Yield-trait and SSR-based genetic diversity and population structure analysis in Northeastern Himalayan germplasm collection of Job's tears (Coix lacryma-jobi L.)

Abstract

Abstract The study characterized 34 Job's tears accessions from the Northeastern Himalayan region using yield-related traits and SSR markers. Genotyping with 17 SSR markers revealed an average of 3.18 alleles per locus, varying from 2 to 4. PIC values ranged from 0.27 to 0.52, averaging 0.41. Clustering and PCoA based on SSR markers grouped the accessions into three major groups. The first three principal coordinates in the PCoA cumulatively explained 41.96% of the variability present in the accessions, with the first and second principal coordinates explaining 22.51% and 10.39% of the molecular variability, respectively. The model-based genetic structure analysis detected the maximal ΔK (80.87) at K = 2, grouping the entire accessions into two subgroups. AMOVA indicated higher genetic variation within individuals (52.86%) than among individuals (47.14%). The high FST value (0.2) suggested significant differentiation between populations. Yield-trait-based analysis resulted in four clusters. Cluster I included six accessions with short height, Cluster II consisted of 12 accessions with high test weight, Cluster III comprised six accessions with high yield, and Cluster IV had nine accessions with early flowering, respectively. PCA extracted three components explaining 67.4% of total variation, with PC1 emphasizing yield and growth-related traits and PC2 highlighting days to flowering and panicle length. Most traits showed positive correlations with yield per plant, especially test weight (0.65, P ≤ 0.01). Path coefficient analysis revealed a strong positive direct effect of test weight and the number of internodes per plant on yield per plant. Cluster analysis and GT biplot analysis showed similar patterns among accessions. However, the Mantel test indicated no significant correlation between genetic and morphological distances (r2 = 0.010, P = 0.41). AMMI analysis and MTSI for yield-related traits identified three promising accessions (IC600638, IC540181, and IC540256) suitable for selection at 10% intensity in future breeding programs.