Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management.

Premise: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification.

Variation in cytonuclear expression accommodation among allopolyploid plants.

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution.

Spontaneous generation of diversity in Arachis neopolyploids (Arachis ipaënsis × Arachis duranensis)4x replays the early stages of peanut evolution.

Polyploidy is considered a driving force in plant evolution and domestication. Although in the genus Arachis, several diploid species were traditionally cultivated for their seeds, only the allotetraploid peanut Arachis hypogaea became the successful, widely spread legume crop. This suggests that polyploidy has given selective advantage for domestication of peanut.

Brazilian Kayabi Indian accessions of peanut, Arachis hypogaea (Fabales, Fabaceae): origin, diversity and evolution.

Peanut is a crop of the Kayabi tribe, inhabiting the Xingu Indigenous Park, Brazil. Morphological analysis of Xingu accessions showed variation exceeding that described for cultivated peanuts. This raised questions as to the origin of the Xingu accessions: are they derived from different species, or is their diversity a result of different evolutionary and selection processes? To answer these questions, cytogenetic and genotyping analyses were conducted.

Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences.

Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements.

Mapping quantitative trait loci (QTLs) and estimating the epistasis controlling stem rot resistance in cultivated peanut (Arachis hypogaea).

A total of 33 additive stem rot QTLs were identified in peanut genome with nine of them consistently detected in multiple years or locations. And 12 pairs of epistatic QTLs were firstly reported for peanut stem rot disease. Stem rot in peanut (Arachis hypogaea) is caused by the Sclerotium rolfsii and can result in great economic loss during production.

The genome sequence of segmental allotetraploid peanut Arachis hypogaea.

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination).

Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA.

The most conspicuous difference among chromosomes and genomes in Arachis species, the patterns of heterochromatin, was mainly modeled by differential amplification of different members of one superfamily of satellite DNAs. Divergence in repetitive DNA is a primary driving force for genome and chromosome evolution. Section Arachis is karyotypically diverse and has six different genomes.

Mapping Late Leaf Spot Resistance in Peanut () Using QTL-seq Reveals Markers for Marker-Assisted Selection.

Late leaf spot (LLS; ) is a major fungal disease of cultivated peanut (). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs.

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

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array 'Axiom_Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study.

Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants.

Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNA-Seq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants.

Tetrasomic recombination is surprisingly frequent in allotetraploid Arachis.

Arachis hypogaea L. (cultivated peanut) is an allotetraploid (2n = 4x = 40) with an AABB genome type. Based on cytogenetic studies it has been assumed that peanut and wild-derived induced AABB allotetraploids have classic allotetraploid genetic behavior with diploid-like disomic recombination only between homologous chromosomes, at the exclusion of recombination between homeologous chromosomes.

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.

Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole-genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms (SNPs) have become popular tools for genetic mapping, discovery and application of SNPs in polyploids has been difficult.

Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance.

Background: Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean.

A reference genome for common bean and genome-wide analysis of dual domestications.

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules.

The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833.

Subtelomeric regions in eukaryotic organisms are known for harboring species-specific tandemly repeated satellite sequences. However, studies on the molecular organization and evolution of subtelomeric repeats are scarce, especially in plants. Khipu is a satellite DNA of 528-bp repeat unit, specific of the Phaseolus genus, with a subtelomeric distribution in common bean, P.

Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.).

Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions.

Nucleotide diversity patterns at the drought-related DREB2 encoding genes in wild and cultivated common bean (Phaseolus vulgaris L.).

Common beans are an important food legume faced with a series of abiotic stresses the most severe of which is drought. The crop is interesting as a model for the analysis of gene phylogenies due to its domestication process, race structure, and origins in a group of wild common beans found along the South American Andes and the region of Mesoamerica. Meanwhile, the DREB2 transcription factors have been implicated in controlling non-ABA dependent responses to drought stress.

Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series.

Background: Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants.

Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers.

Background: Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption and the goal of this study was to integrate a recently constructed physical map for the species with a microsatellite based genetic map using a BAC library from the genotype G19833 and the recombinant inbred line population DOR364 x G19833.

Results: We searched for simple sequence repeats (SSRs) in the 89,017 BAC-end sequences (BES) from the physical map and genetically mapped any polymorphic BES-SSRs onto the genetic map.