Background: Microsatellite (simple sequence repeat -SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.

These authors contributed equally. SUMMARYCowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions. (2), and 90% of its genome was estimated to be repetitive DNA (3). The Ae. tauschii genome and the D genome of hexaploid wheat are closely related due to the recent origin of hexaploid wheat (4). Ae. tauschii is therefore an important resource for wheat breeding, and its genome is an invaluable reference for wheat genomics, as illustrated by the utility of its sequences in the analysis of the wheat gene space (5). The utility of Ae. tauschii for wheat genetics and genomics would be further enhanced by a high-quality draft sequence of its genome. With current technology, the only approach to produce a high-quality de novo draft sequence for a genome of this size and complexity is the orderedclone sequencing approach, which requires a physical map.Physical map construction necessitates fingerprinting multiple genome equivalents of bacterial artificial chromosome (BAC) clones, assembling them into contigs, and anchoring the contigs on a genetic map (6-8). Great strides have been made in BAC fingerprinting techniques (7, 9-12) and software for fingerprint editing and contig assembly (13-16). It is now possible with these technological advances to fingerprint and assemble contigs from hundreds of thousands of BAC clones (7,8,(17)(18)(19). In contrast, contig anchoring remains a weakness in physical mapping of large plant genomes because of their low gene density, extensive gene duplication, and abundance of repetitive DNA. BAC end sequences (BESs) are an effective means of contig anchoring in small genomes (11). In large genomes, however, hundreds of thousands of BESs are needed. DNA hybridization and PCRbased anchoring (6,7,20,21)...

No abstract