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.

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 Insights on the process of reciprocal gene loss in the duplicate DPL genes of rice

2019 ◽  
Author(s):  
Xun Xu ◽  
Song Ge ◽  
Fu-min Zhang
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
Diploid Species ◽  
Recent Common Ancestor ◽  
Duplicate Genes ◽  
Evolutionary Divergence ◽  
Dna Transposons ◽  
B Genome ◽  
A Genome ◽  
History Of

Abstract Background: Reciprocal gene loss (RGL) of duplicate genes is an important genetic resource of reproductive isolation, which is essential for speciation. In the past decades, various RGL patterns have been revealed, but RGL process is still poorly understood. The RGL of the duplicate DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2) gene can lead to BDM-type hybrid incompatibility between two rice subspecies. The evolutionary history of the duplicate genes, including their origin and mechanism of duplication as well as their evolutionary divergence after the duplication, remains unclear. In this study, we investigated the evolutionary history of the duplicate genes for gaining insights into the process of RGL.Results: We reconstructed phylogenetic relationships of DPL copies from all 15 diploid species representing six genome types of rice genus and then found that all the DPL copies from the latest diverged A- and B-genome gather into one monophyletic clade. Southern blot analysis also detected definitely two DPL copies only in A- and B-genome. High conserved collinearity can be observed between A- and B-genomic segments containing DPL1 and DPL2 respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is related to DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective constraint in DPL1 lineage but an enhancement in DPL2 lineage after DPL duplication. Sequence analysis also indicated that quite a few defective DPL1 can be found in 6 wild and cultivated species out of all 8 species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions: DPL duplication of rice originated in the recent common ancestor of A- and B-genome about 6.76 million years ago and the duplication was possibly caused by DNA transposons. The DPL1 is a redundant copy and has being in the process of pseudogenization, suggesting that artificial selection may play an important role in forming the RGL of DPLs between two rice subspecies during the domestication.

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.

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.

Genome analysis in wheat – rye – Aegilops caudata trigeneric hybrids

Genome ◽  
1989 ◽  
Vol 32 (2) ◽  
pp. 169-172 ◽  
Author(s):  
J. Orellana ◽  
J. F. Vazquez ◽  
J. M. Carrillo
Keyword(s):  
Genome Analysis ◽  
Preliminary Data ◽  
Meiotic Metaphase ◽  
Meiotic Pairing ◽  
Hybrid Wheat ◽  
B Genome ◽  
A Genome ◽  
C Genome ◽  
Aegilops Caudata ◽  
Trigeneric Hybrids

Using C-banding, homologous and homoeologous meiotic pairing between wheat (AB), rye (R), and Aegilops caudata (C) genomes were estimated at meiotic metaphase I in trigeneric hybrids (AABBRC; 2n = 6x = 42). In all hybrids, the C-genome chromosomes pair homoeologously only with chromosomes of the A genome, but not with chromosomes of the B genome or R genome. The A – C pairing was restricted to trivalents (0.15 per cell), each composed of two A-genome and one C-genome chromosomes. These preliminary data suggest that the C genome of Ae. caudata is probably more closely related to the A genome than to the B genome of wheat.Key words: trigeneric hybrid, wheat, rye, Aegilops, genome analysis, meiosis.

scholarly journals The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome

2013 ◽  
Vol 112 (3) ◽  
pp. 545-559 ◽  
Author(s):  
David J. Bertioli ◽  
Bruna Vidigal ◽  
Stephan Nielen ◽  
Milind B. Ratnaparkhe ◽  
Tae-Ho Lee ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Sequence Space ◽  
Intergenic Sequence ◽  
Evolutionary Divergence ◽  
B Genome ◽  
A Genome

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 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.

scholarly journals Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽  
2021 ◽  
Author(s):  
Yael S. Rodger ◽  
Alexandra Pavlova ◽  
Steve Sinclair ◽  
Melinda Pickup ◽  
Paul Sunnucks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary History ◽  
Livestock Grazing ◽  
Genetic Connectivity ◽  
Evolutionary Divergence ◽  
Common Component ◽  
A Genome ◽  
Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

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