CAREER: Using a Century Scale Experiment to Decode the Molecular Basis of Crop Competitiveness

职业：利用一个世纪规模的实验来解码作物竞争力的分子基础

• 批准号: 2046256
• 负责人: Daniel Koenig
• 金额: $ 168.66万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2046256&HistoricalAwards=false
• 关键词: CAREER; Using; Century; Scale; Experiment

The food supply is dependent on the ability of plant species to survive in a wide variety of environments. Most crops emerged from limited geographical ranges but were rapidly disseminated into highly variable conditions across the globe. Though selection of crop varieties best adapted to specific locales is critical for maximizing agricultural yields, our understanding of the genetic basis of crop adaptation remains in its infancy. This is partly because the process of plant adaptation occurs over the course of decades making it difficult for plant geneticists to study. To directly observe the process of adaptation, this project will use the barley composite crosses (CCs) common garden experiments, a novel series of agricultural genetics experiments begun nearly a century ago in barley. In these experiments, genetically diverse sets of barley varieties were competed in multiple locations over the course of decades. Using modern genomics techniques, this project will uncover and link the genes that underlie competitive ability revealed in these experiments to changes in important agricultural traits such as flowering time, plant size, and yield. Through this project, hundreds of undergraduate students will participate in the discovery of genetic shifts in the population as part of a reenvisioned introductory biology curriculum that involves hands-on experiments using molecular biology techniques. Plant materials, phenotypic observations, and billions of DNA sequences produced by this project will be made rapidly available for use by researchers and small grains breeders world-wide.The longevity of the composite crosses makes them an unparalleled genetic resource to study the molecular basis of crop adaptation. The primary goals of this project are to identify genes that underlie crop fitness in variable environments, to explore the genetic process of adaptation over time, and to understand how molecular changes translate into phenotypic differences. To achieve these goals, structural and single nucleotide variants that segregated at the beginning of the experiments will be identified by resequencing the genomes of the forty parental barley cultivars using long read sequencing technologies. The evolution of these variants will be monitored as the composite cross populations adapt to two distinct environments, one located in Bozeman (MT), the other in Davis (CA). Using this comparative approach will allow for the characterization of the rate and mode of genetic change throughout the genome and will result in the identification of suites of genes that drive increases in barley fitness. Finally, genotypes will be linked to phenotypes by creating and using a powerful new barley multiparent mapping population from the composite cross material to identify the genomic basis of numerous adaptive traits, to link changes in gene expression to changes in phenotype, and to reveal how the genetic architecture of trait variation shapes adaptive evolution.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.

食物供应取决于植物物种在各种环境中生存的能力。大多数农作物生长在有限的地理范围内，但迅速传播到地球仪各地的高度变化的条件下。虽然选择最适合特定地区的作物品种对于最大限度地提高农业产量至关重要，但我们对作物适应性遗传基础的理解仍处于起步阶段。这部分是因为植物适应的过程需要几十年的时间，这使得植物遗传学家很难研究。为了直接观察适应过程，该项目将使用大麦复合杂交（CC）普通花园实验，这是一系列近世纪前开始的大麦农业遗传学实验。 在这些实验中，遗传多样性的大麦品种在几十年的时间里在多个地点进行了竞争。利用现代基因组学技术，该项目将发现并将这些实验中揭示的竞争能力背后的基因与重要农业性状（如开花时间，植物大小和产量）的变化联系起来。通过这个项目，数百名本科生将参与发现人口中的遗传变化，作为重新设想的生物学入门课程的一部分，该课程涉及使用分子生物学技术的动手实验。该项目产生的植物材料、表型观察结果和数十亿个DNA序列将迅速提供给世界各地的研究人员和小粒谷物育种者使用。复合杂交的寿命使其成为研究作物适应性分子基础的无与伦比的遗传资源。该项目的主要目标是确定在可变环境中作物适应性的基础基因，探索随着时间的推移适应的遗传过程，并了解分子变化如何转化为表型差异。为了实现这些目标，在实验开始时分离的结构和单核苷酸变体将通过使用长读段测序技术对40个亲本大麦栽培品种的基因组进行重测序来鉴定。随着复合杂交群体适应两个不同的环境，一个位于Bozeman（MT），另一个位于Davis（CA），将监测这些变体的演变。使用这种比较方法将允许整个基因组的遗传变化的速率和模式的表征，并将导致在驱动大麦健身增加的基因套件的识别。最后，通过从复合杂交材料中创建和使用强大的新大麦多亲本作图群体，将基因型与表型联系起来，以鉴定许多适应性性状的基因组基础，将基因表达的变化与表型的变化联系起来，并揭示性状变异的遗传结构如何塑造适应性进化。该奖项反映了NSF的法定使命，并被认为值得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。

项目成果

A KARRIKIN INSENSITIVE2 paralog in lettuce mediates highly sensitive germination responses to karrikinolide

• DOI: 10.1101/2021.10.13.464162
• 发表时间: 2021-10
• 期刊: bioRxiv
• 作者: Stephanie E. Martinez;Caitlin E. Conn;Angelica M. Guercio;C. Sepulveda;Christopher J. Fiscus;Daniel Koenig;N. Shabek;David C. Nelson

Measuring hidden phenotype: quantifying the shape of barley seeds using the Euler characteristic transform

• DOI: 10.1093/insilicoplants/diab033
• 发表时间: 2022-01-01
• 期刊: IN SILICO PLANTS
• 影响因子: 3.1
• 作者: Amezquita, Erik J.;Quigley, Michelle Y.;Chitwood, Daniel H.
• 通讯作者: Chitwood, Daniel H.