Question

Case 2: In Ghana, cowpea is a legume plant that is a significant source of nutrition for people in this country. Attempts are being made to improve the yield and hardiness of this plant through a national crop improvement program. What has complicated this effort is the existence of several different collections of cowpea seeds. (Oppong-Konadu E, Akromah I, and Adu-Dapaah O. 2005. African Crop Science Journal 13:117-123) 1. How would you use protein analysis via SDS-polyacrylamide gel electrophoresis to sort through these collections so that duplicates could be eliminated and the remaining specimens could be sorted into subgroups that could then be further studied for properties of value in crop improvement

Answer 1

It is expected that accessions/lines that exhibit the same bands in SDS-PAGE are phylogenetically similar (or even identical, duplicated, accessions) and therefore they can be removed when developing a core collection of germplasm. Subsequently, the accessions of the core collection can be clustered into subgroups (subpopulations) based on the distances observed between lines, reflected by different protein band patterns observed in SDS-PAGE. It is expected that these subpopulations adequately contain the genetic diversity of the core collection (useful in breeding programs).

Step-by-step explanation:

SDS-PAGE (sodium dodecyl sulphate–polyacrylamide gel electrophoresis), is a technique widely used in molecular biology to separate proteins based on their molecular weights. In crop improvement programs, this information can result useful to identify accession lines and develop core collections. A core collection is a limited set of lines or accessions/varieties obtained from a large germplasm collection that is expected to contain the genetic diversity of crop species. In this case, cowpea lines that exhibit the same bands in SDS - PAGE are expected to be phylogenetically similar (or even identical/duplicated accessions), thereby these lines can be removed in order to conserve one accession in the core collection. Subsequently, the remaining lines can be classified by a phenogram based on distance measures clustered by UPGMA (unweighted pair group method with arithmetic mean). This cluster analysis enables the construction of a phylogenetic tree from a distance matrix based on protein patterns in SDS-PAGE, thereby obtaining subpopulations (clusters) which will be useful in breeding programs.