J Integr Plant Biol. ›› 2017, Vol. 59 ›› Issue (3): 190-204.DOI: 10.1111/jipb.12522

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple

Baiquan Ma1,2†, Liao Liao1,3†, Qian Peng1,2, Ting Fang1,2, Hui Zhou1,3, Schuyler S. Korban4 and Yuepeng Han1,3*   

  1. 1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
    2Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
    3Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
    4Department of Biology, University of Massachusetts Boston, Boston Massachusetts 02184, USA
  • Received:2016-11-23 Accepted:2017-01-15 Published:2017-01-17
  • About author:These authors contributed equally to this work.
    *Correspondence: E-mail: Yuepeng Han (yphan@wbgcas.cn)


Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphism with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2-value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.

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