
Scott JacksonUniversity of Georgia | UGA
Scott Jackson
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Publications (269)
Introduction
Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly base...
Machine learning has demonstrated potential in analyzing large, complex biological data. In practice, however, biological information is required in addition to machine learning for successful application.
Development of next-generation crops will be enabled by combining state-of-the-art technologies with speed breeding.
Main conclusion
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...
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...
Background:
Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domestication. Interestingly, domesticated accessions have significantly higher [A] and [T] values across genome-wide polymorphic sites than...
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.
Figure S3 Frequency histogram of the percentage of missing data points in WGRS of 91 RILs with 16 674 polymorphic SNPs in the population.
Figure S4 Distribution of markers on linkage groups.
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).
Figure S2 Percentage reads mapped to the diploid reference A‐ and B‐genome in each RIL and the two parents.
Figure S5 QTL maps showing the major QTL peaks at different LODs on vertical axis.
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...
Figure S1 Phenotypic distribution of ELS, LLS and TSWV in T‐pop RILs during different seasons.
Domesticated species often exhibit convergent phenotypic evolution, termed the domestication syndrome, of which loss of seed dormancy is a component. To date, dormancy genes that contribute to parallel domestication across different families have not been reported. Here, we cloned the classical stay-green G gene from soybean and found that it contr...
Premise of the Study
The genetic bottleneck of polyploid formation can be mitigated by multiple origins, gene flow, and recombination among different lineages. In crop plants with limited origins, efforts to increase genetic diversity have limitations. Here we used lineage recombination to increase genetic diversity in peanut, an allotetraploid lik...
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...
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of m...
Most plants are polyploid due to whole genome duplications (WGD) and can thus have duplicated genes. Following a WGD, paralogs are often fractionated (lost) and few duplicate pairs remains. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high-resolution methylation maps of access...
Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a polyploidy event ~59 MYA, followed by a Glycine-specific WGD ~8-13 MYA. Duplicated genes were classified into five categories: singletons, dispersed, proximal, tandem or WGD/segmental and found strong correlations between gene category and functional annotation. Photosynthesis and t...
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ~2.7 Gb. To understand the genome of the cultivated peanut, it is prerequisite to know the genome organization of its diploid progenitors, A-genome—Arachis duranensis and B-genome—A. ipaensis. Two genome sequencing projects conducted sequenc...
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other pl...
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...
Document S1. Supplemental Results, Supplemental Methods, and Supplemental Figures 1–8
Supplemental Table 2. Re-sequencing Stats for 20 Tetraploid A. hypogaea Genotypes
Supplemental Table 5. Simulated Thresholds for Selection due to Genetic Drift at p < 0.01
Supplemental Table 4. Genotype Calls for Tetrasomic Markers in All Tetraploid A. hypogaea Genotypes Assayed, Related to Figure 3 and Figure 4
Supplemental Table 8. Tracking Ancestor-Specific Alleles through Eight Cycles of Breeding in US Runner Cultivars
Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell...
Peanut genetic improvement is approaching the cusp of rapidly accelerating gains due to application of genomic, transcriptomic, and metabolomic technologies. Yield is a primary target trait for improvement but is impacted by biotic and abiotic stresses, and quality traits specific to different cultural and industrial sectors that must be taken into...
Peanut (Arachis hypogaea; 2n = 4x = 40), is a nutritious food and a good source of vitamins, minerals, and healthy fats. Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high throughput genotyping of Ara...
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application...
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genom...
Background:
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant speci...
Background
The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing symbiotic microbes. With the aim of understanding the underlying molecular mechanisms leading to nodulation, many efforts are under...
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the m...
Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cow...
To understand the variation in genomic patterning of DNA methylation we compared methylomes of 34 diverse angiosperm species. By analyzing whole-genome bisulfite sequencing data in a phylogenetic context it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and r...
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2)...
Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaen...
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common...
Background
Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understoo...
Transposable Elements (TEs) are mobile genomic DNA sequences that are found in almost all living organisms. They so densely populate the genomes of many eukaryotic species that they are often the major components, as in man (more than 50%) or bread wheat (more than 95%). TEs achieve their transposition cycle within their host genome and are thus co...
A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, espec...