Development of a set of SNP markers present in expressed genes of the apple

被引：143

作者：

Chagne, David ^{[2
]}

Gasic, Ksenija ^{[1
]}

Crowhurst, Ross N.

Han, Yuepeng ^{[1
]}

Bassett, Heather C. ^{[2
]}

Bowatte, Deepa R. ^{[2
]}

Lawrence, Timothy J. ^{[3
]}

Rikkerink, Erik H. A. ^{[3
]}

Gardiner, Susan E. ^{[2
]}

Korban, Schuyler S. ^{[1
]}

机构：

[1] Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL 61801 USA

[2] Hort & Food Res Inst New Zealand HortRes, Palmerston North 4442, New Zealand

[3] HortRes Mt Albert, Auckland 1142, New Zealand

来源：

GENOMICS | 2008年 / 92卷 / 05期

关键词：

Malus x domestica; Single nucleotide polymorphisms; Expressed sequence tags; Candidate genes; Bin mapping;

D O I：

10.1016/j.ygeno.2008.07.008

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family. (C) 2008 Elsevier Inc. All rights reserved.

引用

页码：353 / 358

页数：6

共 42 条

[41]

Vision TJ, 2000, GENETICS, V155, P407

[42] A draft sequence of the rice genome (Oryza sativa L. ssp indica) [J].

Yu, J ;

Hu, SN ;

Wang, J ;

Wong, GKS ;

Li, SG ;

Liu, B ;

Deng, YJ ;

Dai, L ;

Zhou, Y ;

Zhang, XQ ;

Cao, ML ;

Liu, J ;

Sun, JD ;

Tang, JB ;

Chen, YJ ;

Huang, XB ;

Lin, W ;

Ye, C ;

Tong, W ;

Cong, LJ ;

Geng, JN ;

Han, YJ ;

Li, L ;

Li, W ;

Hu, GQ ;

Huang, XG ;

Li, WJ ;

Li, J ;

Liu, ZW ;

Li, L ;

Liu, JP ;

Qi, QH ;

Liu, JS ;

Li, L ;

Li, T ;

Wang, XG ;

Lu, H ;

Wu, TT ;

Zhu, M ;

Ni, PX ;

Han, H ;

Dong, W ;

Ren, XY ;

Feng, XL ;

Cui, P ;

Li, XR ;

Wang, H ;

Xu, X ;

Zhai, WX ;

Xu, Z .

SCIENCE, 2002, 296 (5565) :79-92

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