Genetic diversity of peanut (Arachis hypogaeaL.) and its wild relatives based on the analysis of hypervariable regions of the genome

Moretzsohn, Márcio de Carvalho; Hopkins, M. S.; Mitchell, Sharon E.; Kresovich, Stephen; Valls, José Francisco Montenegro; Ferreira, Márcio Elias

doi:10.1186/1471-2229-4-11

Cited by 179 publications

(88 citation statements)

References 52 publications

(53 reference statements)

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“…This attribute was not found in any cultivated groundnut and is conceived as a naive feature in the genus. These observations affirm the possibility that A. monticola is the immediate wild ancestor or an introgressive derivative between the A. hypogaea and wild species as reported in earlier studies (Gregory and Gregory, 1976; Moretzsohn et al, 2004; Koppolu et al, 2010). …”

Section: Discussionsupporting

confidence: 89%

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

et al. 2017

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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.

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Section: Discussionsupporting

confidence: 89%

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

et al. 2017

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“…Peanut is widely grown and ranks fifth among the world oil production crops (Moretzsohn et al 2004). To gain insight into the complex mechanisms of peanut fatty acid biosynthesis, it is a prerequisite to isolate and characterize the ACCase genes.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of Putative Acetyl-CoA Carboxylases in Arachis hypogaea L.

Xia

Zhao

et al. 2009

Plant Mol Biol Rep

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Candidate genes of multisubunit (MS) and multifunctional (MF) acetyl-CoA carboxylase (ACCase) including accB1, accB2, accC, accA, accD, and MF-ACCase were isolated from peanut by sequencing a full-length cDNA library and homology-based cloning. Primary structures of peanut ACCases were highly conserved, especially biochemical function domains, compared with other higher plants and Escherichia coli. The numbers of homologs of each ACCase gene expressed in developing seed of peanut varied from two to five. Two editing sites of peanut accD were identified by comparing genomic DNA and its corresponding cDNAs. The MS-ACCase of Arachis hypogaea and Arabidopsis thaliana shared a conservative structure of gene organization. Semiquantitative reverse transcription polymerase chain reaction analysis indicated that MS-ACCase and MF-ACCase genes were expressed in all peanut tissues examined, but their mRNA expression level were quite different. In peanut seed development, accC, accA, accD, and MF-ACCase mRNAs were expressed strongly at 60 days after pegging.

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“…However, our knowledge of the origin of cultivated peanut is limited compared with other major crops. More than eight diploid species having either the A- or B- genome have been considered to be involved in the origin of peanut (Norden 1973; Gregory and Gregory 1976; Kochert et al 1991, 1996; Fernandez and Krapovickas 1994; Krapovickas and Gregory 1994; Lavia 1998; Raina and Mukai 1999; Raina et al 2001; Moretzsohn et al 2004; Seijo et al 2007; Bertioli et al 2011). More recently, Seijo et al (2007) and Bertioli et al (2011, 2016) provided stronger evidence of A. duranensis and A. ipaënsis being the progenitor species of modern cultivars.…”

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confidence: 99%

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

Chopra

Burow

Simpson³

et al. 2016

G3 Genes|Genomes|Genetics

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To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

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Genetic diversity of peanut (Arachis hypogaeaL.) and its wild relatives based on the analysis of hypervariable regions of the genome

Cited by 179 publications

References 52 publications

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

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

Isolation and Characterization of Putative Acetyl-CoA Carboxylases in Arachis hypogaea L.

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

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