Genetic diversity, population structure and marker-trait associations in Indian kale (Brassica oleracea L. Gp. Acephala) using cross-species microsatellite markers

Kale is known for its exceptional nourishing and functional benefits to human body. However, it is an understudied species from genomic as well as agronomic aspects. It is important to characterize niche kale germplasms around the world to systematically conserve and utilize its genetic variability, especially for commercial traits in the interest of growers, consumers and industry. With this view, genomic and phenotypic characterizations of 62 Kashmiri kale accessions including popular landraces were done to estimate and partition genetic diversity, understand trait relationships, develop population structure and divulge marker-trait associations of economic significance. Sixty-six cross species microsatellite (SSR) markers within Brassica genus amplified 269 alleles in the germplasm. Their polymorphic information content (PIC) ranged from 0.00078 to 0.953 with an average of 0.407. The population structure analysis and neighbour joining tree clustering categorized the germplasm into three sub-populations. AMOVA revealed more within-population variance (67.73%) than among-populations (32.27%) variance. The principal component analysis (PCA) involving 24 agronomical traits revealed seven PCs (PC1 to PC7) having Eigen values more than 1, which explained a cumulative variation of 69.21%. Association mapping with respect to these 24 agronomical traits using mixed linear model and general linear model revealed six overlapping significant marker-trait relationships with five being significant at probability value of 0.001/0.0001. The highly significant associations of two SSRs with economically important traits (siliqua length and seed weight) significantly correlated/ related with leaf yield and seed yield were revealed for their possible utilization in marker assisted breeding for higher leaf and seed yields.