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Genotypic Characterization of the U.S. Peanut Core Collection.
G3: Genes, Genomes, Genetics ( IF 2.6 ) Pub Date : 2020-10-27 , DOI: 10.1534/g3.120.401306
Paul I Otyama 1, 2 , Roshan Kulkarni 1, 2, 3 , Kelly Chamberlin 4 , Peggy Ozias-Akins 5 , Ye Chu 5 , Lori M Lincoln 6 , Gregory E MacDonald 7 , Noelle L Anglin 8 , Sudhansu Dash 9 , David J Bertioli 5 , David Fernández-Baca 10 , Michelle A Graham 2, 6 , Steven B Cannon 2, 6 , Ethalinda K S Cannon 11
Affiliation  

Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.



中文翻译:

美国花生核心收藏的基因型鉴定。

栽培花生(花生))是全球重要的石油,食品和饲料作物。USDA花生种质资源库目前包含8,982个种质。在1990年代,根据表型和原产国,选择了812个种质作为核心收藏。本研究报告了整个可用核心集的基因分型结果。每个品系均使用Arachis_Axiom2 SNP阵列进行基因分型,从而在整个收藏品中产生14,430个高质量,信息丰富的SNP。此外,复制了253个种质的子集,每个种质使用2至5个种子,以评估这些种质内的异质性。核心的基因型多样性主要捕获在五个基因型簇中,它们与植物种类和市场类型有一定的对应关系。按原籍国划分的遗传聚类很少,和19世纪。与鞭毛/赤道/百日咳有关的遗传簇该品种主要来自玻利维亚,秘鲁和厄瓜多尔,与这些最早的地方品种一致。遗传学,表型特征和生物地理学都与玻利维亚东南部四倍体花生的先前报道一致。对基因型数据的分析表明,遗传辐射较早,其次是整个南美地区主要遗传类别的区域分布,然后是全球传播,保留了花生的许多早期遗传多样性。与来自二倍体祖先的等位基因相关的基因型数据的比较还表明,无论大小,亚基因组交换都是花生遗传多样性的主要贡献者。

更新日期:2020-11-06
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