The first genetic map for a psoraleoid legume (Bituminaria bituminosa) reveals highly conserved synteny with phaseoloid legumes

We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes.This research was funded by the Future Farm Industries Cooperative Research Centre (FFI CRC), Department of Primary industries and Regional development (DPIRD) and Meat & Livestock Australia (MLA). This research was supported in part by the US Department of Agriculture, Agricultural Research Service, project 5030-21000-069-00D. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and Employer. AGRF is supported by the Australian Government NCRIS initiative through Bioplatforms Australia

Tedera: From a Promising Novel Species to a Commercial Pasture Option for Mediterranean Southern Australia

Tedera (Bituminaria bituminosa var. albomarginata and var. crassiuscula) is a traditional forage species used for centuries in the Canary Islands (Méndez and Fernández 1990), that has increasingly attracted interest from researchers in regions with Mediterranean-type climates from Spain, Italy, Israel, Greece, Portugal, Morocco, Turkey and Australia. In 2000, Australian pasture researchers started a large and systematic screening process that evaluated about 720 species of exotic and native legumes, grasses and herbs for adaptation and productivity in Mediterranean and temperate environments (Real et al. 2011). Tedera was one of the few novel perennial legumes to show potential for domestication (Real et al. 2008; Real et al. 2011). Now an international multidisciplinary team has come together to take tedera forward towards commercial adoption by farmers in Mediterranean-type environments. This paper provides a technical update and discussion on all research aspects conducted by the tedera research team up to February 2013

Fertile allohexaploid Brassica hybrids obtained from crosses between B. oleracea and B. juncea via ovule rescue and colchicine treatment of cuttings

An allohexaploid Brassica crop (2n = AABBCC) does not exist naturally, but is of interest for its potential to combine useful traits found in the six cultivated Brassica species which share combinations of the A, B and C genomes with additional allelic heterosis. In this study, we aimed to produce 2n = AABBCC hybrids by crosses between B. juncea and a number of Brassica C genome species. We used ovule rescue to overcome hybridization barriers and different colchicine treatment methods to induce chromosome doubling of ABC hybrids to AABBCC allohexaploids, thus restoring fertility. Only the cross B. oleracea x B. juncea was successful, with six triploid hybrids produced from one genotype combination. Colchicine-containing regeneration media was unsuccessful in doubling chromosome number in these hybrids, but treatment of cuttings with 0.05 to 0.25% colchicine successfully produced 200 S-1 allohexaploid seeds. The S-1 plants produced 7-84% viable pollen and set 0-390 seeds per plant, with 23-27 bivalents and 0-3 univalents during metaphase I of meiosis. Our results highlight the difficulties in working with the wild C genome species, but showed tha t our methods have utility for producing euploid, chromosome-doubled progeny in this cross combination. Further, Brassica oleracea x B. juncea allohexaploid hybrids may contain useful genetic factors for improved meiotic stability and fertility in allohexaploid germplasm pools.Key message Ovule rescue followed by 0.05-0.25% colchicine treatment of cuttings successfully produces fertile, partially stable allohexaploid Brassica from the cross B. juncea x B. oleracea

Centromere locations in brassica A and C genomes revealed through half-tetrad analysis

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate

Resistance gene analogs in the brassicaceae: Identification, characterization, distribution, and evolution

The Brassicaceae consists of a wide range of species, including important Brassica crop species and the model plant Arabidopsis (Arabidopsis thaliana). Brassica spp. crop diseases impose significant yield losses annually. A major way to reduce susceptibility to disease is the selection in breeding for resistance gene analogs (RGAs). Nucleotide binding site-leucine rich repeats (NLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are the main types of RGAs; they contain conserved domains and motifs and play specific roles in resistance to pathogens. Here, all classes of RGAs have been identified using annotation and assembly-based pipelines in all available genome annotations from the Brassicaceae, including multiple genome assemblies of the same species where available (total of 32 genomes). The number of RGAs, based on genome annotations, varies within and between species. In total 34,065 RGAs were identified, with the majority being RLKs (21,691), then NLRs (8,588) and RLPs (3,786). Analysis of the RGA protein sequences revealed a high level of sequence identity, whereby 99.43% of RGAs fell into several orthogroups. This study establishes a resource for the identification and characterization of RGAs in the Brassicaceae and provides a framework for further studies of RGAs for an ultimate goal of assisting breeders in improving resistance to plant disease

Trigenomic Bridges for Brassica Improvement

We introduce and review Brassica crop improvement via trigenomic bridges. Six economically important Brassica species share three major genomes (A, B, and C), which are arranged in diploid (AA, BB, and CC) and allotetraploid (AABB, AACC, and BBCC) species in the classical triangle of U. Trigenomic bridges are Brassica interspecific hybrid plants that contain the three genomes in various combinations, either triploid (ABC), unbalanced tetraploid (e.g., AABC), pentaploid (e.g., AABCC) or hexaploid (AABBCC). Through trigenomic bridges, Brassica breeders can access all the genetic resources in the triangle of U for genetic improvement of existing species and development of new agricultural species. Each of the three Brassica genomes occurs in several species, where they are distinguished as subgenomes with a tag to identify the species of origin. For example, the A subgenome in B. juncea (2n = AABB) is denoted as Aj and the A subgenome in B. napus (2n = AACC) as An. Trigenomic bridges have been used to increase genetic diversity in allopolyploid Brassica crop species, such as a new-type B. napus with subgenomes from B. rapa (Ar) and B. carinata (Cc). Recently, trigenomic bridges from several sources have been crossed together as the ‘founders’ of a potentially new allohexaploid Brassica species (AABBCC). During meiosis in a trigenomic bridge, crossovers are expected to form between homologous chromosomes of related subgenomes (for example Ar and An), but cross-overs may also occur between non-homologous chromosomes (for example between A and C genome chromosomes). Irregular meiosis is a common feature of new polyploids, and any new allotetraploid or allohexaploid Brassica genotypes derived from a trigenomic bridge must achieve meiotic stability through a process of diploidisation. New sequencing technologies, at the genomic and epigenomic level, may reveal the genetic and molecular basis of diploidization, and accelerate selection of stable allotetraploids or allohexaploids. Armed with new genetic resources from trigenomic bridges, Brassica breeders will be able to improve yield and broaden adaptation of Brassica crops to meet human demands for food and biofuel, particularly in the face of abiotic constraints caused by climate change