SNP Markers and Their Impact on Plant Breeding

Abstract

The use of molecular markers has revolutionized the pace and precision of plant genetic analysis which in turn facilitated the implementation of molecular breeding of crops. The last three decades have seen tremendous advances in the evolution of marker systems and the respective detection platforms. Markers based on single nucleotide polymorphisms (SNPs) have rapidly gained the center stage of molecular genetics during the recent years due to their abundance in the genomes and their amenability for high-throughput detection formats and platforms. Computational approaches dominate SNP discovery methods due to the ever-increasing sequence information in public databases; however, complex genomes pose special challenges in the identification of informative SNPs warranting alternative strategies in those crops. Many genotyping platforms and chemistries have become available making the use of SNPs even more attractive and efficient. This paper provides a review of historical and current efforts in the development, validation, and application of SNP markers in QTL/gene discovery and plant breeding by discussing key experimental strategies and cases exemplifying their impact.

Applications of molecular markers for bacterial blight resistant varieties in rice (Oryza sativa L.)

“…The variation between two individual it's because of addition/deletion/ substitution of bases. The number of markers is highly abundant as compared to other markers system as a result polymorphism rate is high; detection and assay of SNP automated allows large scale genotyping at a short time (Mammadov et al, 2012). The details of SNP marker of rice are available in OryzaSNP and it needs minimum quantity of DNA, automation of genotype and largest amount of DNA polymorphism (Huq et al, 2016;kurokawa et al, 2016).…”

Applications and challenges of next-generation sequencing in Brassica species

“…Davey et al (2011) reviewed genome-wide marker discovery using NGS in both model organisms and non-model species via reduced representation sequencing methods, including reduced representation libraries (RRLs), complexity reduction of polymorphic sequences (CRoPS) and restriction site-associated DNA sequencing (RAD-seq). The development, validation and application of SNPs had been reviewed systematically (Mammadov et al 2012). Freely available software including SGSAutoSNP ) enable rapid, high-throughput, accurate SNP discovery that can be applied to any species with available NGS data.…”

“…In this case, Brassica unigene sequences were used as a reference and aligned with sequence reads using MAQ software to discover SNPs. In total, 23,330-42,593 putative SNPs with different read depth were detected, and ~90 % of the SNPs detected were termed as hemi-SNPs, which were homozygous in one line but heterozygous in the other line (Mammadov et al 2012). The hemi-SNPs between these two lines could be used for genetic mapping.…”

“…At the same time, 26 out of 31 SNPs (84 %) in 16 RAD clusters were validated by Sanger sequencing (Bus et al 2012). This is simple and effective in genetic mapping, but is limited for genomewide association studies (GwAS) due to the small number of markers (Mammadov et al 2012). …”

KASP^TM genotyping technology and its use in gene­tic-breeding programs (a study of maize)

“…ïðîïóñêíîþ çäàòí³ñòþ é â³äíîñíî íèçüêîìó ð³âíþ ïîìèëêè ãåíîòèïóâàííÿ [2,3], SNP-ìàðêåðè ñòàëè ïîòóaeíèì ³íñòðóìåíòîì äëÿ áàãàòüîõ ãåíåòè÷íèõ ³ ñåëåêö³éíèõ ïðîãðàì, âêëþ÷àþ÷è õàðàêòåðèñòèêó çàðîäêîâî¿ ïëàç-ìè (äîñë³äaeåííÿ ãåíåòè÷íî¿ ð³çíîìàí³òíîñò³, ãåíåòè÷íî¿ ñïîð³äíåíîñò³, ñòðóêòóðè ïîïóëÿ-ö³é), àíàë³ç êîíòðîëþ ÿêîñò³ (àíãë. quality control analysis) (âèçíà÷åííÿ ãåíåòè÷íî¿ ³äåí-òè÷íîñò³, ãåíåòè÷íî¿ ÷èñòîòè, ïåðåâ³ðêà ïî-õîäaeåííÿ), êàðòóâàííÿ ëîêóñ³â ê³ëüê³ñíî¿ îçíàêè (àíãë.…”