Abstract

BackgroundPeanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers.ResultsThe use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2%) of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs) for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed.ConclusionsIn silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp).

Highlights

  • Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop

  • Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) composed of A and B genomes that are derived from two diploids, most likely A. duranensis (A genome) and A. ipaënsis (B genome)

  • We investigated whether in silico polymorphism analysis could increase the efficiency of development of polymorphic Simple sequence repeat (SSR) and transposon markers

Read more

Summary

Introduction

Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but highdensity linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) composed of A and B genomes that are derived from two diploids, most likely A. duranensis (A genome) and A. Low genetic diversity within the species has inhibited the advance of genetic linkage map construction. Tetraploid peanut is thought to have arisen approximately 3,500 years ago [10], and its short history has been considered a source of lower levels of polymorphism compared with diploid Arachis species [11]

Methods
Results
Discussion
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call