**Abstract**

Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

**Keywords:** single nucleotide polymorphisms, molecular breeding, plant germplasm screening, molecular marker, marker assisted selection

## **1. Introduction**

Plant breeders usually screen a large number of plants for traits of economic value as determined by the breeding goal which may include breeding for resistance, biofortification to increase some micronutrients and gene pyramiding. The larger volume of plants screened at early stages of a breeding program can be laborious, capital intensive and time consuming. Germplasm screening is usually an initial step for a number of breeding programs. The aim of screening large collection of plants is for narrowing on those with desired characteristic for advancement to the next stage. It is extremely important to get it right from the beginning in other to meet breeding objectives for crop improvement.

Recently, molecular breeding has brought about a revolution in plant breeding and has been widely applied in plant improvement programs. Molecular breeding also called marker assisted breeding or marker assisted selection (MAS) is the method of using molecular or DNA markers that are closely linked to a phenotype to aid selection for such trait in a breeding scheme. A number of molecular markers have been developed and successfully used in selection due to their association with a phenotype of interest in different plant species. Thus, they have been applied in plant germplasm screening for desirable traits. Because selection is based on target

genes, they provide a higher rate of accuracy during screening, reduce time and labor, therefore bringing about reduced cost.

Several types of molecular markers have been applied to different areas of plant breeding, firstly developed markers include Restriction fragment length polymorphism (RFLPs) and Randomly amplified polymorphic DNA (RAPDs). These gave way to the popular techniques Amplified fragment polymorphism (AFLP) and Simple sequence repeats (SSRs) due to their ease in detection and automation. Simple sequence repeats have been extensively applied to screen for resistant germplasms, biotic and abiotic stress and variety identification in potato, groundnut rice [1–3]. SSR markers are generally PCR-based, their technicality is simple and relatively cheap. The disadvantage of these markers is that they require polyacrylamide gel electrophoresis to achieve a high resolution of allele fragments, which is laborious to perform. They give information about a single locus per assay although multiplexing of more than two markers is possible, it is relatively expensive. The continued automation in sequencing technology has resulted in a shift from first generation DNA based markers to the use of functional and gene targeted single nucleotide polymorphism (SNP) markers. Therefore, this chapter covers ways of discovering new SNPs and their conversion to molecular marker. Also, different methods of SNPs genotyping and their application in some aspects of crop improvement are documented. The discovery of SNP markers is cost effective, it is highly multiplexable and they are availability of high throughput technologies for SNP genotyping. Because SNPs are based on target genes, they are highly reliable in cultivar identification and germplasm screening.
