中国农业科学 ›› 2024, Vol. 57 ›› Issue (21): 4192-4204.doi: 10.3864/j.issn.0578-1752.2024.21.003

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

青海省青稞主栽品种昆仑14与昆仑15的基因组序列多态性比较

徐金青1(), 边海燕1,2, 陈同睿1,2, 王蕾1, 王寒冬1, 尤恩1,2, 邓超1,2, 唐有林1, 沈裕虎1,3()   

  1. 1 中国科学院西北高原生物研究所/中国科学院高原适应与进化重点实验室/青海省作物分子育种重点实验室/青藏高原作物种质资源研究与利用实验室,西宁 810008
    2 中国科学院大学生命科学学院,北京 100049
    3 中国科学院种子创新研究院,西宁 810008
  • 收稿日期:2024-05-02 接受日期:2024-07-12 出版日期:2024-11-01 发布日期:2024-11-10
  • 通信作者:
    沈裕虎,E-mail:
  • 联系方式: 徐金青,E-mail:xujq@nwipb.cas.cn。
  • 基金资助:
    国家自然科学基金青年科学基金(32101714); 青海省基础研究计划青年项目(2021-ZJ-967Q); 中国科学院青年创新促进会(2023451); 中国科学院-青海省人民政府三江源国家公园联合专项(LHZX-2022-03); 青海省“昆仑英才高端创新创业人才”计划培养领军人才项目(青人才字[2023]1号)

Comparison of the Genome Sequence Polymorphisms Between the Main Naked Barley Varieties Kunlun 14 and Kunlun 15 in Qinghai Province

XU JinQing1(), BIAN HaiYan1,2, CHEN TongRui1,2, WANG Lei1, WANG HanDong1, YOU En1,2, DENG Chao1,2, TANG YouLin1, SHEN YuHu1,3()   

  1. 1 Northwest Institute of Plateau Biology, Chinese Academy of Sciences/Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB)/Qinghai Provincial Key Laboratory of Crop Molecular Breeding/Laboratory for Research and Utilization of Qinghai-Tibetan Plateau Germplasm Resources, Xining 810008
    2 College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049
    3 Innovation Academy for Seed Design (INASEED), Chinese Academy of Sciences, Xining 810008
  • Received:2024-05-02 Accepted:2024-07-12 Published:2024-11-01 Online:2024-11-10

摘要:

【目的】昆仑14和昆仑15是目前青海省青稞的主栽品种,也是青稞育种工作中重要的骨干亲本。比较昆仑14和昆仑15的基因组序列,为青稞重要性状区间/位点追溯、系谱分析及其二者在分子设计育种方面的利用提供参考。【方法】在田间调查昆仑14和昆仑15的农艺性状和籽粒性状,并进行全基因组重测序(测序深度≥15×)。系统比较2个品种拷贝数变异(CNV)、单核苷酸多态性(SNP)和插入/缺失(InDel)等序列差异。以SNP分布规律为依据,鉴定二者之间的多态性热点区间和序列相似区间。比较分析多态性热点区间和序列相似区间的突变类型。对2个品种的特有CNV变异区间和多态性热点区间内的基因进行富集分析。【结果】除株高和穗下节长度外,二者在其他农艺性状和籽粒性状上存在较高的相似性。与大麦Morex参考基因组相比,2个品种有83 Mb共有CNV变异区间,昆仑14和昆仑15特有的CNV变异区间总长分别为37和38 Mb。昆仑14特有CNV区间内含有564个基因,显著富集在15个GO条目中。昆仑15特有CNV区间内含有519个基因,显著富集在7个GO条目中。在全基因组水平鉴定出昆仑14和昆仑15存在1 706 Mb多态性热点区间和2 411 Mb序列相似区间。多态性热点区间内含有16 768个基因,其功能主要与植物生长发育相关。多态性热点区间和序列相似区间在SNP变异类型、InDel长度分布、突变影响编码功能的比例上差别不大。多态性热点区间和序列相似区间中基因序列上的SNP与InDel变异的类型主要是错义突变,其次是同义突变。【结论】昆仑14和昆仑15的田间表型相似,全基因组水平上,二者之间存在75 Mb的CNV变异区间,差异多态性热点区间主要分布在3H、6H和7H。

关键词: 青稞, 昆仑14, 昆仑15, 重测序, 多态性

Abstract:

【Objective】At present, Kunlun 14 and Kunlun 15 are the main varieties of the naked barley in Qinghai Province, and also the important backbone parents in the breeding of the naked barley. The genomic sequences of Kunlun 14 and Kunlun 15 were compared to provide references for the trace of important character regions/loci, pedigree analysis and their utilization in molecular design breeding of the naked barley. 【Method】In this study, the agronomic and grain traits of Kunlun 14 and Kunlun 15 were investigated in the field, and the whole genome resequencing were performed (sequencing depth ≥15×). The sequence differences of copy number variation (CNV), single nucleotide polymorphism (SNP) and insertion/deletion (InDel) were compared between the two varieties. According to the SNP distribution patterns, the polymorphism hotspot and genetic similar regions between them were identified. The mutation types of polymorphism hotspot and genetic similar regions were compared and analyzed. The gene enrichment analysis was carried out in the specific CNV regions and the polymorphism hotspots regions of the two varieties. 【Result】In addition to the plant height and peduncle internode length, Kunlun 14 and Kunlun 15 had high similarity in important agronomic and grain traits. Compared with the barley reference genome of Morex, the two varieties had a common CNV variation interval of 83 Mb, and the length of cultivar-specific CNV variation interval in Kunlun 14 and Kunlun 15 was 37 Mb and 38 Mb, respectively. There were 564 genes in the CNV region specific to Kunlun 14, which were significantly enriched in 15 GO terms, while 519 genes were in the CNV region specific to Kunlun 15 and were significantly enriched in 7 GO terms. Based on the SNP distribution patterns, 1 706 Mb polymorphism hotspots and 2 411 Mb sequence similarity intervals of Kunlun 14 and Kunlun 15 were identified at the whole genome level, and the polymorphism hotspots were mainly distributed on 3H, 6H and 7H. The polymorphism hotspots regions contained 16 768 genes, whose functions were mainly related to plant growth and development. There was no significant difference between polymorphism hotspot regions and genetic similar regions in SNP variation type, InDel length distribution and the proportion of mutations affecting coding function. The SNPs and InDel mutations in polymorphism hotspot and genetic similar regions were mainly missense mutations and followed by synonymy mutations. 【Conclusion】The field phenotypes of Kunlun 14 and Kunlun 15 were similar. At the whole genome level, a total of 75 Mb CNV variation regions between them and the polymorphism hotspot regions were mainly distributed at 3H, 6H and 7H.

Key words: naked barley (Hordeum vulgare var. coeleste L.), Kunlun 14, Kunlun 15, re-sequencing, polymorphism