Duarte Jorge, Rivière Nathalie, Baranger Alain, Aubert Grégoire, Burstin Judith, Cornet Laurent, Lavaud Clément, Lejeune-Hénaut Isabelle, Martinant Jean-Pierre, Pichon Jean-Philippe, Pilet-Nayel Marie-Laure, Boutet Gilles
INRA UMR 1349 IGEPP, BP35327, Le Rheu Cedex 35653, France.
BMC Genomics. 2014 Feb 12;15:126. doi: 10.1186/1471-2164-15-126.
Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis.
We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs.We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species.
Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding.
豌豆拥有一个4.3Gb的复杂基因组，迄今为止仅有有限的基因组资源。尽管单核苷酸多态性（SNP）标记目前对于研究和现代育种具有很高的价值，但在豌豆中仅有少数被描述并用于遗传多样性和连锁分析。
我们利用罗氏454技术对8个代表现代育种材料的基因型进行cDNA测序，开发了一个大型资源库，该技术结合了长读长（400bp）和高覆盖率（380万条读长，总计达13.69亿碱基）。对测序数据进行组装，生成了一个68K的单基因集，其中41K通过与模式物种蒺藜苜蓿的最佳比对结果进行了注释。注释的重叠群沿蒺藜苜蓿假染色体呈均匀分布，表明该单基因集能很好地代表豌豆基因组。在被调查的遗传材料中发现10K个豌豆重叠群具有多态性，对应35K个SNP。我们通过GoldenGate分析验证了1538个SNP的一个子集，证明了它们构建育种种质多样性面板的能力。其中，1340个被进行了遗传定位，并用于构建一个新的共有图谱，该图谱总共包含2070个标记。基于比对分析，我们在豌豆共有图谱和蒺藜苜蓿假染色体之间建立了1252个桥梁，这为两个物种之间的共线性提供了新的见解。
我们的方法在豌豆中创建了重要的新资源，即迄今为止与模式物种蒺藜苜蓿紧密连锁的最全面的遗传图谱以及用于学术研究和育种的大型SNP资源。
