A study on genetic diversity and marker trait association analysis in turmeric (Curcuma longa L.)

Abstract

Turmeric (Curcuma longa L.) commonly known as golden spice is an economically important spice crop. Turmeric genotypes exhibit wide intraspecific variation for the biologically active principles coupled with morphological variation. Given the large influence of the environment on phenotypic variability, there is no clear understanding about the relation of genetic base with the observed phenotypic variability. Here, we have studied the genetic diversity in turmeric diversity panel comprising 93 genotypes by examining the phenotypic variability alongside the molecular genetic variability to find marker-trait associations. Phenotypic characterization revealed significant genetic variation among 93 genotypes. Flow cytometric analysis revealed that among the 93 genotypes, majority were triploids (84) and nine were tetraploids. Most of the tetraploids have origins as seedling progenies while few are germplasm collection. It was found that triploids and tetraploids differ significantly in their plant height, number of shoots, number of leaves on main shoot, petiole length, leaf length, length of mother rhizome, length of primary rhizomes, length of secondary rhizomes, girth of secondary rhizomes, inner core diameter of primary rhizome, weight of mother rhizomes per plant, weight of primary rhizomes per plant, total rhizome weight per plant and dry rhizome weight per plant. Genetic variability analysis revealed that characters; number of shoots per plant, length of mother rhizome, total weight of mother rhizomes per plant, total weight of rhizome per plant and dry weight of rhizome per plant were the most important traits for selection across ploidy levels. Here, we have utilized molecular marker based genotyping as well as NGS based genotyping to study the genetic relationship of the genotypes under study. Although, reliable and reproducible, the inherent limitations of molecular marker to achieve the requisite resolution for association studies led us to proceed with NGS based genotypic data. Here, we have optimized a bioinformatics pipeline or workflow for variant calling which have resulted in discovery of 30438 SNP variants. Further, we have analysed the population structure of genotypes understudy (to avoid false positive marker trait associations in downstream analysis) and have found that there are three subpopulations. Further the association mapping for three key traits has revealed nine significant marker trait association for : curcumin content (1), rhizome length (5), and rhizome girth (3). Most marker trait associations were from chromosome 4. Zingiber officinale MADS-box transcription factor 34- like (LOC122034397) can be a putative locus involved in rhizome length morphology. Thus, results obtained here will add onto the understanding of genetic base of these complex traits in turmeric and to further crop improvement efforts in turmeric