Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane

The Challenge of Analyzing the Sugarcane Genome

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5'UTR and in the ORF (about 27%) and a low frequency was observed in the 3'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane.

Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115)

The genome of modern sugarcane cultivars is highly polyploid (approximately 12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers

The presence of a major resistance gene (Bru1) for brown rust in the sugarcane cultivar R570 (2n about 115) was confirmed by analyzing segregation of rust resistance in a large population of 658 individuals, derived from selfing of clone R570. A subset of this population was analyzed with AFLP and bulked segregant analysis (BSA) to develop a detailed genetic map around the resistance gene. Four hundred and forty three primer pairs were used resulting in the identification of eight AFLP markers surrounding the resistance gene in an interval of 10 cM, with the closest markers located at 1.9 and 2.2 cM on each side of the gene. Efficiency of the AFLP/BSA applied to the complex polyploid genome of sugarcane is discussed, as well as the potential of the newly identified AFLP markers for developing a map-based cloning approach exploiting, synteny conservation with sorghum.

DNA markers in plant improvement: an overview

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

A High-Density Genetic Recombination Map of Sequence-Tagged Sites for Sorghum, as a Framework for Comparative Structural and Evolutionary Genomics of Tropical Grains and Grasses

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM (∼300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of ≤50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny—in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4-83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.

Genetic mapping of the Sorghum bicolor vp1 gene and its relationship with preharvest sprouting resistance

The plant vp1 gene encodes a transcription factor originally identified in maize that participates in the control of the transition from embryogenesis to seed germination. Different lines of evidence suggest that vp1 participates in preharvest sprouting (PHS) resistance in cereals, but the genetic relationship is not yet established. Thus, the aim of this study was to investigate if there is a connection between vp1 and the formerly documented quantitative trait loci for PHS in Sorghum bicolor. This gene was mapped in sorghum using two well-studied inbred lines displaying contrasting PHS phenotypes. Linkage analysis revealed that the S. bicolor vp1 (Sbvp1) locus is linked to markers located on chromosomes 3 and 8 in maize. Analysis indicated that this gene is not correlated with PHS at a statistically significant level. Structural analysis of the Sbvp1 gene from both inbred lines showed a high degree of overall conservation (low polymorphism), even in the promoter region. These findings, taken together with the previously observed correlation between the pattern of expression of this gene and PHS performance, suggest that Sbvp1 might act downstream in the signalling pathway that leads to seed germination, or even be differentially regulated as a consequence rather than as a cause of the phenotypic behaviour.

Sugarcane genomics: depicting the complex genome of an important tropical crop

In the past few years, approaches such as molecular cytogenetics and the use of molecular markers have permitted significant advances in the establishment of the evolutionary origin and genome structure of sugarcane, an important polyploid crop. The availability of new resources, such as a bacterial artificial chromosome library and a huge collection of expressed sequence tags, has opened the gateway to promising functional analyses on a genomic scale.

Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes

18S-5.6S-25S and 5S ribosomal DNA (rDNA) sites were located by in situ hybridization to the three main species of the Saccharum genus. For each species and each rDNA family, the position and number of sites in the various cytotypes suggested the presence of one locus and basic chromosome numbers of 10 for Saccharum officinarum and Saccharum robustum and\i 8 forSaccharum spontaneum. The implications of these results for the genetic maps of modern cultivars derived from crosses between the species S. officinarum and S. spontaneum are discussed.Key words: sugarcane, Saccharum, 18S-5.6S-25S rRNA, 5S rRNA, basic chromosome number, in situ hybridization.

To pair or not to pair: chromosome pairing and evolution

Chromosome pairing in wild-type wheat closely resembles the process in both yeast and Drosophila. The recent characterisation of a mutant Ph1 wheat and the observation that chromosome pairing in the absence of Ph1 more closely resembles that of mammals and maize has shed light on the evolution of chromosome pairing in the cereals.

Physical mapping of the liguleless linkage group in Sorghum bicolor using rice RFLP-selected sorghum BACs

Physical mapping of BACs by fluorescent in situ hybridization (FISH) was used to analyze the liguleless (lg-1) linkage group in sorghum and compare it to the conserved region in rice and maize. Six liguleless-associated rice restriction fragment length polymorphism (RFLP) markers were used to select 16 homeologous sorghum BACs, which were in turn used to physically map the liguleless linkage group in sorghum. Results show a basic conservation of the liguleless region in sorghum relative to the linkage map of rice. One marker which is distal in rice is more medial in sorghum, and another marker which is found within the linkage group in rice is on a different chromosome in sorghum. BACs associated with linkage group I hybridize to chromosome It, which was identified by using FISH in a sorghum cytogenetic stock trisomic for chromosome I (denoted It), and a BAC associated with linkage group E hybridized to an unidentified chromosome. Selected BACs, representing RFLP loci, were end-cloned for RFLP mapping, and the relative linkage order of these clones was in full agreement with the physical data. Similarities in locus order and the association of RFLP-selected BAC markers with two different chromosomes were found to exist between the linkage map of the liguleless region in maize and the physical map of the liguleless region in sorghum.