In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

Shirasawa, Kenta; Koilkonda, Padmalatha; Aoki, Koh; Hirakawa, Hideki; Tabata, Satoshi; Watanabe, Masao; Hasegawa, Makoto; Kiyoshima, Hiroyuki; Suzuki, Shigeru; Kuwata, Chikara; Naito, Yoshiki; Kuboyama, Tetsuji; Nakaya, Akihiro; Sasamoto, Shigemi; Watanabe, Akïharu; Kato, Midori; Kawashima, Kumiko; Kishida, Yoshie; Kohara, Mitsuyo; Kurabayashi, Atsushi; Takahashi, Chika; Tsuruoka, Hisano; Wada, Tsuyuko; Isobe, Sachiko

doi:10.1186/1471-2229-12-80

Cited by 123 publications

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“…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.…”

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“…Of the marker sequences from three maps 21,41 , 83%, 83% and 94% were assigned by sequence similarity searches to the expected diploid chromosomal pseudomolecules (Supplementary Data Set 6). When visualized as plots along the chromosomal pseudomolecules, the diploid A-genome chromosomes were distinctly less similar to A. hypogaea sequences than the B-genome chromosomes (Fig.…”

Section: Sequence Comparisons To Tetraploid Cultivated Peanutmentioning

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

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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...

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Section: Sequence Comparisons To Tetraploid Cultivated Peanutmentioning

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

et al. 2016

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“…Resistance to biotic stresses Angular leaf spot QTL 22-64 Oblessuc et al, 2012;Teixeira et al, 2005 (Khedikar et al, 2010;Liang et al, 2009a;Qin et al, 2012;Sujay et al, 2012;Wang et al, 2013 (Gautami et al, 2012b;Ravi et al, 2011;Varshney et al, 2009b) Gautami et al, 2012a;Liang et al, 2009;Ravi et al, 2011;Selvaraj et al, 2009;Shirasawa et al, 2012;Varshney et al, 2009b) (Continued on next page) (Liang et al, 2009;Pandey et al, 2012c;Sarvamangala et al, 2011;Selvaraj et al, 2009;Shirasawa et al, 2012) Pea Plant height QTL 19-65 (Tullu et al, 2008;Tar'an et al, 2003b;Dirlewanger et al, 1994) (Atibalentja et al, 2005;Guo et al, 2006;Guo et al, 2008;Han et al, 2008;Huynh et al, 2010;Kazi et al, 2008;Ruben et al, 2006;Shi et al, 2008;Silva and Danielle, 2008;Vuong et al, 2008;Wang et al, 2010;Winter et al, 2007) (Continued on next page) Funatsuki et al, 2005;Githiri et al, 2006;Githiri et al, 2007;…”

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Translational Genomics in Agriculture: Some Examples in Grain Legumes

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et al. 2014

Critical Reviews in Plant Sciences

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“…In addition to the SSRs mentioned above, Wang et al (2012) have also used 1152 SSRs mined from 36,314 BAC-end sequences (BES) and constructed a genetic map with a total of 318 markers covering 1674.4 cM in a single mapping population. For the creation of the highest density map of a single population of cultivated peanut to date, Shirasawa et al (2012b) reported the use of in silico analysis of DNA sequence data from the parental lines, which increased the efficiency of polymorphic marker development by more than three-fold. In total, 926 (34.2%) of 2702 markers showed polymorphisms between parental lines of the mapping population.…”

Section: Recent Advancement In Genetic Linkage Mapsmentioning

confidence: 99%

“…In total, 926 (34.2%) of 2702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4449 published markers generated 21 linkage groups covering 2166.4 cM with 1114 loci (Shirasawa et al, 2012b).…”

Section: Recent Advancement In Genetic Linkage Mapsmentioning

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Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

et al. 2013

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The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.Key Words: Arachis hypogaea, Arachis species, genomics, genetic maps, molecular markers, molecular breeding, Peanut Genome Consortium (PGC).The world's population is predicted to reach nine billion by 2050 (Nature Editorial, 2010), which means greater demand for food, hence, a continuing need to produce improved cultivars of crop plants. Advances in food production will require greater efforts in agricultural research to increase crop yield with improved genetics for plant protection from biotic and abiotic stresses. Agricultural biotechnology is one tool that holds great promise for sustainability of agricultural production and feeding an ever increasing population.Peanut (Arachis hypogaea L.), or groundnut, is one of the major economically important legumes that is cultivated worldwide for its ability to grow in semi-arid environments with relatively low inputs of chemical fertilizers. On a global basis, peanut also is a major source of protein and vegetable oil for human nutrition, containing about 28% protein, 50% oil and 18% carbohydrates. Peanut is cultivated in more than 100 countries in Asia, Africa and the Americas, grown mostly by resource-limited farmers of the semi-arid regions. India and China together produce almost twothirds of the world's peanuts, and the U...

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In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

Cited by 123 publications

References 61 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

Translational Genomics in Agriculture: Some Examples in Grain Legumes

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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