Phenotypic and genotypic resources for the USDA quinoa (Chenopodium quinoa) genebank accessions

Authors: NEPA, NIRMAN - Purdue University; CONDORI-APFATA, JORGE ALBERTO - National University Of Toribio Rodriguez De Mendoza Of Amazonas; GAIRE, RUPESH - Bayer Cropscience; ANCO, MAYELA ELIZABET - National University Of Saint Augustine; Scofield, Steven - Steve; MOHAMMADI, MOHSEN - Purdue University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: Quinoa is an important source of nutrition that is growing in importance in agriculture. The number of countries cultivating Quinoa is rapidly increasing. Seventy six countries were reported to grow it in 2013 and that increased to 123 by 2018. Its grain is highly nutritious and able to be grown in a wide variety of environments, notably arid regions. In this work reported the genetic diversity of the USDA-ARS's's collection of 148 Quinoa accession was screened for a wide variety of agronomic traits and the genome-wide association studies (GWAS) were performed to identify DNA sequences associated with these traits. This work provides important DNA markers for these traits that can be used by breeders around the world who are working to improve Quinoa qualities and yield.

Technical Abstract: Quinoa is a nutritious grain, with balanced composition of amino acids, and a facultative halophyte. Under greenhouse conditions, we assessed 148 quinoa accessions from the USDA genebank for grain yield, phenological, morphological, and physiological features.. For all traits, an ANOVA revealed a significant difference among accessions. The accessions matured as late as 146 days after planting and yielded up to 19.6 grams per plant. . The accessions were divided into three separate clades using cluster analysis based on phenotypic features, Euclidean distance, and the Ward clustering approach.. By adopting the NsiI/BfaI combination to enhance the genotyping-by-sequencing technique, we were able to generate 92,693 filtered single nucleotide polymorphism markers by mapping to the reference genome.. The unrooted NJ tree confirmed the existence of two large clusters, and the first two principal components explained 38.9% and 8.2% of the molecular variations, respectively.. Linkage disequilibrium analysis on scaffold_1001 showed that the LD persists as high as 0.2 over a range of 1100 kb. Using two principal components as covariates to account for population structure, TASSEL was used to conduct GWAS for days to flowering and maturity, plant height, branching, and grain yield. Marker-trait associations (MTAs) were found at -logP > 4 in these studies. Up to 17.8% of variability in phenotypic features were explained by the MTAs. These findings helps to cataloging and conservation of phenotypic and genotypic diversity of USDA’s quinoa germplasm. Furthermore, quinoa genetic diversity can be harnessed for improvement of quinoa by breeding or genome editing to address future food security.