Aquaculture 350-353 (2012) 200–209 Contents lists available at SciVerse ScienceDirect Aquaculture journal homepage: www.elsevier.com/locate/aqua-online A first-generation linkage map of the Pacific lion-paw scallop (Nodipecten subnodosus): Initial evidence of QTL for size traits and markers linked to orange shell color Jessica L. Petersen a,⁎, Melinda R. Baerwald a, Ana M. Ibarra b, Bernie May a a University of California, Department of Animal Science, One Shields Ave, Davis CA 95616, USA b Centro de Investigaciones Biológicas del Noroeste S.C., Programa de Acuicultura, Mar Bermejo 195, La Paz, B.C.S. 23090, México article info abstract Article history: The first genetic linkage maps of the Pacific lion-paw scallop were created using microsatellite and AFLP gen- Received 25 October 2011 otyping of a full-sibling family spawned from a single, pairwise mating. As an important step in the develop- Received in revised form 16 February 2012 ment of genomic resources for this species, the maps were then used in an effort to identify putative Accepted 30 March 2012 quantitative trait loci (QTL) for the size traits of shell length, height, and width, as well as total mass, soft Available online 9 April 2012 tissue mass, muscle mass, and orange shell color. The female map contains 147 markers on 27 linkage groups, covering 919.7 cM, while the male map contains 149 markers placed on 20 linkage groups spanning 963.7 cM. Keywords: Mollusk Combining all available markers resulted in a consensus map of 320 loci (56 microsatellites and 264 AFLPs) on Selection 22 linkage groups with an average spacing of 3.8 cM and a total map distance of 1124.14 cM. Non-parametric, Genetic map Kruskal–Wallis tests found significant linkage at α=0.005 for two size traits: total biomass in the loci segregat- Linkage ing in the female parent, and shell width in the male. Interval mapping showed chromosome-wide significance Pectinidae for many traits on two primary linkage groups in the female map and one in the male. Highly correlated, 91.7% of the variation among the six size phenotypes could be explained by the first principal component, which explained 9 and 7.8% of the variance in the female and male maps, respectively. With the exception of muscle mass mapped when maturation stage was considered as a covariate, no significant LOD scores for size traits were identified using the combined map. Finally, orange shell color was mapped to a 1 cM region of linkage group Nsub9. The development of these maps and identification of linkage groups linked to size traits provide a foundation for future quantitative studies, which could ultimately result in marker assisted selection to im- prove scallop growth in aquaculture. © 2012 Elsevier B.V. All rights reserved. 1. Introduction associated with heritable traits important to aquaculture. Traits of in- terest include those involved in growth and size, particularly of the While model organisms and many species significant to agricul- adductor muscle, which is marketed for human consumption. While ture have been subject to full genome sequencing, the genomic re- not quantified in the Pacific lion-paw scallop, the heritability of such sources for organisms such as the Pacific lion-paw scallop size traits have been investigated in other species of scallop (Nodipecten subnodosus) are few. With a significant economic value, (Crenshaw et al., 1991; Ibarra et al., 1999; Liang et al., 2010; Perez the large and fast-growing Pacific lion-paw scallop is of interest to and Alfonsi, 1999; Zheng et al., 2004); the results from the aforemen- aquaculture ventures. The development of microsatellite markers tioned studies as well as observed variation within and between fam- (Ibarra et al., 2006; Petersen et al., 2009) has allowed for ilies of N. subnodosus spawned in the laboratory suggests that these population-level investigations of diversity in aquaculture (Petersen traits have a genetic basis in the Pacific lion-paw scallop as well. As et al., 2008) and the wild (Petersen et al., 2010), but still little infor- each individual scallop can spawn as many as 25 million eggs per mation exists regarding the organization of the genome. The creation spawning event (Maldonado-Amparo et al., 2004), the identification of a genetic linkage map is a common first step in the development of of even a few superior spawners could result in a significant increase genetic resources for non-model organisms. Linkage maps specific for in the size of the population. If QTL for growth traits can be identified, this species will allow for the identification of genetic markers a selective breeding program can utilize those loci to increase aqua- culture production, which would benefit producers and potentially reduce harvest pressure on declining natural stocks. ⁎ Corresponding author at: University of Minnesota, College of Veterinary Medicine, Several mollusks have already been the focus of genetic mapping 1365 Gortner Ave, 225 VMC, St Paul, MN 55108, USA. Tel.: +1 612 624 3611; fax: +1 612 625 0204. using microsatellite and/or AFLP markers. These include the blue E-mail address: [email protected] (J.L. Petersen). mussel (Lallias et al., 2007), Pacific oyster (Hubert and Hedgecock, 0044-8486/$ – see front matter © 2012 Elsevier B.V. All rights reserved. doi:10.1016/j.aquaculture.2012.03.039 J.L. Petersen et al. / Aquaculture 350-353 (2012) 200–209 201 Table 1 Table 1 (continued) Linkage group information for (a) combined, (b) female, and (c) male maps. Female NsubM6 9 4 5 58.47 7.31 and male linkage groups are listed next to the combined linkage group to which they NsubM7 13 3 10 57.98 4.83 correspond based upon microsatellite placement. Length and distance measurements NsubM8 7 2 5 52.20 8.70 are given in centiMorgans. NsubM9 7 4 3 50.89 8.48 NsubM10 8 3 5 50.64 7.23 (a) NsubM11 7 3 4 44.56 7.43 Linkage Total Micro- AFLP Total Avg Corresponding LG NsubM12 11 6 5 44.50 4.45 group markers satellites loci length spacing NsubM13 9 1 8 41.26 5.16 Maternal Paternal (cM) NsubM14 7 2 5 39.98 6.66 NsubM15 4 1 3 39.10 13.03 Nsub1 15 5 10 135.41 9.67 15, 19, 26 19, 20 NsubM16 9 3 6 38.40 4.80 Nsub2 28 5 23 99.48 3.68 3, 8 2, 9 NsubM17 5 1 4 34.56 7.89 Nsub3 26 7 19 93.33 3.73 2 12 NsubM18 3 1 2 28.19 14.09 Nsub4 17 4 13 74.25 4.64 5 6 NsubM19 8 3 5 27.20 3.89 Nsub5 16 1 15 71.28 4.75 11 1 NsubM20 2 2 0 0.00 0.00 Nsub6 20 3 17 69.50 3.66 1 8 7.45 2.35 5.10 48.18 8.08 Nsub7 20 2 18 68.09 3.58 4, 12 14 149 47 102 963.66 161.68 Nsub8 10 1 9 65.98 7.33 6 4 a Nsub9 24 4 20 59.56 2.59 14, 24 3 Based exclusively upon AFLP loci. Nsub10 21 1 20 57.58 2.88 10, 23 13 Nsub11 16 3 13 55.68 3.71 16, 21 10 Nsub12 20 5 15 51.54 2.71 1 7 Nsub13 19 3 16 48.81 2.71 9 16 2004; Li and Guo, 2004), eastern oyster (Yu and Guo, 2003), Zhikong Nsub14 16 2 14 47.08 3.14 7 5 Nsub15 20 5 15 35.59 1.87 22 11 scallop (Wang et al., 2004, 2005), and abalone (Baranski et al., 2006; Nsub16 8 1 7 29.33 4.19 18 18 Sekino and Hara, 2007; Shi et al., 2010; Zhan et al., 2011). Some inves- Nsub17 5 0 5 18.95 4.74 13* n/a tigations have also mapped loci associated with sex (Li et al., 2005), Nsub18 6 1 5 18.92 3.78 20 15,16 disease resistance (Yu and Guo, 2006), size (Qin et al., 2007a; Zhan Nsub19 3 0 3 12.08 6.04 17* n/a Nsub20 4 2 2 6.37 2.12 6 n/a et al., 2009), and shell color (Qin et al., 2007b; Zhan et al., 2009). In Nsub21 3 0 3 4.09 2.05 27a n/a mollusk aquaculture, selective breeding has been successful in several Nsub22 3 1 2 1.24 0.62 25 17 species, most often with the goal of achieving larger size and/or faster Average 14.55 2.55 12.00 51.10 3.83 growth (Deng et al., 2009; He et al., 2008; Ibarra et al., 1999; Langdon Total 320 56 264 1124.14 84.21 et al., 2003; Zheng et al., 2004), or to increase a population's resis- tance to disease (Nell and Perkins, 2003; Ragone Calvo et al., 2003). (b) However, marker assisted selection in mollusk aquaculture is thus Linkage Total Micro- AFLP Total Avg far uncommon due largely to the limited availability of genomic group markers satellites loci length (cM) spacing resources. NsubF1 20 7 13 182.56 9.61 The purpose of the current study was to construct the first genetic NsubF2 14 6 8 96.76 7.44 map of the Pacific lion-paw scallop using a full-sibling family. NsubF3 11 4 7 74.74 7.47 NsubF4 6 1 5 74.68 14.94 Seventy-two previously published microsatellite markers (Ibarra et NsubF5 8 4 4 68.37 9.77 al., 2006; Petersen et al., 2009) and one new microsatellite locus NsubF6 7 3 4 59.14 9.86 were available to anchor the map, while AFLP loci were used to link NsubF7 6 2 4 55.57 11.11 microsatellites and facilitate more dense coverage of the genome.