Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear

Huabai Xue,Pujuan Zhang,Long Wang,Suke Wang,Yanli Su,Jian Yang,Yushan Qiao,Ting Shi,Huirong Zhang,Xiugen Li

doi:10.1186/s12864-018-4822-7

Abstract

BackgroundPear (Pyrus spp.) is an economically important temperate fruit tree worldwide. In the past decade, significant progress has been made in pear molecular genetics based on DNA research, but the number of molecular markers is still quite limited, which hardly satisfies the increasing needs of geneticists and breeders.ResultsIn this study, a total of 156,396 simple sequence repeat (SSR) loci were identified from a genome sequence of Pyrus bretschneideri ‘Dangshansuli’. A total of 101,694 pairs of SSR primers were designed from the SSR loci, and 80,415 of the SSR loci were successfully located on 17 linkage groups (LGs). A total of 534 primer pairs were synthesized and preliminarily screened in four pear cultivars, and of these, 332 primer pairs were selected as clear, stable, and polymorphic SSR markers. Eighteen polymorphic SSR markers were randomly selected from the 332 polymorphic SSR markers in order to perform a further analysis of the genetic diversity among 44 pear cultivars. The 14 European pears and their hybrid materials were clustered into one group (European pear group); 29 Asian pear cultivars were clustered into one group (Asian pear group); and the Zangli pear cultivar ‘Deqinli’ from Yunnan Province, China, was grouped in an independent group, which suggested that the cultivar ‘Deqinli’ is a distinct and valuable germplasm resource. The population structure analysis partitioned the 44 cultivars into two populations, Pop 1 and Pop 2. Pop 2 was further divided into two subpopulations. Results from the population structure analysis were generally consistent with the results from the UPGMA cluster analysis.ConclusionsThe results of the present study showed that the use of next-generating sequencing to develop SSR markers is fast and effective, and the developed SSR markers can be utilized by researchers and breeders for future pear improvement.

Highlights

Pear (Pyrus spp.) is an economically important temperate fruit tree worldwide
simple sequence repeat (SSR) can be divided into genomic SSRs and genic SSRs, and genomic SSRs are usually derived from SSRenriched genomic libraries or random genomic sequences, while genic SSRs are derived from coding regions of the transcriptome or expressed sequence tag (EST) sequences [17, 26, 29]
Compared with genomic SSR markers, genic SSR markers are considered to link to the loci of agronomic phenotypes and are more useful for marker assisted selection (MAS), especially when polymorphic genic SSR markers were identified in breeding lines [29, 30]

Summary

Introduction

Pear (Pyrus spp.) is an economically important temperate fruit tree worldwide. In the past decade, significant progress has been made in pear molecular genetics based on DNA research, but the number of molecular markers is still quite limited, which hardly satisfies the increasing needs of geneticists and breeders. Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated units of 1–6 nucleotide sequence motifs flanked by unique sequences [6,7,8]. Given their wide distribution throughout the genome, codominant inheritance, and high polymorphism [7, 9, 10], SSRs have become desirable molecular markers for the construction of genetic linkage maps [11], genetic relationship identification [12], fingerprinting [13] and genetic diversity analyses [14,15,16,17]

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Discussion

Conclusion