Rapid identification and determination of purity of flow-sorted plant chromosomes using C-PRINS

Flow Analysis and Sorting of Plant Chromosomes

Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.

Accessing complex crop genomes with next-generation sequencing

Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.

Flow sorting and molecular cytogenetic identification of individual chromosomes of Dasypyrum villosum L. (H. villosa) by a single DNA probe

Dasypyrum villosum (L.) Candargy (sin. Haynaldia villosa) is an annual wild diploid grass species (2n = 2x = 14; genome VV) belonging to the Poaceae family, which is considered to be an important source of biotic and abiotic stress resistance genes for wheat breeding. Enhanced characterization of D. villosum chromosomes can facilitate exploitation of its gene pool and its use in wheat breeding programs. Here we present the cytogenetic identification of D. villosum chromosomes on slide by fluorescent in situ hybridization (FISH), with the GAA simple sequence repeat (SSR) as a probe. We also describe the isolation and the flow cytometric analysis of D. villosum chromosomes in suspension, resulting in a distinguished flow karyotype. Chromosomes were flow sorted into three fractions, according their DNA content, one of which was composed of a single type of chromosome, namely 6 V, sorted with over 85% purity. Chromosome 6 V is known to carry genes to code for important resistance and seed storage characteristics, and its isolation represents a new source of genetic traits and specific markers useful for wheat improvement.

Chromosomes in the flow to simplify genome analysis

Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.

Inversions of chromosome arms 4AL and 2BS in wheat invert the patterns of chiasma distribution

In many species, including wheat, crossing over is distal, and the proximal regions of chromosome arms contribute little to genetic maps. This was thought to be a consequence of terminal initiation of synapsis favoring distal crossing over. However, in an inverted rye chromosome arm, the pattern of metaphase I chiasmata was also inverted, suggesting that crossover frequencies were specific to chromosome segments. Here, wheat chromosome arms 2BS and 4AL, with essentially entire arms inverted in reverse tandem duplications (rtd), were studied in the MI of meiosis. Inversion-duplication placed the recombining segments in the middle of the arms. While the overall pairing frequencies of the inverted-duplicated arms were considerably reduced relative to normal arms, chiasmata, if present, were always located in the same regions as in structurally normal arms, and relative chiasma frequencies remained the same. The frequencies of fragment or fragment + bridge configurations in AI and AII indicated that of the two tandemly arranged copies of segments in rtds, the more distal inverted segments were more likely to cross over than the segments in their original orientations. These observations show that also in wheat, relative crossover frequencies along chromosome arms are predetermined and independent of the segment location. The segments normally not licensed to cross over do not do so even when placed in seemingly most favorable positions for it.

Flow cytometry in plant breeding

Since the first report on the flow cytometric study of plant material 35 years ago, analyzing the nuclear DNA content of field bean, an ever increasing number of applications of FCM has been developed and applied in plant science and industry, but a similar length of time elapsed before the appearance of the first complete volume devoted to FCM of plant cells. Most published information on the uses of FCM addresses various aspects of animal (including human) cell biology, thus failing to provide a pertinent substitute. FCM represents an ideal means for the analysis of both cells and subcellular particles, with a potentially large number of parameters analyzed both rapidly, simultaneously, and quantitatively, thereby furnishing statistically exploitable data and allowing for an accurate and facilitated detection of subpopulations. It is, indeed, the summation of these facts that has established FCM as an important, and sometimes essential, tool for the understanding of fundamental mechanisms and processes underlying plant growth, development, and function. In this review, special attention is paid to FCM as applied to plant cells in the context of plant breeding, and some new and less well-known uses of it for plants will be discussed.

Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes

The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that the MROS3 gene is located in at least two copies tandemly arranged on the X chromosome with additional copy(ies) on the autosome(s), while MROS1, MROS2, and MROS4 are exclusively autosomal. The specificity of PCR products was checked by digestion with a restriction enzyme or reamplification using nested primers. Homology search of databases has shown the presence of five MROS3 homologues in A. thaliana, four of them arranged in two tandems, each consisting of two copies. We conclude that MROS3 is a low-copy gene family, connected with the proper pollen development, which is present not only in dioecious but also in other dicot plant species.