Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement
Naibin DuanShandong Centre of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of ChinaYang BaiBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. [email protected]Honghe SunBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USANan WangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaYumin MaShandong Centre of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, People's Republic of ChinaMingjun LiState Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of ChinaXin WangBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USAChen JiaoBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USANoah LegallBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USALinyong MaoBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USASibao WanSection of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USAKun WangThe Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125100, People's Republic of ChinaTianming HeCollege of Forestry and Horticulture, Research Centre of Specialty Fruits, Xinjiang Agricultural University, Urumqi, Xinjiang, 830000, People's Republic of ChinaShouqian FengState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaZongying ZhangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaZhiquan MaoState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaXiang ShenState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaXiaoliu ChenState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaYuanmao JiangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaShu-Jing WuState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaChengmiao YinState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaShunfeng GeState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaLong YangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaShenghui JiangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaHaifeng XuState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaJingxuan LiuState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaDe Yun WangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaChangzhi QuState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaYicheng WangState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaWeifang ZuoState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaXiang LiState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaChang LiuMudanjiang Branch of Heilongjiang Academy of Agricultural Science, Mudanjiang, Heilongjiang, 157500, People's Republic of ChinaDaoyuan ZhangKey Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, 830011, People's Republic of ChinaYuan GaoThe Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125100, People's Republic of ChinaYimin XuBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USAKenong XuSection of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USAThomas C. ChaoUSDA-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY, 14456, USAGennaro FazioUSDA-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY, 14456, USAHuairui ShuState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of ChinaGan‐Yuan ZhongUSDA-Agricultural Research Service, Plant Genetic Resources Unit, Geneva, NY, 14456, USALailiang ChengSection of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USAZhangjun FeiBoyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. [email protected]Xuesen ChenState Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271000, People's Republic of China
2017en
ABI
Аннотация
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 is 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 have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a 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.Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.
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