Location: Potato, Pulse and Small Grains Quality Research
Project Number: 3060-21650-002-072-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2025
End Date: Dec 31, 2026
Objective:
The aim of this project is to develop chickpea varieties with large increases to nitrogen fixation rates. Specifically, (1) Refine the genetics of wild alleles conferring efficient nitrogen fixation in Cicer species. (a) More precise definition of genomic intervals. (b) Test interactions and relative benefits of allele combinations, (2) Create new cultivated varieties carrying superior combinations of wild alleles, and (3) Determine the mechanisms of nitrogen fixation efficiency and strain specificity, with the goals of informing effective crop management.
Approach:
The research plan combines (1) a wealth of high quality genetic and genomic resources, (2) well-established greenhouse and laboratory assays to understand both genetic control and the mechanism of enhanced symbiotic performance, and (3) a genomic-assisted breeding pipeline to introgress high-value wild traits for nitrogen fixation into grower-preferred chickpea varieties. This will be accomplished by genotyping large numbers of segregating progeny as seedlings, then advancing only those individuals with informative recombinants for seed increase and phenotyping. Our initial target will be three genetic intervals from C. recitulatum and three from C. echinospermum, but we will refine this target based on outcomes from the intial rounds of genotyping and phenotyping. Recombinant inbred lines with high trait values have already been selected as donor genotypes and these will be backcrossed into two cultivated lineages. For purpose of genotyping, we have aligned PacBio REVIO genomes of each wild x cultivated parent combination and compiled a full list of single nucleotide polymorphisms (SNP) using minimap2 (https://github.com/lh3/minimap2), from which we have designed thousands of PCR allele competitive extension (PACE) primer sets and selected 240 primer sets for testing and validation. To create new cultivated varieties carrying superior allele combinations of wild alleles, breeding will involve the tools and genotypes from objective 1. We will conduct field trials to understand the agronomic value of the wild traits and their interactions. To determine the mechanisms of nitrogen fixation efficiency and strain specificity, with the goals of informing effective crop management, we will combine our multispectral methods with transcriptional profiling and thin section/confocal microscopy methods to better understand the processes and developmental status of effective versus ineffective nodules. Fresh nodules will be imaged, and immediately processed either for RNA analysis of fixed for microscopy.