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

Abstract

Carthamus tinctorius L. (safflower) is an important oilseed crop producing seed oil rich in unsaturated fatty acids. Scarcity of identified marker-trait associations is a major limitation toward development of successful marker-assisted breeding programs in safflower. In the present study, a safflower panel (CartAP) comprising 124 accessions derived from two core collections was assayed for its suitability for association mapping. Genotyping of CartAP using microsatellite markers revealed significant genetic diversity indicated by Shannon information index (H = 0.7537) and Nei's expected heterozygosity (I = 0.4432). In Principal Coordinate Analysis, the CartAP accessions were distributed homogeneously in all quadrants indicating their diverse nature. Distance-based Neighbor Joining analysis did not delineate the CartAP accessions in consonance with their geographical origin. Bayesian analysis of population structure of CartAP demonstrated the unstructured nature of the association panel. Kinship analysis at population (Gij) and individual level (Fij) revealed absence of or weak relatedness between the CartAP accessions. The above parameters established the suitability of CartAP for association mapping. We performed association mapping using phenotypic data for eight traits of agronomic value (viz., seed oil content, oleic acid, linoleic acid, plant height, number of primary branches, number of capitula per plant, 100-seed weight and days to 50% flowering) available for two growing seasons (2011–2012 and 2012–2013) through General Linear Model and Mixed Linear Model. Our study identified ninety-six significant marker-trait associations (MTAs; P < 0.05) of which, several MTAs with correlation coefficient (R2) > 10% were consistently represented in both models and in both seasons for traits viz., oil content, oleic acid content, linoleic acid content and number of primary branches. Several MTAs with high R2-values were detected either in a majority or in some environments (models and/or seasons). Many MTAs were also common between traits (viz., oleic/linoleic acid content; plant height/days to 50% flowering; number of primary branches/number of capitula per plant) that showed positive or negative correlation in their phenotypic values. The marker-trait associations identified in this study will facilitate marker-assisted breeding and identification of genetic determinants of trait variability.

Designing of a mini-core that effectively represents 3004 diverse accessions of rice

“…This purpose is best served by a core collection which is designed to capture maximum available/possible diversity (genetic, phenotypic and geographical) of the entire population, with limited number of individuals having low or no kinship among them (Korte et al, 2012). Core collections have been used as an association panel for GWAS in different studies (El Bakkali et al, 2013;Zhang et al, 2014;Perseguini et al, 2015;Ambreen et al, 2018). In case of rice, limited attempts have been made to use a core collection as an association panel.…”

Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information

“…The representation of safflower accessions from such a wide range of countries in the admixture population might be due to their use in international breeding programs. Other important factors like mutation, migration and selection by humans might also be responsible for the occurrence of admixture populations in safflower accessions of different origin [21,27].…”

“…Earlier studies reported different loci/markers linked with 100-seed weight. Ambreen et al [21] reported two loci (NGSaf_306 and NGSaf_309) associated with 100-seed weight utilizing SSR markers. Mirzahashemi et al [51] identified one QTL (qThsw5) associated with 100-seed weight.…”

“…Great emphasis on the molecular characterization and development of efficient molecular markers in safflower is required to accelerate safflower breeding activities [18][19][20]. Safflower genetic diversity using different molecular markers has been estimated [2,10,18,[21][22][23][24][25][26][27].…”

“…Relationships between plant traits and genetic polymorphisms observed in a heterogeneous assembly of distinct individuals, utilizing naturally occurring recombination events, aid in fine scale mapping of traits. Ambreen et al [21] and Ebrahimi et al [33] identified marker-trait associations in safflower, utilizing SSR and AFLP marker systems, respectively. Yield in any crop is the most important trait that is polygenic and difficult to measure and improve as it is highly influenced by other contributing traits.…”