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

食物供应取决于植物物种在各种环境中生存的能力。大多数作物起源于有限的地理范围，但在全球范围内迅速传播到高度变化的环境中。虽然选择最适合特定地区的作物品种对农业产量最大化至关重要，但我们对作物适应的遗传基础的理解仍处于起步阶段。这部分是因为植物的适应过程发生在几十年的过程中，这使得植物遗传学家很难研究。为了直接观察适应过程，本项目将使用大麦复合杂交（cc）普通园艺试验，这是近一个世纪前开始的大麦一系列新颖的农业遗传学试验。在这些实验中，基因多样化的大麦品种在几十年的时间里在多个地方竞争。利用现代基因组学技术，该项目将揭示这些实验中揭示的竞争能力与重要农业性状（如开花时间、植物大小和产量）变化的基因，并将其联系起来。通过这个项目，数百名本科生将参与到人口遗传变化的发现中，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、表型观察和数十亿个DNA序列将迅速提供给全世界的研究人员和小谷物育种者使用。复合杂交的长寿性使其成为研究作物适应分子基础的无可比拟的遗传资源。该项目的主要目标是鉴定作物在可变环境下适应性的基因，探索适应时间的遗传过程，并了解分子变化如何转化为表型差异。为了实现这些目标，将利用长读测序技术对40个亲本大麦品种的基因组进行重测序，从而鉴定在实验开始时分离的结构和单核苷酸变异。当复合杂交种群适应两个不同的环境时，这些变异的进化将被监测，一个位于Bozeman (MT)，另一个位于Davis （CA）。使用这种比较方法将允许对整个基因组中遗传变化的速率和模式进行表征，并将导致识别驱动大麦适应性增加的基因套件。最后，基因型将与表型联系起来，通过创建和使用一个强大的新的大麦多亲本定位群体，从复合交叉材料中识别许多适应性性状的基因组基础，将基因表达变化与表型变化联系起来，并揭示性状变异的遗传结构如何影响适应性进化。该奖项反映了美国国家科学基金会的法定使命，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。

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.