Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

Abstract

Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15–20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue >2.1×10–6) with wide phenotypic variance (PV) range (5.81–90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.

Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

“…Majority of the genotypes from hypogaea subspecies were grouped together in Cluster-II, both the subspecies i.e., hypogaea and fastigiata genotypes in Cluster-III and genotypes of fastigiata subspecies in Cluster-IV. The grouping of different subspecies genotypes using the SNP array was found much better than the earlier studies conducted with SSR and DArT genotyping on the same germplasm set2627.…”

Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

“…Indeed, four of the accessions screened in this study were chosen from the United States peanut minicore collection. Previous minicore screens have also shown that there is huge variability for traits such as water use efficiency (Singh et al 2014), oil content (Wang et al 2011a,b), bacterial wilt disease (Jiang et al 2014), resistance to abiotic and biotic stresses (Upadhyaya et al 2013), and agronomic traits (Pandey et al 2014). Sufficient variation has been identified among tetraploid accessions through transcriptome sequencing for performing QTL analysis with high density marker linkage maps.…”

“…Evaluation has demonstrated significant phenotypic diversity for numerous traits, including resistance to leaf spots, tomato spotted wilt virus, other biotic stresses, for tolerance to drought or heat stress, and for early maturity (Isleib et al 1995; Anderson et al 1996; Upadhyaya 2003, 2005, Upadhyaya et al 2006a,b; Selvaraj et al 2011; Wang et al 2011a; Jiang et al 2014; Pandey et al 2014; Singh et al 2014). To date, these have not been accompanied by molecular characterization at SNP levels.…”

Identification of two major quantitative trait locus for fresh seed dormancy using the diversity arrays technology and diversity arrays technology‐seq based genetic map in Spanish‐type peanuts

“…The method of genotyping with DArT is explained in detail in Pandey et al. () and at http://www.diversityarrays.com/dart-application. The DArT‐seq method next‐generation sequencing (NGS) platform, deploys sequencing of the representations to achieve higher marker densities for conducting high‐resolution genetic and trait mapping.…”

“…More recently, the DArT markers were deployed for genome‐wide association studies (GWAS) in peanut, leading to the identification of 524 marker–trait associations for 50 agronomical traits in peanut (Pandey et al. ). Therefore, the present study has deployed DArT and next‐generation sequencing (NGS)‐based DArT platform called as DArT‐seq, for mapping FSD in the F 2 mapping population.…”