Genetic mapping methods provide a unique opportunity to study the interactions of differentiated genes and genomes in a hybrid genetic background. After a brief discussion of theoretical and analytical concerns, we review the application of these methods to a wide range of evolutionary issues. Map-based studies of experimental hybrids indicate that most postzygotic reproductive barriers in plants are polygenic and that the expression of extreme or novel traits in segregating hybrids (transgressive segregation) results from the complementary action of divergent parental alleles. However, genetic studies of hybrid vigor do not concur in their interpretations of the relative roles of dominance, overdominance, and epistasis. Map-based studies of natural hybrids are much rarer, but the few existing studies confirm the polygenic basis of postzygotic barriers and demonstrate the utility of genetic linkage for detecting cryptic introgression. In addition, studies of experimental and natural hybrid lineages provide compelling evidence that homoploid hybrid speciation has occurred in nature, and that it represents a rapid and repeatable mode of speciation. Data further indicate that this mode is facilitated by strong fertility selection and high chromosomal mutation rates. We recommend that future studies of hybrid genomes focus on natural hybrids, not only because of the paucity of data in this area, but also because of the availability of highly recombinant hybrid genotypes in hybrid zones. Of particular value will be studies of long-lived or difficult-to-propagate organisms, which previously have not been amenable to genetic study.

Hybridization, introgression, and linkage evolution

Chemically induced non-nodulating nod139 and nn5 mutants of soybean (Glycine max) show no visible symptoms in response to rhizobial inoculation. Both exhibit recessive Mendelian inheritance suggesting loss of function. By allele determination and genetic complementation in nod139 and nn5, two highly related lipo-oligochitin LysM-type receptor kinase genes in Glycine max were cloned; they are presumed to be the critical nodulation-inducing (Nod) factor receptor similar to those of Lotus japonicus, pea and Medicago truncatula. These duplicated receptor genes were called GmNFR5alpha and GmNFR5beta. Nonsense mutations in GmNFR5alpha and GmNFR5beta were genetically complemented by both wild-type GmNFR5alpha and GmNFR5beta in transgenic roots, indicating that both genes are functional. Both genes lack introns. In cultivar Williams82 GmNFR5alpha is located in chromosome 11 and in tandem with GmLYK7 (a related LysM receptor kinase gene), while GmNFR5beta is in tandem with GmLYK4 in homologous chromosome 1, suggesting ancient synteny and regional segmental duplication. Both genes are wild type in G. soja CPI100070 and Harosoy63; however, a non-functional NFR5beta allele (NFR5beta*) was discovered in parental lines Bragg and Williams, which harbored an identical 1,407 bp retroelement-type insertion. This retroelement (GmRE-1) and related sequences are located in several soybean genome positions. Paradoxically, putatively unrelated soybean cultivars shared the same insertion, suggesting a smaller than anticipated genetic base in this crop. GmNFR5alpha but not GmNFR5beta* was expressed in inoculated and uninoculated tap and lateral root portions at about 10-25% of GmATS1 (ATP synthase subunit 1), but not in trifoliate leaves and shoot tips.

Inactivation of duplicated nod factor receptor 5 (NFR5) genes in recessive loss-of-function non-nodulation mutants of allotetraploid soybean (Glycine max L. Merr.).

https://pubag.nal.usda.gov/download/50277/PDF

Applying molecular-based approaches to classical biological control of weeds

Bulk segregant analysis (BSA), random amplified polymorphic DNA (RAPD) and sequence characterized amplified region (SCAR) methods were used to map molecular markers to the sex locus M of asparagus. Two parents, A19 (male, Mm) and MW25 (female, mm), and 63 progeny were used for the study. Two DNA bulks, one male and one female, were made by pooling equal amounts of DNA from 10 randomly selected progeny of each sex type. A total of 760 arbitrary decamer oligonucleotide primers were used for RAPD analysis. Primer OPC15 produced two RAPD markers, OPC15-98 and OPC15-30, both of which were linked to the M locus at a distance of 1.6 cM. Subsequently, amplified RAPD fragment OPC15-98 was cloned and sequenced. The sequence was then used to design flanking 24-mer oligonucleotide SCAR primers SCC15-1 and SCC15-2. Both of these SCAR primers amplified a single 980 bp fragment; the same size as the cloned RAPD fragment. However, the SCAR marker was dominant as was the original OPC15-98 band from which it was derived. These RAPD and SCAR markers could be used for scoring male and female progeny in the mapping population, but were not found to be applicable to other asparagus germplasm studied.

RAPD and SCAR markers linked to the sex expression locus M in asparagus

The leaves of globe artichoke and cultivated cardoon (Cynara cardunculus L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds. Hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase (HQT) encoding genes have been isolated from both globe artichoke and cultivated cardoon (GenBank accessions DQ915589 and DQ915590, respectively) using CODEHOP and PCR-RACE. A phylogenetic analysis revealed that their sequences belong to one of the major acyltransferase groups (anthranilate N-hydroxycinnamoyl/benzoyltransferase). The heterologous expression of globe artichoke HQT in E. coli showed that this enzyme can catalyze the esterification of quinic acid with caffeoyl-CoA or p-coumaroyl-CoA to generate, respectively, chlorogenic acid (CGA) and p-coumaroyl quinate. Real time PCR experiments demonstrated an increase in the expression level of HQT in UV-C treated leaves, and established a correlation between the synthesis of phenolic acids and protection against damage due to abiotic stress. The HQT gene, together with a gene encoding hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT) previously isolated from globe artichoke, have been incorporated within the developing globe artichoke linkage maps. A novel acyltransferase involved in the biosynthesis of CGA in globe artichoke has been isolated, characterized and mapped. This is a good basis for our effort to understand the genetic basis of phenylpropanoid (PP) biosynthesis in C. cardunculus.

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The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway

Genome Mapping and Agriculture (R.C. Shoemaker, L.L. Lorenzen, B.W. Diers, and T.C. Olson). Usefulness of Plant Genome Mapping to Plant Breeding (F.L. Allen). Technology for Molecular Breeding: RAPD Markers, Microsatellites, and Machines (J.A. Rafalski, M.K. Hanafey, S.V. Tingey, and J.G.K. Williams). Multiple Arbitrary Amplicon Profiling Using Short Oligonucleotide Primers (G. Caetano-Anolles, B.J. Bassam, and P.M. Gresshoff). Length Polymorphisms of Simple Sequence Repeat (SSR) DNA as Molecular Markers in Plants (P.B. Cregan, M.S. Akkaya, A.A. Bhagwat, U. Lavi, and J. Rongwen). Approaches to Mapping in Horticultural Crops (N. Weeden). FISH, DNA Amplification Markers and Conifers (J.E. Carlson, Y.-P. Hong, G.R. Brown, and J.C. Glaubitz). Molecular Exploitation of Soybean Genetic Resources (L.O. Vodkin). Molecular Mapping of Soybean Nodulation Genes (P.M. Gresshoff and D. Landau-Ellis). Plant Telomeres as Molecular Markers (A.M. Kolchinsky and P.M. Gresshoff). Plant Yeast Artificial Chromosome Libraries and Their Use: Status and Some Strategic Considerations (R.P. Funke and A.M. Kolchinsky). Duplicate Loci in Soybean: Characterization of the sle and A071 Loci (K.M. Polzin, E.S. Calvo, T.C. Olson, and R.C. Shoemaker). Antisense RNA Inhibition of Photosynthetic Gene Expression (S. Rodermel, C-Z. Jiang, D. Kliebenstein, and J. Qian). Organization and Expression of Mitochondrial DNA Sequences Associated with Cytoplasmic Male Sterility in Phaseolus vulgaris L. (C.D. Chase and M.J. Bassett). Cell Cycle Genes and Their Plant Homologues (J. Deckert, N. Taranenko, and P.M. Gresshoff). The Basics of the Patent Process (L. Terlizzi). Recent Cases and Legislative Initiatives Pertaining to Biotechnology (R.H. Kjeldgaard). Patenting DNA: Is There a Bull in the China Shop? (L.L. Greenlee). Glossary. Index.

Peter M. Gresshoff

Papers

Plant genome analysis