Abstract
Safflower, a minor oilseed crop, is gaining increased attention for food and industrial uses. Safflower genebank collections are an important genetic resource for crop enhancement and future breeding programs. In this study, we investigated the population structure of a safflower collection sourced from the Australian Grain Genebank and assessed the potential of genomic prediction (GP) to evaluate grain yield and related traits using single and multi-site models. Prediction accuracies (PA) of genomic best linear unbiased prediction (GBLUP) from single site models ranged from 0.21 to 0.86 for all traits examined and were consistent with estimated genomic heritability (h2 ), which varied from low to moderate across traits. We generally observed a low level of genome × environment interactions (g × E). Multi-site g × E GBLUP models only improved PA for accessions with at least some phenotypes in the training set. We observed that relaxing quality filtering parameters for genotype-by-sequencing (GBS), such as missing genotype call rate, did not affect PA but upwardly biased h2 estimation. Our results indicate that GP is feasible in safflower evaluation and is potentially a cost-effective tool to facilitate fast introgression of desired safflower trait variation from genebank germplasm into breeding lines.
Highlights
Safflower (Carthamus tinctorius L.) is a member of the family Compositae or Asteraceae, commonly referred to as the aster, daisy, composite, or sunflower family (Ashri, 1975; Elfadl, Reinbrecht, & Claupein, 2010)
Seven groups were revealed by the dendrogram, and the unrooted phylogenetic tree showed that groups 1, 2, and 3 formed one branch, while groups 4, 5, 6, and 7 were more differentiated (Figure 1a)
Our results indicated that applying the g × E genomic best linear unbiased prediction (GBLUP) model could potentially lower the cost of field testing for germplasm evaluation as not all lines need to be grown at all sites
Summary
Safflower (Carthamus tinctorius L.) is a member of the family Compositae or Asteraceae, commonly referred to as the aster, daisy, composite, or sunflower family (Ashri, 1975; Elfadl, Reinbrecht, & Claupein, 2010) It is an annual, self-compatible, diploid (2n = 2x = 24) crop with a cultivation history dating back to 3,000 B.C. in northern and central Syria (Marinova & Riehl, 2009). Safflower is a multi-purpose crop that populated the old world as a dye plant and is grown as a vegetable, cut flower, herbal medicine, animal feed, bird, and oilseed (Li & Mündel, 1996; Zohary, Hopf, & Weiss, 2012) Today, it is mostly grown as an oilseed crop across a broad geographical range, including Africa, America, Europe, and Asia (Emongor, 2010). Genetic diversity analyses have typically been performed using several types of sparse molecular markers including random amplified polymorphic DNAs (RAPDs) (Khan, von WitzkeEhbrecht, Maass, & Becker, 2009), amplified fragment length polymorphisms (AFLPs) (Johnson, Kisha, & Evans, 2007), inter-simple sequence repeats (ISSRs) (Majidi & Zadhoush, 2014), sequence-related amplified polymorphisms (SRAPs)
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