Andrew H Paterson

Athens State University, Афіни, Alabama, United States

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Publications (359)2278.94 Total impact

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    Changsoo Kim · Xiyin Wang · Tae-Ho Lee · Katrin Jakob · Geung-Joo Lee · Andrew H Paterson ·

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    ABSTRACT: An introduced species must contend with enormous environmental variation in its introduced range. In this study, we use niche models and ordination analyses to reconstruct changes in genotype, phenotype, and climatic niche of Johnsongrass (Sorghum halepense), which is regarded as one of the world's most threatening invasive plants. In the United States, Johnsongrass has rapidly evolved within- and among-population genetic diversity; our results show that genetic differentiation in expanding Johnsongrass populations has resulted in phenotypic variation that is consistent with habitat and climatic variation encountered during its expansion. Moreover, Johnsongrass expanded from agricultural to non-agricultural habitat, and now, despite occupying overlapping ranges, extant agricultural and non-agricultural populations are genetically and phenotypically distinct and manifest different plastic responses when encountering environmental variation. Non-agricultural accessions are broadly distributed in climatic and geographic space and their fitness traits demonstrate plastic responses to common garden conditions that are consistent with local specialization. In contrast, agricultural accessions demonstrate “general purpose” plastic responses and have more restricted climatic niches and geographic distributions. They also grow much larger than non-agricultural accessions. If these differences are adaptive, our results suggest that adaptation to local habitat variation plays a crucial role in the ecology of this invader. Further, its success relates to its ability to succeed on dual fronts, by responding simultaneously to habitat and climate variability and by capitalizing on differential responses to these factors during its range expansion.This article is protected by copyright. All rights reserved.
    Ecography 10/2015; DOI:10.1111/ecog.02031 · 4.77 Impact Factor
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    ABSTRACT: The ‘apparently’ simple genomes of many angiosperms mask complex evolutionary histories. The reference genome sequence for cotton (Gossypium spp.) revealed a ploidy change of a complexity unprecedented to date, indeed that could not be distinguished as to its exact dosage. Herein, by developing several comparative, computational and statistical approaches, we revealed a 5× multiplication in the cotton lineage of an ancestral genome common to cotton and cacao, and proposed evolutionary models to show how such a decaploid ancestor formed. The c. 70% gene loss necessary to bring the ancestral decaploid to its current gene count appears to fit an approximate geometrical model; that is, although many genes may be lost by single-gene deletion events, some may be lost in groups of consecutive genes. Gene loss following cotton decaploidy has largely just reduced gene copy numbers of some homologous groups. We designed a novel approach to deconvolute layers of chromosome homology, providing definitive information on gene orthology and paralogy across broad evolutionary distances, both of fundamental value and serving as an important platform to support further studies in and beyond cotton and genomics communities.
    New Phytologist 10/2015; DOI:10.1111/nph.13689 · 7.67 Impact Factor
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    ABSTRACT: Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.
    Plant Biotechnology Journal 09/2015; DOI:10.1111/pbi.12467 · 5.75 Impact Factor
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    R. Ming · S C Liu · J E Bowers · P.H. Moore · J.E. Irvine · A H Paterson ·
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    ABSTRACT: A consensus map of homologous DNA linkage groups from two genotypes in each of two Saccharum species was aligned with the compact diploid genome of Sorghum bicolor (L.) Moench. A set of 439 DNA probes from different Poaceae (grasses) detected 2523 loci in two segregating populations derived from the crosses Saccharum officinarum L.'Green German' x S. spontaneum L. 'IND 81-146', and S. spontaneum 'PIN 84-1' x S. officinarum 'Muntok Java'. Genetic maps of the four Saccharum genotypes, including a total of 289 linkage groups (LGs), were assembled into 13 homologous groups (HGs) on the basis of parallel arrangements of duplicated loci. The consensus map of HGs consisted of 232 probes and 982 mapped loci/alleles in four sugarcane linkage maps. Of the 982 loci/alleles on the consensus map, 845 (86%) of them correspond to a single linkage group of Sorghum, indicating the highly conserved genome structure between these two closely related genera. At least six basic chromosomes, LGs A, D, F, H, I, and J, showed close correspondence to each other in Saccharum and Sorghum. Two possible chromosome fusion events were found in S. spontaneum corresponding to sorghum LG B fused with LG E, and LG B fused with LG G. This consensus map illustrates how the high-density sorghum linkage map can be used to facilitate the mapping and understanding of the complex sugarcane genome.
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    ABSTRACT: Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
    Frontiers in Plant Science 07/2015; 6:563. DOI:10.3389/fpls.2015.00563 · 3.95 Impact Factor
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    ABSTRACT: Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. Herein, a homeodomain leucine zipper gene (HD1) was found to co-segregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern G. barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt sub genomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1, which might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions result in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetic mapping, gene expression and association analysis suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The inter-specific phenotypic difference in stem trichome traits may also be attributable to HD1 inactivation associated with retrotransposon insertion. Copyright © 2015, The Genetics Society of America.
    Genetics 07/2015; 201(1). DOI:10.1534/genetics.115.178236 · 5.96 Impact Factor
  • Andrew H Paterson · Jonathan F Wendel ·

    Nature Biotechnology 05/2015; 33(5):491-493. DOI:10.1038/nbt.3217 · 41.51 Impact Factor
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    Wenqian Kong · Changsoo Kim · Valorie H Goff · Dong Zhang · Andrew H Paterson ·
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    ABSTRACT: • Rhizomes, subterranean stems that grow horizontally, are a storage organ that is highly associated with overwintering and regrowth. This quantitative study aimed to discover genetic determinants of rhizomatousness, an important trait related to perenniality and invasiveness. • A population of 161 individuals of a recombinant inbred line (RIL) derived from morphologically distinct parents, Sorghum bicolor and Sorghum propinquum, which segregates for rhizomatousness, was phenotyped and genetically mapped. • Seven genomic regions influenced rhizomatousness in this population; four were "consensus" regions that correspond with previously detected quantitative trait loci (QTLs) in an F2 population of the same pedigree and with different levels of vegetative branching. Because rhizomatousness is a plastic trait that is greatly influenced by environment, overlap between regions discovered in the RIL and F2 populations validates the position and effect of QTLs. Correspondence with regions influencing vegetative branching indicates that some genes and biochemical pathways may influence both vegetative branching and rhizomatousness, while genes influencing only one trait may confer divergent aspects of development of these organs. • Identifying genes conferring rhizomatousness and understanding their functions may provide opportunities to regulate plant growth for diverse applications. Increasing rhizomatousness may promote the productivity and perenniality of many grasses, especially biomass-dedicated crops, while decreasing rhizomatousness may improve monocarpic grain production and offer means to control many noxious weeds. © 2015 Botanical Society of America, Inc.
    American Journal of Botany 05/2015; 102(5):718-24. DOI:10.3732/ajb.1500035 · 2.60 Impact Factor
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    ABSTRACT: Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved 'hotspots' in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.
    BMC Plant Biology 04/2015; 15(1):107. DOI:10.1186/s12870-015-0477-6 · 3.81 Impact Factor
  • Xiyin Wang · Jingpeng Wang · Dianchuan Jin · Hui Guo · Tae-Ho Lee · Tao Liu · Andrew H Paterson ·
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    ABSTRACT: Multiple comparisons among genomes can clarify their evolution, speciation and functional innovations. To date, the genome sequences of 8 grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding grasses' divergence and speciation. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.
    Molecular Plant 04/2015; 8(6). DOI:10.1016/j.molp.2015.04.004 · 6.34 Impact Factor
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    Changsoo Kim · Hui Guo · Wenqian Kong · Rahul Chandnani · Lan-Shuan Shuang · Andrew H. Paterson ·
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    ABSTRACT: Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species.
    Plant Science 04/2015; DOI:10.1016/j.plantsci.2015.04.016 · 3.61 Impact Factor
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    ABSTRACT: Seed size is closely related to fitness of wild plants, and its modification has been a key recurring element in domestication of seed/grain crops. In sorghum, a genomic and morphological model for panicoid cereals, a rich history of research into the genetics of seed size is reflected by a total of 13 likelihood intervals determined by conventional QTL (linkage) mapping, in 11 non-overlapping regions of the genome. To complement QTL data and investigate whether the discovery of seed size QTLs is approaching "saturation", we compared QTL data to GWAS for seed mass, seed length and seed width, studied in 354 accessions from a sorghum association panel (SAP) that have been genotyped at 265,487 SNPs. We identified 9 independent GWAS-based "hotspots" for seed size associations. Targeted resequencing near four association peaks with the most notable linkage disequilibrium provides further support of the role(s) of these regions in the genetic control of sorghum seed size, and identifies two candidate causal variants with non-synonymous mutations. Of 9 GWAS hotspots in sorghum, 7 have significant correspondence with rice QTL intervals and known genes for components of seed size, on orthologous chromosomes. Identifying intersections between positional and association genetic data is a potentially powerful means to mitigate constraints associated with each approach, and non-random correspondence of sorghum (panicoid) GWAS signals to rice (oryzoid) QTLs adds a new dimension to the ability to leverage genetic data about this important trait across divergent plants. Copyright © 2015 Author et al.
    G3-Genes Genomes Genetics 03/2015; 5(6). DOI:10.1534/g3.115.017590 · 3.20 Impact Factor
  • Andrew H. Paterson ·

    Genomes of Herbaceous Land Plants, Edited by Jean-pierre Jacquot, Pierre Gadal, 12/2014: chapter 7, 9: pages 175, 223; ELSEVIER., ISBN: 978-0-12-417163-3
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    ABSTRACT: Cotton fiber quality traits are controlled by multiple genes of minor effect. Identification of significant and stable quantitative trait loci (QTL) across environments and populations lays foundation for marker-assisted selection for fiber quality improvement and studies of its molecular regulation. Here, a detailed genetic map is constructed and QTL are detected based on an intraspecific recombinant inbred line population derived from a cross between Upland cotton cultivar/line Yumian 1 and 7235. A total of 25,313 SSR primer pairs, including 5,000 developed from G. raimondii BAC-ends sequences, were used to construct the genetic map which finally contained 1,540 loci, spanning 2,842.06 cM, with an average of 1.85 cM between adjacent markers. With 4 year fiber quality traits data, variance analysis revealed that they were significantly affected by genetic and environmental factors. Significant correlations were also detected between them. A total of 62 QTL were identified with combined analysis and single environment analysis. These QTL explain phenotypic variation from 5.0 to 28.1 %. For each trait, favorable alleles were conferred by both parents. Seventeen QTL were detected in more than one environment. The genetic map and stable QTL are valuable for Upland cotton genome research and breeding projects to improve fiber quality.
    Euphytica 12/2014; 201(2):195-213. DOI:10.1007/s10681-014-1189-y · 1.39 Impact Factor
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    ABSTRACT: Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2 and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen encoding genes, ~617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3 and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea and pigeonpea, which diverged from peanut about 50 million years ago (mya) and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species, to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus and Arabidopsis while Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen encoding genes.
    Genome Biology and Evolution 09/2014; 6(9). DOI:10.1093/gbe/evu189 · 4.23 Impact Factor
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    Wenqian Kong · Hui Guo · Valorie H Goff · Tae-Ho Lee · Changsoo Kim · Andrew H Paterson ·
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    ABSTRACT: Key message: We identified quantitative trait loci influencing plant architecture that may be valuable in breeding of optimized genotypes for sustainable food and/or cellulosic biomass production, and advancing resilience to changing climates. We describe a 3-year study to identify quantitative trait loci (QTLs) for vegetative branching of sorghum in a recombinant inbred line population of 161 genotypes derived from two morphologically distinct parents, S. bicolor × S. propinquum. We quantify vegetative branching based on morphological position and physiological status. Different sets of QTLs for different levels of branching were identified. QTLs discovered on chromosomes 1, 3, 7 and 8 affect multiple vegetative branching variables, suggesting that these regions may contain genes that control general axillary meristem initiation. Other regions that only influence one vegetative branching trait could contain genes that influence developmental processes contributing to divergent patterns of plant architecture. We investigate the relationship between vegetative branching patterns and dry biomass, and conclude that tillers with mature panicles and immature secondary branches each show consistent positive correlation with dry biomass. Among 19 branching-related genes from rice, eight sorghum homologs of seven rice genes are in syntenic blocks within branching-related QTL likelihood intervals. Five of these eight genes are within 700 kb of SNPs significantly associated with differences in branching in genome-wide association study of a diversity panel of 377 sorghum accessions, and three contain striking allelic variations between S. bicolor and S. propinquum that are likely to impact gene functions. Unraveling genetic determinants for vegetative branching may contribute to deterministic breeding of optimized genotypes for sustainable food and cellulosic biomass production in both optimal and marginal conditions, which are resilient to future climates that are more volatile and more stressful.
    Theoretical and Applied Genetics 08/2014; 127(11). DOI:10.1007/s00122-014-2384-x · 3.79 Impact Factor
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    Yuannian Jiao · Andrew H Paterson ·
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    ABSTRACT: The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more 'particulate' understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.
    Philosophical Transactions of The Royal Society B Biological Sciences 08/2014; 369(1648). DOI:10.1098/rstb.2013.0355 · 7.06 Impact Factor
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    ABSTRACT: Resistance to root-knot nematodes [Meloidogyne arenaria (Neal) Chitwood] is needed for cultivation of peanut in major peanut-growing areas, but significant resistance is lacking in the cultivated species (Arachis hypogaea L.). Markers to two closely-linked genes introgressed from wild relatives of peanut have been identified previously, but phenotypic evidence for the presence of additional genes in wild species and introgression lines has eluded quantitative trait locus (QTL) identification. Here, to improve sensitivity to small-effect QTLs, an advanced backcross population from a cross between a Florunner component line and the synthetic amphidiploid TxAG-6 [Arachis batizocoi × (A. cardenasii × A. diogoi)]4× was screened for response to root-knot nematode infection. Composite interval mapping results suggested a total of seven QTLs plus three putative QTLs. These included the known major resistance gene plus a second QTL on LG1, and a potentially homeologous B-genome QTL on LG11. Additional potential homeologs were identified on linkage group (LG) 8 and LG18, plus a QTL on LG9.2 and putative QTLs on LG9.1 and 19. A QTL on LG15 had no inferred resistance-associated homeolog. Contrary to expectation, two introgressed QTLs were associated with susceptibility, and QTLs at some homeologous loci were found to confer opposite phenotypic responses. Long-term functional conservation accompanied by rapid generation of functionally divergent alleles may be a singular feature of NBS-LRR resistance gene clusters, contributing to the richness of resistance alleles available in wild relatives of crops. The significance for peanut evolution and breeding is discussed.
    Molecular Breeding 08/2014; 34(2):393-406. DOI:10.1007/s11032-014-0042-2 · 2.25 Impact Factor

Publication Stats

23k Citations
2,278.94 Total Impact Points


  • 2015
    • Athens State University
      Афіни, Alabama, United States
  • 1970-2015
    • University of Georgia
      • • Plant Genome Mapping Laboratory
      • • Center for Applied Genetic Technologies
      • • Department of Crop and Soil Sciences
      Атина, Georgia, United States
  • 1993-2014
    • Texas A&M University
      • Department of Soil and Crop Sciences
      College Station, Texas, United States
  • 2012
    • University of Illinois, Urbana-Champaign
      • Department of Plant Biology
      Urbana, Illinois, United States
  • 2009
    • Jilin University
      • College of Computer Science & Technology
      Yung-chi, Jilin Sheng, China
  • 2003-2008
    • Iowa State University
      • Department of Ecology, Evolution and Organismal Biology
      Ames, IA, United States
  • 2007
    • Catholic University of Louvain
      Walloon Region, Belgium
  • 2006
    • North Carolina State University
      Raleigh, North Carolina, United States
    • University of Wisconsin, Madison
      • Department of Biochemistry
      Madison, MS, United States
  • 2005
    • The University of Arizona
      • Arizona Genomics Institute
      Tucson, Arizona, United States
  • 2002
    • Mississippi State University
      • Department of Plant and Soil Sciences
      Starkville, MS, United States
    • University of Missouri
      • Division of Biological Sciences
      Columbia, Missouri, United States
  • 2001
    • Zhejiang Agricultural University
      Hang-hsien, Zhejiang Sheng, China
  • 1999
    • Alabama A & M University
      Huntsville, Alabama, United States
    • Concordia University–Ann Arbor
      Ann Arbor, Michigan, United States
  • 1988
    • Cornell University
      Ithaca, New York, United States