Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms

Complex duplications in maize lines

Rp1 is a disease resistance complex and is the terminal morphological marker on the short arm of maize chromosome 10. Several restriction fragment length polymorphisms (RFLPs), which map within 5 map units of Rp1, were examined to determine if they are also complex in structure. Two RFLP loci, which mapped distally to Rp1, BNL3.04 and PIO200075, existed in a single copy in all maize lines examined. These two loci cosegregated perfectly in 130 test cross progeny. Two RFLP loci that map proximally to Rp1 had unusual structures, which have not yet been reported for maize RFLPs; the loci were complex, with variable numbers of copies in different maize lines. One of the loci, NP1285, occasionally recombined in meiosis to yield changes in the number of copies of sequences homologous to the probe. The other proximal locus, detected by the probes NPI422, KSU3, and KSU4, was relatively stable in meiosis and no changes in the number of restriction fragments were observed. The similarity in map position between Rp1 and the complex RFLP loci indicate there may be genomic areas where variable numbers of repeated sequences are common. The structure of these complex loci may provide insight into the structure and evolution of Rp1.

Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers

The use of molecular markers to identify quantitative trait loci (QTLs) affecting agriculturally important traits has become a key approach in plant genetics-both for understanding the genetic basis of these traits and to help design novel plant improvement programs. In the study reported here, we mapped QTLs (and evaluated their phenotypic effects) associated with seven major traits (including grain yield) in a cross between two widely used elite maize inbred lines, B73 and Mo17, in order to explore two important phenomena in maize genetics-heterosis (hybrid vigor) and genotype-by-environment (G x E) interaction. We also compared two analytical approaches for identifying QTLs, the traditional single-marker method and the more recently described interval-mapping method. Phenotypic evaluations were made on 3168 plots (nearly 100,000 plants) grown in three states. Using 76 markers that represented 90-95% of the maize genome, both analytical methods showed virtually the same results in detecting QTLs affecting grain yield throughout the genome, except on chromosome 6. Fewer QTLs were detected for other quantitative traits measured. Whenever a QTL for grain yield was detected, the heterozygote had a higher phenotype than the respective homozygote (with only one exception) suggesting not only overdominance (or pseudooverdominance) but also that these detected QTLs play a significant role in heterosis. This conclusion was reinforced by a high correlation between grain yield and proportion of heterozygous markers. Although plant materials were grown and measured in six diverse environments (North Carolina, Iowa and Illinois) there was little evidence for G x E interaction for most QTLs.

Alpha-tubulin gene family of maize (Zea mays L.). Evidence for two ancient alpha-tubulin genes in plants

Among 81 alpha-tubulin cDNA clones prepared from RNA from maize seedling shoot, endosperm and pollen, we identified six different alpha-tubulin coding sequences. The DNA sequence analysis of coding and non-coding regions from the clones showed that they can be classified into three different alpha-tubulin gene subfamilies. Genes within each subfamily encode proteins that are 99 to 100% identical in amino acid sequence. Deduced amino acid sequence identity between genes in different subfamilies ranges from 89 to 93%. The results of hybridizations of genomic DNAs to alpha-tubulin coding region probes and to 3' non-coding region probes constructed from six different alpha-tubulin cDNA clones indicated that the maize alpha-tubulin gene family contains at least eight members. Comparison of deduced alpha-tubulin amino acid sequences from maize and the dicot species Arabidopsis thaliana showed that alpha-tubulin isotypes encoded by genes in maize subfamilies I and II are more similar to specific Arabidopsis gene products (96 to 97% amino acid identity) than to isotypes encoded by genes in the other maize subfamilies. Phylogenetic analyses revealed that genes in these two subfamilies were derived from two ancient alpha-tubulin genes that predate the divergence of monocots and dicots. These same analyses revealed that the gene in maize subfamily III is more closely related to sequences from subfamily I genes than to those from subfamily II genes. However, the subfamily III gene has no close counterpart in Arabidopsis. We found evidence of a transposable element-like insertion in the subfamily III gene in some maize lines.

Genetic diversity for RFLPs in European maize inbreds : II. Relation to performance of hybrids within versus between heterotic groups for forage traits

Restriction fragment length polymorphisms (RFLPs) have been proposed for the prediction of the yield potential of hybrids and the assignment of inbreds to heterotic groups. Such use was investigated in 66 diallel crosses among 6 flint and 6 dent inbreds from European maize (Zea mays L.) germ plasm. Inbreds and hybrids were evaluated for seven forage traits in four environments in the Federal Republic of Germany. Midparent heterosis (MPH) and specific combining ability (SCA) were calculated. Genetic distances (GD) between lines were calculated from RFLP data of 194 clone-enzyme combinations. GDs were greater for flint x dent than for flint x flint and dent x dent line combinations. Cluster analysis based on GDs showed separate groupings of flint and dent lines and agreed with pedigree information, except for 1 inbred. GDs of all line combinations in the diallel were partitioned into general (GGD) and specific (SGD) genetic distances; GGD explained approximately 20% of the variation among GD values. For the 62 diallel crosses (excluding 4 crosses of highly related lines), correlations of GD with F1 performance, MPH, and SCA for dry matter yield (DMY) of stover, ear, and forage were positive but mostly of moderate size (0.09≤r≤0.60) compared with the higher correlations (0.39≤r≤0.77) of SGD with these traits. When separate calculations were performed for various subsets, correlations of GD and SGD with DMY traits were generally small (r<0.47) for the 36 flint x dent crosses, significantly positive (r<0.53) for the 14 flint x flint crosses, and inconclusive for the 12 dent x dent crosses because of the lack of significant genotypic variation. Results indicated that RFLPs can be used for assigning inbreds to heterotic groups. RFLP-based genetic distance measures seem to be useful for predicting forage yield of (1) crosses between lines from the same germ plasm group or (2) crosses including line combinations from the same as well as different heterotic groups. However, they are not indicative of the hybrid forage yield of crosses between unrelated lines from genetically divergent heterotic groups.

Generation of a Brassica oleracea composite RFLP map: linkage arrangements among various populations and evolutionary implications

A composite linkage map of Brassica oleracea was developed from maps of four different populations, derived from 108 DNA, isozyme and morphological loci covering over 747 centimorgans in 11 linkage groups. Of these linkage groups, 8 were assigned to their respective chromosomes by alignment with gene synteny groups of B. oleracea. Distortions in segregation ratios increased with the level of divergence of the parents and were attributed to differentiation of parental chromosomes. Comparison of the individual maps demonstrates that the B. oleracea genome undergoes frequent chromosomal rearrangement, even at the subspecies level. Small inversions were the most frequent form of aberration followed by translocations. The former type of aberration could occur without a noticeable effect on meiotic behavior of chromosomes or on pollen fertility. The obvious deduction from the composite map is that a large fraction of the B. oleracea genome is duplicated, falling into three classes: randomly dispersed, linked-gene families, and blocks duplicated in non-homologous chromosomes. The genealogy of chromosomes sharing duplicated segments was formulated and indicates that B. oleracea is a secondary polyploid species derived from ancestral genome(s) of fewer chromosomes.

Subfamilies of histone H3 and H4 genes are located on most, possibly all of the chromosomes in maize

It has been previously shown that in the genome of maize the multiple copies of the histone H3 and H4 multigenic families are organized into eight to ten subfamilies each containing a variable number of copies. Each subfamily is characterized by a specific proximal environment and thus can be revealed by blot-hybridization with its specific 5' probe. Restriction fragment length polymorphism (RFLP) combined with monosomic analysis was used to localize several H3 and H4 subfamilies on maize chromosomes. H3 and H4 genes were found to be located on most, possibly all of the chromosomes, revealing a remarkably dispersed organization of these multigenic families.

Similarity of maize and sorghum genomes as revealed by maize RFLP probes

Densely saturated genetic maps of neutral genetic markers are a prerequisite either for plant breeding programs to improve quantitative traits in crops or for evolutionary studies. cDNA and genomic clones from maize were utilized to initiate the construction of a RFLP linkage map in Sorghum bicolor. To this purpose, an F2 population was produced from starting parental lines IS 18729 (USA) and IS 24756 (Nigeria) that were differentiated with regard to many morphological and agronomical traits. A total of 159 maize clones were hybridized to the genomic DNA of the two parents in order to detect polymorphism: 154 probes hybridized to sorghum and 58 out of these were polymorphic. In almost all of the cases hybridization patterns were similar between maize and sorghum. The analysis of the segregation of 35 polymorphic clones in an F2 population of 149 individuals yielded five linkage groups. The three principal ones recall regions of maize chromosomes 1, 3 and 5: in general, colinearity was maintained. A possible inversion, involving a long region of maize chromosome 3, was detected. Simulations were also performed to empirically obtain a value for the lowest number of individuals of the F2 population needed to obtain the same linkage data.

RFLP analyses of early-maturing European maize germ plasm : I. Genetic diversity among flint and dent inbreds

Thirty inbred lines representing a wide range of early-maturing European elite germ plasm of maize (Zea mays L.) were assayed for RFLPs using 203 clone-enzyme combinations (106 DNA clones with restriction enzymes EcoR1 and HindIII). The genetic materials comprised 14 flint, 12 dent, and 4 lines of miscellaneous origin. Objectives were to (1) characterize the genetic diversity for RFLPs in these materials, (2) compare the level of genetic diversity found within and between the flint and the dent heterotic groups, and (3) examine the usefulness of RFLPs for assigning inbreds to heterotic groups. All but two DNA clones yielded polymorphism with at least one restriction enzyme. A total of 82 and 121 clone-enzyme combinations gave single-banded and multiple-banded RFLP patterns, respectively, with an average of 3.9 and 7.7 RFLP patterns per clone-enzyme combination across all 30 inbreds, respectively. Genetic similarity (GS) between lines, estimated from RFLP data as Dice's similarity coefficient, showed considerable variation (0.32 to 0.58) among unrelated inbreds. The mean GS for line combinations of type flint x dent (0.41) was significantly smaller than for unrelated flint lines (0.46) and dent lines (0.46), but there was considerable variation in GS estimates of individual line combinations within each group. Cluster and principal coordinate analyses based on GS values resulted in separate groupings of flint and dent lines in accordance with phylogenetic information. Positioning of lines of miscellaneous origin was generally consistent with expectations based on known breeding behavior and pedigrees. Results from this study corroborated that RFLP data can be used for assigning inbreds to heterotic groups and revealing pedigree relationships among inbreds.

Molecular-marker-facilitated investigations of quantitative trait loci in maize : 4. Analysis based on genome saturation with isozyme and restriction fragment length polymorphism markers

Restriction fragment length polymorphisms have become powerful tools for genetic investigations in plant species. They allow a much greater degree of genome saturation with neutral markers than has been possible with isozymes or morphological loci. A previous investigation employed isozymes as genetic markers to infer the location of genetic factors influencing the expression of quantitative traits in the maize population: (CO159×Tx303)F2. This investigation was conducted to examine the inferences that might be derived using a highly saturated map of RFLP markers and isozymes to detect quantitative trait loci (QTLs) in the same maize F2 population. Marker loci that were associated with QTL effects in this investigation generally corresponded well with previous information where such comparisons were possible. Additionally, a number of previously unmarked genomic regions were found to contain factors with large effects on some plant traits. Availability of numerous marker loci in some genomic regions allowed: more accurate localization of QTLs, resolution of linkage between QTLs affecting the same traits, and determination that some chromsome regions previously found to affect a number of traits are likely to be due to linkage of QTLs affecting different traits. Many of the factors that affected plant height quantitatively in this investigation were found to map to regions also including known sites of major genes influencing plant height. Although the data are not conclusive, they suggest that some of the identified QTLs may be allelic to known major genes affecting plant height.

Inheritance of RFLP loci in a loblolly pine three-generation pedigree

A high-density restriction fragment length polymorphism (RFLP) linkage map is being constructed for loblolly pine (Pinus taeda L.). Loblolly pine cDNA and genomic DNA clones were used as probes in hybridizations to genomic DNAs prepared from grandparents, parents, and progeny of a three-generation outbred pedigree. Approximately 200 probes were evaluated for their ability to detect polymorphic loci between DNAs prepared from the two parent trees, 20-1010 and 11-1060, and cut with four different restriction enzymes: BamHI, DraI, EcoRI, and HindIII. More than half of the probes detecting single- or low-copy number sequences (56%) revealed polymorphisms between the two parents with at least one restriction enzyme. If necessary, an additional hybridization to DNAs prepared from the four grandparent trees was conducted to determine the zygosity of parent trees. Ten of these probes were hybridized to progeny DNAs from this cross and, as expected, the markers were inherited as simple codominant Mendelian alleles. Four of the ten probes detected segregation of three alleles at one locus, and four probes detected more than one independently segregating locus. RFLPs can be used immediately to assess genetic diversity in conifer populations and to "efingerprint" genotypes in tree improvement programs.

RFLP maps of potato and their alignment with the homoeologous tomato genome

An RFLP linkage map of the potato is presented which comprises 304 loci derived from 230 DNA probes and one morphological marker (tuber skin color). The self-incompatibility locus of potato was mapped to chromosome I, which is homoeologous to tomato chromosome I. By mapping chromosome-specific tomato RFLP markers in potato and, vice versa, potato markers in tomato, the different potato and tomato RFLP maps were aligned to each other and the similarity of the potato and tomato genome was confirmed. The numbers given to the 12 potato chromosomes are now in accordance with the established tomato nomenclature. Comparisons between potato RFLP maps derived from different genetic backgrounds revealed conservation of marker order but differences in chromosome and total map length. In particular, significant reduction of map length was observed in interspecific compared to intraspecific crosses. The distribution of regions with distorted segregation ratios in the genome was analyzed for four potato parents. The most prominent distortion of recombination was found to be caused by the self-incompatibility locus.

Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat

Sixty-six F2 plants from the cross, Triticum aestivum cv. Chinese Spring (abbrev. CS) x T. spelta var. duhamelianum (Spelta), exhibiting the greatest number of RFLPs among eight common wheats, were analyzed for their RFLP genotypes using genomic DNA clones of CS as probes. In total, 204 RFLP loci were identified and their linkage relationships established. By nulli-tetrasomic analyses, all linkage groups were assigned to one another of the 21 wheat chromosomes. In addition, the carrier chromosomes of 228 non-RFLP loci were identified. The linkage maps of these RFLP loci have a total size of 1800 cM and exceed those of the classical genes in both size and locus number. Twenty loci show distorted segregation, four of which are clustered on chromosome 4A and three on the 2D chromosome. The CS alleles on 4A exhibit preferential transmission, while those on 2D exhibit depressed transmission, compared with Spelta alleles. This suggests the influence of gametic factors in those regions. RFLP loci are much fewer in the D genome than in the A and B genomes, but the numbers of non-RFLP loci are nearly the same in these three genomes. This suggests that Spelta wheat originated from a hybridization between T. dicoccum (spelt emmer) and T. aestivum.

Inheritance of isozyme and RFLP markers in Brassica campestris and comparison with B. oleracea

Using primarily cDNA restriction fragment length polymorphism markers (RFLPs) previously located to Brassica oleracea (cabbage, 2n=18) chromosomes, we initiated a comparative RFLP map in an F2 population of B. campestris (turnip x mock pak-choi, 2n=20). As with B. oleracea, the genome of B. campestris showed extensive gene duplication, and the majority of detected duplicated loci were unlinked. Only 6 of the 49 identified loci were represented as a single copy, and 3 of these 6 were clustered on a single linkage group showing a distorted segregation ratio. Comparison with B. Oleracea indicates this synteny is conserved between species. Two other linkage groups also appeared syntenic between B. oleracea and B. campestris. One single copy locus appears to have changed synteny between B. oleracea and B. campestris. These observations suggest that B. oleracea and B. campestris share a common ancestor, but that chromosome repatterning has occurred during or after speciation. Within B. campestris, 5 loci appeared duplicated in one parent or the other, and 2 of these were linked. Differentiation through subspecies-specific duplication or deletion events is suggested as one mechansim for the evolution of numerous morphotypes within each of these species.

A linkage map ofBrassica rapa (syn.campestris) based on restriction fragment length polymorphism loci

A detailed linkage map ofB. rapa (syn.campestris) was constructed based on segregation of 280 restriction fragment length polymorphism loci, detected by using 188 genomic DNA clones as probes on DNAs from a F2 population of Chinese cabbage 'MichihilF'×'Spring broccoli.' These genetic markers covered 1,850 centiMorgans (cM) and defined ten linkage groups, which equals the haploid chromosome number of this species. Extensive sequence duplication was evident by the detection of two or more segregating loci with each of 69 clones (36.7% of the total). Although some duplicated loci were randomly distributed throughout the genome, many had linkage arrangements that were conserved on different linkage groups, suggesting that large chromosome fragments were present in multiple copies. However, conservation in the linkage arrangement of duplicate loci throughout entire pairs of linkage groups was not observed. Single-copy loci were often found to be located within conserved duplicated regions, and linkage distances between some loci having conserved duplicated arrangements were substantially different between the duplicated regions. Structural rearrangements, such as insertions, deletions, and inversions or combinations of these events, seemed to be related to the alternations of map distances between duplicated loci and to the dispersal of duplicated chromosome fragments. These results suggest thatB. rapa has evolved in part by duplication of chromosomes or large chromosome fragments with subsequent structural rearrangements.

DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L

Genetic variation in Phaseolus vulgaris L. (P. vulgaris) was investigated at the isozyme and DNA levels. We constructed a library of size-selected Pst I clones of P. vulgaris nuclear DNA. Clones from this library were used to examine 14 P. vulgaris accessions for restriction fragment length polymorphisms (RFLPs). DNAs from each accession were analyzed with three restriction enzymes and 18 single copy probes. The same accessions were also examined for variability at 16 isozyme loci. Accessions included four representatives of the T phaseolin group and five representatives each of the C and S phaseolin groups. One member of the S group (the breeding line XR-235-1-1) was derived from a cross between P. vulgaris and P. coccineus. Isozymes and RFLPs revealed very similar patterns of genetic variation. Little variation was observed among accessions with C and T phaseolin types or among those with the S phaseolin type. However, both isozyme and RFLP data grouped accessions with S phaseolin separately from those accessions with C or T phaseolin. The highest degree of polymorphism was observed between XR-235-1-1 and members of the C/T group. RFLP markers will supplement isozymes, increasing the number of polymorphic loci that can be analyzed in breeding, genetic, and evolutionary studies of Phaseolus.

Plant genome studies: restriction fragment length polymorphism and chromosome mapping information

The detection of sequence variation with restriction fragment length polymorphisms is advancing our knowledge of plant genetics on several fronts. In the past year, there has been progress in genetic map construction, phylogeny studies, and the dissection of multigenic traits. In addition, new methods that are independent of restriction sites are being developed for polymorphism detection.

Genetic and molecular analysis of Sn, a light-inducible, tissue specific regulatory gene in maize

The Sn locus of maize is functionally similar to the R and B loci, in that Sn differentially controls the tissue-specific deposition of anthocyanin pigments in certain seedling and plant cells. We show that Sn shows molecular similarity to the R gene and have used R DNA probes to characterize several Sn alleles. Northern analysis demonstrates that all Sn alleles encode a 2.5 kb transcript, which is expressed in a tissue-specific fashion consistent with the distribution of anthocyanins. Expression of the Sn gene is light-regulated. However, the Sn: bol3 allele allows Sn mRNA transcription to occur in the dark, leading to pigmentation in dark-grown seedlings and cob integuments. We report the isolation of genomic and cDNA clones of the light-independent Sn: bol3 allele. Using Sn cDNA as a probe, the spatial and temporal expression of Sn has been examined. The cell-specific localization of Sn mRNA has been confirmed by in situ hybridization using labelled antisense RNA probes. According to its proposed regulatory role, expression of Sn precedes and, in turn, causes a coordinate and tissue-specific accumulation of mRNA of structural genes for pigment synthesis and deposition, such as A1 and C2. The functional and structural relationship between R, B, Lc and Sn is discussed in terms of an evolutionary derivation from a single ancestral gene which gave rise this diverse gene family by successive duplication events.

Directed synthesis of a segmental chromosomal transposition: an approach to the study of chromosomes lethal to the gametophyte generation of maize

Because of the haploid nature of the gametophyte generation of plants, most mutations that are lethal or detrimental to the gametophytes cannot be recovered. Our laboratory is currently developing several techniques to overcome this situation. In this paper, a procedure is described to generate directed segmental chromosomal transpositions. The method involves recovery of recombinants between reciprocal translocation overlaps such that one region of the genome is inserted into a nonhomologous chromosome in a predetermined and directed manner. This duplicated segment then could serve to cover deficiencies or mutations, lethal to the gametophytes, in the region from whence it originated. The manipulation of segmental chromosomal transpositions for analyzing mutants lethal or detrimental to the gametophyte generation is discussed. The procedure to generate transpositions, the translocations between normal A and supernumerary B chromosomes that generate deficiencies in the male gametes, the r-X1 chromosome that generates deficiencies in the female gametes and other techniques available in maize form a system to analyze gametophyte lethal mutations.

Molecular mechanisms underlying the differential expression of maize pyruvate, orthophosphate dikinase genes

I describe here the organization of maize C4 chloroplast and non-C4 cytosolic pyruvate, orthophosphate dikinase (PPDK) genes and the molecular mechanisms underlying their differential expression. The maize C4 chloroplast PPDK gene (C4ppdkZm1) appears to have been created by the addition of an exon encoding the chloroplast transit peptide at a site upstream of a cytosolic PPDK gene (cyppdkZm1). A splice acceptor sequence located in the first exon of cyppdkZm1 allows the fusion of the transit peptide to the cyppdkZm1 sequences. A second cyPPDK gene (cyppdkZm2) shares extensive homology with cyppdkZm1 in the coding region and in the 5' flanking region up to the TATA box. By a novel protoplast transient expression method, I show that the light-inducible expression of C4ppdkZm1 is controlled by two expression programs mediated through separate upstream regulatory elements that are active in leaf, but inactive in root and stem. Light-mediated C4ppdkZm1 expression in maize is apparently uncoupled from leaf development and partially associated with chloroplast development. For cyppdkZm1 expression, distinct upstream elements and a specific TATA promoter element, located in the first intron of C4ppdkZm1, are required. The low expression of cyppdkZm2 can be attributed to an absence of upstream positive elements and weak activity of the TATA promoter element.

RFLP mapping in soybean: association between marker loci and variation in quantitative traits

We have constructed a genetic map for soybean and identified associations between genetic markers and quantitative trait loci. One-hundred-fifty restriction fragment length polymorphisms (RFLPs) were used to identify genetic linkages in an F2 segregating population from an interspecific cross (Glycine max x Glycine soja). Twenty-six genetic linkage groups containing ca. 1200 recombination units are reported. Progeny-testing of F2-derived families allowed quantitative traits to be evaluated in replicated field trials. Genomic regions, which accounted for a portion of the genetic variation (R2 = 16 to 24%) in several reproductive and morphological traits, were linked to RFLP markers. Significant associations between RFLP markers and quantitative trait loci were detected for eight of nine traits evaluated. The ability to identify genes within a continuously varying trait has important consequences for plant breeding and for understanding evolutionary processes.

Identification of Brassica oleracea monosomic alien chromosome addition lines with molecular markers reveals extensive gene duplication

Chromosomes of Brassica oleracea (2n = 18) were dissected from the resynthesized amphidiploid B. napus Hakuran by repeated backcrosses to B. campestris (2n = 20), creating a series of monosomic alien chromosome addition line plants (2n = 21). Using morphological, isozyme and restriction fragment length polymorphism markers (RFLPs), 81 putative loci were identified. Of nine possible synteny groups, seven were represented in the 25 monosomic addition plants tested. Sequences homologous to 26% of the 61 DNA clones utilized (80% were cDNA clones) were found on more than one synteny group, indicating a high level of gene duplication. Anomalous synteny associations were detected in four 2n = 21 plants. One of these plants showed two markers from one B. oleracea chromosome associated with a second complete B. oleracea synteny group, suggesting translocation or recombination between non-homologous chromosomes in Hakuran or the backcross derivatives. The other three 2n = 21 plants each contained two or more B. oleracea synteny groups, suggesting chromosome substitution.

Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea

A detailed genetic linkage map of Brassica oleracea was constructed based on the segregation of 258 restriction fragment length polymorphism loci in a broccoli × cabbage F2 population. The genetic markers defined nine linkage groups, covering 820 recombination units. A majority of the informative genomic DNA probes hybridized to more than two restriction fragments in the F2 population. "Duplicate" sequences having restriction fragment length polymorphism were generally found to be unlinked for any given probe. Many of these duplicated loci were clustered non-randomly on certain pairs of linkage groups, and conservation of the relative linkage arrangement of the loci between linkage groups was observed. While these data support previous cytological evidence for the existence of duplicated regions and the evolution of B. oleracea from a lower chromosome number progenitor, no evidence was provided for the current existence of blocks of homoeology spanning entire pairs of linkage groups. The arrangement of the analyzed duplicated loci suggests that a fairly high degree of genetic rearrangement has occurred in the evolution of B. oleracea. Several probes used in this study were useful in detecting rearrangements between the B. oleracea accessions used as parents, indicating that genetic rearrangements have occurred in the relatively recent evolution of this species.

Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes

Cloned DNA fragments from 14 characterized maize genes and 91 random fragments used for genetic mapping in maize were tested for their ability to hybridize and detect restriction fragment length polymorphisms in sorghum and other related crop species. Most DNA fragments tested hybridized strongly to DNA from sorghum, foxtail millet, Johnsongrass, and sugarcane. Hybridization to pearl millet DNA was generally weaker, and only a few probes hybridized to barley DNA under the conditions used. Patterns of hybridization of low-copy sequences to maize and sorghum DNA indicated that the two genomes are very similar. Most probes detected two loci in maize; these usually detected two loci in sorghum. Probes that detected one locus in maize generally detected a single locus in sorghum. However, maize repetitive DNA sequences present on some of the genomic clones did not hybridize to sorghum DNA. Most of the probes tested detected polymorphisms among a group of seven diverse sorghum lines tested; over one-third of the probes detected polymorphism in a single F2 population from two of these lines. Cosegregation analysis of 55 F2 individuals enabled several linkage groups to be constructed and compared with the linkage relationships of the same loci in maize. The linkage relationships of the polymorphic loci in the two species were usually conserved, but several rearrangements were detected.

Genetic analysis of the obligate parasitic barley powdery mildew fungus based on RFLP and virulence loci

Genome organization of the biotrophic barley powdery mildew fungus was studied using restriction fragment length polymorphism (RFLP). Genomic DNA clones containing either low-or multiple-copy sequences appeared to be the best RFLP markers, as they frequently revealed polymorphisms that could be readily detected. A total of 31 loci were identified using 11 genomic DNA clones as probes. Linkage analysis of the 31 RFLP loci and five virulence loci resulted in the construction of seven groups of linked loci. Two of these contained both RFLP markers and virulence genes. RFLP markers were found to be very efficient in characterizing mildew isolates, as only three markers were necessary to differentiate 28 isolates. The DNA of the barley powdery mildew fungus appeared to contain a considerable number of repetitive sequences dispersed throughout the genome.

Two regulatory genes of the maize anthocyanin pathway are homologous: isolation of B utilizing R genomic sequences

Genetic studies in maize have identified several regulatory genes that control the tissue-specific synthesis of the purple anthocyanin pigments during development. Two such genes, R and B, exhibit extensive allelic diversity with respect to the tissue specificity and developmental timing of anthocyanin synthesis. Previous genetic studies demonstrated that certain B alleles can substitute for R function, and in these cases only one functional allele at either locus is required for pigment synthesis in the aleurone. In addition, biochemical studies have shown that both genes act on the same biosynthetic pathway, suggesting that the genes are functionally duplicate. In this report we describe DNA hybridization experiments that demonstrate that the functionally duplicate nature of B and R is reflected in DNA sequence similarity between the two genes. We took advantage of this homology and used the R genomic sequences to clone B. Two different strategies were pursued and two genomic clones isolated, a 2.5-kilobase BgIII fragment linked to the b allele in W23 inbred stocks and a 1.0-kilobase HindIII fragment linked to the B allele in CM37 stocks. Examination of several independent transposable element insertion mutations in B and revertant derivatives demonstrated that our clones recognize the functional B gene. Genomic clones representing the entire B-Peru allele were isolated, and a detailed restriction map was prepared. Using these clones we have identified a 2.2-kilobase mRNA in husks from plants containing either B-I or B-Peru alleles, but no B mRNA was detected in plants containing a b allele. The transcript is at least 100 times more abundant in strongly pigmented B-I husks than in weakly pigmented B-Peru husk tissue. Expression of functional B alleles in husk tissue correlates with the coordinate increase in mRNA levels of two structural genes of the pathway, A1 and Bz1, consistent with the postulated role of B as a regulatory gene.

The organization and expression of a maize ribosomal protein gene family

We have isolated several Zea mays cDNAs encoding the 40S subunit ribosomal protein S14. In maize, this ribosomal protein is encoded by a small multigene family, at least three members of which are expressed. S14 transcript levels are highest in mitotically active tissues, such as seedling shoot, developing endosperm, and tassel primordia, and lowest in tissues with little cell division, such as mature leaf and root. Very little S14 RNA is present in pollen, suggesting that translation of pollen mRNAs during pollen germination uses preformed ribosomes. During kernel development, the highest levels of S14 transcripts in endosperm tissue are found at 10-12 days postpollination; S14 RNA levels decline continuously from this point onward. The period of maximal expression of the S14 ribosomal protein gene appears to precede the onset of storage protein synthesis and does not correlate with the reported times of increased nucleolar volume or genome amplification.

Linkages between restriction fragment length, isozyme, and morphological markers in lentil

A genetic linkage map of lentil comprising 333 centimorgans (cM) was constructed from 20 restriction fragment length, 8 isozyme, and 6 morphological markers segregating in a single interspecific cross (Lens culinaris × L. orientalis). Because the genotypes at marker loci were determined for about 66 F2 plants, linkages are only reported for estimates of recombination less than 30 cM. Probes for identification of restriction fragment length polymorphisms (RFLPs) were isolated from a cDNA and EcoRI and PstI partial genomic libraries of lentil. The cDNA library gave the highest frequency of relatively low-copy-number probes. The cDNAs were about twice as efficient, relative to random genomic fragments, in RFLP detection per probe. Nine markers showed significant deviations from the expected F2 ratios and tended to show a predominance of alleles from the cultigen. Assuming a genome size of 10 Morgans, 50% of the lentil genome could be linked within 10 cM of the 34 markers and the map is of sufficient size to attempt mapping of quantitative trait loci.

Mapping RFLP loci in maize using B-A translocations

Plants hypoploid for specific segments of each of the maize (Zea mays L.) chromosomes were generated using 24 different B-A translocations. Plants carrying each of the B-A translocations were crossed as male parents to inbreds, and sibling progeny hypoploid or not hypoploid for specific chromosomal segments were recovered. Genomic DNAs from the parents, hypoploid progeny, and nonhypoploid (euploid or hyperploid) progeny for each of these B-A translocations were digested with restriction enzymes, electrophoresed in agarose gels, blotted onto reusable nylon membranes, and probed with nick-translated, cloned DNA fragments which had been mapped previously by restriction fragment length polymorphism (RFLP) analysis to the chromosome involved in the B-A translocation. The chromosomal segment on our RFLP map which was uncovered by each of the B-A translocations was determined. This work unequivocally identified the short and long arms of each chromosome on this map, and it also identified the region on each chromosome which contains the centromere. Because the breakpoints of the B-a translocations were previously known on the cytological and the conventional genetic maps, this study also allowed this RFLP map to be more highly correlated with these maps.

Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms

Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.

New isozyme systems for maize (Zea mays L.): aconitate hydratase, adenylate kinase, NADH dehydrogenase, and shikimate dehydrogenase

Electrophoretic variation and inheritance of four novel enzyme systems were studied in maize (Zea mays L.). A minimum of 10 genetic loci collectively encodes isozymes of aconitate hydratase (ACO; EC 4.2.1.3.), adenylate kinase (ADK; EC 2.7.4.3), NADH dehydrogenase (DIA; EC 1.6.99.-), and shikimate dehydrogenase (SAD; EC 1.1.1.25). At least four loci are responsible for the genetic control of ACO. Genetic data for two of the encoding loci, Aco1 and Aco4, demonstrated that at least two maize ACOs are active as monomers. Analysis of organellar preparations suggests that ACO1 and ACO4 are localized in the cytosolic and mitochondrial subcellular fractions, respectively. Maize ADK is encoded by a single nuclear locus, Adk1, governing monomeric enzymes that are located in the chloroplasts. Two cytosolic and two mitochondrial forms of DIA were electrophoretically resolved. Segregation analyses demonstrated that the two cytosolic isozymes are controlled by separate loci, Dia1 and Dia2, coding for products that are functional as monomers (DIA1) and dimers (DIA2). The major isozyme of SAD is apparently cytosolic, although an additional faintly staining plastid form may be present. Alleles at Sad1 are each associated with two bands that cosegregate in controlled crosses. Linkage analyses and crosses with B-A translocation stocks were effective in determining the map locations of six loci, including the previously described but unmapped locus Acp4. Several of these loci were localized to sparsely mapped regions of the genome. Dia2 and Acp4 were placed on the distal portion of the long arm of chromosome 1, 12.6 map units apart. Dia1 was localized to chromosome 2, 22.2 centimorgans (cM) from B1. Aco1 was mapped to chromosome 4, 6.2 cM from su1. Adk1 was placed on the poorly marked short arm of chromosome 6, 8.1 map units from rgd1. Less than 1% recombination was observed between Glu1 (on chromosome 10) and Sad1. In contrast to many other maize isozyme systems, there was little evidence of gene duplication or of parallel linkage relationships for these allozyme loci.

Gene mapping with recombinant inbreds in maize

Recombinant inbred lines of maize have been developed for the rapid mapping of molecular probes to chromosomal location. Two recombinant inbred families have been constructed from F2 populations of T232 X CM37 and CO159 X Tx303. A genetic map based largely on isozymes and restriction fragment length polymorphisms has been produced that covers virtually the entire maize genome. In order to map a new gene, an investigator has only to determine its allelic distribution among the recombinant inbred lines and then compare it by computer with the distributions of all previously mapped loci. The availability of the recombinant inbreds and the associated data base constitute an efficient means of mapping new molecular markers in maize.