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

<p>Abstract</p> <p>Background</p> <p>Cultivated peanut or groundnut (<it>Arachis hypogaea</it> L.) is an important oilseed crop with an allotetraploid genome (AABB, 2<it>n</it> = 4<it>x</it> = 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 <it>Arachis</it> species (2<it>n</it> = 2<it>x</it> = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of <it>Arachis</it>. 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.</p> <p>Results</p> <p>A 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 <it>Arachis</it>. 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 <it>A</it>. <it>batizocoi</it>. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (<it>A</it>. <it>duranensis</it>) and B (<it>A</it>. <it>batizocoi</it>) 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.</p> <p>Conclusions</p> <p>Our 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.</p

A high-density genetic map of <it>Arachis duranensis</it>, a diploid ancestor of cultivated peanut

<p>Abstract</p> <p>Background</p> <p>Cultivated peanut (<it>Arachis hypogaea</it>) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, <it>A. duranensis</it>, and the B-genome species, <it>A. ipaensis</it>. The very recent (several millennia) evolutionary origin of <it>A. hypogaea</it> has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species <it>A. duranensis</it> based on <it>de novo</it> generated EST databases. <it>Arachis duranensis</it> was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in <it>A. hypogaea</it>.</p> <p>Results</p> <p>More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of <it>A. duranensis</it> were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two <it>A. duranensis</it> accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in <it>A. hypogaea</it> assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between <it>A. duranensis, Medicago</it> and <it>Glycine</it> revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between <it>A. duranensis</it> and <it>Glycine</it> than with <it>Medicago</it>.</p> <p>Conclusions</p> <p>The first high-density, gene-based linkage map for <it>A. duranensis</it> was generated that can serve as a reference map for both wild and cultivated <it>Arachis</it> species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into <it>A</it>. <it>hypogaea</it> from <it>A</it>. <it>cardenasii</it>.</p

Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat cultivar ‘Stephens’ in multi-environment trials

The wheat (Triticum aestivum L.) cultivar 'Stephens' has been grown commercially in the USA Pacific Northwest for 30 years. The durable resistance of 'Stephens' to stripe rust (Puccinia striiformis f. sp. tritici) was believed to be due to a combination of seedling and adult plant resistance genes. Multilocation field trials, diversity array technology (DArT), and simple sequence repeat (SSR) markers were used to identify quantitative trait loci (QTL) for resistance. Recombinant inbred lines were assessed for stripe rust response in eight locations/years, five in 2008 and three in 2009. The data from Mt. Vernon, WA, differed from all other environments, and composite interval mapping (CIM) identified three QTL, QYrst.orr-1AL, QYrst.orr-4BS, and QYrpl.orr-6AL, which accounted for 12, 11, and 6% of the phenotypic variance, respectively. CIM across the remaining six environments identified four main QTL. Two QTL, QYrst.orr-2BS.2 and QYrst.orr-7AS, were detected in five of six environments and explained 11 and 15% of the phenotypic variance, respectively. Two other QTL, QYrst.orr-2AS and QYrpl.orr-4BL, were detected across four and three of six environments, and explained 19 and 9% of the phenotypic variance, respectively. The susceptible parent 'Platte' contributed QYrpl.orr-4BL and QYrpl.orr-6AL, with the remaining QTL originating from 'Stephens'. For each environment, additional minor QTL were detected, each accounting for 6-10% of the phenotypic variance. Different QTL with moderate effects were identified in both 'Stephens' and 'Platte'. Significant QTL × environment interactions were evident, suggesting that specificity to plant stage, pathogen genotype, and/or temperature was important