Institute of Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30605, USA.
BMC Genomics. 2012 Sep 11;13:469. doi: 10.1186/1471-2164-13-469.
Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea 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 A. duranensis based on de novo generated EST databases. Arachis duranensis 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 A. hypogaea.
More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis 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 A. hypogaea 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 A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago.
The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis 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 A. hypogaea from A. cardenasii.
栽培花生（Arachis hypogaea）是一个异源四倍体物种，其祖先基因组很可能来自 A 基因组物种 A. duranensis 和 B 基因组物种 A. ipaensis。A. hypogaea 的最近进化起源（几千年）对栽培种内的等位基因和表型多样性施加了瓶颈效应。然而，野生二倍体近缘种是等位基因的丰富来源，可用于作物改良，其较简单的基因组更容易分析，同时为异源四倍体花生基因组的结构提供了见解。本研究的目的是基于从头生成的 EST 数据库为二倍体物种 A. duranensis 建立高密度遗传图谱。选择 A. duranensis 进行作图，因为它是栽培花生的 A 基因组祖先，同时也可以避免与 A. hypogaea 多倍体相关的基因复制的干扰。
从 A. duranensis 的标准化 cDNA 文库中生成的超过一百万个表达序列标签（EST）序列被组装成 81116 个独特的转录本。从该数据集挖掘出 1236 个 A. duranensis 两个品系 PI 475887 和 Grif 15036 之间的 EST-SNP 标记。还从代表保守豆科同源物的基因组序列中开发了 300 个 SNP 标记。在 1536 个 SNP 标记中，有 1054 个标记被定位在遗传图谱上。此外，在 A. hypogaea 组装中鉴定的 598 个 EST-SSR 标记以及 37 个抗病基因候选物（RGC）和 35 个其他先前发表的标记也被包含在图谱中。总共 1724 个标记分布在 10 个连锁群上，跨越 1081.3cM。使用三个不同数据库中的相似性搜索对提供标记的基因序列进行注释，并使用 Medicago Gene Atlas 和 TAIR 数据库确定基因本体描述。A. duranensis、Medicago 和 Glycine 之间的共线性分析揭示了分布在花生基因组中的大量保守基因簇。在 A. duranensis 和 Glycine 之间检测到的共线性水平高于与 Medicago 的共线性水平。
生成了第一个高密度、基于基因的 A. duranensis 连锁图谱，可作为野生和栽培 Arachis 物种的参考图谱。这里开发的标记对花生具有重要价值，更广泛地说，对豆科研究社区也具有重要价值。A 基因组图谱将对其他花生物种的精细作图有用，并且已经应用于从 A. cardenasii 引入 A. hypogaea 的线虫抗性基因的作图。
