Yiqun Weng

The genome of melon (Cucumis melo L.)

We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site–leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly.

Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.

Extended physical maps and a consensus physical map of the homoeologous group-6 chromosomes of wheat (Triticum aestivum L. em Thell.)

Abstract Extended physical maps of chromosomes 6A, 6B and 6D of common wheat (Triticum aestivum L. em Thell., 2n=6x=42, AABBDD) were constructed with 107 DNA clones and 45 homoeologous group-6 deletion lines. Two-hundred and ten RFLP loci were mapped, including three orthologous loci with each of 34 clones, two orthologous loci with each of 31 clones, one locus with 40 clones, two paralogous loci with one clone, and four loci, including three orthologs and one paralog, with one clone. Fifty five, 74 and 81 loci were mapped in 6A, 6B and 6D, respectively. The linear orders of the mapped orthologous loci in 6A, 6B and 6D appear to be identical and 65 loci were placed on a group-6 consensus physical map. Comparison of the consensus physical map with eight linkage maps of homoeologous group-6 chromosomes from six Triticeaespecies disclosed that the linear orders of the loci on the maps are largely, if not entirely, conserved. The relative distributions of loci on the physical and linkage maps differ markedly, however. On most of the linkage maps, the loci are either distributed relatively evenly or clustered around the centromere. In contrast, approximately 90% of the loci on the three physical maps are located either in the distal one-half or the distal two-thirds of the six chromosome arms and most of the loci are clustered in two or three segments in each chromosome.

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

BackgroundCucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.ResultsUsing two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F2- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.ConclusionsComparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.

Cross-species transferability of microsatellite markers from six aphid (Hemiptera: Aphididae) species and their use for evaluating biotypic diversity in two cereal aphids.

The abundance and distribution of microsatellites, or simple sequence repeats (SSRs) were explored in the expressed sequence tag (EST) and genomic sequences of the pea aphid, Acyrthosiphon pisum (Harris), and the green peach aphid, Myzus persicae (Sulzer). A total of 108 newly developed, together with 40 published, SSR markers were investigated for their cross‐species transferability among six aphid species. Genetic diversity among six greenbug, Schizaphis graminum (Rondani) and two Russian wheat aphid, Diuraphis noxia (Kurdjumov) biotypes was further examined with 67 transferable SSRs. It was found that the pea aphid genome is abundant in SSRs with a unique frequency and distribution of SSR motifs. Cross‐species transferability of EST‐derived SSRs is dependent on phylogenetic closeness between SSR donor and target species, but is higher than that of genomic SSRs. Neighbor‐joining analysis of SSR data revealed host‐adapted genetic divergence as well as regional differentiation of greenbug biotypes. The two Russian wheat aphid biotypes are genetically as diverse as the greenbug ones although it was introduced into the USA only 20 years ago. This is the first report of large‐scale development of SSR markers in aphids, which are expected to have wide applications in aphid genetic, ecological and evolutionary studies.

BAC Libraries from Wheat Chromosome 7D: Efficient Tool for Positional Cloning of Aphid Resistance Genes

Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance gene DnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance gene Gb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective.

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides

Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000–27,000 oligos. These probes spanned 8.3–17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5–3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.

Biotypic Diversity in Greenbug (Hemiptera: Aphididae): Microsatellite-Based Regional Divergence and Host-Adapted Differentiation

ABSTRACT Nineteen isolates of the cereal aphid pest greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae), were collected from wheat, Triticum aestivum L.; barley, Hordeum vulgare L.; or noncultivated grass hosts in five locations from Colorado and Wyoming. Parthenogenetic colonies were established. Biotypic profiles of the 19 isolates were determined based on their abilities to damage a set of host plant differentials, and 13 new biotypes were identified. Genetic diversity among the 19 isolates and five previously designated greenbug biotypes (E, G, H, I, and K) was examined with 31 cross-species transferable microsatellite (simple sequence repeat) markers. Neighbor-joining clustering analysis of marker data revealed host-adapted genetic divergence as well as regional differentiation of greenbug populations. Host associated biotypic variation seems to be more obvious in “agricultural biotypes,” whereas isolates collected from noncultivated grasses tend to show more geographic divergence. It seems that the biotype sharing the most similar biotypic profiles and the same geographic region with current prevailing one may have the greatest potential to become the new prevailing biotype. Close monitoring of greenbug population dynamics especially biotypic variation on both crop plants and noncultivated grasses in small grain production areas may be a useful strategy for detecting potentially new prevailing virulent biotypes of the greenbug.

Comparison of homoeologous group-6 short arm physical maps of wheat and barley reveals a similar distribution of recombinogenic and gene-rich regions

Abstract.Eighty two new loci, mapped with 51 DNA clones, were added to the earlier deletion maps of the homoeologous group-6 short arms of hexaploid wheat (Triticum aestivum L. em Thell., 2n = 6x = 42, AABBDD). There are now 41, 56 and 52 loci mapped on deletion maps of 6AS, 6BS and 6DS, respectively. The linear order of orthologous loci in all three arms appears to be identical. The majority of the loci are located in the distal one-half of the three arms. There seems to be an increased marker/gene density from the centromeric to the telomeric regions in each arm, and the marker density in comparable physical regions is similar on all three maps. Recombination is not uniformly distributed along the chromosome arms; 60% of recombination occurs in the distal one-third of each arm. Recombination increases from the proximal region to the distal end in a nonlinear pattern. The distribution of loci and recombination along each of the three chromosome arms is highly correlated. Comparison of the 6BS deletion map from this study and a 6HS physical map of barley (Hordeum vulgare L., 2n = 2x = 14, HH) reveals a remarkably similar distribution of recombinogenic and gene-rich regions between the two chromosome arms, suggesting that the distribution patterns of genes may be conserved in the homoeologous group-6 chromosome short arms of wheat and barley. A consensus map of wheat group-6 short arms containing 46 orthologous loci was constructed. Comparison of the consensus map with published linkage maps of Triticeae group-6 chromosome short arms indicates that the linear order of the loci on the maps has been largely conserved. Evidence from this study does not support the existence of a 2BS–6BS reciprocal terminal translocation.

Ultrahigh-Density Linkage Map for Cultivated Cucumber (Cucumis sativus L.) Using a Single-Nucleotide Polymorphism Genotyping Array

Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a ‘9930’ × ‘Gy14’ recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.