Peggy Ozias-Akins

Peggy Ozias-Akins
University of Georgia | UGA · Department of Horticulture

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318
Publications
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Publications

Publications (318)
Article
Background: Engineering apomixis in sexually reproducing plants has been long desired because of the potential to fix hybrid vigor. Validating the functionality of genes originated from apomictic species that contribute to apomixis upon transfer to sexually reproducing species is an important step. The PsASGR-BABYBOOM-like (PsASGR-BBML) gene from...
Article
Full-text available
Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core...
Article
Full-text available
Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae . However, less progress has been made for A. flavus . As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL...
Article
Full-text available
Key message: Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection. Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the g...
Article
Full-text available
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...
Article
Full-text available
Key message 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. Abstract Stem rot in peanut (Arachis hypogaea) is caused by the Sclerotium rolfsii and can result in great econom...
Article
Full-text available
Cultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of...
Article
Apomixis or asexual reproduction through seeds, enables the preservation of hybrid vigor. Hybrids are heterozygous and segregate for genotype and phenotype upon sexual reproduction. While apomixis, that is, clonal reproduction, is intuitively antithetical to diversity, it is rarely obligate and actually provides a mechanism to recover and maintain...
Article
Developing markers linked to key traits has been a focus of peanut genomics in the post‐genome era. Multiple disease resistance traits have been found to be qualitative and controlled by major quantitative trait loci (QTL) or even single genes while others are more complex. Southern stem rot (stem rot in short) is a devastating disease of peanut ca...
Article
Full-text available
Pod and seed size are important characteristics for the peanut industry and have been under strong selection pressure since peanut domestication. In order to dissect the genetic control of peanut pod and seed size, a recombinant inbred mapping population from a cross of Florida-07 by GP-NC WS 16 was used to determine the genomic regions associated...
Article
Full-text available
Multi-parental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomics regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were u...
Article
Full-text available
Background Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To broaden the genetic variation in future breeding programs, it is necessary to characterize germplasm accessions for new sources o...
Article
Full-text available
Root-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance allel...
Preprint
Full-text available
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...
Article
Full-text available
Early and late leaf spots (LLSs) are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resista...
Preprint
Background Tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) are three serious peanut diseases in the United States, causing tens of millions of dollars of annual economic losses. However, the genes underlying resistance to those diseases in peanut have not been well studied. We conducted a genome-wide association study (GW...
Article
Full-text available
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...
Preprint
Full-text available
Early and late leaf spots are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resistance in...
Article
Full-text available
Cultivated peanut (Arachis hypogaea L.) is an economically important crop grown around the world. Compared with the entire Arachis genus, cultivated peanut germplasm has low levels of genetic diversity for several economically important traits, resulting in the need for alternative sources of favorable alleles. Wild diploid species of Arachis are a...
Article
Full-text available
Single nucleotide polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and codominant. However, the discovery of true SNPs in polyploid species is difficult. Peanut (Arachis hypogaea L.) is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Axio...
Article
Full-text available
Parthenogenesis is the spontaneous development of an embryo from an unfertilized egg cell. It naturally occurs in a variety of plant and animal species. In plants, parthenogenesis usually is found in combination with apomeiosis (the omission of meiosis) and pseudogamous or autonomous (with or without central cell fertilization) endosperm formation,...
Article
Full-text available
Peanut is one of the most common food triggers of fatal anaphylaxis worldwide although peanut allergy affects only 1‐2% of the general population. Peanuts are the source of highly potent allergenic proteins. It is emerging that the allergenicity of certain proteins is linked to their biological function. Peanut is an unusual crop in that it flowers...
Data
Figure S3 Frequency histogram of the percentage of missing data points in WGRS of 91 RILs with 16 674 polymorphic SNPs in the population.
Data
Figure S4 Distribution of markers on linkage groups.
Data
Figure S6 Genetic and QTL map of major QTLs (>10% PVE) comprising SNP and SSR markers in Tifrunner × GT‐C20 population in peanut (Pandey et al., 2017a).
Data
Figure S2 Percentage reads mapped to the diploid reference A‐ and B‐genome in each RIL and the two parents.
Data
Figure S5 QTL maps showing the major QTL peaks at different LODs on vertical axis.
Data
Table S1 Phenotypic variation of diseases (ELS, LLS and TSWV) in T‐population parents and RILs. Table S2 Overview of the WGRS data and alignment to the reference genome. Table S3 Summary of SNPs detected between Tifrunner and GT‐C20 and SNPs used in RIL population. Table S4 Number of homeologus and translocated markers. Table S5 Effect of major...
Data
Figure S1 Phenotypic distribution of ELS, LLS and TSWV in T‐pop RILs during different seasons.
Article
Full-text available
Background Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled b...
Article
Full-text available
Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs) are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads...
Article
Full-text available
Nat. Biotechnol. 35, 969–976 (2017); published online 18 September 2017; corrected after print 28 February 2018 In the version of this article initially published, in the HTML, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML version of the article.
Article
Full-text available
Whole genome re‐sequencing (WGRS) of mapping populations has facilitated development of high‐density genetic linkage maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases...
Data
The package 'keggseq' was developed to apply KEGG enrichment analysis mainly for ployploids utilizing their sub-genomes. ‘keggseq’ provides some advantages over the available tools (https://github.com/w-korani/keggseq): It allows applying KEGG enrichment analysis for diploids or ployploids with any levels of gene duplications. It generates ready-to...
Article
Full-text available
Post-harvest aflatoxin contamination is a challenging issue that affects peanut quality. Aflatoxin is produced by fungi belonging to the Aspergilli group, and is known as an acutely toxic, carcinogenic and immune-suppressing class of mycotoxins. Evidence for several host genetic factors that may impact aflatoxin contamination has been reported,e.g....
Article
Full-text available
Single Nucleotide Polymorphisms (SNPs) have many advantages as molecular markers since they are ubiquitous and co-dominant. However, the discovery of true SNPs especially in polyploid species is difficult. Peanut is an allopolyploid, which has a very low rate of true SNP calling. A large set of true and false SNPs identified from the Arachis 58k Af...
Article
Full-text available
Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). 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 allotetraploi...
Poster
Full-text available
Improving seed quality traits is one of the most important goals in peanut breeding. Since many of these traits are relatively difficult to phenotype, an alternative indirect selection by markers is needed. Yet, peanut has very low degree of polymorphism especially among cultivated varieties that hindered the development of mapping tools. The aim o...
Chapter
Peanut or groundnut (Arachis hypogaea), an allotetraploid species, recently became the focus of a global genomics initiative with the goal of developing genome-wide molecular resources to facilitate breeding. Publicly available reference genome sequence of peanut’s diploid progenitors (peanutbase.org) is enabling expansion of genotyping tools for g...
Article
Full-text available
Resistance to root-knot nematode was introgressed into cultivated peanut Arachis hypogaea from a wild peanut relative, A. cardenasii and previously mapped to chromosome A09. The highly resistant recombinant inbred RIL 46 and moderately resistant RIL 48 were selected from a population with cv. Gregory (susceptible) and Tifguard (resistant) as female...
Article
Full-text available
Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses in...
Article
Full-text available
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for...
Chapter
Apomixis, commonly defined as asexual reproduction through seed, is a reproductive trait that occurs in only a few minor crops, but would be highly valuable in major crops. Apomixis results in seed-derived progenies that are genetically identical to their maternal parent. The advantage of apomixis would lie in seed propagation of elite food, feed,...
Article
‘TifNV-High O/L’ (Reg. No. CV-132, PI 680611) is a runner-type peanut (Arachis hypogaea L. subsp. hypogaea var. hypogaea) cultivar released by the USDA-ARS and the Georgia Agricultural Experiment Station in 2014. TifNV-High O/L was developed at the University of Georgia Coastal Plain Experiment Station, Tifton, GA. Our research objective was to com...
Article
Full-text available
Tifguard was released in 2008 as a peanut cultivar with a high level of resistance to Meloidogyne arenaria. Our objective was to determine the role of temperature on infection and development of M. arenaria in Tifguard compared to that in the nematode susceptible cultivar, Georgia-06G. Temperature affected the rate of nematode infection and develop...
Data
An image processing software for analyzing seed, leaf, stem, ... coverage infection, this version was designed mainly for analyze peanut seeds which infected by GFP-Aspergillus-flavus strain. The software and full description are available at: https://github.com/w-korani/SICIA.
Data
An extended image processing software of SICIA version I for analyzing seed, leaf, stem, ... coverage infection, SICIA-I was designed mainly for peanut seeds which infected by GFP-Aspergillus-flavus strain. However, this version (SICIA-II) is suitable for a large application, for other species and other methods of infection. The software and full d...
Article
Full-text available
Aflatoxin contamination is a major economic and food safety concern for the peanut industry that largely could be mitigated by genetic resistance. To screen peanut for aflatoxin resistance, ten genotypes were infected with a green fluorescent protein (GFP)—expressing Aspergillus flavus strain. Percentages of fungal infected area and fungal GFP sign...