Research-PGR: dissecting the dynamic evolution of paralogs in shaping trait variation across the solanum pan-genome

Active Project Grant Awarded Last action

Award ID
2216612
Recipient
Awarding agency
Obligated
$4,800,000

Award facts

Assistance listing
47.074 Biological Sciences
Completion date 85% complete
Place of performance
Cold Spring Harbor, NY 11724, USA

Award details come from USAspending.gov.

Description

As the agency reported it.

Abstract
The growing population and climate extremes are threatening food security. Agriculture is largely based on a few major crops, and revolutionary technologies in genome sequencing and crispr genome engineering are accelerating their improvement. These technologies can also improve ?orphan? Crops, which are not widely cultivated or studied but have the potential to increase the diversity and resilience of food production. Orphan crops are related to major crops, allowing translation of knowledge between them. However, orphan crops lack research tools, and an even greater challenge is determining whether specific genetic mutations that benefitted major crops can be engineered to improve traits similarly in orphan crops. This is because gene sequence and function change as species evolve, especially among genes that become duplicated, which is common in plants. This project will take advantage of the nightshade family ? A source of many major and orphan crops, such as eggplant, pepino, and tomato ? To study how duplicated genes evolve and affect agricultural traits in related species. Combining genome sequencing and crispr will reveal sequence diversity among thousands of duplicated genes and enable improved predictability in engineering genes and traits across species. This project will train young scientists with a focus on diversity and inclusion, as well as promote public understanding of genome engineering in plant biology through a community science program on orphan crops. Finally, new curricula and research opportunities for undergraduate students at a small liberal arts college will broaden participation and training of underrepresented groups in the plant sciences. This project will exploit advances in large-scale reference genome sequencing, gene CO-expression analyses, and crispr genome editing to dissect how paralog diversification impacts species-specific phenotypes in a genus of both fundamental and applied importance. Fifty solanum species, including 16 orphan crops, will be sequenced to establish a solanum pan-genome with telomere-to-telomere reference assemblies, providing a foundation for genus-wide comparative genomics and functional genetics. Computational approaches based on genomics data will be developed for precise assembly and comparison of complex genomes, and identification and classification of paralogs and their relationships based on their variants and expression patterns. Simultaneously, transformation protocols and genome editing will be developed and deployed for an array of solanum to test how paralogs impact genotype-to-phenotype relationships within and between species. By focusing on major domestication gene families and the adaptation and productivity traits they control, this synergistic work will provide both a new understanding of paralog diversification in evolution and a more robust translation of agriculturally relevant genotype-to-phenotype relationships to orphan crops. Beyond a valuable community resource of solanum reference genomes, expression data, and crispr lines for plant researchers and breeders, this multidisciplinary project will result in new tools, resources, and principles that will enable the study and engineering of other taxa and traits of significance to both plant biology and crop improvement. 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.

Transactions

Action Obligated Date
Amendment $932,763
Amendment $811,864
Amendment $802,217
Amendment $1,080,511
Amendment $0
Original award $1,172,645

Subawards

Subrecipient Amount Awarded
Boyce Thompson Institute For Plant Research Inc. Amendment incorporates year 5 funding for the period of performance 8/1/2026-7/31/2027 $228,075
The Johns Hopkins University Amendment #5 incorporates year 5 funding for the period of performance 08/01/2026 - 07/31/2027 $223,371
The Trustees Of Mount Holyoke College Amendment #6 incorporates year 5 funding for the period of performance 08/01/2026 - 07/31/2027 $75,057
The Johns Hopkins University Dr. Schatz is an expert in genome sequencing and comparative genomics and will oversee the computational aspects of the project working closely with the… $217,268
The Governing Council Of The University Of Toronto The Gillis lab will collaborate on the Identification and classification of paralogs and their molecular relationships in the Solanum Pan-Genome (Aim 2),… $109,842
Boyce Thompson Institute For Plant Research Inc. Dr. Van Eck is an expert in plant biotechnology and genome editing, especially for species in the Solanaceae family. She will oversee the activities in her… $198,071
The Trustees Of Mount Holyoke College To stimulate undergraduate awareness of and interest in plant research, co-PI Frary will develop a synergistic outreach program at Mount Holyoke College which… $14,483
The Governing Council Of The University Of Toronto The Gillis lab will collaborate on the Identification and classification of paralogs and their molecular relationships in the Solanum Pan-Genome (Aim 2),… $108,968
The Johns Hopkins University Dr. Schatz is an expert in genome sequencing and comparative genomics and will oversee the computational aspects of the project working closely with the… $211,342
The Trustees Of Mount Holyoke College To stimulate undergraduate awareness of and interest in plant research, co-PI Frary will develop a synergistic outreach program at Mount Holyoke College which… $52,821
Boyce Thompson Institute For Plant Research Inc. Dr. Van Eck is an expert in plant biotechnology and genome editing, especially for species in the Solanaceae family. She will oversee the activities in her… $190,234
The Johns Hopkins University Dr. Schatz is an expert in genome sequencing and comparative genomics and will oversee the computational aspects of the project working closely with the… $205,588
Show all 12

Quick answers

Who received award 2216612?

2216612 was awarded to Cold Spring Harbor Laboratory by Division of Integrative Organismal Systems (National Science Foundation) on August 15, 2022.

How much is award 2216612 worth?

$4,800,000 has been obligated on 2216612.

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