SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.) for QTL analysis and comparative mapping

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The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.)

Molecular markers and genetic linkage maps are pre-requisites for molecular breeding in any crop species. In case of peanut or groundnut (Arachis hypogaea L.), an amphidiploid (4X) species, not a single genetic map is, however, available based on a mapping population derived from cultivated genotypes. In order to develop a genetic linkage map for tetraploid cultivated groundnut, a total of 1,145 microsatellite or simple sequence repeat (SSR) markers available in public domain as well as unpublished markers from several sources were screened on two genotypes, TAG 24 and ICGV 86031 that are parents of a recombinant inbred line mapping population. As a result, 144 (12.6%) polymorphic markers were identified and these amplified a total of 150 loci. A total of 135 SSR loci could be mapped into 22 linkage groups (LGs). While six LGs had only two SSR loci, the other LGs contained 3 (LG_AhXV) to 15 (LG_AhVIII) loci. As the mapping population used for developing the genetic map segregates for drought tolerance traits, phenotyping data obtained for transpiration, transpiration efficiency, specific leaf area and SPAD chlorophyll meter reading (SCMR) for 2 years were analyzed together with genotyping data. Although, 2–5 QTLs for each trait mentioned above were identified, the phenotypic variation explained by these QTLs was in the range of 3.5–14.1%. In addition, alignment of two linkage groups (LGs) (LG_AhIII and LG_AhVI) of the developed genetic map was shown with available genetic maps of AA diploid genome of groundnut and Lotus and Medicago. The present study reports the construction of the first genetic map for cultivated groundnut and demonstrates its utility for molecular mapping of QTLs controlling drought tolerance related traits as well as establishing relationships with diploid AA genome of groundnut and model legume genome species. Therefore, the map should be useful for the community for a variety of applications

Constructing and Characterising Solar Structure Models for Computational Helioseismology

In this paper, we construct background solar models that are stable against convection, by modifying the vertical pressure gradient of Model S (Christensen-Dalsgaard et al., 1996, Science, 272, 1286) relinquishing hydrostatic equilibrium. However, the stabilisation affects the eigenmodes that we wish to remain as close to Model S as possible. In a bid to recover the Model S eigenmodes, we choose to make additional corrections to the sound speed of Model S before stabilisation. No stabilised model can be perfectly solar-like, so we present three stabilised models with slightly different eigenmodes. The models are appropriate to study the f and p1 to p4 modes with spherical harmonic degrees in the range from 400 to 900. Background model CSM has a modified pressure gradient for stabilisation and has eigenfrequencies within 2% of Model S. Model CSM_A has an additional 10% increase in sound speed in the top 1 Mm resulting in eigenfrequencies within 2% of Model S and eigenfunctions that are, in comparison with CSM, closest to those of Model S. Model CSM_B has a 3% decrease in sound speed in the top 5 Mm resulting in eigenfrequencies within 1% of Model S and eigenfunctions that are only marginally adversely affected. These models are useful to study the interaction of solar waves with embedded three-dimensional heterogeneities, such as convective flows and model sunspots. We have also calculated the response of the stabilised models to excitation by random near-surface sources, using simulations of the propagation of linear waves. We find that the simulated power spectra of wave motion are in good agreement with an observed SOHO/MDI power spectrum. Overall, our convectively stabilised background models provide a good basis for quantitative numerical local helioseismology. The models are available for download from http://www.mps.mpg.de/projects/seismo/NA4/.Comment: 35 pages, 23 figures Changed title Updated Figure 1

An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for Tetraploid Groundnut (Arachis hypogaea L.)

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut