Quantitative trait loci for sugarcane resistance to the spotted stem borer <Emphasis Type="Italic">Chilo sacchariphagus</Emphasis>

The spotted stem borer (SSB) Chilo sacchariphagus is a major pest of sugarcane, causing substantial losses in cane weight and in sucrose yield. SSB resistance is an important trait to be taken into account for sugarcane breeding programs. In order to analyse the genetic basis of the resistance to SSB, we undertook a quantitative trait allele (QTA) mapping study based on a population of 147 progenies derived from the selfing of the resistant modern cultivar R570. The experimental population was evaluated in a replicated trial for borer damage under natural infestation in two successive crop cycles. A single-factor analysis using 1,405 polymorphic markers was performed to detect marker–trait associations. Statistical thresholds based on permutation tests designed to control type I errors at a low level allowed the detection of nine QTAs whose individual size ranged between 6 and 10% of the total variation. These nine QTAs are distributed over five of the eight homeology groups of the polyploid R570 genome. Two QTAs were found to co-localize with two typical resistance gene analog clusters. Overall, eight QTAs explain altogether 42% of the total phenotypic variance.     

Genetic control of yield related stalk traits in sugarcane

A major focus of sugarcane variety improvement programs is to increase sugar yield, which can be accomplished by either increasing the sugar content of the cane or by increasing cane yield, as the correlation between these traits is low. We used a cross between an Australian sugarcane variety Q165, and a Saccharum officinarum accession, IJ76-514, to dissect the inheritance of yield-related traits in the complex polyploid sugarcane. A population of 227 individuals was grown in a replicated field trial and evaluated over 3 years for stalk weight, stalk diameter, stalk number, stalk length and total biomass. Over 1,000 AFLP and SSR markers were scored across the population and used to identify quantitative trait loci (QTL). In total, 27 regions were found that were significant at the 5% threshold using permutation tests with at least one trait; individually, they explained from 4 to 10% of the phenotypic variation and up to 46% were consistent across years. With the inclusion of digeneic interactions, from 28 to 60% of the variation was explained for these traits. The 27 genomic regions were located on 22 linkage groups (LGs) in six of the eight homology groups (HGs) indicating that a number of alleles or quantitative trait alleles (QTA) at each QTL contribute to the trait; from one to three alleles had an effect on the traits for each QTL identified. Alleles of a candidate gene, TEOSINTE BRANCHED 1 (TB1), the major gene controlling branching in maize, were mapped in this population using either an SSR or SNP markers. Two alleles showed some association with stalk number, but unlike maize, TB1 is not a major gene controlling branching in sugarcane but only has a minor and variable effect.     

Markers associated with stalk number and suckering in sugarcane colocate with tillering and rhizomatousness QTLs in sorghum.

Two important factors influencing sugar yield, the primary focus of sugarcane plant breeding programs, are stalk number and suckering. Molecular markers linked to both of these traits are sought to assist in the identification of high sugar yield, high stalk number, low-suckering sugarcane clones. In this preliminary mapping study, 108 progeny from a biparental cross involving two elite Australian sugarcane clones were evaluated at two sites for two years for both stalk number and suckering. A total of 258 DNA markers, including both restriction fragment length polymorphisms (RFLPs) and radio-labelled amplified fragments (RAFs), were scored and evaluated using single-factor analysis. Sixteen (7 RFLPs and 9 RAFs) and 14 (6 RFLPs and 8 RAFs) markers were identified that were significantly associated (P < 0.01) with stalk number and suckering, respectively, across both years and sites. The seven and six RFLP markers associated with stalk number and suckering, respectively, were generated by eight different RFLP probes, of which seven had been mapped in sorghum and (or) sugarcane. Of significant interest was the observation that all seven RFLP probes could be shown to be located within or near QTLs associated with tillering and rhizomatousness in sorghum. This observation highlights the usefulness of comparative mapping between sorghum and sugarcane and suggests that the identification of useful markers for stalk number and suckering in sugarcane would be facilitated by focussing on sorghum QTLs associated with related traits.     

Characterisation of genome regions incorporated from an important wild relative into Australian sugarcane

Mandalay is an important Saccharum spontaneum clone used historically in Australian sugarcane breeding programs, and has given rise to many valuable cultivars. In order to better understand the genetic contribution of Mandalay to Australian varieties and elite parental material, a combined pedigree and quantitative trait loci (QTL) mapping approach was undertaken. A genetic map containing 400 single-dose markers was constructed for the Australian sugarcane clone MQ77340, one parent of an Australian sugarcane population (Q117 × MQ77340), using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. This cultivar was selected because it is a direct descendent of Mandalay; its grandparents are Korpi, a S. officinarum clone, and Mandalay. The 400 markers were scattered onto 101 linkage groups (LGs) with an estimated map length of 3582 cM. The ancestral origin of all of the markers was determined with approximately 25% of the markers shown to originate from Mandalay, and a similar percentage from Korpi. Of the 101 LGs, 65 contained markers originating from Mandalay and/or Korpi. QTL analysis was undertaken using the map and 3 years of field data for three sugar-related traits (pol, brix, and CCS) and using single year field data for fibre, stalk weight and cane and sugar yield. Markers from both Mandalay and Korpi were found to be associated with both positive and negative effects on all of the traits analysed.     

Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations

As sugarcane is a complex polyaneuploid with many chromosomes, large numbers of markers are required to generate genetic maps with reasonable levels of genome coverage. Comparative mapping was investigated as an approach for both quantitative trait loci (QTL) validation and genetic map enhancement in sugarcane. More than 1000 SSR and AFLP markers were scored in a bi-parental Australian sugarcane population (Q3) that was segregating widely for sugar content-related traits. Two maps were constructed, one for each parent. The Q117 (female) and MQ77-340 (male) maps each contained almost 400 markers distributed onto approximately 100 linkage groups (LGs), of which nearly half could be assigned to homology groups (HGs) on the basis of SSRs. Then, using common SSR and AFLP markers, the two Q3 parental maps were aligned with the maps of the French cultivar, R570, and of the Australian cultivar, Q165^A (A denotes variety covered by Australian plant breeding rights). As a result of comparative mapping, all ten HGs in the Q117 map, and all eleven HGs in the MQ77-340 map could be re-assigned to seven of the expected eight sugarcane HGs, revealing that one sugarcane HG was not covered at all in either Q3 parental map, and that other HGs were poorly represented. QTL analysis in the Q3 population identified approximately 75 marker-trait associations (MTAs) from approximately 18 chromosomal regions or putative QTL in each map for three sugar content-related traits. QTL location appeared to be consistent between the 4 maps; two of the eight HGs were observed to contain MTAs for brix in two or three maps, strongly suggesting the location of sugar content-related trait loci in these HGs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps

Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes.     

Chromosome evolution in perissodactyla

Comparative painting has provided a wealth of useful information and helped to reconstruct the pathways of karyotype evolution within major eutherian phylogenetic clades. New data have come from gene localizations, BAC mapping and high throughout sequencing projects that enrich and provide new details of genome evolution. Extensive research on perissodactyl genomes has revealed not only increased rates of chromosomal rearrangements, but also an exceptionally high number of centromere repositioning events in equids. Here were combined new physical mapping, comparative painting and genome sequencing data to refine the putative ancestral karyotype maps and to revise the previously proposed scenario of perissodactyl karyotype evolution.     

Whole-genome association mapping in elite inbred crop varieties

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley (Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.     

Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era

Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community.     

Characterisation of single nucleotide polymorphisms in sugarcane ESTs

Commercial sugarcane cultivars (Saccharum spp. hybrids) are both polyploid and aneuploid with chromosome numbers in excess of 100; these chromosomes can be assigned to 8 homology groups. To determine the utility of single nucleotide polymorphisms (SNPs) as a means of improving our understanding of the complex sugarcane genome, we developed markers to a suite of SNPs identified in a list of sugarcane ESTs. Analysis of 69 EST contigs showed a median of 9 SNPs per EST and an average of 1 SNP per 50 bp of coding sequence. The quantitative presence of each base at 58 SNP loci within 19 contiguous sequence sets was accurately and reliably determined for 9 sugarcane genotypes, including both commercial cultivars and ancestral species, through the use of quantitative light emission technology in pyrophosphate sequencing. Across the 9 genotypes tested, 47 SNP loci were polymorphic and 11 monomorphic. Base frequency at individual SNP loci was found to vary approximately twofold between Australian sugarcane cultivars and more widely between cultivars and wild species. Base quantity was shown to segregate as expected in the IJ76-514 × Q165 sugarcane mapping population, indicating that SNPs that occur on one or two sugarcane chromosomes have the potential to be mapped. The use of SNP base frequencies from five of the developed markers was able to clearly distinguish all genotypes in the population. The use of SNP base frequencies from a further six markers within an EST contig was able to help establish the likely copy number of the locus in two genotypes tested. This is the first instance of a technology that has been able to provide an insight into the copy number of a specific gene locus in hybrid sugarcane. The identification of specific and numerous haplotypes/alleles present in a genotype by pyrophosphate sequencing or alternative techniques ultimately will provide the basis for identifying associations between specific alleles and phenotype and between allele dosage and phenotype in sugarcane.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Evolution of plant mitochondrial genomes via substoichiometric intermediates

Comparison of the modern fertile maize mitochondrial genome (N) with an ancestral maize mitochondrial genome (RU) reveals a 12 kb duplication (containing the atpA gene) in the modern genome that is absent from the ancestor. Cloning, mapping, and sequencing of the relevant portions of the ancestral genome shows that this duplication probably arose via a three-stage recombination process involving substoichiometric intermediates. Comparison with analogous observations on yeast mitochondrial genomes suggests that this three-stage model of genome reorganization can be generally applied to plant mitochondrial genomes to explain both deletions and the creation of novel repeats, common features of plant mitochondrial genome evolution.     

Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae

An in silico comparative genomics approach was used to identify putative orthologs to genetically mapped genes from the mosquito, Aedes aegypti, in the Drosophila melanogaster and Anopheles gambiae genome databases. Comparative chromosome positions of 73 D. melanogaster orthologs indicated significant deviations from a random distribution across each of the five A. aegypti chromosomal regions, suggesting that some ancestral chromosome elements have been conserved. However, the two genomes also reflect extensive reshuffling within and between chromosomal regions. Comparative chromosome positions of A. gambiae orthologs indicate unequivocally that A. aegypti chromosome regions share extensive homology to the five A. gambiae chromosome arms. Whole-arm or near-whole-arm homology was contradicted with only two genes among the 75 A. aegypti genes for which orthologs to A. gambiae were identified. The two genomes contain large conserved chromosome segments that generally correspond to break/fusion events and a reciprocal translocation with extensive paracentric inversions evident within. Only very tightly linked genes are likely to retain conserved linear orders within chromosome segments. The D. melanogaster and A. gambiae genome databases therefore offer limited potential for comparative positional gene determinations among even closely related dipterans, indicating the necessity for additional genome sequencing projects with other dipteran species.     

Linking porcine microsatellite markers to known genome regions by identifying their human orthologs.

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.     

Mapping quantitative trait loci for principal components of bone measurements and osteochondrosis scores in a wild boar x large white intercross

Data on osteochondrosis and femur dimensions from 195 F2 pigs from a wild boar x Large White intercross were analysed with the aim of detecting quantitative trait loci (QTLs) for normal and disturbed bone formation. The information from numerous recorded traits was summarized by principal component analysis and analysed by least-squares interval mapping. An increase in the proportion of wild boar alleles across the genome increased length versus width of femur and reduced the prevalence of osteochondrosis. The presence of QTLs with an impact on femur dimensions was indicated on chromosomes 2, 4, 16 and 17 and on osteochondrosis on chromosomes 5, 13 and 15. A substantial effect of the chromosome 5 QTL calls for further studies within commercial populations to evaluate whether marker-assisted selection could be used to reduce the prevalence of osteochondrosis.     

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

Mapping quantitative trait loci (QTLs) is a foundation for molecular marker-assisted selection and map-based gene cloning. During the past decade, numerous QTLs for seed yield (SY) and yield-related traits in Brassica napus L. have been identified. However, integration of these results in order to compare QTLs from different mapping populations has not been undertaken, due to the lack of common molecular markers between studies. Using previously reported Brassica rapa and Brassica oleracea genome sequences, we carried out in silico integration of 1,960 QTLs associated with 13 SY and yield-related traits from 15 B. napus mapping experiments over the last decade. A total of 736 SY and yield-related QTLs were mapped onto 283 loci in the A and C genomes of B. napus. These QTLs were unevenly distributed across the 19 B. napus chromosomes, with the most on chromosome A3 and the least on chromosome C6. Our integrated QTL map identified 142 loci where the conserved QTLs were detected and 25 multifunctional loci, mostly for the traits of flowering time (FT), plant height, 1,000-seed weight, maturity time and SY. These conserved QTLs and multifunctional loci may result from pleiotropism or clustered genes. At the same time, a total of 146 genes underlying the QTLs for FT and other yield-related traits were identified by comparative mapping with the Arabidopsis genome. These results facilitate the retrieval of B. napus SY and yield-related QTLs for research communities, increase the density of targeted QTL-linked markers, validate the existence of QTLs across different populations, and advance the fine mapping of genes.     

Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae)

BACKGROUND: Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. GENETIC RESOURCES: The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.     

Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.