

Ribosomal DNA inheritance and recombination in Neurospora crassa

The genetic segregation of ribosomal DNA (rDNA) in Neurospora crassa was analyzed by exploiting restriction fragment length polymorphisms in the nontranscribed spacer (NTS) sequences of nine laboratory wild-type strains and wild-collected strains. In an analysis of random spore progeny from seven crosses, and of ordered tetrads from two of those crosses the rDNA was shown to be inherited in a simple, stable Mendelian fashion, exhibiting an approximately 1:1 ratio of the two parental rDNA types. No meiotic recombinants were detected among the progeny, indicating that non-sister-chromatid crossing over is highly suppressed in the rDNA region. The basis for this suppression of meiotic recombination is not known.

Cytogenetic analysis of structural rearrangements in three varieties of common wheat, Triticum aestivum

The winter wheat varieties 'Starke' and 'Cappelle Desprez' and the spring wheat 'Chinese Spring' were analysed for structural chromosome rearrangements that resulted in the formation of multivalents in F1 hybrids. The analyses were carried out using hybrids involving euploids, monosomic and ditelosomic stocks, and double-monotelodisomic constructs. The study confirmed that 'Cappelle Desprez' differs from 'Chinese Spring' in a reciprocal translocation between chromosomes 5B and 7B (Riley et al. 1967); a translocation involving chromosomes 3B and 3D could not be verified. Furthermore, the analysis showed that 'Starke' differs from 'Chinese Spring' in a reciprocal translocation between chromosomes 7A and 7D. Both translocations have a coefficient of multivalent realisation of about 0.84. Further multivalents in euploid 'Starke', in euploid and some aneuploid stocks of 'Cappelle Desprez', and in euploid as well as various types of aneuploid hybrids between all three varieties could nearly all be explained hypothesizing that chromosome 2B of both 'Starke' and 'Cappelle Desprez' is a duplication-deficiency chromosome. In the hypothesis a part of the long arm of 2B is missing and replaced by a duplicated part of the long arm of chromosome 2D. The multivalents of this rearrangement showed an average coefficient of realisation of about 0.09.

Variability and genetics of spacer DNA sequences between the ribosomal-RNA genes of hexaploid wheat (Triticum aestivum)

Using restriction enzyme digests of genomic DNA extracted from the leaves of 25 hexaploid wheat (Triticum aestivum L. em. Thell.) cultivars and their hybrids, restriction fragment length polymorphisms of the spacer DNA which separates the ribosomal-RNA genes have been examined. (From one to three thousand of these genes are borne on chromosomes 1B and 6B of hexaploid wheat). The data show that there are three distinct alleles of the 1B locus, designated Nor-B1a, Nor-B1b, and Nor-B1c, and at least five allelic variants of the 6B locus, designated Nor-B2a, Nor-B2b, Nor-B2c, Nor-B2d, and Nor-B2e. A further, previously reported allele on 6B has been named Nor-B2f. Chromosome 5D has only one allelic variant, Nor-D3. Whereas the major spacer variants of the 1B alleles apparently differ by the loss or gain of one or two of the 133 bp sub-repeat units within the spacer DNA, the 6B allelic variants show major differences in their compositions and lengths. This may be related to the greater number of rDNA repeat units at this locus. The practical implications of these differences and their application to wheat breeding are discussed.

Distribution, inheritance and linkage relationships of ribosomal DNA spacer length variants in pea

DNA restriction endonuclease fragment analysis is used to examine the genetic organization, inheritance and linkage associations of the ribosomal DNA in pea. The substantial variation observed in the length of the intergenic spacer region is shown to segregate in Mendelian fashion involving two independent genetic loci, designated Rrn1 and Rrn2. Linkage between Rrn1 and two marker loci on chromosome 4 establishes the approximate location of this tandem array. Rrn2 shows linkage with a set of isozyme loci which assort independently of other markers on all seven chromosomes. Combining these observations with previous cytological data, we suggest that Rrn2 and the isozyme loci linked to it constitute a new linkage group on chromosome 7. The general absence of spacer length classes common to both rRNA loci in any of the lines we examined indicates that little or no genetic exchange occurs between the nonhomologous nucleolar organizer regions.

Mapping the nucleolus organizer region, seed protein loci and isozyme loci on chromosome 1R in rye

The nucleolus organizer region located on the short arm of chromosome 1R of rye consists of a large cluster of genes that code for ribosomal RNA (designated the Nor-R1 locus). The genes in the cluster are separated by spacer regions which can vary in length in different rye lines. Differences in the spacer regions were scored in two families of F2 progeny. Segregation also occurred, in one or both of the families, at two seed protein loci and at two isozyme loci also located on chromosome 1R. The seed protein loci were identified as the Sec 1 locus controlling ω-secalins located on the short arm of chromosome 1R and the Sec 3 locus controlling high-molecular-weight secalins located on the long arm of 1R. The two isozyme loci were the Gpi-R1 locus controlling glucose-phosphate isomerase isozymes and the Pgd 2 locus controlling phosphogluconate dehydrogenase isozymes. The data indicated linkage between all five loci and map distances were calculated. The results indicate a gene order: Pgd 2 ... Sec 3 ... [centromere] ... Nor-R1 ... Gpi-R1 ... Sec 1. Evidence was obtained that rye possesses a minor 5S RNA locus (chromosome location unknown) in addition to the major 5S RNA locus previously shown to be located on the short arm of chromosome 1R.

Repetitive DNA and chromosome evolution in plants

Most higher plant genomes contain a high proportion of repeated sequences. Thus repetitive DNA is a major contributor to plant chromosome structure. The variation in total DNA content between species is due mostly to variation in repeated DNA content. Some repeats of the same family are arranged in tandem arrays, at the sites of heterochromatin. Examples from the Secale genus are described. Arrays of the same sequence are often present at many chromosomal sites. Heterochromatin often contains arrays of several unrelated sequences. The evolution of such arrays in populations is discussed. Other repeats are dispersed at many locations in the chromosomes. Many are likely to be or have evolved from transposable elements. The structures of some plant transposable elements, in particular the sequences of the terminal inverted repeats, are described. Some elements in soybean, antirrhinum and maize have the same inverted terminal repeat sequences. Other elements of maize and wheat share terminal homology with elements from yeast, Drosophila, man and mouse. The evolution of transposable elements in plant populations is discussed. The amplification, deletion and transposition of different repeated DNA sequences and the spread of the mutations in populations produces a turnover of repetitive DNA during evolution. This turnover process and the molecular mechanisms involved are discussed and shown to be responsible for divergence of chromosome structure between species. Turnover of repeated genes also occurs. The molecular processes affecting repeats imply that the older a repetitive DNA family the more likely it is to exist in different forms and in many locations within a species. Examples to support this hypothesis are provided from the Secale genus.