Introgression browser: high-throughput whole-genome SNP visualization

GenoTypeMapper: graphical genotyping on genetic and sequence-based maps

BACKGROUND

The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable.

RESULTS

We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time.

CONCLUSIONS

In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.

Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing

Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non-coding regions in the gene promoter and 5'UTR regions of genes. Poly-A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non-crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non-homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.

Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato

Genome editing technologies are being widely adopted in plant breeding¹. However, a looming challenge of engineering desirable genetic variation in diverse genotypes is poor predictability of phenotypic outcomes due to unforeseen interactions with pre-existing cryptic mutations^2-4. In tomato, breeding with a classical MADS-box gene mutation that improves harvesting by eliminating fruit stem abscission frequently results in excessive inflorescence branching, flowering and reduced fertility due to interaction with a cryptic variant that causes partial mis-splicing in a homologous gene^5-8. Here, we show that a recently evolved tandem duplication carrying the second-site variant achieves a threshold of functional transcripts to suppress branching, enabling breeders to neutralize negative epistasis on yield. By dissecting the dosage mechanisms by which this structural variant restored normal flowering and fertility, we devised strategies that use CRISPR-Cas9 genome editing to predictably improve harvesting. Our findings highlight the under-appreciated impact of epistasis in targeted trait breeding and underscore the need for a deeper characterization of cryptic variation to enable the full potential of genome editing in agriculture.

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom

A better understanding of genomic features influencing the location of meiotic crossovers (COs) in plant species is both of fundamental importance and of practical relevance for plant breeding. Using CO positions with sufficiently high resolution from four plant species [Arabidopsis thaliana, Solanum lycopersicum (tomato), Zea mays (maize) and Oryza sativa (rice)] we have trained machine-learning models to predict the susceptibility to CO formation. Our results show that CO occurrence within various plant genomes can be predicted by DNA sequence and shape features. Several features related to genome content and to genomic accessibility were consistently either positively or negatively related to COs in all four species. Other features were found as predictive only in specific species. Gene annotation-related features were especially predictive for maize, whereas in tomato and Arabidopsis propeller twist and helical twist (DNA shape features) and AT/TA dinucleotides were found to be the most important. In rice, high roll (another DNA shape feature) and low CA dinucleotide frequency in particular were found to be associated with CO occurrence. The accuracy of our models was sufficient for Arabidopsis and rice (area under receiver operating characteristic curve, AUROC > 0.5), and was high for tomato and maize (AUROC ≫ 0.5), demonstrating that DNA sequence and shape are predictive for meiotic COs throughout the plant kingdom.

BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene

A mutant line, bifurcate flower truss (bif), was recovered from a tomato genetics programme. Plants from the control line produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The control line and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed, and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a mitogen-activated protein (MAP) kinase, contained a leucine to stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato.

IntroMap: a signal analysis based method for the detection of genomic introgressions

BACKGROUND

Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.

RESULTS

We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionally we show, through targeted marker-based assays, validation of the IntroMap predicted regions for the hybrid cultivar.

CONCLUSIONS

This approach can be used to automate the screening of large populations, reducing the time and labor required, and can improve the accuracy of the detection of introgressed regions in comparison to a marker-based approach. In contrast to other approaches that generally rely upon a variant calling step, our method achieves accurate identification of introgressed regions without variant calling, relying solely upon alignment.

Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium

We determined the crossover (CO) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent-assigned variants of 52 F₆ recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum, and its wild relative, Solanum pimpinellifolium. The interspecific CO frequency was 80% lower than reported for intraspecific tomato crosses. We detected regions showing a relatively high and low CO frequency, so-called hot and cold regions. Cold regions coincide to a large extent with the heterochromatin, although we found a limited number of smaller cold regions in the euchromatin. The CO frequency was higher at the distal ends of chromosomes than in pericentromeric regions and higher in short arm euchromatin. Hot regions of CO were detected in euchromatin, and COs were more often located in non-coding regions near the 5' untranslated region of genes than expected by chance. Besides overrepresented CCN repeats, we detected poly-A/T and AT-rich motifs enriched in 1-kb promoter regions flanking the CO sites. The most abundant sequence motifs at CO sites share weak similarity to transcription factor-binding sites, such as for the C2H2 zinc finger factors class and MADS box factors, while InterPro scans detected enrichment for genes possibly involved in the repair of DNA breaks.

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line

The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.

Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping

A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.

Gramene Database: Navigating Plant Comparative Genomics Resources

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

Tracing ancestor rice of Suriname Maroons back to its African origin

African rice (Oryza glaberrima) and African cultivation practices are said to have influenced emerging colonial plantation economies in the Americas^1,2. However, the level of impact of African rice practices is difficult to establish because of limited written or botanical records^2,3. Recent findings of O. glaberrima in rice fields of Suriname Maroons bear evidence of the high level of knowledge about rice among African slaves and their descendants, who consecrate it in ancestor rituals^4,5. Here we establish the strong similarity, and hence likely origin, of the first extant New World landrace of O. glaberrima to landraces from the Upper Guinean forests in West Africa. We collected African rice from a Maroon market in Paramaribo, Suriname, propagated it, sequenced its genome⁶ and compared it with genomes of 109 accessions representing O. glaberrima diversity across West Africa. By analysing 1,649,769 single nucleotide polymorphisms (SNPs) in clustering analyses, the Suriname sample appears sister to an Ivory Coast landrace, and shows no evidence of introgression from Asian rice. Whereas the Dutch took most slaves from Ghana, Benin and Central Africa⁷, the diaries of slave ship captains record the purchase of food for provisions when sailing along the West African Coast⁸, offering one possible explanation for the patterns of genetic similarity. This study demonstrates the utility of genomics in understanding the largely unwritten histories of crop cultures of diaspora communities.

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Background

Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results

We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on genome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100 % identification accuracy at supra-species level and 78 % accuracy at the species level.

Conclusion

CNIDARIA allows for fast, resource-efficient comparison and identification of both raw and assembled genome and transcriptome data. This can help answer both fundamental (e.g. in phylogeny, ecological diversity analysis) and practical questions (e.g. sequencing quality control, primer design).

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0806-7) contains supplementary material, which is available to authorized users.