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CIMMYT新引进合成小麦株高性状全基因组关联分析
张红杰1, 邓中印2, 陶姝2, 孙国梁2, 贾美玲2, 王振玉2, 廖如意2, 郑兴卫1, 李爱丽2, 毛龙2, 郑军1, 耿帅锋2
0
(1.山西大学生物工程学院;2.中国农业科学院作物科学研究所)
摘要:
株高是影响小麦产量的重要农艺性状。本研究对从国际玉米与小麦改良中心(CIMMYT)新引进的152份合成小麦在三个环境下的株高进行了观察和统计,并利用55 K单核苷酸多态性(SNP,Single nucleotide polymorphism)芯片进行全基因组关联分析(GWAS,Genome-wide association study),以挖掘与株高相关的新的遗传位点。结果表明:合成小麦株高呈正态分布,变异丰富。不同环境下的平均株高为97.9 cm,显著高于栽培小麦(70.5 cm),但低于黄淮麦区农家小麦(114.8 cm)。方差分析显示合成小麦株高在基因型、环境、环境与基因型互作方面的差异均达极显著水平。对获得的55K SNP标记经最大杂合率、最小等位基因频率及最大等位基因频率过滤,我们在合成小麦群体中发现 37916个有效SNP,其中A、B和D三个亚基因组上各有14404、14566和8946个。群体结构分析结果表明,152份合成小麦可分为三个亚群。利用混合线性模型(MLM,Mixed liner model)对不同环境下平均株高和最佳线性无偏预测值(BLUP,Best linear unbiased prediction)进行GWAS分析,筛选到24个显著标记(P≤0.0001),分别位于1A、3B、4A、4B、4D、5A、5B、6A、6D和7B染色体上,单个标记可解释12.33%-20.1%的表型变异。对BLUP值分析获得的10个显著标记左右3 Mb距离内的669个基因进行转录组数据筛查,得到131个在茎或叶中高表达(TPM≥5)。通过与水稻同源基因的比较,明确其中5个基因可能与小麦株高发育有关。鉴于这些位点与以往已定位的株高数量性状位点并不重叠,我们的工作可为小麦株高改良提供新的种质和分子标记。
关键词:  合成小麦  株高  55K SNP芯片  全基因组关联分析
DOI:10.13430/j.cnki.jpgr.20201208002
投稿时间:2020-12-08修订日期:2021-01-06
基金项目:国家自然科学基金(31661143007);山西省国际合作项目(201803D421021)
Genome-wide association study (GWAS) for plant height traits in synthetic wheat lines introduced in CIMMYT
ZHANG Hong-jie1, DENG Zhong-yin2, TAO Shu2, SUN Guo-liang2, JIA Mei-ling2, WANG Zhen-yu2, LIAO Ru-yi2, ZHENG Xing-wei, LI Ai-li2, MAO Long2, ZHENG Jun1, GENG Shuai-feng2
(1.College of Bioengineering,Shanxi University;2.Institute of Crop Sciences,Chinese Academy of Agricultural Sciences)
Abstract:
Plant height is an important agronomic trait that affects wheat yield. To identify new genetic loci that are significantly associated to plant height, the genome-wide association study (GWAS) was conducted using 152 newly introduced synthetic wheat lines from International Maize and Wheat Improvement Center (CIMMYT). This population was subjected for measuring plant height at three environments and genotyping using 55K single nucleotide polymorphism (SNP) chip. The plant height was observed with a a normal distribution in synthetic genotypes, with the mean value of 97.9 cm, which was higher than that of modern cultivars (70.5 cm) but lower than that of local landraces (114.8 cm) in Huanghuai zone. Analysis of variance showed significant differences in the plant height of synthetic wheat in genotype, environment and interaction between environment and genotype. 37916 markers were qualified using filtering parameters to be polymorphic including 14404, 14566 and 8946 SNPs on the A, B and D sub-genome respectively. Population structure analysis of 152 synthetic wheat lines suggested three groups. GWAS using the mixed liner model (MLM) on the best linear unbiased prediction values (BLUP) revealed 24 significant SNPs (P≤0.0001), which were found on chromosomes 1A, 3B, 4A, 4B, 4D, 5A, 5B, 6A, 6D and 7B, each explaining12.33%-20.1% of the phenotypic variation. The annotation in a physical interval of 3 Mb querying significant SNPs suggested a total of 669 genes, among which 131 genes were found highly expressed in wheat stems or leaves (TPM≥5) in public transcriptome data. According to the functional annotation of wheat gene models and rice gene homologs, we speculated that five genes were possibly involved in plant height development. Since these significant loci did not overlap with previously reported QTLs, they may represent new genetic loci in controlling plant height. Collectively, these results provided new germplasm and selection markers in order to improve plant height in wheat.
Key words:  synthetic wheat  plant height  55K SNP chip  Genome-wide association study

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