Utilization of Molecular, Phenotypic, and Geographical Diversity to Develop Compact Composite Core Collection in the Oilseed Crop, Safflower (Carthamus tinctorius L.) through Maximization Strategy

Abstract

Safflower (Carthamus tinctorius L.) is a dryland oilseed crop yielding high quality edible oil. Previous studies have described significant phenotypic variability in the crop and used geographical distribution and phenotypic trait values to develop core collections. However, the molecular diversity component was lacking in the earlier collections thereby limiting their utility in breeding programs. The present study evaluated the phenotypic variability for 12 agronomically important traits during two growing seasons (2011–12 and 2012–13) in a global reference collection of 531 safflower accessions, assessed earlier by our group for genetic diversity and population structure using AFLP markers. Significant phenotypic variation was observed for all the agronomic traits in the representative collection. Cluster analysis of phenotypic data grouped the accessions into five major clusters. Accessions from the Indian Subcontinent and America harbored maximal phenotypic variability with unique characters for a few traits. MANOVA analysis indicated significant interaction between genotypes and environment for both the seasons. Initially, six independent core collections (CC1–CC6) were developed using molecular marker and phenotypic data for two seasons through POWERCORE and MSTRAT. These collections captured the entire range of trait variability but failed to include complete genetic diversity represented in 19 clusters reported earlier through Bayesian analysis of population structure (BAPS). Therefore, we merged the three POWERCORE core collections (CC1–CC3) to generate a composite core collection, CartC1 and three MSTRAT core collections (CC4–CC6) to generate another composite core collection, CartC2. The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon's diversity index, and Nei's gene diversity for CartC1 were 11.2, 43.7, 132.4, 93.4, 0.47, and 0.306, respectively while the corresponding values for CartC2 were 9.3, 58.8, 124.6, 95.8, 0.46, and 0.301. Each composite core collection represented the complete range of phenotypic and genetic variability of the crop including 19 BAPS clusters. This is the first report describing development of core collections in safflower using molecular marker data with phenotypic values and geographical distribution. These core collections will facilitate identification of genetic determinants of trait variability and effective utilization of the prevalent diversity in crop improvement programs.

Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L.) Core Collection Using Microsatellite Markers

“…Another advantage offered by core collections is that these collections often include unrelated individuals (accessions) which decreases the chances of identifying spurious marker-trait associations due to pre-existing population structure. In safflower, evaluation of global germplasm collections identified significant diversity for most of the desirable traits (oil content, fatty acid composition, resistance to biotic and abiotic stresses, and spines) (Ashri, 1975 ; Dwivedi et al, 2005 ; Kumar et al, 2016 ). To facilitate genetic dissection of complex traits, small, operational core collections have been developed in safflower (Johnson et al, 1993 ; Dwivedi et al, 2005 ; Kumar et al, 2016 ).…”

“…In safflower, evaluation of global germplasm collections identified significant diversity for most of the desirable traits (oil content, fatty acid composition, resistance to biotic and abiotic stresses, and spines) (Ashri, 1975 ; Dwivedi et al, 2005 ; Kumar et al, 2016 ). To facilitate genetic dissection of complex traits, small, operational core collections have been developed in safflower (Johnson et al, 1993 ; Dwivedi et al, 2005 ; Kumar et al, 2016 ). These core collections can be effectively used for association mapping provided they demonstrate presence of high genetic variance (for better mapping resolution) and possess weak population structure and low kinship association among individuals (to avoid spurious associations between molecular markers and functional loci) during association analysis (Pritchard et al, 2000 ).…”

“…The present study describes evaluation of a safflower panel of 124 accessions derived from two core collections (reported earlier from our group; Kumar et al, 2016 ) for its suitability for association mapping and identification of SSR loci associated with eight traits of agronomic value (plant height, number of primary branches, number of capitula per plant, 100-seed weight, days to 50% flowering, seed oil content, oleic acid content and linoleic acid content) in the crop. The current work will facilitate mining of elite genes or loci for safflower breeding and conservation.…”

Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats

“…The identification, selection, and preservation the genetic of diversity within forest trees species is therefore of particular interest due to the long life spans of these organisms, which require adaption to different environments and climate. These characteristics can be successfully used to inform conservation, efforts, including targeted breeding programs seeking to improve genetic diversity within a provenance [ 5 , 6 , 7 , 8 ].…”

Wide hybridization and introgression breeding in safflower: Effectiveness of different selection methods

“…For example Kumar et al () assessed 531 safflower accessions collected from 43 countries and reported high genetic variability in the collection of safflower germplasm with a global distribution. In another study they described development of core collections in safflower using molecular marker data with phenotypic values and geographical distribution (Kumar et al, ). Nevertheless, safflower exhibits somewhat reduced nucleotide diversity as compared to its progenitor, consistent with the occurrence of a population genetic bottleneck during domestication (Chapman & Burke, ).…”