Quantitative Trait Loci for Genetically Correlated Seed Traits are Tightly Linked to Branching and Pericarp Pigment Loci in Sunflower Shunxue Tang, Alberto Leon, William C. Bridges, and Steven J. Knapp* ABSTRACT The seed oil concentrations of large-seeded, low-oil and small- seeded, high-oil sunflower (Helianthus annuus L.; x 5 17) cultivars differ by 180 to 280 g kg 21 . We identified quantitative trait loci (QTL) for seed oil and other seed traits in a low- 3 high-oil (RHA280 3 RHA801) recombinant inbred line (RIL) mapping population segre- gating for apical branching (B), phytomelanin pigment (P), and hypo- dermal pigment (Hyp) loci. B, Hyp, and P mapped to linkage groups 10, 16, and 17, respectively. The seed oil concentrations of RHA280 and RHA801 were 254 and 481 g kg 21 , respectively. Composite inter- val mapping (CIM) identified 40 QTL for seed oil concentration, 100-seed weight, seed length, width and depth, kernel and pericarp weight, and kernel-to-pericarp weight ratio in 14 DNA marker inter- vals on 10 of 17 linkage groups. Twenty-four of the QTL were tightly linked to B, P , and Hyp and may have been partly or wholly caused by the pleiotropic effects of B, P , and Hyp. Multilocus QTL analyses were performed using B, P , Hyp, and four DNA marker loci as independent variables in mixed linear models. Seventy percent of the additive effects (39/56) and 42% of the additive 3 additive and additive 3 additive 3 additive effects (189/448) were significant ( p , 0.05). The linked, pleiotropically acting, and epistatically interacting QTL iden- tified for seed traits in RHA280 3 RHA801 were presumably targeted by selection in the transition from large-seeded, low-oil to small- seeded, high-oil cultivars in sunflower. T HE ACHENES (seeds) of cultivated or common sun- flower (Helianthus annuus L.) are a rich source of oil and an historically important source of food and pigment for Native Americans (Heiser, 1951, 1977). The seeds of unbranched (single-headed) Native American land races, the earliest cultigens, are significantly larger than the seeds of wild populations, partly because un- branched biotypes have larger capitula and seeds than branched biotypes, and partly because sunflower was domesticated by selecting for larger seeds (Ross, 1939; Heiser, 1951, 1977; Dedio, 1980). Shellable, large- seeded, low-oil (confectionery) land races developed in eastern Europe were introduced to North America in 1880 and had seed oil concentrations in the 260 to 280 g kg 21 range. Mennonite, an early confectionery cultivar, CM 612 (PI 546351), an inbred directly isolated from Mennonite (Dedio and Rashid, 1991), and numer- ous other confectionery cultivars and inbred lines have seed oil concentrations in the 240 to 290 g kg 21 range (http://www.ars-grin.gov; verified 2 December 2005). Unshellable, small-seeded, high-oil (oilseed) cultivars were developed between 1920 and 1955 by direct selec- tion for increased seed oil concentration and indirect selection for small seeds and thin pericarps (hulls) in open-pollinated populations (Putt, 1940, 1997; Heiser, 1951, 1977; Pustovoit, 1964). Cultivars producing 380 g kg 21 of seed oil may have been developed as early as 1915; however, the seed oil concentrations of cultivars commonly grown between 1900 and 1915 re- portedly ranged from 200 to 300 g kg 21 (Putt, 1997). Selection in open-pollinated populations increased seed oil concentrations to 430 g kg 21 by 1935 and 490 g kg 21 by 1955 (Pustovoit, 1964; Heiser, 1977; Seiler, 1985, 1994; Putt, 1997; Seiler and Brothers, 1999), thereby greatly increasing the economic importance of sunflower as an oilseed and further differentiating the confectionery and oilseed market classes (Pustovoit, 1964; Putt, 1997). Seeds of confectionery and oilseed cultivars are dis- tinguished by differences in shellability, hull color, seed weight and morphology, and kernel-to-pericarp weight ratio, in addition to seed oil concentration (Beard, 1981; Seiler, 1997). The seeds of confectionery cultivars are typically gray or white, black or brown striped, and easily dehulled or shelled, whereas the seed of oilseed cultivars are typically black (dark purple) and difficult to dehull. Seeds of confectionery cultivars are larger and have lower kernel-to-pericarp weight ratios than seeds of oilseed cultivars. Hull color differences are produced by pigments in the epidermal, hypodermal, and phyto- melanin layers (Johnson and Beard, 1977; Leon et al., 1996; Miller and Fick, 1997). The epidermis is either unpigmented, solid brown or black, or black- or brown- striped, the hypodermis is either anthocyanin pigmented (black) or unpigmented, and phytomelanin is either present (black) or absent (Johnson and Beard, 1977; Leon et al., 1996; Miller and Fick, 1997). Several hull pigment loci have been identified through phenotypic analyses of mutations (reviewed by Miller and Fick, 1997). The allelism of many of the mutations is not known, and only Hyp, a hypodermis pigment locus, has been genetically mapped (Leon et al., 1996). The first high-oil cultivars were apparently developed by introgressing allelic diversity from wild populations into open-pollinated, low-oil cultivars (Pustovoit, 1964; Heiser et al., 1969; Semelczi-Kovacs, 1975; Putt, 1997). Selection within domesticated, low-oil populations per se cannot be completely ruled out—land race selec- tion between 1880 and 1915 could have played a role in Shunxue Tang and Steven J. Knapp, Center for Applied Genetic Technologies, 111 Riverbend Road, The University of Georgia, Athens, GA, 30602, USA; Alberto Leon, Advanta Seeds, Balcarce Research Station, Ruta 226, KM 60.3 (7620), Balcarce PCIA DE BS. AS., ARGENTINA; William C. Bridges, Department of Experimen- tal Statistics, Clemson University, Clemson, SC 29634. Received 4 Jan. 2005. *Corresponding author (sjknapp@uga.edu). Published in Crop Sci. 46:721–734 (2006). Genomics, Molecular Genetics & Biotechnology doi:10.2135/cropsci2005.0006-7 ª Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: INDEL, insertion-deletion; LG, linkage group; QTL, quantitative trait locus; RIL, recombinant inbred line; SSR, simple sequence repeat. Reproduced from Crop Science. Published by Crop Science Society of America. All copyrights reserved. 721 Published online February 24, 2006