Characterization and Transferable Utility of Microsatellite Markers in the Wild and Cultivated Arachis Species.

Li Huang,Yuning Chen,Xiaoping Ren,Haitao Li,Jiaojiao Zhao,Boshou Liao,Huifang Jiang,Bei Wu,Yong Lei,Weigang Chen,Xiaojing Zhou,Yanli Zheng,David D Fang

doi:10.1371/journal.pone.0156633

Abstract

Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data. The GSS-SSRs had a density of 159.9–239.8 SSRs/Mb for wild Arachis and 1,015.8 SSR/Mb for cultivated Arachis, whereas the EST-SSRs had the density of 173.5–384.4 SSR/Mb and 250.9 SSRs/Mb for wild and cultivated Arachis, respectively. The trinucleotide SSRs were predominant across Arachis species, except that the dinucleotide accounted for most in A. hypogaea GSSs. From Arachis GSS-SSR and EST-SSR sequences, we developed 2,589 novel SSR markers that showed a high polymorphism in six diverse A. hypogaea accessions. A genetic linkage map that contained 540 novel SSR loci and 105 anchor SSR loci was constructed by case of a recombinant inbred lines F6 population. A subset of 82 randomly selected SSR markers were used to screen 39 wild and 22 cultivated Arachis accessions, which revealed a high transferability of the novel SSRs across Arachis species. Our results provided informative clues to investigate microsatellite patterns across A. hypogaea and its wild relative species and potentially facilitate the germplasm evaluation and gene mapping in Arachis species.

Highlights

Cultivated peanut (Arachis hypogaea L.) is an important oil crop in the world for its direct consumption in the food industry and edible oil in cooking
Through searching the di, tri, tetra, and pentanucleotide simple sequence repeat (SSR) repeats in genome survey sequences (GSSs) sequence, a total of 4,401, 377 and 7,251 SSR-containing sequences were identified in A. duranensis, A. batizocoi and A. hypogaea, respectively (Table 1)
By integrating the contigs and singletons, we identified 4,826, 454 and 11,155 unique GSS-SSRs with an overall frequency of 159.9, 239.8 and 1,015.8 SSRs/Mb in A. duranensis, A. batizocoi and A. hypogaea, respectively (Table 1)

Summary

Introduction

Cultivated peanut (Arachis hypogaea L.) is an important oil crop in the world for its direct consumption in the food industry and edible oil in cooking. It is widely cultivated in more than 100 countries with a global annual production of 45.7 Mt over an area of 25.4 Mha (http:// faostat.fao.org/faostat/collectons?subset=argriculture 2013). All wild Arachis species are diploid (2n = 2x = 18, 2n = 2x = 20) except A. monticola and certain species in section Rhizomatosae, whereas peanut is an allotetraploid species (AABB, 2n = 4x = 40) harboring A and B genomes [1].

Objectives

Methods

Results

Conclusion