Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

Ooijen, J. W. Van

doi:10.1017/s0016672311000279

Cited by 446 publications

(313 citation statements)

References 13 publications

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“…Further filtering was done by selecting only SNP markers with a missing rate of < 0.09 that were separated by at least 2000 bp. After such stringent filtering, a total of 6088 SNP markers were obtained and subsequently used to develop a linkage map using JoinMap 4.1 65 . The limit of detection (LOD) score = Z = log(probability of sequence with linkage/probability of sequence with no linkage) for the occurrence of linkage was set to 4-20 (start-end).…”

Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.

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Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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“…Linkage analysis was performed via maximum likelihood mapping using JoinMap software package and default parameters, except that the number of optimization rounds was increased from three to five to ensure accurate internal ordering of large numbers of tightly linked markers (Stam 1993;Van Ooijen 2011). In order to circumvent limitations of the software package related to computational overhead, efficiently anchor the map to the existing assembly, and permit robust integration of female and male maps, we limited our analyses to markers that (1) aligned to the published genome assembly (>95% identity over ≥90 bp via BLAST) (Altschul et al 1990), (2) yielded informative segregation phasing, and (3) yielded genotypic information for at least 20 of 30 offspring.…”

Section: Linkage Analysismentioning

confidence: 99%

“…In order to circumvent limitations of the software package related to computational overhead, efficiently anchor the map to the existing assembly, and permit robust integration of female and male maps, we limited our analyses to markers that (1) aligned to the published genome assembly (>95% identity over ≥90 bp via BLAST) (Altschul et al 1990), (2) yielded informative segregation phasing, and (3) yielded genotypic information for at least 20 of 30 offspring. These were further supplemented with markers that were specifically informative for one or both parents, regardless of alignment to the genome assembly, permitted that they were genotyped for at least 27 of 30 offspring for biallelic markers (llxlm, nnxnp, or hkxhk) (Maliepaard et al 1997;Van Ooijen 2011) or at least 25 of 30 offspring for tri-and tetra-allelic markers (efxeg or abxcd) (Maliepaard et al 1997;Van Ooijen 2011). The maximum likelihood mapping algorithm for mapping of a full sib family from outbred parents (CP) (Van Ooijen 2011) was used to generate a linkage map from a total of 7215 potentially informative markers.…”

Section: Linkage Analysismentioning

confidence: 99%

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

2015

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It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ∼550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ∼ 99), spanning a total of 5570.25 cM. Comparative mapping data yield strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, but do not strongly support a hypothetical second event. Rather, these comparative maps reveal several evolutionarily independent segmental duplications occurring over the last 600+ million years of chordate evolution. This refined history of vertebrate genome duplication should permit more precise investigations of vertebrate evolution.

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“…A custom PERL script identified segregating polymorphic patterns. A genotype file formatted for JoinMap (v. 3.0) 77 was produced. Scaffolds were assigned onto corresponding linkage groups on the basis of the alignment result with the RAD alleles (Supplementary Table 9).…”

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confidence: 99%

A heterozygous moth genome provides insights into herbivory and detoxification

et al. 2013

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l e t t e r sHow an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants 1 , but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood 2 . We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.The global pest P. xylostella (Lepidoptera: Yponomeutidae) is thought to have coevolved with the crucifer plant family 3 ( Supplementary Fig. 1) and has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage 4 . Recently, the total cost of damage and management worldwide was estimated at $4-5 billion per annum 5,6 . This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s 7 and to Bacillus thuringiensis (Bt) toxins in the 1990s 8 and has developed resistance to all classes of insecticide, making it increasingly difficult to control 9,10 . P. xylostella provides an exceptional system for understanding the genetic and molecular bases of how insect herbivores cope with the broad range of plant defenses and chemicals encountered in the environment (Supplementary Fig. 2).We used a P. xylostella strain (Fuzhou-S) collected from a field in Fuzhou in southeastern China (26.08 °N, 119.28 °E) for sequencing ( Supplementary Fig. 1). Whole-genome shotgun-based Illumina sequencing of single individuals (Supplementary Table 1), even after ten generations of laboratory inbreeding, resulted in a poor initial assembly (N50 = 2.4 kb, representing the size above which 50% of the total length of the sequences is included), owing to high levels of heterozygosity ( Supplementary Figs. 3 and 4 and Supplementary Table 2). Subsequently, we sequenced 100,800 fosmid clones (comprising ~10× the genome length) to a depth of 200× ( Supplementary Fig. 5 and Supplementary Tables 3-5), assembling the resulting sequence data into 1,819 scaffolds, with an N50 of 737 kb, spanning ~394 Mb of the genome sequence (version 1; Supplementary Fig. 6 and Supplementary Table 6). The assembly covered 85.5% of a set of protein-coding ESTs (Supplementary Tables 7 and 8) generated by transcriptome sequencing 11 . Alignment of a subject scaffold against a 126-kb BAC (GenBank GU058050) from an altern...

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Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

Cited by 446 publications

References 13 publications

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

A heterozygous moth genome provides insights into herbivory and detoxification

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