Yanyan Zhang, Xiaoya Huang, Long Zhang, Weidong Gao, Jingfu Ma, Tao Chen, Delong Yang
{"title":"小麦(Triticum aestivum L.)菱形样基因家族的全基因组鉴定、基因表达和单倍型分析。","authors":"Yanyan Zhang, Xiaoya Huang, Long Zhang, Weidong Gao, Jingfu Ma, Tao Chen, Delong Yang","doi":"10.1002/tpg2.20435","DOIUrl":null,"url":null,"abstract":"<p><p>The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":3.9000,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.).\",\"authors\":\"Yanyan Zhang, Xiaoya Huang, Long Zhang, Weidong Gao, Jingfu Ma, Tao Chen, Delong Yang\",\"doi\":\"10.1002/tpg2.20435\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.</p>\",\"PeriodicalId\":49002,\"journal\":{\"name\":\"Plant Genome\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2024-06-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Genome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1002/tpg2.20435\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/2/13 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/tpg2.20435","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/13 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.).
The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through various approaches, including gene structure analysis, evolutionary relationship analysis, promoter cis-acting element analysis, expression pattern analysis, and haplotype analysis. The 41 TaRBL genes were identified and divided into five subfamilies in the wheat genome. RBL family genes were expanded through segmented duplication and purification selection. The cis-element analysis revealed their involvement in various stress responses and plant development. The results of RNA-seq and quantitative real-time-PCR showed that TaRBL genes displayed higher expression levels in developing spike/grain and were differentially regulated under polyethylene glycol, NaCl, and abscisic acid treatments, indicating their roles in grain development and abiotic stress response. A kompetitive allele-specific PCR molecular marker was developed to confirm the single nucleotide polymorphism of TaRBL14a gene in 263 wheat accessions. We found that the elite haplotype TaRBL14a-Hap2 showed a significantly higher 1000-grain weight than TaRBL14a-Hap11 in at least three environments, and the TaRBL14a-Hap2 was positively selected in wheat breeding. The findings will provide a good insight into the evolutionary and functional characteristics of the TaRBL genes family in wheat and lay the foundation for future exploration of the regulatory mechanisms of TaRBL genes in plant growth and development, as well as their response to abiotic stresses.
期刊介绍:
The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.