Utility of SSRs for Determining Genetic Similarities an Relationships in Maize Using an Agarose Gel System

TLDR

Maize breeders need to preserve genetic diversity, but traditional markers such as RFLPs and isozymes are limited and labor‑intensive, so SSRs resolved on agarose gels offer a cost‑effective alternative. The study genotyped 94 elite inbred lines from Corn Belt and Southern Dent races at 70 SSR loci on agarose gels, yielding 365 alleles that were used to compute genetic similarities. SSR polymorphisms reproduced known pedigrees, clustered the lines into nine groups matching heterotic classes, allowed unique fingerprints with as few as five loci, and proved as useful or superior to RFLPs for diversity assessment, heterotic assignment, and fingerprinting.

Abstract

Among maize ( Zea maize L.) breeders, there is a heightened awareness of the necessity for both maintaining genetic diversity for crop improvement and improving the quality of genetic resource management. Restriction fragment length polymorphisms (RFLPs) and isozymes can serve as genetic markers for estimating divergence or diversity; however, the limited number of polymorphic isozyme loci available and the labor intensive and time consuming nature of RFLPs make their use for this purpose prohibitive. Simple sequence repeats (SSRs), when resolved using agarose gels, may be a viable and costeffective alternative to RFLPs and isozymes. Ninety‐four elite maize inbred lines, representative of the genetic diversity among lines derived from the Corn Belt Dent and Southern Dent maize races, were assayed for polymorphism at 70 SSR marker loci using agarose gels. The 365 alleles identified served as raw data for estimating genetic similarities among these lines. The patterns of genetic divergence revealed by the SSR polymorphisms were consistent with known pedigrees. A cluster analysis placed the inbred lines in nine clusters that correspond to major heterotic groups or market classes for North American maize. A unique fingerprint for each inbred line could be obtained from as few as five SSR loci. The utility of polymerase chain reaction (PCR)‐based markers such as SSRs for measuring genetic diversity, for assigning lines to heterotic groups and for genetic fingerprinting equals or exceeds that of RFLP markers, a property that may prove a valuable asset for a maize breeding program.