NEW YORK (GenomeWeb News) – In a paper scheduled to appear online this week in the Proceedings of the National Academy of Sciences, international researchers reported that they have developed a high-density consensus linkage map for the legume Vigna unguiculata, commonly known as cowpea.
A team of researchers from the US, Nigeria, and Senegal integrated sequence data on nearly 200,000 expressed sequence tags, identifying thousands of possible genetic markers. After weeding through these, they developed an array that evaluated about 1,500 of the markers. By genotyping almost 1,000 plants from six cowpea lines, the team came up with a genetic map that they then compared with genetic resources for a few other legume and non-legume plants.
"[W]e report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes," senior author Timothy Close, a plant science researcher at the University of California at Riverside, and his colleagues wrote.
Cowpea is a legume grown on several continents, but particularly important in parts of sub-Saharan Africa. Despite it's importance to income and food security in some parts of the developing world, cowpea is considered an orphan crop for which few genetic or genomic resources have been developed so far, the team noted, though past studies have identified 11 cowpea linkage groups.
Close and his team argued that cowpea may prove useful as a model legume in the future, since it can withstand drought, heat, low soil fertility and other stresses that are deleterious to other crop plants
As such, they set about developing cowpea genetic resources, using the Sanger approach to sequence 141,538 ESTs from 11 cowpea complementary DNA libraries. After incorporating ESTs sequenced by others, the team had information from 183,118 cowpea ESTs.
From these, the researchers found roughly 10,000 high-confidence SNPs — 1,536 of which were used to develop an Illumina Golden Gate genotype array for cowpea.
When the researchers applied this array to 742 recombinant inbred cowpea lines from six populations, they found that 1,375 of the SNPs — about 90 percent — appeared to be dependable cowpea genetic markers. The team then integrated 928 of the markers into a consensus cowpea genetic linkage map.
The researchers also annotated 921 cowpea genes based on comparisons between the cowpea genetic map and genetic information from the better-characterized soybean, a related legume.
Next, the team compared the cowpea map to soybean, the legume model Medicago trunculata, and the higher plant model Arabidopsis. They reported that cowpea shared between 82 percent and 85 percent macrosynteny and extensive microsynteny with soybeans and M. trunculata. On the other hand, widespread rearrangements were apparent when they compared cowpea with Arabidopsis, although they did see some microsynteny between the two.
"EST-derived SNP markers provide an additional level of utility in genomic studies because they tag actual genes that, when incorporated into genetic maps, may be used for synteny-based cross-genome comparison," the researchers wrote.
In the future, they predict, the cowpea linkage map will be useful not only for comparing cowpea to other plants but also for understanding different cowpea populations and improving cowpea breeding and selection.