Molecular biogeographic study of recently described B- and A-genome Arachis species, also providing new insights into the origins of cultivated peanut

Genome ◽  
2009 ◽  
Vol 52 (2) ◽  
pp. 107-119 ◽  
Author(s):  
Mark D. Burow ◽  
Charles E. Simpson ◽  
Michael W. Faries ◽  
James L. Starr ◽  
Andrew H. Paterson
Keyword(s):  
Wild Species ◽  
Rflp Markers ◽  
Species Variation ◽  
Additional Species ◽  
Marker Haplotype ◽  
Genome Species ◽  
B Genome ◽  
A Genome ◽  
Cultivated Peanut ◽  
Arachis Batizocoi

The cultivated peanut Arachis hypogaea is a tetraploid, likely derived from A- and B-genome species. Reproductive isolation of the cultigen has resulted in limited genetic variability for important traits. Artificial hybridizations using selected diploid parents have introduced alleles from wild species, but improved understanding of recently classified B-genome accessions would aid future introgression work. To this end, 154 cDNA probes were used to produce 1887 RFLP bands scored on 18 recently classified or potential B-genome accessions and 16 previously identified species. One group of B-genome species consisted of Arachis batizocoi , Arachis cruziana , Arachis krapovickasii , and one potential additional species; a second consisted of Arachis ipaënsis , Arachis magna , and Arachis gregoryi . Twelve uncharacterized accessions grouped with A-genome species. Many RFLP markers diagnostic of A. batizocoi group specificity mapped to linkage group pair 2/12, suggesting selection or genetic control of chromosome pairing. The combination of Arachis duranensis and A. ipaënsis most closely reconstituted the marker haplotype of A. hypogaea, but differences allow for other progenitors or genetic rearrangements after polyploidization. From 2 to 30 alleles per locus were present, demonstrating section Arachis wild species variation of potential use for expanding the cultigen’s genetic basis.

scholarly journals Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability

2016 ◽  
Vol 6 (12) ◽  
pp. 3825-3836 ◽  
Author(s):  
Ratan Chopra ◽  
Gloria Burow ◽  
Charles E Simpson ◽  
Jennifer Chagoya ◽  
Joann Mudge ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Wild Species ◽  
De Novo ◽  
Genome Species ◽  
Phenotypic Differences ◽  
B Genome ◽  
A Genome ◽  
Cultivated Peanut ◽  
Allele Specific ◽  
Cultivated Species

Abstract To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

Further data on the genomic relationships among wild perennial species (2n = 40) of the genus Glycine Willd.

Genome ◽  
1988 ◽  
Vol 30 (2) ◽  
pp. 166-176 ◽  
Author(s):  
R. J. Singh ◽  
K. P. Kollipara ◽  
T. Hymowitz
Keyword(s):  
Current Status ◽  
Evolutionary Divergence ◽  
Similar Species ◽  
Meiotic Pairing ◽  
Perennial Species ◽  
Genome Species ◽  
B Genome ◽  
A Genome ◽  
Genomic Relationships ◽  
Hybrid Weakness

The present study furnishes information about the current status of knowledge concerning the genomic relationships among 9 of the 12 wild perennial species (2n = 40) of the subgenus Glycine. Crossability rate, hybrid inviability, and meiotic pairing in intra- and inter-specific F1 hybrids revealed that genomically similar species, though morphologically distinct, crossed readily to produce hybrid progeny that were vigorous, fertile, and normal in meiotic pairing (20 bivalents at metaphase I). However, a chromatin bridge and acentric fragment were recorded in certain hybrid combinations, suggesting that the evolutionary divergence in genomically similar species occurred because of paracentric inversions. In contrast, crosses between genomically dissimilar species set pods that often aborted, showed hybrid weakness, seedling and vegetative lethality, seed inviability, and complete sterility. The sterility was attributed to disturbed meiotic pairing. It is obvious from this study that A-genome species such as G. canescens (AA) G. clandestina (intermediate pod, A1A1, and long pod, A2A2), and G. argyrea (A3A3), and B-genome species such as G. microphylla (BB), G. latifolia (B1B1), and G. tabacina (B2B2) predominate in the subgenus Glycine. Glycine cyrtoloba (CC) showed stronger genome homology to B-genome species than to A-genome species. Likewise, G. tomentella (DD) appeared to be more closely associated with A-genome species than to B-genome species. Although tomentellas with 38 and 40 chromosomes were indistinguishable morphologically, they differed genomically. Therefore, genome symbol EE was assigned to the 38-chromosome G. tomentella. Glycine falcata (FF) was found to be the most unusual species because it showed negligible chromosome homology with A- and B-genome species and did not set pods when cross-pollinated by C-, D-, and E-genome species.Key words: Glycine spp., genome, hybridization.

scholarly journals An overview of peanut and its wild relatives

2011 ◽  
Vol 9 (01) ◽  
pp. 134-149 ◽  
Author(s):  
David J. Bertioli ◽  
Guillermo Seijo ◽  
Fabio O. Freitas ◽  
José F. M. Valls ◽  
Soraya C. M. Leal-Bertioli ◽  
...  
Keyword(s):  
Wild Species ◽  
Crop Improvement ◽  
Genomic Analysis ◽  
Linkage Drag ◽  
Root Knot Nematode ◽  
Hybrid Identities ◽  
B Genome ◽  
Cultivated Peanut ◽  
Recent Origin ◽  
The Tropics

The legumeArachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and sub-tropics. The genus is endemic to South America being mostly associated with the savannah-like Cerrado. All species in the genus are unusual among legumes in that they produce their fruit below the ground. This profoundly influences their biology and natural distributions. The species occur in diverse habitats including grasslands, open patches of forest and even in temporarily flooded areas. Based on a number of criteria, including morphology and sexual compatibilities, the 80 described species are arranged in nine infrageneric taxonomic sections. While most wild species are diploid, cultivated peanut is a tetraploid. It is of recent origin and has an AABB-type genome. The most probable ancestral species areArachis duranensisandArachis ipaënsis, which contributed the A and B genome components, respectively. Although cultivated peanut is tetraploid, genetically it behaves as a diploid, the A and B chromosomes only rarely pairing during meiosis. Although morphologically variable, cultivated peanut has a very narrow genetic base. For some traits, such as disease and pest resistance, this has been a fundamental limitation to crop improvement using only cultivated germplasm. Transfer of some wild resistance genes to cultivated peanut has been achieved, for instance, the gene for resistance to root-knot nematode. However, a wider use of wild species in breeding has been hampered by ploidy and sexual incompatibility barriers, by linkage drag, and historically, by a lack of the tools needed to conveniently confirm hybrid identities and track introgressed chromosomal segments. In recent years, improved knowledge of species relationships has been gained by more detailed cytogenetic studies and molecular phylogenies. This knowledge, together with new tools for genetic and genomic analysis, will help in the more efficient use of peanut's genetic resources in crop improvement.

scholarly journals The Use of DNA Sequences from the β-Amylase Gene to Determine the Genetic Relationship among Sweetpotato, I. batatas and Other Ipomoea Species in Series Batatas (Convolvulaceae)

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1121E-1122
Author(s):  
Sriyani Rajapakse ◽  
Janice Ryan-Bohac ◽  
Sasanda Nilmalgoda ◽  
Robert Ballard ◽  
Daniel F. Austin
Keyword(s):  
Dna Sequences ◽  
Ipomoea Batatas ◽  
Dna Flow Cytometry ◽  
Amylase Gene ◽  
Genome Species ◽  
B Genome ◽  
A Genome ◽  
Nucleotide Sequence Variation ◽  
In Series ◽  
True Hybrid

The sweet potato Ipomoea batatas (L.) Lam. is classified in series Batatas (Choisy) in Convolvulaceae, with 12 other species and an interspecific true hybrid. The phylogenetic relationships of a sweetpotato cultivar and 13 accessions of Ipomoeas in the series Batatas were investigated using the nucleotide sequence variation of the nuclear-encoded β-amylase gene. First, flowers were examined to identify the species, and DNA flow cytometry used to determine their ploidy. The sweetpotato accession was confirmed as a hexaploid, I. tabascana a tetraploid, and all other species were diploids. A 1.1–1.3 kb fragment of the β-amylase gene spanning two exons separated by a long intron was PCR-amplified, cloned, and sequenced. Exon sequences were highly conserved, while the intron yielded large sequence differences. Intron analysis grouped species currently recognized as A and B genome types into separate clades. This grouping supported the prior classification of all the species, with one exception. The species I. tiliacea was previously classified as a B genome species, but this DNA study classifies it as an A genome species. From the intron alignment, sequences specific to both A and B genome species were identified. Exon sequences indicated that I. ramosissima and I. umbraticola were quite different from other A genome species. Placement of I. littoralis was questionable: its introns were similar to other B genome species, but exons were quite different. Exon evolution indicated the B genome species evolved faster than A genome species. Both intron and exon results indicated the B genome species most closely related to sweetpotato (I. batatas) were I. trifida and I. tabascana.

scholarly journals A Microsatellite Map of Wheat

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2007-2023 ◽  
Author(s):  
Marion S Röder ◽  
Victor Korzun ◽  
Katja Wendehake ◽  
Jens Plaschke ◽  
Marie-Hélène Tixier ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Population ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
D Genome ◽  
B Genome ◽  
Microsatellite Map ◽  
A Genome ◽  
Polymorphic Microsatellite ◽  
Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

scholarly journals ValSten: a new wild species derived allotetraploid for increasing genetic diversity of the peanut crop (Arachis hypogaea L.)

2021 ◽  
Author(s):  
Dongying Gao ◽  
Ana C. G. Araujo ◽  
Eliza F. M. B. Nascimento ◽  
M. Carolina Chavarro ◽  
Han Xia ◽  
...  
Keyword(s):  
High Resistance ◽  
Wild Species ◽  
Chromosome Doubling ◽  
Crop Improvement ◽  
Snp Array ◽  
Great Majority ◽  
Morphological Variations ◽  
Peanut Crop ◽  
Cultivated Peanut ◽  
Wild Peanut

AbstractIntrogression of desirable traits from wild relatives plays an important role in crop improvement, as wild species have important characters such as high resistance to pests and pathogens. However, use of wild peanut relatives is challenging because almost all wild species are diploid and sexually incompatible with cultivated peanut, which is tetraploid (AABB genome type; 2n = 4x = 40). To overcome the ploidy barrier, we used 2 wild species to make a tetraploid with the same allotetraploid genome composition as cultivated peanut. Crosses were made between 2 diploid wild species, Arachis valida Krapov. and W.C. Greg. (BB genome; 2n = 2x = 20) and Arachis stenosperma Krapov. and W.C. Greg. (AA genome; 2n = 2x = 20). Cuttings from the diploid F1 AB hybrid were treated with colchicine to induce chromosome doubling thus generating an induced allotetraploid. Chromosome counts confirmed polyploidy (AABB genome; 2n = 4x = 40). We named the new allotetraploid ValSten. Plants had well-developed fertile pollen, produced abundant seed and were sexually compatible with cultivated peanut. ValSten exhibits the same high resistance to early and late leaf spot and rust as its diploid parents. Notably, we observed morphological variations, including flower width and branch angles in the earliest generation (S0) of allotetraploids. A SNP array was used to genotype 47 S0 allotetraploids. The great majority of markers showed the additive allelic state from both parents (AABB). However, some loci were AAAA or BBBB, indicating homeologous recombination. ValSten provides a new, vigorous, highly fertile, disease resistant germplasm for peanut research and improvement.

scholarly journals Three founding ancestral genomes involved in the origin of sugarcane

2021 ◽  
Author(s):  
Nicolas Pompidor ◽  
Carine Charron ◽  
Catherine Hervouet ◽  
Stéphanie Bocs ◽  
Gaëtan Droc ◽  
...  
Keyword(s):  
Evolutionary Model ◽  
Saccharum Officinarum ◽  
Modern Cultivar ◽  
Ploidy Levels ◽  
Saccharum Spp ◽  
Bac Clones ◽  
B Genome ◽  
A Genome ◽  
Genomic Regions ◽  
Complex Genome

Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

Putative diploid ancestors of 80-chromosome Glycine tabacina

Genome ◽  
1992 ◽  
Vol 35 (1) ◽  
pp. 140-146 ◽  
Author(s):  
R. J. Singh ◽  
K. P. Kollipara ◽  
F. Ahmad ◽  
T. Hymowitz
Keyword(s):  
Adventitious Roots ◽  
Chromosome Doubling ◽  
Colchicine Treatment ◽  
Meiotic Pairing ◽  
B Genome ◽  
Specific Hybridization ◽  
A Genome ◽  
Genome Homology ◽  
Glycine Tabacina ◽  
Natural Mutation

The objective of this study was to discover the diploid progenitors of 80-chromosome Glycine tabacina with adventitious roots (WAR) and no adventitious roots (NAR). Three synthetic amphiploids were obtained by somatic chromosome doubling. These were (i) (G. latifolia, 2n = 40, genome B1B1,) × (G. microphylla, 2n = 40, genome BB) = F1(2n = 40, genome BB1) – 0.1% colchicine treatment (CT) – 2n = 80, genome BBB1B1; (ii) (G. canescens, 2n = 40, genome AA) × G. microphylla, 2n = 40, genome BB) = F1 (2n = 40, genome AB) – (CT) – 2n = 80, genome AABB; (iii) (G. latifolia, 2n = 40, B1B1) × G. canescens, 2n = 40, AA) = F1 (2n = 40, genome AB1) – (CT) – 2n = 80, genome AAB1B1. The segmental allotetraploid BBB1B1 was morphologically similar to the 80-chromosome G. tabacina (WAR), but meiotic pairing data in F1 hybrids did not support the complete genomic affinity. Despite normal diploid-like meiosis in allotetraploids AABB and AAB1B1, AABB was completely fertile, while pod set in AAB1B1 was very sparse. Morphologically, allotetraploid AABB was indistinguishable from the 80-chromosome G. tabacina (NAR) but in their F1 hybrids, the range of univalents at metaphase I was wide (4–44). The allotetraploid AAB1B1 did not morphologically resemble the 80-chromosome G. tabacina (NAR). However, the F1 hybrid of AABB × AAB1B1 showed normal meiosis with an average chromosome association (range) of 1.7 I (0–4) + 39.2 II (38–40). Based on this information, we cannot correctly deduce the diploid progenitor species of the 80-chromosome G. tabacina (NAR). The lack of exact genome homology may be attributed to the geographical isolation, natural mutation, and growing environmental conditions since the inception of 80-chromosome G. tabacina. Thus, it is logical to suggest that the 80-chromosome G. tabacina (NAR) is a complex, probably synthesized from A genome (G. canescens, G. clandestina, G. argyrea, G. tomentella D4 isozyme group) and B genome (G. latifolia, G. microphylla, G. tabacina) species, and the 80-chromosome G. tabacina (WAR) complex was evolved through segmental allopolyploidy from the B genome species.Key words: Glycine spp., allopolyploidy, colchicine, genome, intra- and inter-specific hybridization, polyploid complex.

scholarly journals Isoenzymes and polyploidy I. Qualitative and quantitative isoenzyme studies in the Triticinae

1971 ◽  
Vol 18 (1) ◽  
pp. 57-69 ◽  
Author(s):  
R. Mitra ◽  
C. R. Bhatia
Keyword(s):  
Enzyme Activity ◽  
Parental Species ◽  
Gene Dosage ◽  
Species Variation ◽  
Polyploid Species ◽  
Qualitative And Quantitative ◽  
B Genome ◽  
Genome Donor ◽  
Variant Enzyme ◽  
Seed Extracts

SUMMARYIsoenzymes of alcohol (ADH), malate (MDH), glutamate (GDH) and isocitrate (IDH) dehydrogenases, and a fast migrating esterase (EST-l) were separated by disk electrophoresis from dry seed extracts of diploid, tetraploid, hexaploid and octaploid species or amphiploids belonging to the subtribe Triticinae. Only ADH and EST-l isoenzymes showed inter-species variation; the other dehydrogenases, which show stringent substrate specificities (‘critical’ enzymes), revealed the same pattern in all diploid and polyploid species. The qualitative zymogram studies showed that (1) the number of variant enzyme bands increased with the level of ploidy, (2) the amphiploid isoenzyme pattern was additive of the parental species, (3) enhancement in the number of bands was due to the presence of not only parental bands, but also hybrid bands formed by association between heteromonomers. Quantitative data were obtained by densitometry of the enzyme bands as well as spectrophotometric measurements of enzyme activity in crude extracts. Increase in the level of enzyme activity was observed with ploidy level. In spite of the evidence that all duplicate/triplicate genes are expressed, increased enzyme activity observed in the polyploid species was not proportional to the level of ploidy or expected gene dosage. On the basis of ADH and EST-l zymograms obtained in 2 × and 4 × wheat, probable zymograms for these enzymes in the B-genome donor to 4 × wheat were extrapolated. Neither Ae. speltoides nor Ae. bicornis showed the extrapolated ADH pattern. Amphiploids involving Ae. speltoides and Triticum monococcum or T. aegilopoides fully reproduced the EST-l zymogram of 4 × wheat, but not the ADH. Ae. bicornis × T. aegilopoides amphiploid showed an ADH zymogram similar to that of 4 × wheat, but the EST-l bands were different.

Flavor Profiles of Wild Species-Derived Peanut Breeding Lines

2008 ◽  
Vol 35 (2) ◽  
pp. 81-85 ◽  
Author(s):  
S. P. Tallury ◽  
H. E. Pattee ◽  
T. G. Isleib ◽  
H. T. Stalker
Keyword(s):  
Wild Species ◽  
Interspecific Hybrid ◽  
Diploid Species ◽  
Sensory Attributes ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut ◽  
Important Quality

Abstract Several diploid wild species of the genus Arachis L. have been used as sources of resistance to common diseases of cultivated peanut (Arachis hypogaea L.). Because flavor is among the most important quality attributes for commercial acceptance of roasted peanuts, sensory attributes of interspecific hybrid derived breeding lines were evaluated to determine if transfer of disease resistance from wild species is associated with concomitant changes in flavor. Sixteen interspecific hybrid derivatives with five diploid species in their ancestries and the commercial flavor standard, NC 7 were evaluated for sensory quality. Significant variation among entries was found for the roasted peanut, sweet, and bitter sensory attributes, but not for the overall contrast between NC 7 and the wild species-derived breeding lines. The variation was either between two groups of wild species-derived breeding lines or within one or both groups. Introduction of disease and pest resistance traits from Arachis species did not result in degradation or improvement of the flavor profile. This suggests that flavor of wild species-derived germplasm will not prevent its use either as parents in peanut breeding programs or as cultivars.

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