A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

Hong, Yanbin; Chen, Xiaoping; Liang, Xuanqiang; Liu, Haiyan; Guiyuan, Zhou; Li, Shaoxiong; Wen, Shaoqing; Holbrook, C. Corley; Guo, Bao‐Zhu

doi:10.1186/1471-2229-10-17

Cited by 125 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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The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

et al. 2016

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

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“…ESTs are considered ideal candidates for rapid and economical SSR marker development using computational approaches since a large number of SSRs are found in coding regions (Morgante et al 2002). As a result, several efforts were made by many researchers to develop SSRs from ESTs in Brassica napus (Kaur et al 2009), peanut (Hong et al 2010), Hordeum vulgare (Castillo et al 2008), cassava (Raji et al 2009), pearl millet (Senthivel et al 2008) and many other plant species (Varshney et al 2005). However, due to the problem of sequence redundancy yielding multiple sets of markers at the same locus, random EST sequences are being assembled into unique gene sequences called unigenes (http://www.…”

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Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L.

Ramchiary

Wang

et al. 2011

Breed. Sci.

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Brassica rapa plants are highly important as vegetables, sources of oilseeds and fodder crop. Here, we developed 450 unigene derived microsatellite (UGMS) markers in B. rapa using unigenes downloaded from the National Center for Biotechnology Information database. Of the 450 UGMS primer pairs, 428 (95.1%) produced repeatable and reliable amplifications of expected size in at least one parental line of B. rapa, and 70 UGMS markers gave 72 polymorphic loci between the two contrasting parental lines. Cross-species transferability analysis of these 70 polymorphic UGMS markers in five other cultivated Brassica species showed varying transferability rates ranging from 82.9% in B. nigra to 97.1% in B. juncea and B. napus, and overall 53 UGMS markers amplified targets in all five species. The B. rapa linkage map was constructed using the 72 UGMS polymorphic loci and 154 previously developed SSRs. The newly developed UGMS markers and linkage map in this study would help in future studies to better understand the organization and evolution of Brassica genomes with respect to unigenes, in addition to mapping, tagging and cloning of economically important trait QTL/gene(s) and marker-assisted breeding in Brassica crops.

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“…Varshney et al (2009) screened 1145 SSR markers and mapped 135 loci onto 22 linkage groups spanning 1271 cM onto a RIL population developed from two parental genotypes, TAG 24 and ICGV 86031. Later a composite map containing 175 SSR markers in 22 linkage groups was developed from three cultivated crosses (Hong et al, 2010). Another composite map was constructed with 101 SSR markers in 17 linkage groups from four populations in China (Zhang, 2011).…”

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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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A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

Cited by 125 publications

References 51 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

Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L.

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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