Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis

Abstract

Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2–10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of “K” genome, although distinct from both the “A” and “B” genomes, but more similar to “B” genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.

Translational genomics for achieving higher genetic gains in groundnut

“…The IPGI-led diploid genomes of A. duranensis (A genome) and A. ipaensis (B genome) were mined for SSRs leading to identification of 135,529 and 199,957 SSRs, respectively (Zhao et al 2017). Further comparative diploid genome analysis with each other also identified 515,223 InDels, i.e., 269,973 insertions and 245,250 deletions by comparing A. duranensis with A. ipaënsis (Vishwakarma et al 2017b). The genome sequence can also be used as reference genome for The developed genetic markers can be used in various purposes for enhancing breeding efficiency such as molecular breeding product development as well as in ensuring genetic purity in seed chain 1 3 single nucleotide polymorphism (SNP) calling which are the most abundant structural variation across the genome.…”

Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut (Arachis hypogaea L.)

“…Availability of reference genome and high density genotyping assay are the most important milestones for understanding genome architecture, trait mapping, gene discovery, and molecular breeding (Varshney et al, 2013). The major genomic resources that have been developed in recent years include 1) reference genome of cultivated tetraploid (Bertioli et al, 2019;Chen et al, 2019;Zhuang et al, 2019); 2) reference genome of allotetraploid wild groundnut, Arachis monticola (Yin et al, 2018); 3) reference genomes of diploid progenitors of cultivated groundnut i.e., A. duranensis (Bertioli et al, 2016;Chen et al, 2016) and A. ipaensis (Bertioli et al, 2016;Lu et al, 2018); 4) "Axiom_Arachis" array, a high density genotyping assay with >58K highly informative SNPs (Pandey et al, 2017a); 5) gene expression atlas for cultivated tetraploid (Clevenger et al, 2016); 6) molecular/ genetic markers (Pandey et al, 2016;Pandey et al, 2017a;Vishwakarma et al, 2017;Zhao et al, 2017;Lu et al, 2019;Pandey et al, 2019b;Pandey et al, 2019c); and 7) diverse genetic populations such as MAGIC and nested association mapping (NAM) populations to conduct high resolution genetic mapping and breeding (Pandey et al, 2017a;Pandey et al, 2017b;Pandey et al, 2017c); and 8) trait linked diagnostic markers for use in genomics-assisted breeding (GAB) (Pandey et al, 2017c). As a result, the next-generation sequencing based trait discovery (Pandey et al, 2017b) and sequence-based breeding (Varshney et al, 2019) will enhance breeding speed and precision for greater genetic gains.…”

Groundnut Entered Post-genome Sequencing Era: Opportunities and Challenges in Translating Genomic Information from Genome to Field

“…There has been tremendous progress in the development of genomic resources for peanut over the last decade, and details of these resources have been reviewed time to time (see Pandey et al 2012Pandey et al , 2014Varshney et al 2013;Ozias-Akins et al 2017;Vishwakarma et al 2017a). Six major resources are very useful for peanut research community including (i) reference genome of diploid progenitor species, i.e., Arachis duranensis (Bertioli et al 2016;Chen et al 2016) and A. ipaensis of cultivated groundnut (Bertioli et al 2016), (ii) high-density genotyping array "Axiom_ Arachis" with >58 K highly informative single nucleotide polymorphisms (SNPs) (Pandey et al 2017a), (iii) gene expression atlas (Clevenger et al 2016), (iv) genome-wide simple sequence repeat (SSR) and insertion/deletion markers (Zhao et al 2017;Vishwakarma et al 2017b), (v) next-generation genetic populations for high-resolution genetic mapping and breeding (see Pandey et al 2016), and (vi) trait-linked diagnostic markers for use in GAB (see Vishwakarma et al 2017a).…”