Registration of the Flyer × Hartwig Recombinant Inbred Line Mapping Population

Abstract

The Southern Illinois University at Carbondale (SIUC) released a genetic map of soybean [Glycine max (L.) Merr.] in May 2006, FxH92 (Reg. No. MP-3, NSL 441378 MAP). The mapping population was constructed using a recombinant inbred line (RIL) mapping population from the cross ‘Flyer MAP’ (PI 642421 MAP) by ‘Hartwig MAP’ (PI 642422 MAP). Hartwig has been used extensively. The population was released by the Southern Illinois University at Carbondale (SIUC) in May 2006. ‘Flyer’ was registered as PI534646 by McBlain et al. (1990) and ‘Hartwig’ was registered as PI 543795 by Anand (1992) The FxH92 population was related to ExF96 (Lightfoot et al., 2005) in that ‘Forrest’ was the recurrent parent used to develop Hartwig (Anand 1992), and ‘Essex’ appeared to share many alleles with Flyer (Yuan et al., 2002). Like ExF96 morphological traits do not vary greatly (Table 1). The FxH92 RIL population has been used extensively to confirm quantitative trait loci (QTL) detected in ExF96 (Table 1) and to map genes underlying additional biochemical and physiological traits (Kazi and Lightfoot, unpublished data, 2006). The genetic marker data encompass hundreds of polymorphic markers and sequence-tagged sites (STS) that were collected at SIUC by Dr. Lightfoot's group (Table 2). Several genetic maps of FxH92 have been constructed (Prabhu et al., 1999; Yuan et al., 2002; Kazi 2005; Kazi et al., 2007a, 2007b) and will continue to be developed. The mapping population was used to identify QTL (Table 3) including those underlying biochemical and physiological traits that include resistance to soybean sudden death syndrome (SDS) [caused by Fusarium virguliforme (Aoki et al., 2004) previously called F. solani (Mart.) Sacc. f. sp. glycines (Fsg)], soybean cyst nematode (SCN), Heterodera glycine Ichinohe (Prabhu et al., 1999; Yuan et al., 2002; Kazi 2005; Kazi et al., 2007a, 2007b), seed yield (Yuan et al., 2002), and seed quality traits (Kazi and Lightfoot, unpublished data, 2006). Soybean genome analysis uses the mapping population (Kazi et al., 2007a, 2007b; Shultz et al., 2006, 2007). The map and RILs were used to help anchor contigs to builds of a physical map of soybean (http://soybeangenome.siu.edu/ verified 11 July 2007). The map and RILs were used for positional cloning of Rpg5 (Ashfield et al., 2003), Rhg1, Rhg2, Rhg3, Rhg4, Rhg5, and Rfs4 (Lightfoot and Meksem, 1999; Kazi, 2005; Ruben et al., 2006). The mapping population was used to develop an assay for marker-assisted selection for SCN resistance (Prabhu et al., 1999). Near-isogeneic line populations have been created from 13 of the RILs (13, 18, 19, 20, 33, 35, 39, 60, 70, 71, 72, 78, 93) for fine mapping and verification of QTL detected in the RIL population (Table 2; Kazi, 2005; Kazi et al., 2007a, 2007b). The mapping population was very important for the analysis of seed yield QTL and other agronomic traits because it segregates across maturity groups 4 and 5 and for growth habit from determinate to indeterminate. The effects of maturity and determinacy loci that are associated with, amplify, or confound yield QTL effects can be measured. In contrast, ExF96 does not segregate for determinacy and has a very restricted maturity date range. The registration of this mapping population allows public access to the population and data generated from it. Hartwig was an F5-derived line from the cross ‘Forrest(3)’ × PI 437654 and was developed by Missouri Agricultural Experiment Stations (Anand, 1992). It was mid-group V in maturity and was characterized by determinate growth habit, white flowers, tawny pubescence, brown pods, shiny yellow seed coats, and black hila. It was released for resistance to SCN (all HG Types permutations from 1.2.3.4.5.6.7; all common races 1, 2, 3, 4, 5, 6, 9, and 14 of SCN; Niblack et al., 2002), resistance to root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] and resistance to reniform nematode [Rotenlenchulus reniformis Linford & Oliviera]. Hartwig was resistant to SDS leaf symptoms (Prabhu et al., 1999). Like it's recurrent parent Forrest, Hartwig was expected to be resistant to bacterial pustule [caused by Xanthomonas axonopodis pv. glycines (Nakano) Vauterin, Hoste, Kersters & Swings], wildfire [caused by Pseudomonas syringae pv. tabaci (Wolf & Foster 1917) Young, Dye & Wilkie 1978], target spot [caused by Corynespora cassiicola (Berk. & M.A. Curtis) C.T. Wei], and have moderate resistance to Phytophthora root rot (caused by Phytophthora sojae Kaufmann & Gerdemann). Lending support to the expected resistance, these diseases have not been severe on Hartwig planted in southern Illinois from 1995 to present (Lightfoot, unpublished data, 2006). Hartwig was found to be resistant to root borne SDS (Prabhu et al., 1999), root infection (infection severity, IS > 20%) by F. virguliforme (Njiti et al., 1997), and F. tucumanes (Aoki et al., 2004; Covert et al., 2007). Hartwig has excellent pod-shatter resistance (Anand, 1992). Hartwig was susceptible to Meloidogyn arenaria (Neal) Chitwood, and to stem canker [caused by Diaporthe phaseolarum (Cook & Ellis) Sacc.]. Flyer was a BC3F2-derived line from the cross ‘A3127’ × ‘L24’ and released by the Ohio Experiment Station (McBlain et al., 1990). It was initially released for high seed yield, good lodging resistance, and multi-race resistance to Phythopthora megasperma f. sp. glycines (with the Rps1-k gene for resistance to 19 of 25 races but susceptible to races 12, 16, 19, 20, and 25). Flyer was a maturity group IV soybean and was characterized by an indeterminate growth habit, purple flower, tawny pubescence, dull yellow seed coat, and black hila. It was moderately resistant to powdery mildew [caused by Microsphaera diffusa Cke. & Pk.], purple seed strain disease [caused by Cercospora kikuchii (Mastsumoto & Tomoyasu) M.W. Gardner], and pod and stem blight [caused by Diaporthe phaselorum Cke. & Ell.]. It has been found to be susceptible (DX > 10%) to SDS (Prabhu et al., 1999), root infection (IS > 40%) by F. virguliforme (Njiti et al., 1997), and F. tucumanes (Aoki et al., 2004; Lightfoot, unpublished data, 2006). The cross Flyer X Hartwig was made in 1991 at SIUC using seed of the parents obtained from the originating programs. About 2000 F2 plants were inbred to the F5 generation by single seed descent (Brim, 1966) and modified as follows. In 1991 a single pod was harvested from each F2 plant. Pods contained one or two seeds. Seeds were pooled for planting and harvesting at the F3 and F4 In 1994, 739 F5 plants, each tracing to a F2 plant, were harvested by hand, intentionally excluding none of the undesirable extremes. The larger population was retained at SIUC. Seeds of each plant were planted in a progeny row and in 1995, 94 lines were selected based on adaptation to growth in southern Illinois for agronomic trials (plants of a range of heights and with a range of pod numbers). The 94 recombinant inbred lines were used for evaluation of morphological and agronomic traits, stress resistance, and construction of genetic map and QTL discovery from 1996 to 2007. The FxH94 population was at the F5:12 generation in 2006. The RILs were identified as FxH1 to FxH94. FxH35 has been released as disease-resistant germplasm under the SDX trademark. Ninety-two of these 94 lines have been officially released by SIUC and all individuals interested in studying these lines may request seeds from Dr. Lightfoot for the next five years. Large samples are available each biennium when the seed source is refreshed. For security, lines are stored at the National Center for Genetic Resources Preservation, 1111 S. Mason Street, Fort Collins, CO 80521-4500. The population has a 17-d spread in maturity (118–135 d after planting). Thirty-eight RILs produce white flowers, 40 produce purple flowers, and 14 are heterogeneous for flower color. All RILs produce tawny pubescence and seed with yellow coats and black hila. All RILs have a determinate or semi-determinate growth habit. Line mean plant height ranges from 71 to 106 cm for full season planting and lodging score ranges from 1.0–4.88 on a five point scale. Mean seed yield ranges from 1.99 to 3.54 Mg ha−1 The RILs show differential response to many SCN HG Types (Niblack et al., 2002). For HG Type 0 (race 3) isolate AP3, there were 10 resistant [index of parasitism (IP) 10], 59 susceptible (IP > 10), and 13 heterogeneic (based on individual plant IP). For HG Type 1.3.5.7 (race 14) isolate AP14, there were 4 resistant [index of parasitism (IP) 10], 85 susceptible (IP > 10), and 3 heterogeneic (based on individual plant IP). For HG Type 1.2.3.5.6.7 (race 2) isolate AP2, there were 2 resistant [index of parasitism (IP) 10], 88 susceptible (IP > 10), and 2 heterogeneic (based on individual plant IP). The RILs show differential response to SDS, with line mean disease incidence ranging from 0 to 62.8% and disease index (DX) ranging from 1 to 24%. The population segregates for resistance to Phytophthora root rot (races 1–11, 13–15, 21–24), salt tolerance, water deficit tolerance, seed isoflavone (daidzein, genistein, and glycitein) protein and oil content (data not shown). The FxH RIL genetic map contained 145 linked markers in 2007 and 107 were high quality Beltsville Agricultural Research Center (BARC)-microsatellite markers that have been scored repeatedly (Kazi 2005; Kazi et al., 2007a, 2007b). The average distance between markers was 18 cM, and there are about 7 markers per linkage group. The polymorphic markers include 33 BAC end sequence (BES) derived SIUC-microsatellite markers, 8 sequence characterized amplified regions (SCAR) markers, and 104 BARC- microsatellite markers. All are publicly available on the web at Soybase http://www.soybase.org (verified 11 July 2007), on the physical map at http://bioinformatics.siu.edu (verified 11 July 2007), and their sequences are deposited in Genbank at http://www.ncbi.nlm.nih.gov (verified 11 July 2007). Updates to the integrated genetic and physical map are publicly available at http://bioinformatics.siu.edu (Shultz et al., 2006). BAC libraries exist for both parents of Hartwig, from Forrest (Meksem et al., 2000) and PI437654 (Tomkins et al., 1999). Twenty-six QTL among eight traits identified in this population included six QTL for resistance to SDS (Prabhu et al., 1999; Kazi 2005, Kazi et al., 2007a, 2007b), three QTL for high yield in southern Illinois (Yuan et al., 2002; Kazi 2005, Kazi et al., 2007a), two QTL for determinacy (Kazi et al., 2007a), four QTL for resistance to SCN HG Type 1.2.3.5.6.7 (race 2), three QTL for resistance to SCN HG Type 1.3.5.7 (race 14), and two for bigenic resistance to SCN HG Type 0 (race 3; Prabhu et al., 1999; Niblack et al., 2002; Kazi et al., 2007b). Among these QTL, we have verified in a second population the positions of 4 of 6 SDS resistance QTL (Njiti et al., 1998, 2001), 2 of 3 yield QTL (Yuan et al., 2002; Kassem et al., 2007), and all four SCN resistance genes (Webb et al., 1995). Verification by testing the remaining QTL has not been performed to date. No QTL have been detected for height and only one for lodging. There were a large number of unlinked markers. Therefore, the genetic and QTL maps have not yet been completed. Seed and updated DNA marker scores in a spreadsheet can be obtained from Dr. David A. Lightfoot on request from The Department of Plant Soil and Agricultural Systems, SIUC, Carbondale, IL 62901. The authors acknowledge diverse contributions toward the research reported in this registration notice: for funding from 1991 to 2007 the ISA, USB, IMBA, NSF, and NCSRB; for assistance by Dr. O. Myers Jr., Dr. M.E. Schmidt, and all members of the SIUC field teams from 1983 to 2007. This material was based on work supported by the National Science Foundation under Grant No. 9872635. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.