Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

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The draft genome and transcriptome of Cannabis sativa

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps Mapping populations were derived from one interspecific backcross and five inter-subspecific (indica/japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population Mapping data for each population consisted of 129-629 markers Segregation distortion was determined based on chi-square analysis (P < 001) and was observed at 68-318%, of the mapped marker loci Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S) Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated

Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

[...] The purpose of this paper is to describe available marker types and examine factors critical for their use in map construction and MAS [marker-assisted selection]. This review clarifies how genetic markers are used in map construction and defines the potential use of genetic maps for MAS [...]

/pdf/genetic-markers-map-construction-and-their-application-in-4o5p9bm5xw.pdf

Genetic Markers, Map Construction, and Their Application in Plant Breeding

A genetic linkage map consisting of 399 RFLP-defined loci was generated from a cross between resynthesized Brassica napus (an interspecific B. rapa × B. oleracea hybrid) and "natural" oilseed rape. The majority of loci exhibited disomic inheritance of parental alleles demonstrating that B. rapa chromosomes were each pairing exclusively with recognisable A-genome homologues in B. napus and that B. oleracea chromosomes were pairing similarly with C-genome homologues. This behaviour identified the 10 A genome and 9 C genome linkage groups of B. napus and demonstrated that the nuclear genomes of B. napus, B. rapa, and B. oleracea have remained essentially unaltered since the formation of the amphidiploid species, B. napus. A range of unusual marker patterns, which could be explained by aneuploidy and nonreciprocal translocations, were observed in the mapping population. These chromosome abnormalities were probably caused by associations between homoeologous chromosomes at meiosis in the resynthesized parent a...

Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape).

Comparative genomics, the study of similarities and differences in structure and function of the hereditary information in different taxa, uses molecular tools to investigate notions that far preceded the discovery that DNA was the hereditary molecule. Vavilov’s (1922) “law of homologous series in variation” was an early suggestion of the possibility of underlying commonality in the genetic blueprints of different (plant) species. In plants, genetic analysis based upon morphological and isozyme markers provided early hints that the arrangements of genes along the chromosomes of various taxa may have retained parallels since their divergence from common ancestors. DNA-level investigations in diverse taxa point to two broad messages: 

(1)

The small but essential portion of most plant genomes encoding genes evolves relatively slowly, with corresponding genes retaining recognizable DNA sequences and similar order along the chromosomes of taxa that have been reproductively-isolated for millions of years.




(2)

A wide range of factors, such as DNA sequence mobility, gene deletion, and localized rearrangements, are superimposed on the relatively slow tempo of chromosomal evolution and cause many deviations from co-linearity.




(3)

Genetic loci that account for common phenotypes in different taxa are often at corresponding genomic locations, and may represent orthologous genes or members of orthologous clusters of genes.

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Comparative Genomics of Plant Chromosomes

F2 segregation analyses of DNA restriction fragment length polymorphisms (RFLPs) detected between a cabbage line (No. 86-16-5) resistant to race 2 of Plasmodiophora brassicae (Woronin), the fungus ...

A genetic map for Brassica oleracea based on RFLP markers detected with expressed DNA sequences and mapping of resistance genes to race 2 of Plasmodiophora brassicae (Woronin)

F2 segregation analyses of DNA restriction fragment length polymorphisms (RFLPs) detected between two cultivars of canola ('Westar' × Topas') was used to construct a detailed genetic map of Brassic...

A genetic map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences

In garlic, molecular markers associated with the trait of pollen fertility were searched, using random amplified polymorphic DNA (RAPD). Twelve pollen fertile and sterile garlic clones were screened, using 60 RAPD primers to find the DNA fragments related to pollen fertility. With the 60 arbitrary 10-mer primers, 625 discrete fragments of DNA were amplified, and 397 (64%) of them showed polymorphisms among the 12 clones. Two RAPD markers, OPJ121300 and OPJ121700 were amplified only in the pollen fertile clones with the primer OPJ12 (5'-GTCCCGTGGT-3'). The selected primers were tested on 60 pollen fertile and sterile garlic clones. The two RAPD markers were present commonly in all of the 31 pollen fertile clones, and they were not amplified in the 29 sterile clones with the exception of one, No. 395-2 which produces sterile pollen. The two RAPD markers were related to the pollen fertility of male organ, but the female fertility was not confirmed in this clone yet. The first step towdrds marker-assisted selection of fertile clones of garlic was made in this study.

Takeomi Etoh

Papers

A genetic map for Brassica oleracea based on RFLP markers detected with expressed DNA sequences and mapping of resistance genes to race 2 of Plasmodiophora brassicae (Woronin)

A genetic map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences

RAPD Markers Related to Pollen Fertility in Garlic (Allium sativum L.)