Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding

文献类型： 外文期刊

第一作者： Zhou, Degui

作者： Zhou, Degui;Wang, Chongrong;Li, Hong;Li, Kanghuo;Zhou, Shaochuan;Chen, Wei;Lin, Zechuan;Chen, Haodong;Yu, Renbo;Zhen, Gang;He, Hang;Deng, Xing Wang;Chen, Wei;Lin, Zechuan;Chen, Haodong;Yu, Renbo;Zhen, Gang;He, Hang;Deng, Xing Wang;Chen, Wei;Chen, Haodong;Yu, Renbo;Zhen, Gang;Tang, Xiaoyan;He, Hang;Deng, Xing Wang;Zhang, Fengyun;Yi, Junliang;Zhou, Shaochuan;Liu, Yaoguang;Terzaghi, William;He, Hang;Deng, Xing Wang

作者机构：

关键词： genetic improvement;resequencing;single nucleotide polymorphisms;pedigree;artificial selection;breeding

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：9.803； 五年影响因子：9.555 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6x depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design.

分类号： Q7

  • 相关文献

[1]Genetic improvement and breeding of tea plant (Camellia sinensis) in China: from individual selection to hybridization and molecular breeding. Chen, Liang,Zhou, Zhi-Xiu,Yang, Ya-Jun. 2007

[2]Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers. Wang, K.,Zhuang, J. Y.,Huang, D. R.,Ying, J. Z.,Fan, Y. Y.. 2015

[3]Genetic variability assessed by microsatellites in the breeding populations of the shrimp Penaeus (Fenneropenaeus) chinensis in China. Zhang, Tianshi,Kong, Jie,Wang, Weiji,Wang, Qingyin,Zhang, Tianshi.

[4]Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Lei Fang,Hao Gong,Yan Hu,Chunxiao Liu,Huang, Xuehui,Zhang, Tianzhen,Baoliang Zhou,Tao Huang,Yangkun Wang,Shuqi Chen,David D. Fang,Xiongming Du,Hong Chen,Jiedan Chen,Sen Wang,Qiong Wang,Qun Wan,Bingliang Liu,Mengqiao Pan,Lijing Chang,Huaitong Wu,Gaofu Mei,Dan Xiang,Xinghe Li,Caiping Cai,Xiefei Zhu,Z. Jeffrey Chen,Bin Han,Xiaoya Chen,Wangzhen Guo,Tianzhen Zhang,Xuehui Huang. 2017

[5]Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars. Yuan, Yang,Yuan, Yang,Zeng, Shuiyun,Gu, Longjiang,Si, Weina,Zhang, Xiaohui,Tian, Dacheng,Yang, Sihai,Wang, Long,Zhang, Qijun. 2017

[6]Application of resequencing to rice genomics, functional genomics and evolutionary analysis. Guo, Longbiao,Gao, Zhenyu,Qian, Qian. 2014

[7]Pooled mapping: an efficient method of calling variations for population samples with low-depth resequencing data. Fu, Lixia,Cai, Chengcheng,Cui, Yinan,Wu, Jian,Liang, Jianli,Cheng, Feng,Wang, Xiaowu.

[8]Deep resequencing reveals allelic variation in Sesamum indicum. Wang, Linhai,Zhang, Yanxin,Li, Donghua,Wei, Xin,Ding, Xia,Zhang, Xiurong,Han, Xuelian,Han, Xuelian. 2014

[9]Biparental Resequencing Coupled With SNP Genotyping of a Segregating Population Offers Insights Into the Landscape of Recombination and Fixed Genomic Regions in Elite Soybean. Li, Ying-hui,Liu, Yu-lin,Liu, Zhang-xiong,Liu, Bo,Chang, Ru-zhen,Qiu, Li-juan,Reif, Jochen C.,Mette, Michael F.. 2014

[10]GPOPSIM: a simulation tool for whole-genome genetic data. Zhang, Zhe,Li, Jiaqi,Li, Xiujin,Ding, Xiangdong,Zhang, Qin. 2015

[11]Pedigree tracing of Fenneropenaeus chinensis by microsatellite DNA markers genotyping. Dong Shirui,Kong Jie,Zhang Qingwen,Liu Ping,Meng Xianhong,Wang Rucai. 2006

[12]Tracing sources of dwarfing genes in barley breeding in China. Zhang, J,Zhang, WX. 2003

[13]Inbreeding and coancestry of the major commercial fresh market peach cultivars in China. Ma, Ruijuan,Yu, Mingliang,Du, Ping,Shen, Zhijun,Byrne, David H.. 2006

[14]Genetic diversity among a founder parent and widely grown wheat cultivars derived from the same origin based on morphological traits and microsatellite markers. Li, X. J.,Xu, X.,Yang, X. M.,Li, X. Q.,Liu, W. H.,Gao, A. N.,Li, L. H.,Li, X. J.,Xu, X..

[15]Genetic relatedness among Aechmea species and hybrids inferred from AFLP markers and pedigree data. Zhang, Fei,Wang, Weiyong,Ge, Yaying,Shen, Xiaolan,Tian, Danqing,Liu, Jianxin,Liu, Xiaojing,Yu, Xinyin,Zhang, Zhi.

[16]QTL mapping for fiber quality traits across multiple generations and environments in upland cotton. Fu-Ding Sun,Jian-Hong Zhang,Shu-Fang Wang,Wan-Kui Gong,Yu-Zhen Shi,Ai-Ying Liu,Jun-Wen Li,Ju-Wu Gong,Hai-Hong Shang,You-Lu Yuan.

[17]Analysis of Fitness Predominance for Gaoyou Duck's Double Yolk Egg. Zhang, Tangjie,Chang, Hong,Li, Hui-Fang,Chen, Kuanwei,Zhao, Yonggao,Xuec, Minkai,Zhang, Shengfu. 2011

[18]A genomic perspective on the important genetic mechanisms of upland adaptation of rice. Lyu, Jun,Gou, Zhiheng,Wang, Wen,Li, Baoye,Zhang, Shilai,Zhang, Jing,Tao, Dayun,Huang, Wangqi,Hu, Fengyi,He, Weiming,Meng, Liyun,Li, Xin. 2014

[19]Functional markers in wheat: current status and future prospects. Liu, Yanan,He, Zhonghu,Xia, Xianchun,He, Zhonghu,Appels, Rudi.

[20]A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata. Zou, Keshu,Zhang, Dianchang,Guo, Huayang,Zhu, Caiyan,Li, Min,Jiang, Shigui,Zou, Keshu,Zhang, Dianchang,Li, Min,Jiang, Shigui.

作者其他论文 更多>>

微信小程序