Janet A. Condie

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

Isolation, expression and phylogenetic inheritance of an acetolactate synthase gene from Brassica napus

SummaryAn acetolactate synthase gene was isolated and characterized from Brassica napus. This B. napus acetolactate synthase gene encodes a deduced polypeptide sequence of 637 amino acids which is 85% homologous to the corresponding proposed gene product from Arabidopsis thaliana. Peptide domains recently associated with herbicide resistance/sensitivity are conserved between the two sequences. From Southern analysis we conclude that the gene isolated is one member of a multigene acetolactate synthase gene family comprising four or five members. A probe spanning the presumptive transit peptide sequence of this gene was shown by Southern analysis to hybridize to a unique sequence in the B. napus genome. This unique probe was used to analyse DNA from B. campestris and B. oleracea, the presumed progenitors of B. napus. On the basis of restriction fragment length polymorphism, we conclude that the B. napus gene isolated here originated in B. campestris. Total acetolactate synthase-homologous transcripts were analysed in a variety of B. napus tissues, and showed preferential accumulation in rapidly growing material. The genomic clone was mutated in vitro at codon 173 to replace a proline residue with serine. This was re-introduced into plants, using Agrobacterium vectors, producing a herbicide-resistant phenotype which is characteristic of the predicted gene product.

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

This study identified multiple whole-genome duplication (WGD) events among Brassicaceae species. Remarkably, these events, as well as previously identified WGD events, are synchronized in age, coincident with epoch transitions, adding to the evidence suggesting the environmental instability associated with these transitions favors polyploidy and rapid species diversification. The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (∼7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.

Gene‑based SNP discovery and genetic mapping in pea

Key messageGene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance.AbstractPea (Pisum sativum L.) is one of the world’s oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.

Sequence of a lepidopteran toxin gene of Bacillus thuringiensis subsp kurstaki NRD-12

Three classes of HindIII hybridizing fragments of 4.5, 5.3 and 6.6 kb in size have been identified in the Bacillus thuringiensis (B.t.) kurstaki NRD-12 strain, a situation similar to the one found in the well-studied B.t. kurstaki HD-1 strain. The probes used were short, synthetic oligodeoxynucleotides derived from the published HD-1 4.5 class delta-endotoxin gene sequence. We have cloned the NRD-12 5.3 class gene in the Escherichia coli plasmid, pUC8, and determined its nucleotide sequence. An open reading frame of 1155 amino acid residues was identified as the delta-endotoxin coding sequence based on its overall homology with the deduced amino acid sequences from the HD-1 4.5 gene and a 6.6 gene from the related kurstaki HD-73 strain. The NRD-12 5.3 gene appears to be a hybrid of the former two genes but displays a unique 78 by deletion and a 12 by insertion in the 3′-coding region. These characteristics have also been reported in two other recently reported genes isolated from B.t. berliner 1715 and kurstaki HD-1. Potential transmembrane segments have been predicted for the three classes of toxins.

Isolation, structure and expression of a cDNA for acetolactate synthase from Brassica napus

Acetolactate synthase (EC 4.1.3.18) catalyzes the first enzymatic step in a bifurcated pathway for the synthesis of the branched-chain amino acids. In plants, biochemical and genetic evidence have strongly implicated the involvement of a highly conserved 68 kDa subunit with ALS activity, and several structurally conserved genomic sequences encoding this ALS subunit have been isolated from Saccharomyces cerevisiae [2], Arabidopsis thaliana [ 3 ], Nicotiana tabacum [ 6, 8 ] and Brassica napus [12]. Mutational analyses of these genes have shown they are involved in phenotypic tolerance in vivo and in vitro to three specific classes of herbicides and inhibitors of ALS activity: the sulfonylureas, imidazolinones and triazolopyrimidinesulfonanilides [ 3, 5, 13 ]. On the basis of Southern analysis using an isolated Brassica ALS genomic sequence as probe, we have previously shown that, relative to A. thaliana (one copy) and N. tabacum (two copies), B. napus probably contains a more complex genomic complement of four or more genes [ 12]. We report here the isolation of a second member of the B. napus ALS gene family as a near full-length cDNA, and propose a nomenclature for this gene (als2). A cDNA library was constructed of Brassica napus L. (cv Westar) in 2gt 11 [ 10 ] using poly(A) ÷ m R N A isolated from 5-day seedlings, and was the generous gift of Dr S. Hemmingsen (Plant Biotechnology Institute, Saskatoon). The properties of the library have been previously described [7]. The library was screened for ALShomologous cDNAs using 32p-labelled probes derived from an existing B. napus ALS sequence [12]. Recombinant inserts were recovered from 2gt l l as Eco RI fragments, and subcloned into the phagemid vector pTZ18R (PharmarciaLKB). Approximately 2.0 × 10 5 recombinant plaques from a B. napus 5-day seedling cDNA library were screened through three levels of plaque purification, resulting in the identification fthree hybridization-positive plaques of which one was chosen for further study. The approximate 2.0 kb Eco RI fragment carried by the selected recombinant phage was subcloned into the phagemid pTZ18R in both orientations, yielding pBI-283 and pBI-284. The sequencing strategy and corresponding complete nucleotide sequence for the recombinant pBI-283 insert is shown in Figs 1A and 1B respectively. The recombinant insert

Data on draft genome sequence of chickpea (Cicer arietinum)

The dataset contains genome sequence of the ~738 Mb chickpea genome from CDC Frontier, a kabuli variety, which contains an estimated 28,269 genes. Re-sequencing and analysis of 90 cultivated and wild genotypes from 10 different countries identifies both targets of breeding-associated genetic sweeps and targets of breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main classes of cultivated chickpea- desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding, and provide insights into both genome diversity and domestication. GBrowse Visualization Links: Chickpea genome at LIS Research Article