EST sequencing and SSR marker development from cultivated peanut ( Arachis hypogaea L.)

Song, Guo Qi; Li, Meng Jun; Han, Xiao; Wang, Xing Jun; Tang, Rong Hua; Xia, Han; Zhao, Chuan Zhi; Bi, Yu

doi:10.2225/vol13-issue3-fulltext-10

Cited by 35 publications

(27 citation statements)

References 26 publications

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“…We found 7,413 perfectly repeated di-, tri-, tetra-, penta-, and hexa-nucleotide motifs (7.3% of the unigenes contained SSRs). The SSR frequency in the above EST resources is comparable with previous reports in cultivated peanut [36,37], and wild Arachis species [38]. The overall SSR density was 3,190 bp per Mb and corresponded to approximately 1 per 5 kb of the genic region, which is similar to a previous report of 1/5.5 kb in cultivated peanut [15].…”

Section: Resultssupporting

confidence: 89%

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Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

et al. 2012

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BackgroundCultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut.ResultsA total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution.ConclusionsOur findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.

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Section: Resultssupporting

confidence: 89%

“…The motif types (AG)n and (AAG)n have been reported as the most common di- and tri-nucleotide repeats identified in other plant EST databases [43,45-47], including peanut ( A . hypogaea ) [15,30,37,40,48,49]. …”

Section: Resultsmentioning

confidence: 99%

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

et al. 2012

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“…The first studies were based on isozymes and proteins (Krishna and Mitra 1988;Grieshammer and Wynne 1990;Lu and Pickersgill 1993), followed by Restriction Fragment Length Polymorphism-RFLPs Paik-Ro et al 1992;Kochert et al 1996), Random Amplified Polymorphic DNARAPDs (Halward et al , 1992Hilu and Stalker 1995;Subramanian et al 2000), Amplified Fragment Length Polymorphism-AFLPs (He and Prakash, 1997;Gimenes et al 2000;He and Prakash 2001;Gimenes et al 2002;Herselman, 2003;Milla et al 2005aMilla et al , 2005bTallury et al 2005), and more recently microsatellite markers (Hopkins et al 1999;Palmieri et al 2002;He et al 2003;Ferguson et al 2004;Moretzsohn et al 2004;He et al 2005;Moretzsohn et al 2005;Palmieri et al 2005;Bravo et al 2006;Budiman et al 2006;Gimenes et al 2007;Proite et al 2007;Wang et al 2007;Cuc et al 2008;Naito et al 2008;Liang et al 2009;Moretzsohn et al 2009;Song et al 2010;Yuan et al 2010;Koilkonda et al 2012;Macedo et al 2012;Pandey et al 2012) and...…”

Section: Molecular Markers For Arachismentioning

confidence: 99%

Marker‐Assisted Selection for Biotic Stress Resistance in Peanut

Burow¹,

Leal‐Bertioli²,

Simpson³

et al. 2013

Translational Genomics for Crop Breeding

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Peanut is the second-most important legum e grown worldwide. Cultivated peanut is a disomic tetraploid, 2n-4 x -40, with limited genetic diversity due to a genetic bottleneck in formation o f the polyploid from ancestors A. duranensis and A. ipaensis. Consequently, resistance_to biotic stresses is limited in the cultigen; however, w ild species possess strong resistances. Transfer o f these re sistances is hindered by differences o f ploidy, but production o f synthetic amphidiploids, coupled with use o f m olecular markers, enables efficient gene transfer. Marker maps have been made from interspecific crosses, and SSR-based maps from cultivated parents have been developed recently. At least 410 resistance gene analogues have been identified. The first markers for biotic stress tolerance were for root-knot nematode resistance and introgressed from one A. cardenasii chromosome. These and improved markers have been used for marker-assisted backcrossing, contributing to release o f three cultivars. Additional QTLs have been identified since.Early and late leafspots cause significant yield losses worldwide, and resistance depends on multiple genes. U sing interspecific populations, five resistance QTLs for early leafspot were identified using greenhouse inoculations, and five QTLs for late leafspot were identified using detached leaf assays. U sing cultivated species populations, 28 QTLs were identified for LLS resistance; all but one w ere minor QTLs; the major QTL was donated by an interspecific introgression line parent. Rust often occurs alongside leafspots, and rust resistance was characterized as one major QTL, plus several smaller QTLs. Marker-assisted backcrossing o f this major QTL has been performed into different populations. QTLs for resistance to other biotic stresses have been identified, namely to groundnut rosette virus, Sclerotinia blight, afiatoxin contamination, aphids, and tomato spotted w ilt virus. Marker-assisted breeding is still in early stages, and develop ment o f more rapid and inexpensive markers from transcriptome and genom e sequencing is expected to accelerate progress.

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“…Of them, the development and use of DNA markers is the frontrunner with significant applications in developing new crop varieties with considerable genetic gain (Yuan et al, 2017). Though several types of marker systems are available in groundnut, most of them suffer from low polymorphism especially in cultivated groundnut (Song et al, 2010;Khera et al, 2013) over the wild types (Moretzsohn et al, 2009), which limits their application in crop improvement (for review, Holbrook et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Utility of AhTE Markers for Genetic and Genomic Studies in Groundnut (Arachis hypogaea L.)

Hake¹,

Bhat²

2017

Int.J.Curr.Microbiol.App.Sci

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EST sequencing and SSR marker development from cultivated peanut ( Arachis hypogaea L.)

Cited by 35 publications

References 26 publications

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

Marker‐Assisted Selection for Biotic Stress Resistance in Peanut

Utility of AhTE Markers for Genetic and Genomic Studies in Groundnut (Arachis hypogaea L.)

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