小麦主栽品种济麦22与良星99的基因组序列多态性比较分析  

Comparative analysis of the genomic sequences between commercial wheat varieties Jimai 22 and Liangxing 99

作　　者：杨正钊 王梓豪 胡兆荣 辛明明 姚颖垠 彭惠茹 尤明山 宿振起 郭伟龙 YANG Zheng-Zhao;WANG Zi-Hao;HU Zhao-Rong;XIN Ming-Ming;YAO Ying-Yin;PENG Hui-Ru;YOU Ming-Shan;SU Zhen-Qi;GUO Wei-Long(College of Agronomy and Biotechnology/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization,Ministry of Education,China Agricultural University,Beijing 100193,China)

机构地区：[1]中国农业大学农学院/农业生物技术国家重点实验室/杂种优势研究与利用教育部重点实验室,北京100193

出　　处：《作物学报》2020年第12期1870-1883,共14页Acta Agronomica Sinica

基　　金：国家重点研发计划项目(2018YFD0100803);国家自然科学基金项目(31701415);中央高校基本科研业务费专项资助。

摘　　要：济麦22和良星99是我国黄淮冬麦区和北部冬麦区大面积推广的高产小麦品种,也是目前小麦杂交育种的重要亲本。虽然济麦22和良星99的来源和系谱不同,但在重要农艺、产量等性状上存在较高的相似性。为了从全基因组水平研究其遗传组成的异同,本研究采用IlluminaHiSeq2500测序平台对上述两个品种进行了全基因组测序(平均测序深度为5.8×),并系统地比较了两个品种拷贝数变异(CNV)、单核苷酸多态性(SNP)和插入/缺失(InDel)的序列差异。与中国春参考基因组序列相比,两个品种除了具有总长466 Mb的共有CNV变异区间外,济麦22和良星99的特有CNV变异区间的总长分别为91Mb和45Mb,这些特有CNV区间主要集中在2B和4B染色体上;济麦22和良星99间存在1,547,371个SNP差异位点和137,817个InDel差异位点。以差异SNP分布规律为依据,在全基因组水平鉴定出济麦22和良星99间存在14.2%的差异多态性热点区间,这些区间集中分布在1D、2B和4B染色体上。通过对5个控制小麦株高和穗长基因的序列分析,发现有2个位于多态性热点区间的基因在品种间存在移码突变。本研究为利用重测序数据在基因组水平上比较小麦品种间遗传差异提供了重要参考,同时揭示了济麦22和良星99在全基因组的遗传相似区间和差异区间,为今后小麦育种改良中更好利用济麦22与良星99提供了重要遗传信息。Jimai 22 and Liangxing 99 are high-yield wheat varieties widely planted in the North Huang-Huai Rivers Valley Winter Wheat Zone and Northern Winter Wheat Zone in China,and are currently used as important parents in wheat breeding programs.Although the origins and pedigrees of Jimai 22 and Liangxing 99 are different,they are highly similar in many important agronomic traits,yield-associated traits,and so on.To identify the genomic differences between the two varieties,we performed whole-genome sequencing using the Illumina HiSeq2500 platform,with an average sequencing depth of 5.8×.We aligned the raw sequencing data against the Chinese Spring reference genome and identified the difference of copy-number variation(CNV)regions,single-nucleotide polymorphisms(SNPs)and InDels in sequence between the two varieties.Lengths of 466 Mb CNV intervals were shared by the two varieties.The lengths of cultivar-specific CNV intervals in Jimai 22 and Liangxing 99 were 91 Mb and 45 Mb,respectively,and these intervals are mainly located on chromosomes 2B and 4B.Beyond the CNV intervals,1,547,371 SNPs and 137,817 InDels were different between the two cultivars.Based on the distribution of SNP densities in the intervals,we identified the polymorphic hotspot regions on chromosomes 1D,2B,and 4B,making up 14.2%of the whole genome.The sequences of five previous cloned dwarf genes and spike length related genes were investigated,and two genes located in the polymorphic hotspot regions were detected with the frame shift variations.This study provides an important guidance for evaluating the genetic differences between two wheat varieties in the genomic level,and also identified both genetic similarity regions and polymorphic hotspot regions between Jimai 22 and Liangxing 99,which provided a valuable genetic information for future genetic improvement utilizing Jimai 22 and Liangxing 99 as parents.

关 键 词：小麦 济麦22 良星99 全基因组重测序 SNP CNV 

分 类 号：S512.1[农业科学—作物学]