Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

Abstract

The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.Key Words: Arachis hypogaea, Arachis species, genomics, genetic maps, molecular markers, molecular breeding, Peanut Genome Consortium (PGC).The world's population is predicted to reach nine billion by 2050 (Nature Editorial, 2010), which means greater demand for food, hence, a continuing need to produce improved cultivars of crop plants. Advances in food production will require greater efforts in agricultural research to increase crop yield with improved genetics for plant protection from biotic and abiotic stresses. Agricultural biotechnology is one tool that holds great promise for sustainability of agricultural production and feeding an ever increasing population.Peanut (Arachis hypogaea L.), or groundnut, is one of the major economically important legumes that is cultivated worldwide for its ability to grow in semi-arid environments with relatively low inputs of chemical fertilizers. On a global basis, peanut also is a major source of protein and vegetable oil for human nutrition, containing about 28% protein, 50% oil and 18% carbohydrates. Peanut is cultivated in more than 100 countries in Asia, Africa and the Americas, grown mostly by resource-limited farmers of the semi-arid regions. India and China together produce almost twothirds of the world's peanuts, and the U...

Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers

“…There was substantial diversity among cultivated peanut in morphological, physiological, agronomic traits, and at molecular levels. This study provided the resource of 111 highly informative SSR markers, which was selected from a larger available genomic pool as a community effort to develop molecular markers for peanut genetic and genomic research (Guo et al , ), and these markers could be used in the primary assessment of the diversity of breeding lines in each program.…”

“…Peanut is grown mostly in the semiarid area of the world that utilizes self‐sufficiency farming, and there is a requirement to increase the production and productivity in order to meet the demand of the increasing world population. During the years, efforts have been made to improve peanut yield, quality, disease resistance, and other agronomic traits resulting in great improvement of many traits in peanut (Guo et al ; Varshney et al ). Cultivar improvement by conventional breeding selection, intra‐specific or inter‐specific hybridization remain to play an important role in the increase of peanut yield (Tang et al ; Guo et al ).…”

“…In addition, intron‐exon splice junction (ISJ), universal rice primer (URP), and directed amplification of minisatellite region DNA (DAMD) techniques also have been used for detecting peanut polymorphisms (Xiong et al ). Among the different types of molecular markers used in peanut, SSRs have been effective and more informative in producing considerable higher polymorphic information content (PIC), and to date it is the most commonly used molecular marker in the peanut community (Guo et al ). It is notable here that one of the key factors for crop improvement efforts depends on the amount and the use of genetic variability in breeding programs.…”

High‐density genetic map using whole‐genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut

“…These foliar diseases cause yield losses of up to 70%, resulting in approximately $600 million in losses (Food and Agriculture Organization (FAO), 2004;Ogwulumba et al, 2008). While insecticides and fungicides have been used as part of an integrated pest management approach, breeding disease-resistant cultivars with high yield and good agronomic performance is the most economical and sustainable solution (Guo et al, 2013;Pandey et al, 2012;Varshney et al, 2013).…”

Establishment and evaluation of a peanut association panel and analysis of key nutritional traits

“…Over the years, breeders have aimed to improve the yield, quality, and stress resistance of cultivated peanut (Guo et al ; Wang et al ). Many breeding studies have aimed to find simple genetic polymorphisms that can explain the phenotypic variation of target traits, thereby enabling the use of marker‐assisted selection (MAS) combined with traditional methods to increase selection efficiency (Myles et al ; Guo et al ). Breeders are also making great efforts to develop novel peanut lines with high yield and high oil content.…”