Unraveling the genetic basis of amino acid composition in dry Arabidopsis seeds

揭示干燥拟南芥种子氨基酸组成的遗传基础

• 批准号: 1754201
• 负责人: Ruthie Angelovici
• 金额: $ 82.78万
• 依托单位: University of Missouri-Columbia
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1754201&HistoricalAwards=false
• 关键词: Unraveling; genetic; basis; amino; acid

Essential amino acids are necessary for human health but must come from dietary sources, as the human body cannot produce them. A lack of these essential amino acids in a diet leads to malnutrition. Much of the world's human and livestock populations rely on seeds for protein, but most staple crops seeds are deficient in several essential amino acids. Efforts to fortify the amino acid composition of staple crop seeds have had limited success since plants respond to induced protein composition alterations by activating a regulatory mechanism that "resets" it back to an original state. While beneficial to the plant growth and development, this mechanism has been a major hurdle to biofortification efforts. Fortunately, it is also known that different cultivars/varieties display natural variation in their seed amino acid composition, which means that the regulation of these compounds is genetically driven and thus should be amenable to manipulation. Therefore, this project aims to identify the key genes involved in this regulatory mechanism by analyzing hundreds of Arabidopsis strains, which display natural genetic and seed amino acid composition variation. Subsequently the potential role of the identified candidate genes will be tested using classical physiological and genetic approaches. Identifying new genetics targets will help facilitate the breeding of new crop varieties that can support our nation's and world's growing population.It is important to identify the genes that underlie the amino acid composition of dry seeds. Doing so will shed new light on a complex regulatory mechanism in plants as well as facilitate efforts to fortify staple seed crops. While much is known about amino acid metabolic pathways, little is known about their regulation, especially in seeds. So far, it is known that alterations to the composition of seed storage proteins (i.e., the major amino acid sink) lead to proteomic reprogramming and activation of a rebalancing mechanism, a response that suggests tight regulation of this trait. Seed amino acid composition varies substantially across genotypes within the same genus. This observation implies that the genetic architecture responsible for this natural variation includes, at least in part, the genes involved in responding to amino acid sink alteration and activation of the rebalancing mechanism. This project aims to elucidate key components of this genetic architecture in Arabidopsis thaliana using two approaches: (1) a GWAS on amino acid composition measured from dry seeds of an 800-accession association panel and (2) an amino acid/gene expression correlation-based network analysis of wildtype and two storage protein mutants with active rebalancing phenotypes. The candidate genes identified from each approach will be compared, and the top candidate genes will be tested for involvement in amino acid regulation via knockdown and overexpression experiments. The identified genetic regulators will provide new targets for breeding programs.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

必需氨基酸是人体健康所必需的，但必须来自饮食来源，因为人体不能产生它们。饮食中缺乏这些必需氨基酸会导致营养不良。世界上大部分的人类和牲畜都依赖种子来获取蛋白质，但大多数主食作物的种子都缺乏几种必需氨基酸。强化主食作物种子的氨基酸组成的努力取得了有限的成功，因为植物通过激活调节机制将其“重置”回原始状态来响应诱导的蛋白质组成改变。虽然这种机制有利于植物的生长和发育，但它一直是生物强化努力的主要障碍。幸运的是，还已知不同的栽培种/品种在其种子氨基酸组成中显示出天然变异，这意味着这些化合物的调节是遗传驱动的，因此应该易于操纵。因此，本项目旨在通过分析数百个拟南芥菌株来确定参与这种调控机制的关键基因，这些菌株显示天然遗传和种子氨基酸组成变异。 随后，将使用经典的生理学和遗传学方法来测试所识别的候选基因的潜在作用。确定新的遗传学目标将有助于促进新作物品种的培育，以支持我们国家和世界不断增长的人口。重要的是要确定干种子氨基酸组成的基因。这样做将为植物中复杂的调节机制提供新的线索，并促进加强主食种子作物的努力。虽然人们对氨基酸代谢途径了解很多，但对其调节却知之甚少，尤其是在种子中。到目前为止，已知改变种子贮藏蛋白的组成（即，主要氨基酸库）导致蛋白质组重编程和再平衡机制的激活，这一反应表明该性状的严格调节。同一属内不同基因型的种子氨基酸组成差异很大。这一观察结果意味着，负责这种自然变异的遗传结构至少部分包括参与响应氨基酸库改变和再平衡机制激活的基因。该项目旨在阐明拟南芥中这种遗传结构的关键组成部分，使用两种方法：（1）从800个登录关联面板的干种子中测量的氨基酸组成的GWAS和（2）野生型和两个具有主动再平衡表型的存储蛋白突变体的基于氨基酸/基因表达相关性的网络分析。将比较从每种方法中鉴定的候选基因，并通过敲低和过表达实验测试最佳候选基因是否参与氨基酸调控。 该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS

HAPPI GWAS：集成前后 GWAS 的整体分析

• DOI: 10.1093/bioinformatics/btaa589
• 发表时间: 2020
• 期刊: Bioinformatics
• 影响因子: 5.8
• 作者: Slaten, Marianne L;Chan, Yen On;Shrestha, Vivek;Lipka, Alexander E;Angelovici, Ruthie
• 通讯作者: Angelovici, Ruthie

A High-Throughput Absolute-Level Quantification of Protein-Bound Amino Acids in Seeds

种子中蛋白质结合氨基酸的高通量绝对水平定量

• DOI: 10.1002/cppb.20084
• 发表时间: 2018
• 期刊: Current Protocols in Plant Biology
• 作者: Yobi, Abou;Angelovici, Ruthie
• 通讯作者: Angelovici, Ruthie

Assessment of two statistical approaches for variance genome-wide association studies in plants

• DOI: 10.1038/s41437-022-00541-1
• 发表时间: 2022-05-10
• 期刊: HEREDITY
• 影响因子: 3.8
• 作者: Murphy，Matthew D.;Fernandes，Samuel B.;Lipka，Alexander E.
• 通讯作者: Lipka，Alexander E.

A High‐Throughput Absolute Quantification of Protein‐Bound Tryptophan from Model and Crop Seeds

对模型和作物种子中的蛋白质结合色氨酸进行高通量绝对定量

• DOI: 10.1002/cpz1.862
• 发表时间: 2023
• 期刊: Current Protocols
• 作者: Ansaf, Huda;Yobi, Abou;Angelovici, Ruthie
• 通讯作者: Angelovici, Ruthie

A High‐Throughput Absolute Quantification of Protein‐Bound Sulfur Amino Acids from Model and Crop Plant Seeds

对模型和作物种子中的蛋白质结合硫氨基酸进行高通量绝对定量

• DOI: 10.1002/cpz1.861
• 发表时间: 2023
• 期刊: Current Protocols
• 作者: Yobi, Abou;Ansaf, Huda;Angelovici, Ruthie
• 通讯作者: Angelovici, Ruthie