Mining genomic regions associated with agronomic and biochemical traits in quinoa through GWAS

Abstract

Quinoa (Chenopodium quinoa Willd.), an Andean crop, is a facultative halophyte food crop recognized globally for its high nutritional value and plasticity to adapt to harsh conditions. We conducted a genome-wide association study on a diverse set of quinoa germplasm accessions. These accessions were evaluated for the following agronomic and biochemical traits: days to 50% flowering (DTF), plant height (PH), panicle length (PL), stem diameter (SD), seed yield (SY), grain diameter (GD), and thousand-grain weight (TGW). These accessions underwent genotyping-by-sequencing using the DNBSeq-G400R platform. Among all evaluated traits, TGW represented maximum broad-sense heritability. Our study revealed average SNP density of ≈ 3.11 SNPs/10 kb for the whole genome, with the lowest and highest on chromosomes Cq1B and Cq9A, respectively. Principal component analysis clustered the quinoa population in three main clusters, one clearly representing lowland Chilean accessions, whereas the other two groups corresponded to germplasm from the highlands of Peru and Bolivia. In our germplasm set, we estimated linkage disequilibrium decay to be ≈ 118.5 kb. Marker-trait analyses revealed major and consistent effect associations for DTF on chromosomes 3A, 4B, 5B, 6A, 7A, 7B and 8B, with phenotypic variance explained (PVE) as high as 19.15%. Nine associations across eight chromosomes were also found for saponin content with 20% PVE by qSPN5A.1. More QTLs were identified for PL and TGW on multiple chromosomal locations. We identified putative candidate genes in the genomic regions associated with DTF and saponin content. The consistent and major-effect genomic associations can be used in fast-tracking quinoa breeding for wider adaptation across marginal environments.

Keywords: Abiotic stress; GWAS; LD; Marginal environment; QTL; Quinoa; Saponin.

Figure 1

Frequency distribution, histogram of residuals, and normal Q–Q plot for various phenotypic traits: (a) panicle length, (b) plant height, (c) seed yield, (d) stem diameter, (e) thousand-grain weight, and (f) days to flowering.

Figure 2

(a) SNP density across 18 chromosomes of quinoa representing the number of SNPs within a 0.5-Mbp window size; (b) genome-wide linkage disequilibrium decay of r² values against physical distance (bp); the LD decay has been considered as the distance at which r² dropped to half of its maximum value (0.4691).

Figure 3

(a) PCA analysis; (b) neighbor joining tree of association mapping panel. Group I contains the genotypes from lowlands majorly, whereas group II and III were dominated by accessions that originated in highlands.

Figure 4

Manhattan and Q–Q plots of genome-wide association mapping of measured traits. The y-axis in each graph represents − log10P for the p-value of the MTAs, while chromosome numbers are indicated on the x-axis. The red dashed line presents the threshold − log10P value (= 4) which was used for declaring the significant associations along with another criterion i.e. number of SNPs within LD decay region.

Figure 5

Various genomic regions identified through GWAS associated with various traits of interest. Green; purple and red text of the genomic regions indicates the genomic region identified in both individual as well as combined analysis; in either of the individual season and combined analysis and through metabolomic data respectively.