QTL Analysis of Adventitious Root Formation in Common Bean under Contrasting Phosphorus Availability Ivan E. Ochoa, Matthew W. Blair, and Jonathan P. Lynch* ABSTRACT Low phosphorus availability is a primary constraint to crop pro- duction in developing countries. Adventitious roots play an important role in phosphorus acquisition, as they are localized near the soil surface where phosphorus is relatively abundant. A population of recombinant inbred lines of Phaseolus vulgaris L. (G2333/G19839) was screened under high- and low-phosphorus conditions in the greenhouse and field. We observed phenotypic variation and transgressive segregation for adventitious root traits in both environments. Allometric analysis re- vealed that although the taproot and basal roots are closely linked to shoot growth, recombinant inbred line (RILs) differ substantially in bio- mass allocation for adventitious roots. A linkage map with 149 genetic markers and a total cumulative map length of 1175 cM was used to identify a total of 19 QTL across 8 of the 11 linkage groups. Together these quantitative trait loci (QTL) accounted for 19 to 61% of the total phenotypic variation for adventitious root traits in the field and 18 to 39% under greenhouse conditions. Two major QTL for adventitious rooting under low phosphorus conditions in the field were observed on linkage groups B2 and B9 that together accounted for 61% of the observed phenotypic variation. We conclude that adventitious rooting under low phosphorus is a feasible target for bean breeding. C OMMON bean is the most important legume for di- rect human consumption in the world. For over 500 million people in Latin America and Africa, common bean is an important source of nutrients and dietary protein (Broughton et al., 2003; Graham and Ranalli, 1997). Low soil fertility is a primary constraint to com- mon bean production in many developing countries, af- fecting at least 80% of global bean production (CIAT, 2001; Wortmann et al., 1998). Of the several edaphic stresses affecting bean production, low phosphorus avail- ability is the most important limitation, affecting over half of all bean production area in Africa and Latin America (Wortmann and Allen, 1994). Substantial ge- netic variation exists within common bean for growth under low phosphorus conditions (Lynch and Beebe, 1995). Cultivated bean accessions are less sensitive to low phosphorus availability than their wild ancestors (Lynch and Beebe, 1995). This suggests that the tol- erance observed in cultivated common bean probably evolved after plant domestication where early land- races were moved from their original environment into phosphorus-deficient environments (Beebe et al., 1997; Gerloff and Gabelman, 1983; Lynch and Beebe, 1995). Plants display a variety of adaptations to low phos- phorus availability, including changes in root morphol- ogy and architecture (Bonser et al., 1996; Fan et al., 2003; Lynch and Brown, 2001, 2005; Miller et al., 2003; Nielsen et al., 1998), increased production and secretion of root exudates (Jones, 1998; Yan et al., 1996), in- creased proliferation and elongation of root hairs (Bates and Lynch, 1996; Ma et al., 2001a), modification of car- bon metabolism and alternative respiratory pathways (Rychter and Mikulska, 1990; Wanke et al., 1998), and enhanced expression of P i transporters (Ragothama, 2005). Selection for specific traits that improve phos- phorus acquisition is preferable to yield trials where G 3 E interaction and a multiplicity of factors affect- ing yield have complicated the identification and se- lection for phosphorus efficiency in the past (Lynch and Beebe, 1995). Marker assisted selection would be an option to select for root traits that are difficult to eval- uate phenotypically. Phosphorus is relatively immobile in soil and its avail- ability is typically greater in topsoil and declines sub- stantially with depth (Lynch and Brown, 2001). Root architectural traits that enhance topsoil foraging such as shallower basal root growth angle (Bonser et al., 1996) or adventitious rooting (Lynch and Brown, 2001; Miller et al., 2003) may therefore enhance phosphorus acqui- sition in low phosphorus environments. In addition to exploring the topsoil, adventitious roots have lower metabolic cost than other root types (Miller et al., 2003), which is important since root costs are an important component of plant adaptation to low phosphorus envi- ronments (Lynch and Ho, 2005; Miller et al., 2003). Genotypic variation in adventitious root formation has been observed in several crops including common bean (Miller et al., 2003), soybean [Glycine max (L.) Merr.: Bacanamwo and Purcell, 1999], Rumex ssp. (Vis- ser et al., 1996), tomato (Lycopersicon esculentum L.: McNamara and Mitchell, 1990), and maize (Zea mays L.: Mano et al., 2005). In common bean phosphorus availability regulates adventitious rooting (Miller et al., 2003); however, there is a lack of information regard- ing the genetic basis for adventitious rooting and re- lated traits. In this study, we analyze QTL controlling variation for adventitious root traits in a RIL population developed from a cross between G2333 3 G19839 and estimate I.E. Ochoa and J.P. Lynch, Department of Horticulture, The Penn- sylvania State University, University Park, PA 16802, USA; M.W. Blair, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia. Received 1 Dec. 2005. *Corresponding author (Fax: +1 814 863 6139. E-mail: JPL4@psu.edu). Published in Crop Sci. 46:1609–1621 (2006). Crop Breeding & Genetics doi:10.2135/cropsci2005.12-0446 ª Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA Abbreviations: QTL, quantitative trait locus (loci); RIL(s), recombinant inbred line(s); PCR, polymerase chain reaction; SSR, simple sequence repeat; RAPD, random amplified polymorphic DNA; SCAR, sequence characterized amplified region; STS, sequence tagged site; PAGE, poly- acrylamide gel electrophoresis; CTAB, cetyl trimethyl ammonium bro- mide; LOD, logarithm of odd; CIM, composite interval mapping; MIM, multiple interval mapping; cM, centimorgan; GxE, genotype by environ- ment interaction; DAS, days after sowing; SRL, specific root length. Reproduced from Crop Science. Published by Crop Science Society of America. All copyrights reserved. 1609 Published online May 18, 2006