Supernumerary B chromosomes (Bs) are a major source of intraspecific variation in nuclear DNA amounts in numerous species of plants. They favour large genomes, and create polymorphisms for DNA variation in natural populations. By studying Bs we can gain useful knowledge about the organization, function and evolution of genomes. There are also significant biological questions concerning the origin and structural organization of Bs, and the way in which these selfish elements can establish themselves by exploiting the replicative machinery of their host genome nucleus. It is a sine qua non that Bs originate from the A chromosomes, in a variety of ways. We can study their modes of drive and ask how it is that chromosomes which apparently lack genes can have control over their own drive process which leads to their survival in natural populations. Molecular cytogenetic studies are opening up new avenues of investigation. Population equilibria for B frequencies are determined by a balance between accumulation and harmful effects. Bs are also subject to meiotic loss due to polysomy and to elimination at meiosis as univalents. These balancing forces can be seen in the context of host/parasite interaction, based on a dissection of the genetic elements in both As and Bs (in maize) which interact to bring about a stable equilibrium, at least for a snapshot in time. Aside from their intrinsic enigmatic properties, B chromosomes make useful experimental tools to study genome organization. Thus far they have not been exploited for their applications, other than through the use of A-B translocations used for gene mapping in maize; but there are opportunities to use them to modulate the frequency and distribution of recombination, to diploidize allopolyploids, to study centromeres and to be developed as plant artificial chromosomes; given that they can be structurally modified and their inheritance stabilized.

Contents Summary 935 I. Introduction 936 II. Survey of genetic variation – sources and resources 936 III. Survey of molecular marker types 939 IV. Mapping approaches and tools 948 V. Survey of bioinformatics and computer resources 954 VI. Bringing it all together: stay‐green gene case study 961 VII. The future of mapping 962 Acknowledgements 962 References 962

Summary: This is a review of genetic mapping with molecular markers aimed at the non‐specialist who wishes to use, or at least grasp the concepts behind, this powerful analytical tool. Restriction fragment length polymorphisms (RFLPs) are defined and used to illustrate the different aspects of mapping. The principles of segregation, recombination and linkage are considered and related to the idea of a molecular marker map. A description of a typical mapping population and how it is analysed follows. Traits to be mapped are divided into those controlled by ‘major’ genes and those governed by quantitative trait loci (QTLs). Exploitation of the map for marker‐assisted selection, gene cloning and synteny comparisons is discussed, as are some of the limitations to the usefulness of molecular marker maps. Finally other marker systems are introduced, namely minisatellites or variable number tandem repeats (VNTRs); randomly amplified polymorphic DNA (RAPDs); microsatellites or simple sequence repeats (SSRs); and amplified fragment length polymorphisms (AFLPs).

The chapter describes the early part of Barbara McClintock’s work on DNA transposons in maize, in which she uncovered the Ac-Ds family of mobile “controlling elements”. As a basis to understanding the work there is a preamble on the reproductive biology of maize, which explains the particular qualities of the maize plant as an experimental organism for genetics. An account is then given of the cytology of the system that was used to generate intact chromosomes having “sticky” (broken) ends, which is the starting point of the story. Cytogenetic aspects of the chromatid and chromosome breakage-fusion-bridge cycles, deriving from breakage, are then described; this leads on to a discussion about the way in which variegation phenotypes of the maize kernels can be “read” in terms of chromosome breakage. The “genetic earthquake” event of 1944, triggered by introducing broken chromosomes into a zygote from both parents, is then described; and the sequence of events leading to the discovery of Ds and Ac is traced. Finding mobility of Ds from one chromosomal location to another was pure serendipity, and the transposition showed itself while experiments were being undertaken to accurately map Ds. A similar chance observation revealed transposition of Ac as well, and then the relationship between the two elements was elucidated in terms of their autonomous and non-autonomous nature. The chapter concludes with a brief reference to the molecular cloning of Ac and Ds.