Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

Wang, Hui; Penmetsa, R. Varma; Yüan, Ming; Gong, Limin; Zhao, Yanni; Guo, Bao‐Zhu; Farmer, Andrew; Rosen, Benjamin D.; Gao, Jinliang; Isobe, Sachiko; Bertioli, David J.; Varshney, Rajeev K.; Cook, Douglas R.; Guo, He

doi:10.1186/1471-2229-12-10

Cited by 90 publications

(89 citation statements)

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“…BESs have been proven to be valuable sources of SSRs [48, 49]. In our study, a total of 3,846 SSRs were identified from the 2,698 sweetpotato BESs.…”

Section: Discussionmentioning

confidence: 90%

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

Huo

et al. 2016

BMC Genomics

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BackgroundSweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species.ResultsThe BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana.ConclusionsThe first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.

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“…BESs have been proven to be valuable sources of SSRs [48, 49]. In our study, a total of 3,846 SSRs were identified from the 2,698 sweetpotato BESs.…”

Section: Discussionmentioning

confidence: 90%

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

Huo

et al. 2016

BMC Genomics

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“…In case of cultivated peanut, the first SSR-based genetic map was constructed using only 135 SSR markers, covering a total of 1,270.5 cM map distance which covers half of the peanut integrated consensus map29. In the past decade, thousands of SSR markers have been developed in peanut from complementary DNAs (cDNAs), SSR-enriched genomic DNA libraries, and BAC-ends25323334353637, which greatly accelerated the construction of genetic map and QTL analysis in peanut21232425272829383940. Since the polymorphism of SSRs in a specific population largely depended on the genetic diversity between the parents of an experimental population, several such efforts were required to make available large number of SSRs in the public domain for genetic and QTL mapping studies.…”

Section: Discussionmentioning

confidence: 99%

“…Subsequently, we constructed a high-density linkage map with a total of 1,219 loci with the map length of 2,038.75 cM, covering nearly 80% of peanut genetic map represented by the integrated peanut map29. More than 85% of the 1,219 loci segregated in the population at the expected ratio of 1:1, which was significantly more than that of other studies2325293940. The high proportion of mapped loci following Mendelian segregation has provided good quality and precise genetic map for conducting QTL analysis.…”

Section: Discussionmentioning

confidence: 99%

“…The SSR markers with prefixes XY, POCR, AGGS and AHGA were developed by our laboratory434445. Remaining SSR markers with the prefixes pPGPseq, pPGSseq, TC, IPAHM, Ah, RI, EE, EM, GA, GM, GNB, AC, Ad, ARS, gi, AHBGS, PM, AHS, AHGS and HAS were obtained from the literatures25293233343536373940. PCR reactions were performed as previously described24.…”

Section: Methodsmentioning

confidence: 99%

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Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)

Huang

Ren

et al. 2016

Sci Rep

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Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

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“…An integrated map was then constructed with 324 marker loci covering 1352 cM genetic distance (Qin et al, 2012). 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.…”

Section: Recent Advancement In Genetic Linkage Mapsmentioning

confidence: 99%

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...

show abstract

Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

Cited by 90 publications

References 59 publications

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition

Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.)

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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