Updating the maize karyotype by chromosome DNA sizing

Carica papaya L. sex chromosome review and physical mapping of the serk 2, svp-like and mdar 4 sequences

Physical mapping evidences the chromosome organization and structure. Despite the data about plant cytogenomics, physical mapping has been conducted from single-copy and/or low-copy genes for few species. Carica papaya cytogenomics has been accomplished from BAC-FISH and repeatome sequences. We aimed to map the serk 2, svp-like and mdar 4 sequences in C. papaya. The sequences were amplified and the amplicons sequenced, showing similarity in relation to serk 2, svp-like and mdar 4 genes. Carica papaya diploidy was confirmed and the mitotic chromosomes characterized. The chromosome 1 exhibited the secondary constriction pericentromeric to the centromere of the long arm. So, we concluded that it is the sex chromosomes. serk 2 was mapped in the long arm interstitial portion of the sex chromosomes, and the interphase nuclei showed two fluorescence signals. Considering these results and the sequencing data from the C. papaya sex chromosomes, svp-like and mdar 4 genes were mapped in the interstitial region of the sex chromosome long arm. Both sequences showed only one fluorescence signal in the interphase nuclei. The procedure adopted here can be reproduced for other single-copy and/or low-copy genes, allowing the construction of cytogenetic maps. In addition, we revisited the cytogenomics data about C. papaya sex chromosomes, presenting a revised point of view about the structure and evolution to these chromosomes.

Genome size estimation of false daisy, cheek weed, pot marigold and marigold

We report the genome size estimated using flow cytometry for four closely related species, including false daisy (Eclipta prostrate), cheek weed (Ageratum conyzoides), pot marigold (Calendula officinalis), and marigold (Tagetes erecta) belonging to Asteraceae family. The detected genome size for false daisy, cheek weed, pot marigold, and marigold was, 2.435, 3.266, 3.413, and 1.897, Gbp, respectively, while their respective 2C DNA content was 2.5, 3.3, 3.5, and 1.9, pg. The information on genome size presented here will be useful for understanding genomic evolution and will also clear the way for additional genomic research in these species.

Genome size, chromosome number variation and its correlation with stomatal characters for assessment of ploidy levels in a core subset of mulberry (Morus spp.) germplasm

The large size of the germplasm collection along with scanty information on their cytological and genome constitution have hindered well-planned breeding schemes in mulberry. To address the issue, a study was undertaken to investigate the variability in DNA content and genome size, chromosome number, ploidy and its relation with important stomatal characteristics among 162 mulberry germplasm. These germplasm comprise a core subset of 150 collections along with a representative collection of different mulberry species including the wild. Among the germplasm belonging to 16 species, we identified 122 diploids (2n = 28), 4 aneuploids (2n = 30), 13 triploids (2n = 42), 15 tetraploids (2n = 56), 7 hexaploids (2n = 84) and 1 dodecosaploid (2n = 308) based on the chromosome count. Most of the cultivated mulberries are found to be diploids. The mean nuclear 2C DNA content estimated by Flow cytometry, varied from 0.723±0.006 pg (M. australis, 2n = 2x) to 7.732 pg (M. nigra, 2n = 22x). The 2C DNA content positively correlated with the ploidy status and stomatal length (r = 0.814, p<0.001). Based on the 1Cx value, the study also suggests that the majority of the polyploid species have experienced genome downsizing in relation to their diploid progenitors. This study provides the most essential information on chromosome number, ploidy and DNA content to facilitate the utilization of a core subset of germplasm in the mulberry breeding program.

3-D Nucleus Architecture in Oat × Maize Addition Lines

The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids.

Repetitive sequences and structural chromosome alterations promote intraspecific variations in Zea mays L. karyotype

LTR-retrotransposons, knobs and structural chromosome alterations contribute to shape the structure and organization of the Zea mays karyotype. Our initial nuclear DNA content data of Z. mays accessions revealed an intraspecific variation (2 C = 2.00 pg to 2 C = 6.10 pg), suggesting differences in their karyotypes. We aimed to compare the karyotypes of three Z. mays accessions in search of the differences and similarities among them. Karyotype divergences were demonstrated among the accessions, despite their common chromosome number (2n = 20) and ancestral origin. Cytogenomic analyses showed that repetitive sequences and structural chromosome alterations play a significant role in promoting intraspecific nuclear DNA content variation. In addition, heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower nuclear 2 C value. Besides this, translocation was also observed in the short arm of chromosome 1. Differently, higher 2 C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphism involving the number and position of the 180-bp knob sequence was found among the accessions. Taken together, we provide insights on the pivotal role played by repetitive sequences and structural chromosome alterations in shaping the karyotype of Z. mays.

Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality?

Painting plant chromosomes through chromosomal in situ suppression (CISS) hybridization has long been considered impracticable. Seeking to build specific and complex probes from a single microdissected chromosome, we employed human chromosomes as models to standardize all the necessary steps for application in plants. Human metaphases were used to define the adequate conditions for microdissection, chromosome DNA amplification and labeling through degenerate oligonucleotide-primed PCR, and in situ hybridization stringency. Subsequently, these methodologies were applied in the plant species Zea mays (chromosome 1) and Capsicum annuum (chromosome 7 or 8). The high quality of human and plant cytogenetic preparations and the meticulous standardization of each step, especially the most critical ones - microdissection and first round of DNA amplification - were crucial to eliminate the signs of non-specific hybridization and for direct application in plants. By overcoming these challenges, we obtained chromosome-specific probes, which allowed to achieve a clear and uniform painting of the entire target chromosomes with little or no background, evidencing their complexity and specificity. Despite the high amount of ubiquitous repetitive sequences in plant genomes, the main drawback for chromosome painting, we successfully employed our methodology on two plant species. Both have more than 80% repetitive sequences, which is compared to the human genome (66-69%). This is the first time that plant chromosome-specific probes were successfully obtained from a single A mitotic or meiotic microdissected chromosome. Thereby, we assume that chromosome painting through microdissection and CISS hybridization can now be considered a reality in the field of plant cytogenetics.