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Jose Francisco Montenegro Valls - One of the best experts on this subject based on the ideXlab platform.
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Organography of greenhouse and field accessions of wild Arachisspecies (section Arachis)
Instituto Agronômico de Campinas, 2017Co-Authors: Renato Ferraz De Arruda Veiga, Jose Francisco Montenegro Valls, Leonardo De Grazia Faria, Alessandra Pereira FáveroAbstract:ABSTRACT Peanut or groundnut (Arachis hypogaea L.) is a globally important oilseed crop, with important nutritional qualities, and a rich source of amino acids and protein. Another 80 species have been described in the genus Arachis, 64 of which are found in Brazil, and even though their morphology and agronomic traits remain largely unknown, they have been cultivated for forage and for landscaping and have great potential for breeding with cultivated peanut. Thus, the morphological characterization of wild Arachis species is essential for their conservation and use. In this study, we present a morphological and agronomic characterization of 29 diploid accessions of eleven wild Arachis species and one of the tetraploid A. monticola (section Arachis) with A and B genomes and determine their intra- and interspecific variability in greenhouse and field conditions. In total, 35 morphological descriptors were developed a priori from greenhouse accessions in the first crop year and used in field accessions in the second crop year. Significant differences in descriptors compiled in the greenhouse and the field support the use of different descriptors for different experimental conditions. PCA analysis showed that the distribution of accessions accorded with the taxonomy of species. The ten morphological descriptors that were important in differentiating section Arachis accessions were seed length, lateral branch length, right apical leaflet length, right apical leaflet width, height and diameter of main stem, branch color, standard petal base color, number of flowers, and presence of bristles on rachis
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Arachis veigae fabaceae la especie silvestre del genero mas dispersa sin embargo pasada por alto taxonomicamente
Bonplandia, 2015Co-Authors: Suzi Helena De Santana, Jose Francisco Montenegro VallsAbstract:A new Brazilian species of Arachis L. is described. Arachis veigaeS.H. Santana & Valls nov. sp, morphologically close to A. pusilla Benth., is distinguished by the absence of a prominent basal disc at the base of the fruit segments and non concaulescent cotyledonary buds. The synonymization of A. sylvestris (A. Chev.) A. Chev. and A. pusilla is discussed.
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a study of the relationships of cultivated peanut Arachis hypogaea and its most closely related wild species using intron sequences and microsatellite markers
Annals of Botany, 2013Co-Authors: Marcio C Moretzsohn, Jose Francisco Montenegro Valls, Soraya C M Lealbertioli, Ediene G Gouvea, Peter W Inglis, David J. BertioliAbstract:Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components.
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a linkage map for the b genome of Arachis fabaceae and its synteny to the a genome
BMC Plant Biology, 2009Co-Authors: Marcio C Moretzsohn, Soraya C M Lealbertioli, Patricia M Guimaraes, Dione M T Alvesfreitas, Rinaldo Wellerson Pereira, Andrea V G Barbosa, Cristiane De Camargo Teixeira, Catalina Romero Lopes, Marcelo Mattos Cavallari, Jose Francisco Montenegro VallsAbstract:Background Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability.
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characterization of rust early and late leaf spot resistance in wild and cultivated peanut germplasm
Scientia Agricola, 2009Co-Authors: A P Favero, Jose Francisco Montenegro Valls, Sergio Almeida De Moraes, Antonio Augusto Franco Garcia, Natal Antonio VelloAbstract:Groundnut (Arachis hypogaea) has an AB genome and is one of the most important oil crops in the world. The main constraints of crop management in Brazil are fungal diseases. Several species of the genus Arachis are resistant to pests and diseases. The objective of our experiments was to identify wild species belonging to the taxonomic section Arachis with either A or B (or " non-A" ) genomes that are resistant to early leaf spot (Cercospora arachidicola), late leaf spot (Cercosporidium personatum) and rust (Puccinia arachidis). For the identification of genotypes resistant to fungal diseases, bioassays with detached leaves were done in laboratory conditions, with artificial inoculation, a controlled temperature of 25oC and a photoperiod of 10 h light/14 h dark, for 20-42 days, depending on the fungi species. Most of the accessions of wild species were more resistant than accessions of A. hypogaea for one, two or all three fungi species studied. Arachis monticola, considered to be a possible tetraploid ancestor or a derivative of A. hypogaea, was also more susceptible to Cercosporidium personatum and Puccinia arachidis, as compared to most of the wild species. Therefore, wild germplasm accessions of both genome types are available to be used for the introgression of resistance genes against three fungal diseases of peanut.
Marcio C Moretzsohn - One of the best experts on this subject based on the ideXlab platform.
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integrated consensus map of cultivated peanut and wild relatives reveals structures of the a and b genomes of Arachis and divergence of the legume genomes
DNA Research, 2013Co-Authors: Kenta Shirasawa, David J. Bertioli, Manish K. Pandey, Rajeev K Varshney, Marcio C Moretzsohn, Soraya C M Lealbertioli, Mahendar Thudi, Jeanfrancois Rami, Daniel Fonceka, M V C GowdaAbstract:The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in gen- etics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaensis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaensis 3 A. duranensis) 43 , were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci whichwas anchoredto20consensusLGscorresponding totheA andBgenomes.Thecomparativegenomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
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a study of the relationships of cultivated peanut Arachis hypogaea and its most closely related wild species using intron sequences and microsatellite markers
Annals of Botany, 2013Co-Authors: Marcio C Moretzsohn, Jose Francisco Montenegro Valls, Soraya C M Lealbertioli, Ediene G Gouvea, Peter W Inglis, David J. BertioliAbstract:Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components.
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identification of candidate genome regions controlling disease resistance in Arachis
BMC Plant Biology, 2009Co-Authors: Soraya C M Lealbertioli, Marcio C Moretzsohn, Patricia M Guimaraes, Ana Carolina V F Jose, Dione M T Alvesfreitas, Stephan Nielen, Bruna Vidigal, Rinaldo Wellerson Pereira, Jodie PikeAbstract:Background: Worldwide, diseases are important reducers of peanut (Arachis hypogaea) yield. Sources of resistance against many diseases are available in cultivated peanut genotypes, although often not in farmer preferred varieties. Wild species generally harbor greater levels of resistance and even apparent immunity, although the linkage of agronomically un-adapted wild alleles with wild disease resistance genes is inevitable. Marker-assisted selection has the potential to facilitate the combination of both cultivated and wild resistance loci with agronomically adapted alleles. However, in peanut there is an almost complete lack of knowledge of the regions of the Arachis genome that control disease resistance. Results: In this work we identified candidate genome regions that control disease resistance. For this we placed candidate disease resistance genes and QTLs against late leaf spot disease on the genetic map of the A-genome of Arachis, which is based on microsatellite markers and legume anchor markers. These marker types are transferable within the genus Arachis and to other legumes respectively, enabling this map to be aligned to other Arachis maps and to maps of other legume crops including those with sequenced genomes. In total, 34 sequence-confirmed candidate disease resistance genes and five QTLs were mapped. Conclusion: Candidate genes and QTLs were distributed on all linkage groups except for the smallest, but the distribution was not even. Groupings of candidate genes and QTLs for late leaf spot resistance were apparent on the upper region of linkage group 4 and the lower region of linkage group 2, indicating that these regions are likely to control disease resistance.
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a linkage map for the b genome of Arachis fabaceae and its synteny to the a genome
BMC Plant Biology, 2009Co-Authors: Marcio C Moretzsohn, Soraya C M Lealbertioli, Patricia M Guimaraes, Dione M T Alvesfreitas, Rinaldo Wellerson Pereira, Andrea V G Barbosa, Cristiane De Camargo Teixeira, Catalina Romero Lopes, Marcelo Mattos Cavallari, Jose Francisco Montenegro VallsAbstract:Background Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability.
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an analysis of synteny of Arachis with lotus and medicago sheds new light on the structure stability and evolution of legume genomes
BMC Genomics, 2009Co-Authors: David J. Bertioli, Marcio C Moretzsohn, Soraya C M Lealbertioli, Lene H Madsen, Niels Sandal, Patricia M Guimaraes, Birgit K Hougaard, Jakob Fredslund, Leif Schauser, Anna Marie NielsenAbstract:Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes Lotus and Medicago (both with substantially sequenced genomes). In contrast, peanut (Arachis hypogaea) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of Arachis with Lotus and Medicago and improve our understanding of the Arachis genome and legume genomes in general. To do this we placed on the Arachis map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed. The Arachis genetic map was substantially aligned with Lotus and Medicago with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of Arachis from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The Arachis and model legume genomes comparison made here, together with a previously published comparison of Lotus and Medicago allowed all possible Arachis-Lotus-Medicago species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in Medicago and possibly also in Lotus, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more conserved regions, some harbor high densities of the fast evolving disease resistance genes. We suggest that gene space in Papilionoids may be divided into two broadly defined components: more conserved regions which tend to have low retrotransposon densities and are relatively stable during evolution; and variable regions that tend to have high retrotransposon densities, and whose frequent restructuring may fuel the evolution of some gene families.
David J. Bertioli - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut
Molecular plant, 2016Co-Authors: Josh Clevenger, Ye Chu, Carolina Chavarro, Gaurav Agarwal, David J. Bertioli, Soraya C. M. Leal-bertioli, Manish K. Pandey, Justin N. Vaughn, Brian Abernathy, Noelle A. BarkleyAbstract: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 Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.
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the genome sequences of Arachis duranensis and Arachis ipaensis the diploid ancestors of cultivated peanut
Nature Genetics, 2016Co-Authors: David J. Bertioli, Steven B Cannon, Lutz Froenicke, Guodong Huang, Andrew Farmer, Ethalinda K S Cannon, Xin Liu, Dongying Gao, Josh ClevengerAbstract: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 ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
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integrated consensus map of cultivated peanut and wild relatives reveals structures of the a and b genomes of Arachis and divergence of the legume genomes
DNA Research, 2013Co-Authors: Kenta Shirasawa, David J. Bertioli, Manish K. Pandey, Rajeev K Varshney, Marcio C Moretzsohn, Soraya C M Lealbertioli, Mahendar Thudi, Jeanfrancois Rami, Daniel Fonceka, M V C GowdaAbstract:The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in gen- etics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaensis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaensis 3 A. duranensis) 43 , were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci whichwas anchoredto20consensusLGscorresponding totheA andBgenomes.Thecomparativegenomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.
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a study of the relationships of cultivated peanut Arachis hypogaea and its most closely related wild species using intron sequences and microsatellite markers
Annals of Botany, 2013Co-Authors: Marcio C Moretzsohn, Jose Francisco Montenegro Valls, Soraya C M Lealbertioli, Ediene G Gouvea, Peter W Inglis, David J. BertioliAbstract:Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components.
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an analysis of synteny of Arachis with lotus and medicago sheds new light on the structure stability and evolution of legume genomes
BMC Genomics, 2009Co-Authors: David J. Bertioli, Marcio C Moretzsohn, Soraya C M Lealbertioli, Lene H Madsen, Niels Sandal, Patricia M Guimaraes, Birgit K Hougaard, Jakob Fredslund, Leif Schauser, Anna Marie NielsenAbstract:Most agriculturally important legumes fall within two sub-clades of the Papilionoid legumes: the Phaseoloids and Galegoids, which diverged about 50 Mya. The Phaseoloids are mostly tropical and include crops such as common bean and soybean. The Galegoids are mostly temperate and include clover, fava bean and the model legumes Lotus and Medicago (both with substantially sequenced genomes). In contrast, peanut (Arachis hypogaea) falls in the Dalbergioid clade which is more basal in its divergence within the Papilionoids. The aim of this work was to integrate the genetic map of Arachis with Lotus and Medicago and improve our understanding of the Arachis genome and legume genomes in general. To do this we placed on the Arachis map, comparative anchor markers defined using a previously described bioinformatics pipeline. Also we investigated the possible role of transposons in the patterns of synteny that were observed. The Arachis genetic map was substantially aligned with Lotus and Medicago with most synteny blocks presenting a single main affinity to each genome. This indicates that the last common whole genome duplication within the Papilionoid legumes predated the divergence of Arachis from the Galegoids and Phaseoloids sufficiently that the common ancestral genome was substantially diploidized. The Arachis and model legume genomes comparison made here, together with a previously published comparison of Lotus and Medicago allowed all possible Arachis-Lotus-Medicago species by species comparisons to be made and genome syntenies observed. Distinct conserved synteny blocks and non-conserved regions were present in all genome comparisons, implying that certain legume genomic regions are consistently more stable during evolution than others. We found that in Medicago and possibly also in Lotus, retrotransposons tend to be more frequent in the variable regions. Furthermore, while these variable regions generally have lower densities of single copy genes than the more conserved regions, some harbor high densities of the fast evolving disease resistance genes. We suggest that gene space in Papilionoids may be divided into two broadly defined components: more conserved regions which tend to have low retrotransposon densities and are relatively stable during evolution; and variable regions that tend to have high retrotransposon densities, and whose frequent restructuring may fuel the evolution of some gene families.
Guillermo Seijo - One of the best experts on this subject based on the ideXlab platform.
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Species relationships among the wild B genome of Arachis species (section Arachis) based on FISH mapping of rDNA loci and heterochromatin detection: a new proposal for genome arrangement
Theoretical and Applied Genetics, 2010Co-Authors: Germán Robledo, Guillermo SeijoAbstract:Arachis hypogaea is an allotetraploid species with low genetic variability. Its closest relatives, all of the genus Arachis , are important sources of alleles for peanut breeding. However, a better understanding of the genome constitution of the species and of the relationships among taxa is needed for the effective use of the secondary gene pool of Arachis . In the present work, we focused on all 11 non-A genome (or B genome sensu lato ) species of Arachis recognized so far. Detailed karyotypes were developed by heterochromatin detection and mapping of the 5S and the 18S–25S rRNA using FISH. On the basis of outstanding differences observed in the karyotype structures, we propose segregating the non-A genome taxa into three genomes: B sensu stricto (s.s.), F and K. The B genome s.s. is deprived of centromeric heterochromatin and is homologous to one of the A. hypogaea complements. The other two genomes have centromeric bands on most of the chromosomes, but differ in the amount and distribution of heterochromatin. This organization is supported by previously published data on molecular markers, cross compatibility assays and bivalent formation at meiosis in interspecific hybrids. The geographic structure of the karyotype variability observed also reflects that each genome group may constitute lineages that have evolved through independent evolutionary pathways. In the present study, we confirmed that Arachis ipaensis was the most probable B genome donor for A. hypogaea , and we identified a group of other closely related species. The data provided here will facilitate the identification of the most suitable species for the development of prebreeding materials for further improvement of cultivated peanut.
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Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization
Sociedade Brasileira de Genética, 2008Co-Authors: Germán Robledo, Guillermo SeijoAbstract:Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH) of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI) positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome) of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes
Hari D Upadhyaya - One of the best experts on this subject based on the ideXlab platform.
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draft genome of the peanut a genome progenitor Arachis duranensis provides insights into geocarpy oil biosynthesis and allergens
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Xiaoping Chen, Hari D Upadhyaya, Manish K. Pandey, Q Yang, Xiyin Wang, X Chi, Dadakhalandar Doddamani, Yanbin Hong, Hui Guo, Aamir W KhanAbstract:Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.
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single nucleotide polymorphism based genetic diversity in the reference set of peanut Arachis spp by developing and applying cost effective kompetitive allele specific polymerase chain reaction genotyping assays
The Plant Genome, 2013Co-Authors: Pawan Khera, Hari D Upadhyaya, Manish K. Pandey, Manish Roorkiwal, Manda Sriswathi, Pasupuleti Janila, Yufang Guo, Michael R Mckain, Ervin D Nagy, Steven J KnappAbstract:Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species. P
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abundant microsatellite diversity and oil content in wild Arachis species
PLOS ONE, 2012Co-Authors: Li Huang, Huifang Jiang, Xiaoping Ren, Yuning Chen, Yingjie Xiao, Xinyan Zhao, Mei Tang, Jiaquan Huang, Hari D Upadhyaya, Boshou LiaoAbstract:The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.
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genetic relationships among seven sections of genus Arachis studied by using ssr markers
BMC Plant Biology, 2010Co-Authors: Ravi Koppolu, Hari D Upadhyaya, S L Dwivedi, David A Hoisington, Rajeev K VarshneyAbstract:Background The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis.
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variability for drought resistance related traits in the mini core collection of peanut
Crop Science, 2005Co-Authors: Hari D UpadhyayaAbstract:where drought is a potential constraint for crop production (Smartt, 1994), and productivity ranges from 0.7 to Peanut (Arachis hypogaea L.) productivity is low in the semiarid