The suitability of restriction fragment length polymorphisms as genetic markers in maize

Molecular marker technologies for plant improvement

The exploitation of DNA polymorphisms by an ever-increasing number of molecular marker technologies has begun to have an impact on plant genome research and breeding. Restriction fragment length polymorphisms, micro- and mini-satellites and PCR-based approaches are used to determine inter- and intra-specific genetic diversity and construct molecular maps of crops using specially designed mapping populations. Resistance genes and other agronomically important loci are tagged with tightly linked DNA markers and the genes isolated by magabase DNA technology and cloning into yeast artificial chromosomes (YAC). This review discusses some recent developments and results in this field.

Developmental impact on trans-acting dosage effects in maize aneuploids

The reduction in vigor or viability caused by aneuploidy may be the result of trans-acting dosage effects that reduce gene expression. To investigate the molecular and developmental parameters of aneuploid syndromes, the expression of sucrose synthase1 (sus1) and shrunken1 (sh1) was studied in 2-week-old plants. Expression of sus1 and sh1 was first investigated in euploids, where it was found that both transcripts varied in a diurnal fashion. Chromosome arm number can be varied in a series from one to three doses in maize. In the 14 aneuploid dosage series examined, most caused changes in sus1 and sh1 RNA levels that were both gene and tissue specific. Results were compared to previous data from embryo and endosperm tissue. More dosage effects were detected and the magnitude of RNA level modulation was greater in 2-week-old plant tissue. These findings suggest that the molecular consequences of aneuploidy might become more severe as development progresses.

Complex structure of a maize Myb gene promoter: functional analysis in transgenic plants

The maize P gene encodes a Myb-like transcription factor that regulates synthesis of red flavonoid pigments in floral organs. To study the transcriptional regulation of the P gene, candidate regulatory sequences of the P1-rr gene promoter were identified by Ac insertional mutagenesis and subjected to functional testing in transgenic maize plants. The results indicate that a 561 bp fragment (Pb) encompassing the transcription start site (-235 to +326) supports weak expression of a GUS reporter gene in floral organs, including husk, silk, kernel pericarp, cob and male inflorescence. Two other fragments, located approximately 1 and 5 kb 5' of the transcription start site, increased the levels of GUS activity in floral tissues and thus appear to contain enhancer elements. All of the tested constructs gave similar patterns of GUS expression, suggesting that the 561 bp Pb fragment that is common among the transgene constructs contains regulatory elements that promote activation in floral organs. The basal promoter and proximal enhancer fragments contain putative binding sites for bZip regulatory factors, and a complex arrangement of palindromes including a large inverted repeat of two tRNA-like genes. Possibly, interconversions between linear and cruciform conformations of the palindromes may affect protein/DNA interactions and thereby modulate P1-rr expression.

Characterization of a maize tonoplast aquaporin expressed in zones of cell division and elongation

We studied aquaporins in maize (Zea mays), an important crop in which numerous studies on plant water relations have been carried out. A maize cDNA, ZmTIP1, was isolated by reverse transcription-coupled PCR using conserved motifs from plant aquaporins. The derived amino acid sequence of ZmTIP1 shows 76% sequence identity with the tonoplast aquaporin gamma-TIP (tonoplast intrinsic protein) from Arabidopsis. Expression of ZmTIP1 in Xenopus laevis oocytes showed that it increased the osmotic water permeability of oocytes 5-fold; this water transport was inhibited by mercuric chloride. A cross-reacting antiserum made against bean alpha-TIP was used for immunocytochemical localization of ZmTIP1. These results indicate that this and/or other aquaporins is abundantly present in the small vacuoles of meristematic cells. Northern analysis demonstrated that ZmTIP1 is expressed in all plant organs. In situ hybridization showed a high ZmTIP1 expression in meristems and zones of cell enlargement: tips of primary and lateral roots, leaf primordia, and male and female inflorescence meristems. The high ZmTIP1 expression in meristems and expanding cells suggests that ZmTIP1 is needed (a) for vacuole biogenesis and (b) to support the rapid influx of water into vacuoles during cell expansion.

Characterization of the molecular defect in a null allele of the opaque-2 locus of maize

The molecular defect in an opaque-2 (o2) mutant, previously characterized as a null allele, has been identified as containing an insertion of the transposable element of the Bergamo (Bg) family. Restriction mapping and partial sequence analysis of the Bg in the o2 null allele indicates that this element is distinct from the previously described Bg as well as the defective Bg (rbg) of the o2m(r) allele. It is, however, inserted at the same site in O2 as the rbg of o2m(r) and can transpose when Bg is present. This study shows that, depending on genetic background, this allele may not behave as a stable null which could dramatically influence the conclusions drawn from experiments based on this particular mutant.

Genetic diversity of maize inbred lines within and among heterotic groups revealed by RFLPs

The objectives of this study were (1) to investigate genetic diversity for RFLPs in a set of important maize inbreds commonly used in Italian breeding programs, (2) to compare genetic similarities between unrelated lines from the same and different heterotic groups, and (3) to examine the potential of RFLPs for assigning maize inbreds to heterotic groups. Forty inbreds were analyzed for RFLPs with two restriction enzymes (EcoRI and HindIII) and 82 DNA clones uniformly distributed over the maize genome. Seventy clone-enzyme combinations gave single-banded RFLP patterns, and 79 gave multiple-banded RFLP patterns. The average number of RFLP patterns detected per clone-enzyme combination across all inbreds was 5.8. RFLP data revealed a wide range of genetic diversity within the two heterotic groups assayed, Iowa Stiff Stalk Synthetic (BSSS) and Lancaster Sure Crop (LSC). Genetic similarity (GS) between lines was estimated from binary RFLP data according to the method of Nei and Li (1979). The mean GS for line combinations of type BSSS × LSC (0.498) was substantially smaller than for unrelated line combinations or type BSSS × BSSS (0.584) but almost as great as for un-related line combinations of type LSC × LSC (0.506). Principal coordinate and cluster analyses based on GS values resulted in the separate groupings of lines, which is consistent with known pedigree information. A comparison between both methods for multivariate analyses of RFLP data is presented.

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.

Restriction fragment length polymorphism in plants and its implications

In the last decade RFLP analysis has evolved from an idea that seemed promising to a well-established tool that has led to fundamental advances in several fields. Construction of genetic maps has now become feasible in many organisms where it would previously have been impractical. Since genetic maps are of general utility for many sorts of biological research, they cannot fail to have a significant impact in the immediate future. As genetic maps become reconciled with physical maps in several plants, it will become possible to clone virtually any gene. For a plant breeder this will have the effect of broadening the gene pool available for plant improvement to include virtually all organisms, including animals and microorganisms. Much remains to be done, however. We need basic studies of the biochemistry, physiology, and genetics of plants and the insects and pathogens infesting them to be able to identify target genes for cloning. We need basic studies of transformation and gene expression to be able to have introduced genes expressed in transformed plants in the proper amounts and in the desired tissues. It must also be kept in mind that the best of our present technologies only suffice to clone and transform single genes. We will have to make another large jump in capabilities to be able to transfer QTL between plants. Since the most important agronomic traits are controlled by QTL, this effort will have to be undertaken. However, the future looks promising for plant breeding and RFLP analysis. The molecular genetic revolution now has every indication of being transferrable to practical problems such as plant breeding, and the first steps in this transferral have already occurred through the medium of RFLP analysis.

Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare)

In order to determine the extent of polymorphism in barley (Hordeum vulgare), DNA from 48 varieties was analyzed with 23 genomic, single-copy probes, distributed across all seven chromosomes. Upon hybridization to wheat-barley addition lines, the probes showed different degrees of homology compared to the wheat genome. Polymorphisms were detected in the barley genome at a frequency of 43% after digestion with EcoRI, BamHI, and HindIII. Subgroups of spring and winter barley and of two- and six-rowed types showed less diversity which, in most cases, was due to shifts in allelic frequencies. One probe (MWG1H504) hybridized to an EcoRI restriction fragment exclusively observed in winter barley. A comparison of six different restriction enzymes revealed clear differences with regard to their efficiency in detecting polymorphisms. The respective frequencies were between 13% (HindIII) and 37% (EcoRV). A significant correlation between the efficiency of a restriction enzyme and the mean fragment size detected by the different probes identified insertion/deletion events as the major factor causing polymorphism in barley.

Relationship of restriction fragment length polymorphisms to single-cross hybrid performance of maize

Isozymes and restriction fragment length polymorphisms (RFLPs) have been proposed for use in varietal identification and selection for agronomic traits. Although the use of isozymes for these purposes has been well documented, evaluation of the efficacy of RFLP technology as applied to crop improvement is far from complete. This investigation was conducted to study the relationship between RFLP-derived genotypes and heterotic patterns of a group of maize (Zea mays L.) inbred lines. A total of 22 inbreds was crossed to four testers (B73, B76, Mo17, and Va26) in combinations that minimized crossing within heterotic groups. Forty-seven single-cross progeny were subsequently evaluated for several agronomic traits (including grain yield and moisture, ear height, and root lodging) over 2-4 consecutive years at two to four Iowa locations in a randomized complete-block design. The inbred lines were subjected to RFLP analysis, which involved 47 genomic clones and the restriction enzymes EcoRI and HindIII. Hybrid RFLP patterns were predicted from their inbred parents. Modified Roger's distances were computed to estimate genetic distance among the inbred lines. Principal component analysis facilitated ascertainment of relative dispersion of the inbreds based on the frequency of variants at specific RFLP loci. Evident associations of variants with genes affecting agronomic traits were identified by principal component regression analysis, in which adjusted hybrid means were regressed on the matrix of hybrid variants frequencies. The hybrid means were adjusted by removing environmental effects, using residuals as dependent variables in the regression analysis. Results from this study suggest that RFLP analysis may be of value in allocating maize inbreds to heterotic groups, but no relationship between RFLP-based genetic distance and hybrid performance was apparent. Principal component regression identified variants potentially linked to genes that control specific agronomic traits.

Identification of 2n breeding lines and 4n varieties of potato (Solanum tuberosum, ssp. tuberosum) with RFLP-fingerprints

The possibility of genotype identification with RFLP fingerprints was examined with 20 tetraploid potato varieties and 38 diploid potato lines. By using a sensitive detection system for small restriction fragment length differences and highly variable potato sequences as probes, all genotypes (diploids and tetraploids) were distinguished by a minimum of two probe/enzyme combinations. The best single probe/enzyme combination distinguished 19 out of 20 4n varieties and 33 out of 38 2n lines. Intravarietal variability was very small compared to the intervarietal variability, and patterns obtained with different DNA sources of the same genotype were identical.

cDNAs of two non-allelic sucrose synthase genes in maize: cloning, expression, characterization and molecular mapping of the sucrose synthase-2 gene

cDNA clones of the two non-allelic sucrose synthase (Ss) genes, Ss2 and Sh, have been isolated from λgt11 expression libraries derived from immature kernel poly(A)(+) RNA of sh-deletion and Sh/Sh genotypes of maize respectively. Recombinant clones containing the longest Ss2 and Sh cDNA inserts, each of approximately 2.5 kb size, were characterized and comparatively analyzed. Although the Sh cDNA insert expresses as a sucrose synthase-1 (SS1) β-galactosidase fusion protein (∼ 200 kD) in λ lysogens, the Ss2 cDNA failed to form such a chimeric protein and instead showed a ∼ 70 kD SS2 polypeptide. The Ss2 and Sh cDNAs as hybridization probes on RNA blots of immature kernels detected a larger Ss2 transcript (∼ 2900 b) than the Sh transcript (∼ 2750 b). Because SS1 and SS2 protein subunits are known to be of identical size, the significance of difference in transcript size is not apparent. A comparative restriction enzyme mapping of the two cDNA clones and a genomic Ss2 clone show sequence diversity over the entire lengths of Ss2 and Sh clones. Interestingly, restriction endonuclease sites around the 3' ends are more conserved than the 5' ends of these two genes. Genetic data indicate that the Ss2 locus is on chromosome 9 and molecular mapping using the Ss2 cDNA clone on recombinant inbred lines and B-A translocations stocks suggest that Ss2 is about 20 map units away from the Wx locus on 9L.

ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification

Bacteriophage T7 RNA polymerase is stable in Escherichia coli but very susceptible to cleavage by at least one endoprotease after cell lysis. The major source of this endoprotease activity was found to be localized to the outer membrane of the cell. A rapid whole-cell assay was developed to screen different strains for the presence of this proteolytic activity. Using this assay, we identified some common laboratory strains that totally lack the protease. Genetic and Southern analyses of these null strains allowed us to conclude that the protease that cleaves T7 RNA polymerase is OmpT (formerly termed protein a), a known outer membrane endoprotease, and that the null phenotype results from deletion of the OmpT structural gene. A recombinant plasmid carrying the ompT gene enables these deletion strains to synthesize OmpT and converts them to a protease-positive phenotype. The plasmid led to overproduction of OmpT protein and protease activity in the E. coli K-12 and B strains we used, but only weak expression in the E. coli C strain, C1757. This strain-dependent difference in ompT expression was investigated with respect to the known influence of envZ on OmpT synthesis. A small deletion in the ompT region of the plasmid greatly diminishes the amount of OmpT protein and plasmid-encoded protease present in outer membranes. Use of ompT deletion strains for production of T7 RNA polymerase from the cloned gene has made purification of intact T7 RNA polymerase routine. Such strains may be useful for purification of other proteins expressed in E. coli.

Advantages and limitations of using Spm as a transposon tag

Transposon tagging has become the method of choice for isolating genes whose products are in low abundance. We have recently used the transposable element Spm to tag and clone maize regulatory loci. Our choice of Spm was dictated by several factors: The frequency of transposition of Spm is high enough to obtain detectable transposition events, into loci affecting kernel traits, in populations of less than 10(6) seed. Although the copy number of Spm is high in the maize genome, insertions into the gene of interest can be distinguished from other Spm copies by digesting DNAs from segregating populations with methyl-sensitive restriction enzymes, and hybridizing with Spm-specific probes. Since all members of the Spm family thus far examined share DNA homology, hybridization with appropriate probes allows detection of insertions of both autonomous and defective elements. Thus, if a mutable allele can be shown to be under Spm control, one can be reasonably confident of successfully cloning that allele.

Transposon tagging and molecular analysis of the maize regulatory locus opaque-2

Genetic analyses suggested that the opaque-2 (o2) locus in maize acts as a positive, transacting, transcriptional activator of the zein seed storage-protein genes. Because isolation of the gene is requisite to understanding the molecular details of this regulation, transposon mutagenesis with the transposable element suppressor-mutator (Spm) was carried out, and three mutable o2 alleles were obtained. One of these alleles contained an 8.3-kilobase autonomous Spm, another a 6.8-kilobase nonautonomous Spm, and the third an unidentified transposon that is unrelated to Spm. A DNA sequence flanking the autonomous Spm insertion was verified to be o2-specific and provided a probe to clone a wild-type allele. Northern blots indicated that the gene is expressed in wild-type endosperm but not in leaf tissues or in endosperms homozygous for a mutant allele of the O2 gene. A transcript was detected in endosperms homozygous for mutations at opaque-7 and floury-2, an indication that O2 expression is independent of these two other putative regulators of zein synthesis.

Comparison of restriction endonucleases and sources of probes for their efficiency in detecting restriction fragment length polymorphisms in lettuce (Lactuca sativa L.)

As a first step in developing a detailed genetic map of lettuce (Lactuca sativa L.), 156 cDNA and 123 genomic DNA clones of lettuce were compared for their efficiency to detect restriction fragment length polymorphism (RFLP) between four lines of lettuce. Polymorphism was detected 2.5 times more frequently with cDNA probes than random genomic probes. Less polymorphism was detected with cDNA clones homologous to single copy than with cDNA clones homologous to multiple copy DNA sequences. A lower percentage of polymorphism was detected with genomic DNA clones homologous to repetitive sequences than with other types of probes. Digests with each of nine restriction endonucleases were compared; increased polymorphism was not correlated with the presence of a CpG dimer in the recognition sequence of the restriction endonuclease. Digests with enzymes recognizing four base pairs, however, displayed RFLPs less frequently. The six pairwise comparisons of the four lettuce lines showed different frequencies of polymorphism which only approximately corresponded to genetic distances obtained from previous isozyme analyses.