Genomic relationships between the cultivated peanut (<i>Arachis hypogaea</i>, Leguminosae) and its close relatives revealed by double GISH

Seijo, Guillermo; Lavia, Graciela Inés; Fernández, Amparo Ygual; Krapovickas, Antonio; Ducasse, Daniel Adrián; Bertioli, David J.; Moscone, Eduardo A.

doi:10.3732/ajb.94.12.1963

Cited by 205 publications

(226 citation statements)

References 44 publications

Supporting

Mentioning

206

Contrasting

Unclassified

Order By: Relevance

“…4 and Supplementary Table 11). In accordance with cytogenetic observations 8,26 , A08 could be assigned as the characteristic small ' A chromosome' (cytogenetic chromosome A09; Supplementary Fig. 23).…”

Section: Analysis Of Chromosomal Structure and Syntenymentioning

confidence: 89%

“…13), makes the assembly of the peanut genome sequence very challenging. However, the A and B subgenomes appear to have undergone relatively few changes since polyploidization: genomic in situ hybridization (GISH), using genomic DNA from the diploid species as probes, clearly distinguishes A and B chromosomes and does not show large A-B mosaics 7,8 . Also, the genome size of A. hypogaea is close to the sum of those for A. duranensis and A. ipaensis (1.25 and 1.56 Gb, respectively 14 ), indicating that there has been no large change in genome size since polyploidy.…”

Section: Openmentioning

confidence: 99%

See 1 more Smart Citation

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

et al. 2016

View full text Add to dashboard Cite

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. A r t i c l e s npg © 2016 Nature America, Inc. All rights reserved.Nature GeNetics VOLUME 48 | NUMBER 4 | APRIL 2016 4 3 9 subgenomes of A. hypogaea. Progeny are vigorous, phenotypically normal and fertile and showed lower segregation distortion 16,17 than has been observed for some populations derived from A. hypogaea intraspecific crosses [18][19][20][21] . Therefore, as a first step to characterizing the genome of cultivated peanut, we sequenced and analyzed the genomes of the two diploid ancestors of cultivated peanut. RESULTS Sequencing and assembly of the diploid A and B genomesConsidering that A. duranensis V14167 and A. ipaensis K30076 are likely good representatives of the ancestral species of A. hypogaea, we sequenced their genomes. After filtering, the data generated from the seven paired-end libraries corresponded to an estimated 154× and 163× base-pair coverage for A. duranensis and A. ipaensis, respectively (Supplementary Tables 1-6). The total assembly sizes were 1,211 and 1,512 Mb for A. duranensis and A. ipaensis, respectively, of which 1,081 and 1,371 Mb were represented in scaffolds of 10 kb or greater in size (Supplementary Table 7). Ultradense genetic maps were generated through genotyping by sequencing (GBS) of two diploid recombinant inbred line (RIL) populations (Supplementary Data Set 1). SNPs within scaffolds were used to validate the assemblies and confirmed their high quality; 190 of 1,297 initial scaffolds of A. duranensis and 49 of 353 initial scaffolds of A. ipaensis were identified as chimeric, on the basis of the presence of diagnostic population-wide switches in genotype calls occurring at the point of misjoin. Chimeric scaffolds were split, and their components were remapped. Thus, approximate chromosomal placements were obtained for 1,692 and 459 genetically verified scaffolds, respectively. Conventional molecular marker maps (Supplementary Data Set 2) and syntenic inferences were then used to refine the ordering of scaffolds within the initial genetic bins. Generally, agreement was good for maps in euchromatic arms and poorer in pericentromeric regions (although one map 22 showed large inversions in two lin...

show abstract

Section: Analysis Of Chromosomal Structure and Syntenymentioning

confidence: 89%

Section: Openmentioning

confidence: 99%

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

et al. 2016

View full text Add to dashboard Cite

show abstract

“…These taxa are more diverse in karyotype formula and in the presence and distribution of heterochromatin (Raina and Mukai, 1999;Seijo et al, 2004). Tetraploid species have an AABB genome constitution, and it has been demonstrated that they originated by hybridization of two wild diploid species, one with the A genome and the other with the B genome Gregory, 1976, 1979;Seijo et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization

Robledo

Seijo

2008

Genet. Mol. Biol.

View full text Add to dashboard Cite

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.

show abstract

“…Domestication of this wild allotetraploid is hypothesized to have resulted in the present day cultivated peanut (Arachis hypogaea L.) (Seijo et al 2007). This cross was successfully re-created, and resulted in fertile tetraploid progeny (Fávero et al 2006).…”

mentioning

confidence: 99%

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

et al. 2011

View full text Add to dashboard Cite

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipae¨nsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance-and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Modelbased clustering identified four subgroups-one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P \ 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r 2 C 0.1). Of the syntenic marker pairs separated by distances \ 10 cM, 11-20 cM, 21-50 cM, and [ 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P B 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r 2 [ 0.035 was found to distinguish mean r 2 values of linkage distance groups statistically from the mean r 2 values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r 2 values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using Vikas Belamkar-This work was performed in partial fulfillment of the requirements for the Master of Science degree.

show abstract

Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH

Cited by 205 publications

References 44 publications

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Contact Info

Product

Resources

About