Past and recent advances in sugarcane cytogenetics

The Saccharum genus comprises species with large and variable chromosome numbers, leading to challenges in genomic studies and breeding improvement. Cytogenetics, including classical and molecular approaches, has played a central role in deciphering the genome structure, classification, and evolution of the genus Saccharum. The application of fluorescence in situ hybridization using oligonucleotide probes significantly improved our understanding of the complex genomes of Saccharum species. This paper reviews the application and progress of cytogenetic techniques in Saccharum. Future applications of cytogenetics are discussed, as they could benefit both genomic studies and breeding of sugarcane as well as other plants with complex genomes.

Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation

Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy,and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide(oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization(FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I(MI) in autotetraploid,autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploidized chromosome behavior;so that homologous chromosomes formed almost exclusively bivalents during MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants.

Multivariate Based Variability within Diverse Indian Mustard (<i>Brassica juncea</i>L.) Genotypes

Indian mustard (Brassica juncea L.) germplasm consisting 167 accessions including one check cultivar was evaluated for qualitative and quantitative traits. The present study was conducted to investigate genetic diversity and correlation among studied genotypes of B. juncea L. based on agro-morphological at NARC, Islamabad, Pakistan. To investigate the genetic diversity based on morphological characters, data was recorded on 20 quantitative and 12 qualitative traits. The calculated data was analyzed through two complementary methods, i.e. PCA (Principal Component Analysis) and cluster analysis. Among all the studied cultivars, significant diversity was recorded for different agro-morphological characters. Among all the parameters, maximum variance was recorded for pod shattering (427.2) followed by plant height (345.6), days to 100% flowering (336.2) and main raceme length (210.0). Among all the characters, the greatest and highly significant association (0.99) was found between days to maturity 50% and days to maturity 100% followed by correlation (0.86) among days to flowering 50% and days to flowering 100%, correlation value (0.71) was calculated among leaf length and leaf width. Using cluster analysis all the genotypes were divided into five major groups. It was observed that 7 out of 20 principal components with an Eigen value of ≥1.0 calculated for 73.92% of the total diversity observed between 167 accessions of Indian mustard (B. juncea L.). The contribution of first three PCs in the total PCs was 23.25, 12.87 and 11.24, respectively. Among all the investigated accessions two genotypes 26,813 and 26,817 showed great potential for seeds/silique, 1000-seed weight and seed yield/plant, respectively, so these genotypes are recommended for future breeding programs for achieving promising results.

Assessment of Genetic Variation Within Indian Mustard (Brassica juncea) Germplasm Using Random Amplified Polymorphic DNA Markers

Genetic diversity among 45 Indian mustard （Brassica juncea L.） genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA （RAPD） technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 （88%） were polymorphic. Of these, 13 were unique to accession ‘Pak85559＇. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li＇s similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.