Aneuploid Mapping in Diploids - Plants and Crops Science

Aneuploid Mapping in Diploids


Genetic mapping in crop plants (both diploids and polyploids) initially involved the use of recombination frequencies that were treated to be in proportion with genetic distances and, therefore, could be converted into centiMorgan units with the help of a mapping function (Kosambi’s mapping function has generally been used). These genetic maps each had a number of linkage groups that generally equaled the haploid chromosome number of the organism concerned.

Later, the individual linkage groups could be assigned to specific chromosomes using aneuploids, which are organisms that have a somatic chromosome number that is not an exact multiple of a basic chromosome number. The aneuploids that have been used for mapping differed in diploid and polyploid crops. While trisomics has been used in a large number of diploids such as barley and tomato, monosomies has been more frequently used in polyploids such as bread wheat, cotton, and tobacco. 

In the case of maize, which was treated earlier as a diploid and is now known to be an archeo-tetraploid, both trisomics and monosomies have been used. Such genetic mapping of chromosomes makes use of abnormal segregation ratios that are obtained in aneuploids, relative to normal diploids, if the gene of interest is located on the chromosome that is involved in aneuploidy. A variety of these aneuploids have been utilized for mapping in diploids. Because much literature is available on the subject, only a summary will be presented in this section. Only a brief account of the different types of trisomics, their methods of production, and their use in chromosome mapping (both genetic and physical) are given here. Detailed information is available elsewhere.


The term trisomic originally referred to a condition in an organism where a particular chromosome is present in three doses, in contrast to each of the other chromosomes being present as a pair.[3] These trisomics were later described as simple primary trisomics to distinguish them from complex primary trisomics (where the extra chromosome is normal, but the remaining constitution is not), and also from the type of trisomics where the extra chromosome is not normal (e.g., secondary, tertiary, telo-, and compensating trisomics).

A number of other trisomic types have also been produced and used for mapping. For instance, a complete set of telotrisomics in rice, a variety of compensating trisomics and haplo-triplo disomic in tomato, and a number of acrotrisomics and metatrisomics in barley have been produced and used (discussed later). Balanced tertiary trisomics have also been produced in crops such as barley and utilized for hybrid seed production, but they have rarely been used for mapping.


Methods for the production of trisomics differ depending upon the type of trisomics desired. However, in most diploids, the simple primary trisomics have generally been produced using triploids, often derived from a tetraploiddiploid cross. These triploids, when selfed or crossed (as the female parent) with diploids, yield a fairly large number of trisomic plants that can be assembled into a complete set of trisomics and are always equal to the haploid number of chromosomes in the species concerned.

Other types of trisomics, including secondary trisomics, telotrisomics, and compensating trisomics, often have been obtained in the progeny of simple primary trisomics. Tertiary trisomics, however, have been obtained in the progeny of interchange heterozygotes, due to the rare 3:1 meiotic disjunction of interchange quadrivalent, which is characteristic of a translocation heterozygote.


Simple primary trisomics and other trisomic types have been characterized using one or more of the following criteria:

1) morphological deviations from the normal diploids;

2) karyotype alterations;

3) crosses with known interchange testers; and

4) crosses with the genetic stocks carrying known markers (including molecular markers).

However, the most important criterion has been a morphological deviation. Meiotic behavior also has been used to distinguish the different types of trisomics (e.g., primary, secondary, tertiary, and compensating trisomics).


Due to the presence of three homologous chromosomes instead of two, a trisomic can have two heterozygous genotypes (AAa, Aaa), which give segregation ratios (described as trisomic ratios) that are different from those obtained in normal diploids (disomic ratios) and thus facilitate chromosome mapping.

Trisomic Genotypes and Segregation Ratios 

If the gene to be mapped occurs on the chromosome that is present in an extra dose in a trisomic, and a cross is made between this trisomic and the normal diploid, the resulting F1 trisomic can be duplex (AAa) or simplex (Aaa) depending upon whether the trisomic carries a dominant or a recessive allele. The segregation ratio for this gene in F2 deviates from the expected Mendelian ratio in a normal diploid. The ratios that are expected in two types of trisomics have been established. These ratio deviations have been used for assigning genes to specific chromosomes.

Assigning Linkage Groups to Specific Chromosomes

Linkage groups already established in a species through conventional linkage analysis can be assigned to specific chromosomes when at least one marker from each linkage group gives abnormal segregation in one of the trisomics in the F2 generation. Multiple genetic marker stocks (having markers from more than one linkage group) could be used and would reduce the work involved. This method has been used successfully in a number of crops, including maize, tomato, and barley.

Assigning Genes to Specific Arms of Chromosomes

Once a gene is already assigned to a specific chromosome, secondary, tertiary, and telotrisomics can be used to map this gene to either the short or the long arm of this chromosome. If the dominant allele is present on the arm involved in the extra chromosome of a secondary, tertiary, or telotrisomic, all trisomic progeny in an F2 population derived from a cross of this trisomic with a recessive genetic stock will exhibit the dominant character (A:a = all:0), thus indicating that the gene is present on this arm. Segregation for this character will suggest that the gene is present on the other arm, which can be confirmed by using telotrisomic for that chromosome arm.

Location of Centromere and Orientation of Linkage Groups

If the linear order of three or more closely linked genes located on two different arms of a chromosome is known, the position of the centromere and the orientation of the chromosome map can be determined. For example, if out of three linked genes a-b-c, a is on the short arm and b and c are on the long arm, the orientation would be a-b-c. In the reverse situation (if a is on the long arm and b and c are on the short arm), the orientation would be c-b-a, the centromere being between a and b in both cases (the genes are read from the end of the short arm to the end of the long arm).

Physical Mapping Using Acro- or Metatrisomics

Physical mapping of genes on chromosomes in diploid crops such as maize and tomato has been accomplished by studying structural changes in chromosomes at pachytene. However, in barley, acrotrisomics (the extra chromosome has one complete arm and a small segment of the other arm) and metatrisomics (having terminal deficiencies in both arms of the extra chromosome) have been produced and used successfully to map individual genes physically on chromosomes. 

When genes are already assigned to a specific chromosome arm, and acrotrisomics and metatrisomics with segmental deficiencies for this arm are used, they can be mapped physically due to the absence of a trisomic ratio if the gene is present in the deficient region of the extra chromosome.


Individual alien chromosome-addition lines have been produced for a number of diploid crops by adding an individual chromosome from the diploid crop to a related polyploid that could tolerate the addition of an extra chromosome. In some cases, telocentric additions have also been successfully produced. Chromosomes of a number of diploid species including rye and barley have been added to tetraploid and hexaploid wheat, and individual maize chromosomes have been added to the oat genome for the purpose of mapping.

Alien chromosome additions have also been obtained in rice, Brassica, sugar beet, and cotton. Addition lines have been utilized for mapping molecular markers using barley and rye additions to wheat and maize additions to oat. Deletions produced in the alien chromosomes in these additional lines can also be used for physical mapping.


Monosmics in diploid crops has been produced only sparingly because the loss of a chromosome has a more drastic effect on a diploid than on a polyploid. However, monosomies for some chromosomes in tomato and for all the 10 chromosomes in maize have been successfully produced and used for mapping. For instance, at least three primary monosomies and 25 tertiary monosomic were produced in tomatoes, and some of them were used for mapping. Similarly, in maize, a complete set of monosomies has been produced using either the B-chromosome system to cause the elimination of chromosomes or an r-xi deficiency. These monosomies have been used to map genes and molecular markers.


Translocation stocks in maize and barley have also been used for mapping. In maize, the linkage between a gene and semisterility due to translocation was observed and facilitated the mapping of genes with respect to the translocation breakpoint. B–A translocations (translocation between B-chromosomes and autosomes) were also used for mapping. More recently, translocation stocks were used for physical mapping of restriction fragment length polymorphism (RFLP) markers in relation to the translocation breakpoints in barley.

Individual microdissected translocation chromosomes were used for (PCR) driven by primers designed from RFLP markers so that the positions of translocation breakpoints could be located by identification of closely linked markers (already mapped genetically) that were found to be present on two different chromosomes involved in translocation.


In diploid plants, hyperaneuploids such as trisomics have generally been used for the preparation of genetic and physical maps of chromosomes, although in tomato and maize, monosomics have also been produced and successfully used for mapping. The presence of genes on chromosomes or chromosome arms that are in three doses in a trisomic and a single dose in a monosomic, in contrast to a double dose in a normal diploid, leads to segregation ratios that deviate from normal Mendelian ratios, thus facilitating the assignment of genes to specific chromosomes or chromosome arms.

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