文献类型：期刊文献

中文题名：日本落叶松SNP和InDel位点及其所在抗生物胁迫基因挖掘

英文题名：Identification of SNP,Indel and Their Located Biotic Stress Resistance Genes in Larix kaempferi

作者：王昕昊[1] 邢俊霞[1,2] 史胜青[1] 杨玲[1,2] 李万峰[1]

第一作者：王昕昊

机构：[1]林木遗传育种全国重点实验室、国家林业和草原局林木培育重点实验室、中国林业科学研究院林业研究所,北京100091;[2]林木遗传育种全国重点实验室东北林业大学,黑龙江哈尔滨150040

年份：2024

卷号：37

期号：5

起止页码：54-64

中文期刊名：林业科学研究

外文期刊名：Forest Research

收录：CSTPCD;;Scopus;北大核心:【北大核心2023】；CSCD:【CSCD2023_2024】；

基金：科技创新2030-重大项目(2022ZD0401602,2022ZD0401705)。

语种：中文

中文关键词：日本落叶松;分子标记;抗性基因;转录组

外文关键词：Larix kaempferi;molecular marker;resistance gene;transcriptome

分类号：S722;S791.223

摘要：[目的]挖掘日本落叶松SNP和InDel位点及其所在抗生物胁迫基因,为日本落叶松分子育种提供分子标记和候选基因。[方法]使用158份来自中国、日本和英国地区的日本落叶松转录组数据,首先进行分子标记位点的鉴定和分类,随后比较了活动期和休眠期基因的表达水平,最后将带有可靠分子标记的差异表达基因进行功能注释。[结果]本研究共鉴定到515935个SNP位点和1056个InDel位点,它们分布在35827个基因上。通过比较不同地区的位点数量,推测日本地区的日本落叶松遗传多样性较为丰富。至少在50份转录组中出现的非同义突变SNP位点有6444个,InDel位点为10个,它们分布在3742个基因上,可以作为可靠的分子标记进行利用。活动期和休眠期的转录组比较后,发现带有可靠分子标记的2569个基因差异表达;GO注释后发现其中101个基因与植物对真菌、细菌、卵菌、病毒、昆虫和线虫的抗性反应有关。[结论]这些结果不仅为日本落叶松全基因组关联分析和全基因组选择育种提供了分子标记,也为利用转基因和基因编辑手段进行遗传育种提供了候选基因。
[Objective]The SNPs,InDels and their located biotic stress resistance genes were investigated in Larix kaempferi to provide molecular markers and candidate genes for the molecular breeding of Larix kaempferi.[Method]158 transcriptome data generated from Larix kaempferi trees grown in China,Japan and the United Kingdom were used to identify SNPs and InDels firstly.Subsequently,the gene expression levels between the active and dormant stage were compared.Finally,the differentially expressed genes with reliable markers were functionally annotated.[Result]A total of 515935 SNPs and 1056 InDels were identified,and they were located in 35827 genes.Based on the number of SNP and InDel in the transcriptome from different regions,we speculated that the genetic diversity of Larix kaempferi was high in Japan.There were 6444 non-synonymous mutant SNPs and 10 InDels in at least 50 transcriptomes,which were located in 3742 genes,and these markers were reliable and could be used further.After comparing the transcriptomes of the active and dormant periods,a total of 2569 genes with reliable markers were differentially expressed,and 101 genes of them were associated with plant response to fungus,bacterium,oomycetes,virus,insect and nematode based on GO annotation.[Conclusion]These data provide molecular markers for genome-wide association study and genomic selection in Larix kaempferi,as well as candidate genes for genetic breeding by means of transgene and gene editing.