Aneuploid Mapping in Polyploids - Plants and Crops Science
INTRODUCTION
Aneuploidy denotes the condition of having extra or missing chromosomes. For specific aneuploid states that are not overly debilitating, the altered genetic constitution enables gross genome mapping through the localization of genes and sequences to specific genomic, subgenomic, chromosomal, and subchromosomal regions. The information from these analyses lends itself to divide-and-conquer strategies that expedite mapping and other forms of genome analysis that impact the efficacy of research, cloning, genetic engineering, interspecific germplasm introgression, and marker-assisted selection, and other aspects of breeding. Plant genomes range about 2500-fold in size, from about 50 Mbp to 125,000 Mbp, with chromosome numbers ranging about 300-fold, from 2 to close to 600. The process of mapping eukaryotic genomes is biologically and technically complex.
All mapping methods suffer from technical, statistical, and human limitations. To create robust maps, several orthogonal mapping methods must be extensively integrated, e.g., segregation analysis, aneuploid analysis, molecular cytogenetics, radiation hybrids, contig assembly, and sequencing. Only then is it possible to harness the synergistic benefits from their complementary strengths and weaknesses?
The integration of aneuploid-based mapping with linkage mapping and other orthogonal approaches is especially beneficial and applicable to disomic polyploid plant species, genomes of which are larger and involve many more gene and sequence duplications than diploid-related taxa. Aneuploid-based mapping provides a means to establish a sound biological footing to the maps and reduce the complexity of the target. Polyploid genomes are more tolerant of the various genic imbalances associated with aneuploidy, and therefore more amenable to aneuploid-based mapping.
ANEUPLOIDY
The most common types of aneuploids are presented diagrammatically in Fig. 1. They can be broadly categorized by whether they have increased or decreased chromosomal (genetic) content, though some involve both. Hypoaneuploids have chromosomal deficiencies, e.g., 2x 1, whereas hyperaneuploids have chromosomal excesses, e.g., 2x + 1. Hypoaneuploids (deficient for chromosomes or chromosome segments) are generally preferred to hyperaneuploids because they offer greater efficacy for mapping, as well as for chromosome substitution-mediated germplasm introgression. Irrespective of ploidy, individuals with chromosomally imbalanced sets are called aneuploids. This imbalance may arise from deviations that affect whole chromosomes, chromosome arms, and/or chromosome segments.
Certain terms denote changes in chromosome number by indicating the abnormal content remaining, e.g., monosomy for 2n 1 and trisomy 2n + 1. Modifiers indicate the content of the affected chromosome, e.g., primary for an intact chromosome and tertiary for a translocated chromosome.
Segmental aneuploids may or may not have a normal chromosome number, but all are genetically imbalanced because of the abnormal dosage of one or more specific segment(s). Telosomes lack essentially an entire chromosome arm. Other segmental aneuploids have an excess/deficiency of specific chromosome segment(s), due directly to deletion or duplication, or derived indirectly from ancestral heterozygosity for translocations or other rearrangements.
The size and type of each chromosomal abnormality are important to mapping because it determines not only the physical scope of localization, but also what kinds of genes or markers are most amenable to analysis, the method of analysis, and the difficulty and time requirements of the analysis. Some give immediate results, while others require follow-up analysis, e.g., progeny testing and/or segregation analysis. Where segregation data are gathered, their statistical efficacy can also differ markedly according to the type of analysis and map distances involved.
COMMON ANEUPLOID-BASED MAPPING APPLICATIONS
Aneuploids are commonly applied to five kinds of mapping objectives:
1. Localization of individual mutants or small numbers of loci, e.g., a specific marker, or simple or oligogenic trait.
2. Genomics and other large-scale genetic endeavors to localize many loci and/or gene products.
3. Centromere mapping.
4. Broad surveys for major chromosome- or segment-specific effects on one or more complex traits, through the development of chromosome substitutions or chromosome additions.
5. Development of chromosome-specific mapping populations for genetic dissection of alien germplasm for effects on complex traits, through the development of phenotypically characterized mapping populations from chromosome substitutions.
The various types of aneuploids, e.g., whole-chromosome versus telosome aneuploids, differ in their effectiveness for specific mapping goals. The localization of molecular markers and linkage groups to specific chromosomes establishes a biological, cytological, and macromolecular foundation, and enables a logical basis for the development of a common nomenclature for linkage groups among research laboratories. Intrachromosomal analyses with telosomes enable the placement of centromeres on linkage maps. Telosomes and other segmental aneuploids can be used to establish the orientations of linkage groups with respect to the two arms of each chromosome. Through the accumulation of many segmental aneuploids, the mapping process can be extended to small subchromosomal regions, as in wheat.
PRINCIPLES OF ANEUPLOID-BASED MAPPING
The methods of aneuploid mapping rely on cytogenetic types that are deficient for one or both copies of a locus (hypoaneuploid), or have extra copies (hyperaneuploid). The procedures used for aneuploid-based mapping are determined partly by the type of gene action or marker detection and by the type of aneuploid. Deletion mapping entails the removal of a locus or allele, the use of which is most efficient when the subject allele or marker is dominant or co-dominant, and not obscured by allele(s) at other loci. Under these circumstances, both the nulli- and the hemizygous states are directly informative about the absence or presence of the particular DNA sequence.
Common strategies and goals used in aneuploid-based mapping. All sorts of aneuploids enable localization of a comprehensive linkage groups to specific chromosomes. Full-chromosome aneuploids enable detection of all loci and linkage groups. Telosomes are often used to orient linkage groups and delimit the location of the centromeres where the latter activity is to be accomplished with opposing telosomes. Segmental aneuploids enable similar localization and mapping at subchromosomal levels. Tertiary chromosomes enable mapping to segments of two chromosomes at once.
Effectiveness of direct versus indirect detection systems for mapping by hyper- and hypoaneuploid conditions, according to type of aneuploidy and type of gene or locus ‘‘action.’’ Hypoaneuploids that are lacking or deficient for a segment offer the most widely effective means of mapping; elimination allows for direct manifestation of dominant and co-dominant alleles, but not recessive alleles (progeny testing required). In general, hyperaneuploids do not allow for direct mapping in most instances, and must be augmented by progeny testing for polysomic versus disomic inheritance to be effective. Co-dominant alleles and markers are relatively amenable to analysis with both classes of aneuploids.
When the deleted allele or marker is recessive or null, hypoaneuploid deficiency mapping requires progeny testing, because there is no change in phenotype or marker status in the hypoaneuploid. Progeny testing and segregation analysis are generally required for hyperaneuploids, unless 1) new alleles are introduced on the extra chromatin, e.g., as for alien chromosomes or segments from a related species, or 2) sufficiently accurate dosage analysis is possible.
Progeny tests can also be used to confirm deletion mapping results from dominant and co-dominant alleles and, thus, bolster reliability of results. In rare instances, recessive traits must be homozygous to be expressed, i.e., they will not be expressed when hemizygous, as when the dominant allele is deleted through monosomy. In these cases, too, deletion mapping alone is insufficient, and progeny testing is required. When a marker is obscured by other similar alleles at the same or different loci, further analysis is often difficult. However, if the marker is readily quantified and present at levels proportional to dosage, then it may be possible to localize the marker by quantitative analysis.
Hypoaneuploids: Nullisomics and Other Deficiency Homozygotes
Where available, nullisomics, ditelosomics, and homozygous deletions are often the tools of choice, because they eliminate a locus or gene. Thus, all molecular markers unique to a nullisomic region are completely absent. For dominant and co-dominant genes and markers, the absence is directly detectable. Deletions of null mutants and recessive alleles are not directly detectable, but can be ascertained by progeny testing. Although nullisomics can be derived in bread wheat, a disomic hexaploid species, they are not available for most plants due to severe effects on viability and fertility. Maintenance across sexual generations requires viability and function of nullihaploid micro- and mega-gametophytes.
Hypoaneuploids: Monosomics and Other Deficiency Hemizygotes
Less severe effects result from monosomy, monotelodisomy, and heterozygosity for segmental deletions. The affected loci are hemizygous, not heterozygous or homozygous. For large-scale mapping applications, the most useful approach has often been to screen for hemizygosity among hypoaneuploids recovered after wide-cross hybridization. For example, a set of different monosomic plants would be mated as female with a divergent genotype, e.g., a different biotype, race, or closely related species. Each hypoaneuploid F1 hybrid would be highly heterozygous, except for the respective hypoaneuploid chromosome, arm, or segment(s), which must be hemizygous for all loci in it. Differential absence of maternal dominant and co-dominant markers and alleles from a hypoaneuploid but not euploid F1 hybrids indicates that the locus is associated with the respective chromosome. Progeny tests can be used to confirm results for dominant and co-dominant markers and to detect deletion of cryptic alleles, e.g., null alleles. Highly distorted self and testcross progeny ratios often result due to reduction or absence of sexual transmission, especially through pollen
Hyperaneuploids
For crops in which hypoaneuploids are not available, hyperaneuploids can usually be obtained. Their use typically entails progeny-segregation analysis to discern between disomic and polysomic inheritance. For example, consider tests of recessive allele ‘‘a’’ across a series of trisomics; if closely linked with the centromere, segregation from the respective A-bearing trisomic will be about 8:1 (A-phenotype : a-phenotype), versus just 3:1 for the euploid and the other trisomics. Hyperaneuploids may also result from interspecific introgression. If the alien genome does not recombine with the genome of the recurrent parent, monosomic addition lines may be obtainable by iterative backcrossing, and, if transmissible through both gametophytes, disomic additions may be derived from selfing the monosomic additions. These aneuploids and similar segmental derivatives offer high rates of polymorphism relative to the host genome, and thus present an effective tool for direct analysis of the alien genome, and by way of comparative mapping, of the host genome, too.
SOURCES OF ANEUPLOIDS
Because the occurrence of specific aneuploids are typically an unusual or rare event, collections of aneuploid stocks have been developed systematically for a number of organisms, e.g., arabidopsis, corn, cotton, potato, soybean, rice, tomato, and wheat. In some cases, these have been maintained either independently or as part of public genetic or germplasm collections for a number of organisms. Collections may be maintained in the plant, seed, vegetative, and/or DNA form. Otherwise, the aneuploids must be generated anew, distinguished, and identified. Typical sources include 1) crosses with an odd-ploid genotype, 2) mutations affecting chromosome or chromatid disjunction in meiosis or mitosis, and treatments with 3) physical mutagens (e.g., X-rays or gamma-rays) or 4) chemicals, e.g., certain mutagens or spindle inhibitors.
SEARCH ENGINE
A panel of aneuploids is useful as a search engine, e.g., to localize grossly one gene, hundreds of genes, or thousands of genes to specific chromosomes or regions. If the panel includes all chromosomes, the search will be comprehensive. Because genomes of most plants contain 5–26 chromosomes per genome, each chromosome represents a significant proportion of a genome, e.g., from 2–20% for most chromosomes. Given a tentative estimate that the basic angiosperm genome contains approximately 30,000 genes, a typical angiosperm chromosome must contain 600–6,000 genes. Thus, aneuploid-based methods are very efficient for large-scale mapping of genes, and yield a ‘‘big picture,’’ whereas complementary methods are typically used to provide higher resolution and detail.