Advances in Arachis genomics for peanut improvement

Abstract

Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.

Assessing the genetic diversity of 48 groundnut (Arachis hypogaea L.) genotypes in the Guinea savanna agro-ecology of Ghana, using microsatellite-based markers

“…Polymerase chain reaction was performed with the 53 SSR-based primers as described by Pandey et al (2012b). The reaction was conducted in a 10 µl reaction volume containing 5 ng of genomic DNA, 0.5 µmoles of each primer, 1.0 µl 10X PCR buffer, 0.25 mM of each dNTPs, 2 mM MgCl2 and 1.0 U Taq DNA Polymerase (Sib enzyme, Russia).…”

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

“…Advances in other marker types, such as randomly amplified polymorphic DNA (RAPD) (Halward and Stalker, 1991;Halward et al, 1992), restriction fragment length polymorphism (RFLP) (Halward and Stalker, 1991;Kochert et al, 1996;Burow et al, 2009), amplified fragment length polymorphism (AFLP) (Herselman et al, 2004), simple sequence repeat (SSR) (He et al, 2003;Gimenes et al, 2007;Cuc et al, 2008;Liang et al, 2009), sequence-related amplified polymorphism (SRAP) , single strand conformational polymorphism (SSCP) (Nagy et al, 2010), and single nucleotide polymorphism (SNP) (Nagy et al, 2012), soon replaced the early exploration with proteins. During the past two decades, much effort has been made to develop genetic and genomic tools in cultivated peanut, such as construction of BAC libraries (Yuksel and Paterson, 2005;Guimarães et al, 2008), cDNA libraries (Luo et al, 2005;Proite et al, 2007;Guo et al, 2008Guo et al, , 2009Koilkonda et al, 2012), RNAseq using next generation sequencing technology (Guimaraes et al, 2012;Zhang et al, 2012) and development of DNA markers (see reviews of Feng et al, 2012;Pandey et al, 2012;Zhao et al, 2012; (Table 1). Among the various molecular markers investigated to date, simple sequence repeats (SSR) have emerged as one of the preferred DNA marker system for conducting genetic and genomic studies in cultivated peanut.…”

“…To date, 15,518 SSRs have been developed by various research groups, although some are likely to be redundant (Table 1). Several reviews have recently summarized progress in peanut genetics and genomics tool and resource development (see reviews of Feng et al, 2012;Pandey et al, 2012;Zhao et al, 2012. Feng et al (2012) reported on EST progress and application (Fig.…”

“…1). Pandey et al (2012) and reported that the last five years have witnessed accelerated expansion of genomic resources such as development of molecular markers, genetic and physical maps, generation of ESTs, development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding efforts have been initiated for several traits for development of superior genotypes (Chu et al, 2011;Pasupuleti et al, 2013).…”

“…Although it is still a challenge to assemble whole complex genome using NGS, the technology has facilitated cost-effective, large scale generation of ESTs. Since the reports of Pandey et al (2012) and Zhao et al (2012), there have been two publications of using NGS to generate EST-SSRs Guimaraes et al, 2012) (Table 1) and for SNP development (Nagy et al, 2012). Zhang et al (2012) …”