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Title: Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

Author
item DUAN, NAIBIN - Shandong Agricultural University
item BAI, YANG - Boyce Thompson Institute
item SUN, HONGHE - Boyce Thompson Institute
item WANG, NAN - Shandong Agricultural University
item MA, YUMIN - Shandong Academy Of Agricultural Sciences
item JIAO, CHEN - Boyce Thompson Institute
item LEGAL, NOAH - Boyce Thompson Institute
item MAO, LINYONG - Boyce Thompson Institute
item WAN, SIBAO - Cornell University
item WANG, KUN - Chinese Academy Of Sciences
item HE, TIANMING - Xinjiang Agricultural University
item FENG, SHOUQIAN - Shandong Agricultural University
item ZHANG, ZONGYING - Shandong Agricultural University
item MAO, ZHIQUAN - Shandong Agricultural University
item SHEN, XIANG - Shandong Agricultural University
item CHEN, XIAOLIU - Shandong Agricultural University
item JIANG, YUANMAO - Shandong Agricultural University
item WU, SHUJING - Shandong Agricultural University
item YIN, CHENGMIAO - Shandong Agricultural University
item GE, SHUNFENG - Shandong Agricultural University
item YANG, LONG - Shandong Agricultural University
item JIANG, SHENGHUI - Shandong Agricultural University
item XU, HAIFENG - Shandong Agricultural University
item JIANG, YUANMAO - Shandong Agricultural University
item WU, SHUJING - Shandong Agricultural University
item YIN, CHENGMIAO - Shandong Agricultural University
item LIU, JINGXUAN - Shandong Agricultural University
item WANG, DEYUN - Shandong Agricultural University
item QU, CHANGZHI - Shandong Agricultural University
item WANG, YICHENG - Shandong Agricultural University
item ZUO, WEIFANG - Shandong Agricultural University
item XIANG, LI - Shandong Agricultural University
item LIU, CHANG - Heilongjiang Bayi Agricultural University (HLAU)
item ZHANG, DAOYUAN - Chinese Academy Of Sciences
item GAO, YUAN - Chinese Academy Of Agricultural Sciences
item XU, YIMIN - Boyce Thompson Institute
item LI, MINGJUN - Northwest Agricultural & Forestry University
item XU, KENONG - Cornell University
item Chao, Chihcheng
item SHU, HUAIRUI - Shandong Agricultural University
item Zhong, Gan-Yuan
item CHENG, LAILIANG - Cornell University
item FEI, ZHANGJUN - Boyce Thompson Institute
item CHEN, XUESEN - Shandong Agricultural University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2017
Publication Date: 8/15/2017
Citation: Duan, N., Bai, Y., Sun, H., Wang, N., Ma, Y., Jiao, C., Legal, N., Mao, L., Wan, S., Wang, K., He, T., Feng, S., Zhang, Z., Mao, Z., Shen, X., Chen, X., Jiang, Y., Wu, S., Yin, C., Ge, S., Yang, L., Jiang, S., Xu, H., Jiang, Y., Wu, S., Yin, C., Liu, J., Wang, D., Qu, C., Wang, Y., Zuo, W., Xiang, L., Liu, C., Zhang, D., Gao, Y., Xu, Y., Li, M., Xu, K., Chao, C.T., Shu, H., Zhong, G., Cheng, L., Fei, Z., Chen, X. 2017. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nature Communications. 8:A249.

Interpretive Summary: Apple is an important fruit crop in the world. Where apple was originated and how it was distributed through-out history is among one of many interesting questions in the minds of many apple researchers. This study investigated the genetic makeup of 117 diverse apple accessions from many countries, including several along the Silk Road, and concluded that cultivated apples likely originated from Malus sieversii (a wild apple species) in Kazakhstan, followed by intensive introgressions from M. sylvestris (another wild apple species). We also identified several genetic factors important for apple fruit texture and flavor and provided evidence that apple fruit size evolution went through two major events with one occurring prior to domestication and the other during domestication. The knowledge obtained from this study will provide valuable information for apple improvement.

Technical Abstract: Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road was proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an ‘ancient’ isolated ecotype not directly contributing to apple domestication. We identified selective sweeps underlying QTLs/genes of important fruit quality traits including fruit texture and flavor, and provided evidences supporting a novel model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.