DOI 10.1007/s11032-014-0116-1 Construction of dense linkage maps on the fly using early generation wheat breeding populations J. T. Eckard J. L. Gonzalez-Hernandez S. Chao P. St Amand G. Bai Received: 4 March 2014 / Accepted: 15 May 2014 Ó Springer Science+Business Media Dordrecht 2014 Abstract In plant species, construction of framework linkage maps to facilitate quantitative trait loci mapping and molecular breeding has been confined to experimental mapping populations. However, development and evaluation of these populations is detached from breeding efforts for cultivar development. In this study, we demonstrate that dense and reliable linkage maps can be constructed using extant breeding populations derived from a large number of crosses, thus eliminating the need for extraneous population development. Using 565 segregating F 1 progeny from 28 four-way cross breeding populations, a linkage map of the hexaploid wheat genome consisting of 3,785 single nucleotide polymorphism (SNP) loci and 22 simple sequence repeat loci was developed. Map estimation was facilitated by application of mapping algorithms for general pedigrees Electronic supplementary material The online version of this article (doi:10.1007/s11032-014-0116-1) contains supplementary material, which is available to authorized users. J. T. Eckard J. L. Gonzalez-Hernandez (&) Department of Plant Science, South Dakota State University, Brookings, SD, USA e-mail: jose.gonzalez@sdstate.edu S. Chao USDA, Agricultural Research Service, Fargo, ND, USA P. St Amand G. Bai USDA, Agricultural Research Service, Manhattan, KS, USA implemented in the software package CRI-MAP. The developed linkage maps showed high rank-order concordance with a SNP consensus map developed from seven mapping studies. Therefore, the linkage mapping methodology presented here represents a resource efficient approach for plant breeding programs that enables development of dense linkage maps on the fly to support molecular breeding efforts. Keywords Linkage mapping Consensus map Pedigree analysis Wheat breeding High-throughput genotyping Introduction Genetic linkage maps, consisting of linked marker loci ordered along chromosomes, provide the essential framework for identifying genomic regions involved in trait expression and detection of marker-trait associations to enable molecular breeding. For plant species, linkage mapping has largely been confined to an experimental paradigm, in which a purpose-built population derived from a cross between two inbred lines is used for map construction. These experimental mapping populations have been attractive tools for genetic mapping due to their simplicity of development, power for quantitative trait loci (QTL) detection and applicability of available mapping algorithms and user-friendly software implementations (Doerge
2002). Despite these attractive attributes, experimental mapping populations have important limitations for the development of genetic linkage maps owing to their narrow genetic base and detachment from applied breeding efforts (Crepieux et al. 2004). The increasing availability of high-throughput marker genotyping platforms (Kilian et al. 2003; Akbari et al. 2006; Akhunov et al. 2011; Allen et al. 2011; Deschamps et al. 2012) provides a means for the development of dense linkage maps (Bowers et al. 2012). However, the narrow genetic base of conventional mapping populations means that only a small fraction of these marker loci are polymorphic and thus informative for mapping in any given population. Development of a linkage map with dense marker coverage has therefore required integration of maps from several experimental populations to form a consensus map (Wu et al. 2008). However, the process of developing and genotyping several large populations that have no direct contribution to cultivar development is inefficient from the perspective of an applied breeding program. Furthermore, conventional mapping algorithms can only facilitate joint likelihood estimation of the linkage map if each of the constituent populations is of the same structure (Wu et al. 2008). Therefore, consensus mapping is computationally inefficient since it often relies on interpolation of disparate estimates from each constituent population. To overcome the limitations of conventional mapping populations, researchers have proposed using broad-based populations derived from multi-parent crosses. For example, the maize nested association mapping (NAM) population consists of 5,000 recombinant inbred lines derived by crossing 25 diverse founders to a single common founder (Yu et al. 2008). Early generation four-way cross populations have been used for genetic mapping in cotton and wheat, facilitating the development of higher density genetic maps relative to biparental populations (Trebbi et al. 2008; Qin et al. 2008). This concept of developing nway intercross mapping populations has been extended to recombinant inbred lines, with such populations referred to multi-parent advanced generation intercross (MAGIC) populations (Cavanagh et al. 2008). A MAGIC population of over 1,500 RILs from a four-way cross among elite wheat cultivars was used to map 1,162 simple sequence repeat (SSR), single nucleotide polymorphism (SNP) and DArT loci (Huang et al. 2012) and later used to map 4,300 SNPs (Cavanagh et al. 2013). MAGIC populations have also been developed for rice using eight-way crosses among elite indica and japonica lines (Bandillo et al. 2013). These rice populations enabled the identification 17,387 polymorphic SNP loci using genotype-bysequencing methods (Bandillo et al. 2013). The preceding results indicate that multi-parent mapping populations, also referred to as second generation (Rakshit et al. 2012) or next generation (Morrell et al. 2012) mapping populations, provide a powerful resource for the construction of dense linkage maps. A major motivation for utilizing these multi-parent mapping populations is that they more closely resemble the broad genetic base and multiallelic/multi-genic inheritance of breeding populations and thus provide more direct inference for QTL mapping applications (Holland 2007). However, considerable time and resources are required for the development and evaluation of these complex experimental populations, which detracts from applied breeding efforts for cultivar development. For example, development of an n-way cross for deriving a MAGIC population requires n/2 generations of intercrossing to generate the base population, followed by 6 7 generations of inbreeding to develop the RILs (Rakshit et al. 2012). Plant breeders are continually developing a large number of segregating populations through carefully planned crosses among numerous elite parents. Primary segregating populations from these crosses consist of relatively small sibships that have yet to be subjected to intense selection by breeders. Collectively, these early generation breeding populations represent a substantial pool of informative genetic recombinations that can be used for the development of dense genetic maps. Linkage maps developed using a large number of early generation breeding populations should therefore provide comparable marker density and reliability to those developed using consensus mapping or multi-parent mapping populations. Thus, utilizing existing populations available in plant breeding programs for the purpose of genetic linkage mapping should provide an efficient alternative to development of experimental mapping populations. In combination with high-throughput and nondestructive genotyping technologies, this strategy would allow breeders to develop dense linkage maps on the fly to support their molecular breeding efforts.
Development of linkage maps using plant breeding populations requires mapping algorithms that can handle partially informative marker data, ambiguous linkage phases and simultaneous analysis of numerous small sibships of arbitrary population structure. Due to the prevailing experimental paradigm, such generalized mapping algorithms are not incorporated into software used for linkage mapping in plant populations (Cheema and Dicks 2009). However, these mapping algorithms are commonly used for linkage analysis in humans and animals populations, where purpose-built populations are not available. Therefore, mapping algorithms used for multi-point linkage analysis in general pedigrees (Lander and Green 1987; Weaver et al. 1992) can be adopted for the purpose of constructing linkage maps in plant breeding populations. In this study, we apply multi-point linkage analysis of general pedigrees to develop a dense genetic linkage map from a 9,000 SNP array using early generation wheat breeding populations. Our objectives are to (1) confirm that dense linkage maps can be obtained using primary segregating populations from breeding programs and (2) assess the accuracy of such derived linkage maps by evaluating their concordance with a recently released SNP consensus map of the wheat genome. Materials and methods Plant materials Segregating F 1 populations were developed from 28 four-way crosses among 10 winter wheat founder lines (Table 1). These wheat breeding populations were developed for the purpose of pyramiding resistance loci for Fusarium head blight. Founders included two backcross derived lines Wesley-Fhb1-BC06 and Wesley-Fhb1-BC56 (Wesley/2*ND2928), an experimental line AL-107-6106 (Alsen/NE00403//NE02583-107), hard winter wheat cultivars Lyman (KS93U134/Arapahoe), Overland (Millennium sib//seward/archer), NE06545 (KS92-946-B-I5-1/Alliance), NI08708 (CO980829/Wesley), McGill (NE92458/Ike), and soft winter wheat cultivars Ernie (Pike/MO9965) and Freedom (GR876/OH217). A total of 565 four-way F 1 plants were derived from the 28 four-way crosses, with an average of 20 four-way F 1 plants per cross (Table 1). Founder lines and four-way F 1 plants were vernalized and then transplanted as individual plants in 4 9 4 inch pots in a greenhouse. DNA extraction Approximately 2 g of healthy leaf tissue was collected from each founder and four-way F 1 plant. For founder lines, tissue samples from multiple plants were pooled into a single sample. Leaf tissue was transferred to liquid nitrogen immediately upon collection and subsequently stored at -80 C to prevent degradation. DNA was isolated from the leaf tissue using a midiprep phenol/chloroform extraction protocol adapted from Karakousis and Langridge (2003). Briefly, leaf tissue was flash frozen in liquid nitrogen and then ground to a fine powder using a mortar and pestle. Ground leaf tissue was then mixed with 5 ml of DNA extraction buffer (1 % n-lauroylsarcosine, 100 mm Tris-base, 100 mm NaCl, 10 mm EDTA, 2 % polyvinyl polypyrrolidone, ph 8.5) and 5 ml of phenol/chloroform/isoamyl alcohol 25:24:1 saturated with 10 mm Tris (ph 8.0) for nucleic acid separation. After mixing and centrifugation, the supernatant was transferred to a 10:1 solution of isopropanol and sodium acetate for overnight precipitation of nucleic acids. Precipitated nucleic acid was pelletized by centrifugation and washed with 70 % molecular grade ethanol to remove salts. After drying, the pellet was suspended in 10 mm Tris buffer (ph 8.0) containing 40 lg/ml of RNase A. Genotyping Founder lines and all 565 four-way F 1 plants were genotyped at 26 polymorphic simple SSR marker loci. SSR genotyping was conducted at the USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, KS. PCR was conducted in 14 ll PCR, consisting of 40 ng of template DNA, 0.1 lm of each primer, 0.2 mm of each dntp, 19 ammonium sulfide PCR buffer, 2.5 mm MgCl 2 and 0.6 unit of Taq polymerase. A touchdown PCR program described by Zhang et al. (2012) was used for amplification. Differentially labeled primers were used for fluorescence detection of SSR amplicons from multiplex PCR as described by Zhang et al. (2012). PCR products were separated and detected using an ABI Prism 3730 Genetic Analyzer, and allele calls were made from resulting fluorescence
Table 1 Summary of breeding populations used for linkage map development, including the pedigrees, number of progeny and number of plants used for SNP genotyping Population Pedigree Four-way F1 plants SNP genotyped 01 Wesley-Fhb1-BC56/NE06545//Ernie/Overland 20 19 03 Ernie/Wesley-Fhb1-BC06//Ernie/NE06545 26 05 Ernie/Wesley-Fhb1-BC06//Lyman/AL-107-6106 22 16 06 Ernie/Wesley-Fhb1-BC56//Ernie/Lyman 40 37 09 Ernie/Wesley-Fhb1-BC56//NI08708/Lyman 40 38 10 Ernie/Lyman//Ernie/Wesley-Fhb1-BC06 12 14 Ernie/Overland//Freedom/Wesley-Fhb1-BC56 5 16 Ernie/Overland//Overland/Wesley-Fhb1-BC56 24 23 17 Ernie/Overland//NI08708/Wesley-Fhb1-BC06 33 30 20 Ernie/NE06545//McGill/Wesley-Fhb1-BC56 28 23 Ernie/McGill//Lyman/Wesley-Fhb1-BC06 12 9 26 Freedom/Wesley-Fhb1-BC06//Ernie/Overland 12 9 27 Freedom/Wesley-Fhb1-BC06//Lyman/AL-107-6106 7 7 28 Freedom/Wesley-Fhb1-BC06//Overland/Wesley-Fhb1-BC56 11 9 30 Freedom/Wesley-Fhb1-BC56//Ernie/NE06545 4 35 Freedom/Ernie//Overland/Wesley-Fhb1-BC56 34 30 36 Freedom/Ernie//NI08708/Wesley-Fhb1-BC06 29 40 Freedom/Overland//Lyman/AL-107-6106 8 8 41 Freedom/NI08708//Wesley-Fhb1-BC56/NE06545 7 45 AL-107-6106/Overland//Lyman/Wesley-Fhb1-BC06 11 10 48 AL-107-6106/Overland//NI08708/Lyman 14 14 54 Lyman/Wesley-Fhb1-BC56//Ernie/Lyman 37 35 57 Lyman/Wesley-Fhb1-BC56//NI08708/Lyman 31 64 Overland/Wesley-Fhb1-BC56//Ernie/Lyman 44 41 65 Overland/Wesley-Fhb1-BC56//Ernie/NE06545 5 67 Overland/McGill//Lyman/Wesley-Fhb1-BC06 12 9 71 NI08708/Wesley-Fhb1-BC06//Ernie/NE06545 8 76 NI08708/Lyman//Overland/Wesley-Fhb1-BC56 29 28 Total population 565 372 peaks using GeneMarker version 1.6 (SoftGenetics, LLC). SSR marker genotypes were scored after visual assessment of fluorescence profiles to correct erroneous and ambiguous allele calls. A subset of 18 populations consisting of 372 fourway F 1 plants (Table 1) were genotyped for approximately 9,000 SNP marker loci. SNP genotyping was conducted using an Infinium 9,000 SNP iselect Beadchip assay developed for wheat (Cavanagh et al. 2013). The assay was performed using the Illumina BeadStation and iscan instruments at the USDA-ARS Biosciences Research Laboratory, Fargo, ND. GenomeStudio version 2011.1 (Illumina) was used for cluster analysis and SNP genotype calling. The minimum GenTrain score (a measure of the reliability of SNP calling based on cluster distribution) was reduced to 5 in GenomeStudio to facilitate delineation of compressed but unambiguous SNP clusters. Genotype clusters were then visually assessed for each SNP and manually revised to improve genotype calling. SNP loci represented by more than three genotypic clusters, and those SNP loci with[20 % deviation from the expected heterozygote frequency under Mendelian segregation were excluded from the analysis to avoid complications of polyploid inheritance. Mendelian inheritance errors for both SSR and SNP loci were detected using the prepare function of
CRI-MAP version 2.504 (Green et al. 1990). Genetic impurities in the founders were diagnosed as outliers (i.e., samples with a low GenTrain score) within the respective homozygote cluster and by unexpected segregation patterns. For those cases where genotyping errors could not be rectified, including cases where a founder line conferred more than one allele at a locus within the same population, the genotypic data were replaced with missing values. Linkage mapping Linkage analysis was performed using the software package CRI-MAP version 2.504 (Green et al. 1990). CRI-MAP provides an interactive environment for multi-point maximum-likelihood estimation of linkage maps in general pedigrees. For the purpose of constructing the required pedigree data, each four-way cross was considered as a separate pedigree. The assumption of independence among pedigrees was made without any loss of generality, since the founder lines were phase known. The sex designation of founders and single-cross F 1 hybrids was generally assigned corresponding to the actual crossing scheme, while four-way F 1 plants were arbitrarily designated as females. All linkage analysis in CRI-MAP was conducted on an IBM 93755 M2 server with 24 processor cores and 128 GB of RAM. Maximum-likelihood estimates of pairwise recombination fractions among marker loci were obtained using the twopoint option of CRI-MAP. Pairwise recombination fractions and associated LOD scores were exported to JoinMap version 4.0 (van Ooijen 2006) for identification of linkage groups. Marker loci were hierarchically clustered in JoinMap based on independence test LOD scores (van Ooijen 2006). Linkage groups were designated as the hierarchical nodes beyond which no significant disaggregation occurred. This point was reached at LOD scores ranging from 1 to 35.0 for different linkage groups. Cross linkage statistics computed by JoinMap were used to combine fragmented linkage groups and unassigned marker loci. Chromosomal assignment of the linkage groups was enabled by cross referencing loci from each linkage group with available SSR and expressed sequence tag (EST) mapping data. Pairwise recombination fractions were then used to cluster marker loci with recombination fractions \01 into genetic bins. From each genetic bin, the locus with the greatest number of informative, phaseknown meioses was identified and considered to be the primary locus representing the genetic bin. These primary loci were used to estimate a linkage map of uniquely ordered loci, prior to incorporating the remaining loci to derive the final linkage map. This strategy reduced the number of possible marker orders that had to be initially interrogated, thus increasing the efficiency of the mapping algorithm. Linkage maps were constructed using the CRI- MAP build option. For each chromosome, several pairs of highly informative primary loci with a recombination fraction of 0.30 0.40 were selected to initialize the map order. A framework linkage map was then constructed from each selected pair of loci by sequentially incorporating the remaining primary loci in decreasing order of informativeness. For this first round of map development, only those loci that mapped to an interval with a likelihood ratio 1,000:1 compared to all other intervals were retained in the map. The resulting set of linkage maps was compared, and the most complete map with the highest likelihood was retained for further development. The stringent likelihood threshold and interrogation of multiple initial map orders provided a reliable framework of highly informative markers for subsequent rounds of map development. Successive rounds of map development were performed to incorporate the primary loci that could not be uniquely ordered in the first round. The likelihood threshold for incorporation of loci was reduced between each round of map development. Specifically, the successive rounds of map development were conducted using likelihood thresholds of 100:1, 10:1 and 2:1. Between each round of map development, the CRI-MAP flips4 option was used to test the 24 possible permutations for each set of 4 consecutive loci in the current map order. Any local rearrangements that increased the likelihood were used to revise the current map order prior next round of map development. Any loci that mapped to end of the chromosome with a distance of[30 cm to the nearest locus were removed from the map and were assumed to either be misclassified to the chromosome or belong to unlinked regions of the same chromosome. After determining the most likely order of the primary loci, the CRI-MAP chrompic function was used to detect loci and individuals resulting in unlikely recombination patterns. Double recombination events
between a set of 3 consecutive loci were considered to be the result of genotyping errors, and these data were replaced with missing values. Double recombinations between loci separated by uninformative regions were retained. Unlikely crossover events that were prevalent at a locus within a specific pedigree were considered to be the result of genotyping errors on the founder lines, and the data for the entire pedigree were replaced with missing values for the locus in question when the errors could not be rectified. Finally, the remaining loci within genetic bins were incorporated into the linkage map. Unmapped loci having a zero estimated recombination fraction with a primary locus were incorporated as a haplotyped system, with the primary locus. CRI-MAP only considers the primary locus in each haplotyped system when evaluating marker orders, whereas all loci were used in likelihood calculations (Green et al. 1990). Genetic distances were not forced to zero between markers within haplotyped systems. Unmapped loci with nonzero estimated recombination fractions with the primary locus were incorporated into the map order to the right of the primary locus, in decreasing order of informativeness. The CRI-MAP flips4 option was then iteratively used to permutate the local marker orders until no higher likelihood map order could be obtained. The final linkage maps were charted using MapChart version 2.2 (Voorrips 2002). from the TCAP consensus map to visually compare patterns of recombination and locus ordering, as well as diagnose causes of poor concordance. Results Of the approximately 9,000 SNPs assayed, 3,977 were polymorphic and produced clusters that facilitated reliable scoring of SNP genotypes. Additionally, 22 of the 26 SSR loci amplified a product that could be reliably scored, resulting in a total of 3,999 informative loci for subsequent linkage analysis. The average number of informative meioses per SNP locus was 320 and ranged from 20 to 604 (Fig. 1). Hierarchical clustering of these loci in JoinMap resulted in the identification of 31 linkage groups. Cross linkage statistics provided by JoinMap combined with previous SSR and EST mapping data enabled the combination of these linkage groups and unassigned marker loci into 21 groups, putatively representing the 21 wheat chromosomes. Evaluation of recombination fractions identified a total of 1,269 unique genetic bins, with an average bin size of 5 loci. Therefore, 67 % of the interrogated loci were found to be colocalized, resulting from tight linkage among the marker loci as well as markers that interrogated the same locus. Comparatively, only 38 % of these SNP Concordance analysis A consensus map of the wheat genome has been developed for the iselect 9,000 SNP assay through the Triticeae Coordinated Agricultural Project (TCAP) as described by Cavanagh et al. (2013). The TCAP consensus map incorporates a four-way MAGIC population and 6 biparental mapping populations with a combined population size of 2,486 fixed lines. The TCAP consensus map was used as the standard for evaluating the accuracy of linkage maps developed in this study. For each chromosome, Spearman s rankorder correlation coefficient was computed as a measure of concordance for locus ordering between the TCAP consensus map and the linkage map developed in this study. For each linkage map, relative genetic distances were computed as the locus position in cm divided by the total map length in cm. The relative genetic distances estimated from the breeding populations in this study were plotted against those Fig. 1 Distribution of the number of informative meioses for polymorphic SNP loci. Primary loci are the most informative loci from each genetic bin used for initial map development, whereas secondary loci are the remaining loci in the genetic bins
Table 2 Summary of the estimated genetic maps for each chromosome Chromosomes Loci mapped Centimorgans Recombination Total Genetic bins Total Mean interval Informative meioses Observed crossovers Singletons (\20 cm) 1A 350 88 174.3 2.0 29,086 1,074 19 1B 193 59 160.5 2.8 20,150 919 18 1D 110 30 92.1 3.2 10,532 464 2 2A 214 92 225.3 2.5 30,299 1,450 13 2B 364 72 142.8 2.0 25,932 917 12 2D 50 25 103.2 4.3 9,613 596 7 3A 231 76 171.6 2.3 27,134 1,107 8 3B 288 116 156.9 1.4 40,886 1,245 17 3D 30 11 78.3 7.8 2,762 205 2 4A 104 56 151.8 2.8 20,438 994 7 4B 104 47 140.6 3.1 18,667 901 18 4D 9 7 39.9 6.6 2,325 58 1 5A 296 104 255.5 2.5 41,824 1,750 15 5B 335 113 212.5 1.9 32,417 1,284 12 5D 39 22 190.1 9.1 7,337 747 1 6A 242 72 176.8 2.5 25,239 926 13 6B 338 85 133.7 1.6 29,899 840 7 6D a 44 16 45.4 3.0 5,618 104 0 7A 316 105 206.6 1.9 32,964 1,263 4 7B 189 58 186.8 3.3 20,273 1,161 7 7D a 29 15 36.2 2.7 3,748 189 1 Overall 3,875 1,269 3,080.9 2.5 437,143 18,194 184 a The chromosome was represented by multiple linkage groups markers were colocalized on the TCAP consensus map. Primary loci from each of the genetic bins provided approximately 437,000 of the uniquely informative data points, from which over 18,000 recombination events could be observed (Table 2). Linkage maps estimated from the breeding populations are summarized in Table 2 and depicted in Fig. 2a g. The estimated linkage maps included 3,875 loci and covered a total genetic distance of 3,080 cm, with an average interval of 2.5 cm between genetic bins. Marker coverage was relatively poor for the D genome. After curating the data to remove doublecrossover events among consecutive marker trios, a total of 184 singletons remained within partially informative regions of 20 cm or less. This number of observed singletons represents a double-crossover rate of 4 % within a span of 20 cm, which is consistent with the expected maximum recombination rate (0.2 2 = 4). Therefore, the majority singletons remaining in the data were assumed to result from genuine recombination events. Poor marker coverage on the D genome resulted in multiple linkage groups per chromosome for both the TCAP consensus map and the map estimated in this study. Therefore, only the A and B genomes were used for analysis of concordance with the consensus map. Linkage maps of the A and B genomes developed from the breeding populations in this study exhibited high concordance with the TCAP consensus maps (Fig. 3a c). Excluding chromosomes 2B and 6B, the average rank-order correlation with the consensus maps was 0.98, indicating a high level of agreement regarding the locus ordering between the two sets of linkage maps. Chromosome 6B had the lowest rank-order correlation with the consensus map (0.52), due to a large centromeric inversion of the locus order (Fig. 3b). The linkage map for chromosome 2B had a region of highly suppressed centromeric recombination compared to
A 1A 1B 1D 4643, 4754 4715 5996 13.8 18.4 20.8 22.2 22.6 23.0 24.5 30.4 33.8 34.5 36.5 41.5 49.0 52.5 56.0 57.6 57.8 60.4 65.8 66.0 66.1 66.2 66.4 66.6 66.9 67.3 67.4 67.8 68.7 69.2 69.6 75.0 75.7 75.8 75.9 76.1 76.2 76.4 76.7 81.6 83.9 85.0 85.2 85.7 86.1 87.4 87.9 90.4 91.7 92.1 93.7 94.7 96.9 97.3 10 105.1 106.1 109.0 110.5 112.1 112.2 114.3 116.1 116.9 117.1 118.2 118.3 118.4 118.5 118.9 150.9 151.6 159.2 159.7 161.2 161.6 162.0 162.6 166.9 167.7 17 170.5 172.1 172.9 173.7 174.3 6644, 1602, 3181 1376 7559, 8622, 5150 6645, 1375, 5065 1603 3180 6444 4321 5702, 7385, 6110, 1566, (9) 5593 764 4506, 1934, 4579, 5509, (5) 7796 217 6441 1388, 1387, 7377 4164, 4163, 4644, 513 7151, 3375 2655, 2656, 710, 7421, (8) 3347 3398 1580 639, 6887, 7879, 7922, (7) 7505 2651, 1991, 8071 2438 1450, 1582, 1583, 7115, (8) 1811, 2057, 2247, 2289, (48) 1078, 2630, 3473, 356, (22) 3144, 498 2981, 2982, 3532, 3533, (24) 7021, 4326, 4328 459, 4126, 268, 5839, (8) 1307 5310 6497 7577 4117, 3134, 3891, 4116, (7) 1594, 3475, 3613, 3820, (11) 7956, 2584, 5138, 6609, (7) 6708, 5174, 6707 162 560, 163, 6553, 7871, (13) 2540, 4511, 605 931 3406 2487, 2488, 2490, 2484, (9) 601 2314 6341 339 3405, 7145, 3859, 5493, (6) 7144, 6624 530, 531 8212 1081, 4537, 6933 577, 578, 5832 7754 6042, 3434, 3435, 3804, (5) 3060, 8334 5047, 5046 691 5822 6081 1225, 3146, 2404, 2405, (5) 1619, 6253, 735, 2818, (20) 1587 7428 7591 672 2994, 4978, 5491 3377, 4021, 3378 4897, 4898 3089 1560, 8051, 2035, 5318, (10) 3590 2015 5097, 4944, 5407, 1710, (5) 4518, 8523 4271, 7290 1645, 6916, 1644 3764 5405, 4121, 4, 4120, (5) 3661 3977 3215, 3799 5734, 5806 15.9 34.6 37.2 37.5 38.0 40.1 42.3 43.1 48.9 49.1 49.9 50.8 56.1 57.1 57.8 58.6 60.7 61.2 62.1 62.6 62.7 62.9 63.1 64.6 65.3 66.1 66.6 68.5 69.9 70.6 72.6 74.7 75.1 78.7 80.4 82.1 89.6 102.4 105.2 105.8 109.3 110.9 111.2 112.1 118.5 122.7 128.9 129.4 130.6 132.2 133.9 144.6 145.7 147.2 148.5 158.4 160.2 160.5 4240 5301, 406 1480 6836, 5370 7331 4349, 6787 1883, 63, 64 2282 1191 1949, 3443, 7480, 1578, (9) 7048 7117, 2578, 2577 3738 6728, 7280, 6703, 4389, (8) 131, 15, 6290, 353, (6) 8619 6063, 5348, 8081, 8082, (9) 128, 7721, 2517, 3502, (26) 7017, 4556, 4557 3307 4316 554 6107, 491, 3945, 269, (14) 5076, 2861 854 540, 515 4681, 4680, 5962, 5229, (26) 1313 5382, 5383 3120, 4488 6646 2411, 7037, 255, 2308, (8) 5186, 368 415 5749, 5915 8507 4999, 4139 5445, 3095, 5448, 3096, (5) 7422 6663, 7141, 4031 695 3097, 5447, 5446 7619 8543, 696 1020, 8542 1092 8461, 3998 919, 920 7992, 8332 3660 3893 1791 724 7892 5758 1504, 4694, 545, 4935 6512, 6511, 2928, 198 2077, 6647 21.6 22.1 23.4 23.7 28.0 58.5 59.1 60.3 60.6 60.8 63.7 64.3 64.4 66.8 69.3 80.3 80.5 80.6 81.0 84.2 85.6 86.1 87.0 88.0 88.9 89.1 89.3 89.7 92.1 407 2449 817 5372, 6500, 1397 4716, 7533, 713 1572 6675 362, 5019, 5018, 5020, (6) 7425 1221, 830, 642 1192, 1193 5698 3446 3481 7154 5232 5234 2340, 2021, 5235, 2341, (6) 6186, 1736, 3014, 3058, (26) 4886, 7838, 4885 1386 6955, 4938, 7675, 3465, (9) 4960, 2043, 4024, 5514, (21) 8002 5182, 7023, 8485, 5541, (5) 7848 474, 3420 532 7702, 3548, 3547, 3549 Fig. 2 a Estimated genetic maps for homeologous group 1 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if[4. See supplemental data for a complete list. b Estimated genetic maps for homeologous group 2 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if [4. See supplemental data for a complete list. c Estimated genetic maps for homeologous group 3 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if[4. See supplemental data for a complete list. d Estimated genetic maps for homeologous group 4 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if [4. See supplemental data for a complete list. e Estimated genetic maps for homeologous group 5 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if [4. See supplemental data for a complete list. f Estimated genetic maps for homeologous group 6 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if [4. See supplemental data for a complete list. g Estimated genetic maps for homeologous group 7 chromosomes. Genetic bins are followed by the number of constituent markers in parentheses if[4. See supplemental data for a complete list
B 2A 2B 2D 2.1 2.3 2.6 2.9 7.8 9.7 10.2 12.9 13.4 15.9 25.6 35.0 43.7 51.5 54.1 54.2 56.9 58.2 67.0 67.9 77.5 78.3 78.7 84.1 84.9 85.1 85.6 86.7 87.6 87.8 87.9 88.5 90.1 92.1 92.9 98.0 98.3 103.1 104.4 106.2 113.1 113.4 113.7 114.7 116.4 118.0 119.4 120.8 122.1 122.7.0 141.0 145.4 145.9 146.1 146.3 148.1 153.8 154.3 157.3 160.6 161.7 164.3 17 170.4 171.1 173.7 174.1 174.8 175.3 175.8 176.0 176.3 186.2 189.8 191.2 194.8 195.0 195.1 195.2 196.1 196.4 199.5 202.8 203.2 203.4 6745, 2426 4989, 6922, 1511 1563 7370 2427, 2425, 2428 barc212 6391, 5341 1512 1830 4990 3468, 3469, 3382 681 3047, 8274, 422, 423, (5) gwm359 3235 2696, 2059, 7410 5087 wmc598 2526 2798, 3280 6478, 6477, 6727 wmc522 6566, 2067, 2731, 6565, (6) 6564, 630 5022, 5893, 5023, 901 3193, 3194 5495, 5824, 562 6332, 2531, 3569, 4026, (8) 7248, 1597, 4410, 5585, (10) 5378, 534, 2758, 533 2948 3842 5273, 2733, 3368, 5092, (8) 3839, 6753 3151, 1174, 488, 7947 2807 240 241 6270 3199, 5574, 5640, 6090, (7) 2612 2092, 200, 4562 3597 4732 4733, 1275 2640 5856, 5855 3629 2835, 3988, 6503, 7540, (18) 8157 970, 2157, 7864 4373 1960, 8385 1539 684, 3752 6931 5066 5959, 2938 8040, 8041, 5685, 5686 5872, 4336, 7727, 3897 2051, 3920 756 4475, 227 5840, 5007, 7761, 5271 8036, 2602 2601 6798, 6797 1348 3596 6600, 2555 1349 6839, 7142 5588, 7143, 319 6620, 1350, 1347, 1351 5161 5759 5894 4461 4463, 6963, 4491 4492, 4493 4664, 5879, 3687, 7327, (6) 3809 5082, 2983 2777, 3688 4459 4460 7885 2.1 2.4 9.7 1 13.4 13.8 24.4 25.2 35.6 40.5 44.0 46.3 49.6 49.9 54.6 54.8 54.9 55.0 55.1 55.2 58.7 59.1 67.9 77.7 78.2 78.4 82.0 82.3 82.5 82.8 83.2 84.0 84.2 84.4 84.6 85.3 85.7 86.2 86.6 87.3 87.4 87.5 87.6 87.9 88.3 88.8 89.1 89.6 90.1 90.5 95.1 95.4 95.7 96.0 96.2 96.7 97.0 98.8 118.8.3 124.8 125.1 125.9 129.2 13 132.7 133.8 135.9 136.1 136.3 142.8 4953 1413, 6263 6262, 7633 4723 2973, 4808, 7656, 2482 4855 7544,3589,5921 2407,2846,7936 5137 749 3723 5554, 2110, 2088, 2111, (6) wmc154 5736, 2440, 2442, 5721 2443,2441,7120 2116, 2115, 5410, 4284, (7) 1931, 5737, 1929, 6048 888 3838 7800 2117 6740, 4420, 4421, 6739, (8) 1360 438, 1210 gwm429 1407, 6893 6026 6462,1204,429,328 6427, 5811, 7076, 4388, (5) 6209,2766,535,5436 5939, 6317 7825, 5506, 2237, 5397, (6) 3924, 4894 7263, 3908, 7661, 1763, (5) 4720, 4642 2671, 4323 169 170, 1102, 1127, 1128, (25) 7951, 8244, 6875, 4983, (12) 1981, 4303, 561, 3452, (5) 2253, 2236, 2184, 5254, (15) 5464 5723 6093, 671, 3236, 6076, (103) 310 837, 8085 2676, 2678, 3395, 5850, (8) 7909, 8270 470, 4256, 4956, 652, (29) 1389 4356, 4357, 4890, 4948, (8) 3148, 1707, 5051, 1291, (6) 2872 3075 2502,3233,7955 3938, 5675, 3937, 5024 5809, 6778, 1599, 2052, (9) 7113,7112,5081 31 5738 7671 1535 6656 3474 746 2377, 3982, 8504, 5093 3252 3206, 1668, 4118, 3773, (7) 988 3315 2094, 7335, 5694, 6852 5991, 5989 0.3 0.9 1.2 3.6 4.1 8.1 20.8 30.4 31.7 46.7 47.0 47.2 52.4 56.5 58.2 61.8 65.5 75.3 77.1 77.5 85.6 90.3 103.2 1601 4711 4746, 4530 4354, 1107 2160, 7790 1855 6302, 6301 5905 760 927 6452 7418, 7273, 1975, 4496 3248 6374 563, 209 144 1858, 6520 2722 2961, 5637, 8562 7332 1072 4789 5252 5919, 1083, 5205, 5630, (15) 8365 220.7 223.0 225.3 7412 7156 6841, 5072, 4229, 6840 Fig. 2 continued
0.2 1.7 2.5 3.1 7.5 13.5 17.9 20.2 22.0 47.4 48.7 49.0 49.8 53.3 54.1 56.5 56.6 56.9 57.3 57.7 58.9 59.0 59.3 59.5 60.5 60.6 61.2 61.4 61.8 62.1 62.4 62.5 62.7 62.8 62.9 63.6 63.9 64.8 65.5 66.5 66.7 66.8 67.5 67.8 69.3 69.5 69.6 7 70.5 73.5 74.7 78.9 80.4 80.8 81.5 86.9 87.4 87.9 89.3 91.4 95.5 101.9 107.4 120.3 134.7 149.7 152.3 158.3 159.6 159.9 161.5 162.1 166.3 170.8 171.6 C 3A 5443, 7771 447, 5427, 4927, 5430, (8) 7861 6387, 2993, 8280 2737, 2738 4066 8127, 851 8105, 8106, 3939 4804 4257 1996 6340 3448, 5642, 3739 885 4334, 4335, 4333, 7552 6413 5399 5151 7022 443 1972 5763, 8526, 6334, 1812, (9) 6877 2763, 2095, 335 5387, 5444, 90 1614 6306, 637 720 143, 2156, 1922, 4912, (5) 3794 6187, 5316 2153, 2154 2023 7012 6256 3071, 6923, 7010, 3069, (5) 5164 1487, 3156, 4397, 462, (13) 7319 2617, 234, 1085 4923, 2750, 2886, 3930, (13) 3836, 6170, 6783 4075 8580, 7114 8465, 133, 743, 5124 5315, 7541, 2801, 5994, (14) 3250, 4110 3999, 1701, 1536, 1700, (22) 5286, 7159, 5285, 1678, (11) 3198 1831 8374 8162 1778 925, 4926, 4851, 1260, (5) 4053 5419, 5596, 8455, 1892, (6) 7169 1891 1611, 855 6996, 6997, 1294 7696, 3524, 5456 5980, 5213, 5982, 5212, (5) 524, 799, 523, 2029, (5) 6396 7297, 1207, 2372 7812, 1367 95, 94 3559, 3560 3493 5111 5112 4258, 7835, 2949 8000, 7999, 2396, 6716, (5) 3949 4407, 1457, 602, 2870 3.6 5.8 9.8 10.6 12.0 16.0 20.6 35.5 39.7 46.7 46.8 52.8 56.5 59.4 59.9 61.4 61.6 62.3 63.5 64.5 64.9 65.1 66.1 66.2 66.4 69.3 69.6 70.6 71.7 72.0 72.1 72.3 73.0 73.1 73.4 74.0 75.3 75.5 75.7 75.9 77.4 78.0 78.2 81.8 83.2 83.6 84.9 85.2 85.6 85.8 86.2 87.1 87.3 87.4 87.5 87.7 88.2 88.3 88.5 88.7 89.8 91.7 92.2 92.3 92.4 92.5 92.6 92.7 92.9 94.9 96.5 96.6 96.7 96.8 96.9 97.0 97.1 97.2 102.7 102.9 104.3 115.3 117.6 118.4 119.1 125.0 133.1 133.3 134.6 139.5 139.9 140.2 141.0 141.5 149.0 152.6 156.9 3B gwm389, 195 6651 barc133 5426 5299 2908, 758 gwm493 288, 289, 2493 1187, 716 8303 663, 280, 4625, 5618, (5) 7342 3983 6632, 3425, 3426 4235 2662, 2663, 4054, 3787 5325, 3117, 3716, 347, (5) 3904 6192, 3150, 3149, 6919 5843 748, 747 6482, 3731, 3732, 7267 1458, 4838, 3390, 1459 2409, 2408, 4843 2074, 2119, 7748, 1416, (7) 4040, 4310, 7860, 4039, (5) 4755, 7294, 6165, 6243, (14) 380, 376, 5351, 729, (6) 210, 377, 5638 6017, 91 gwm285, 2990 3021, 6814, 6655, 2494 2622 1206 1383, 1607, 7247, 4193, (10) 6793, 2329, 6677, 4452, (15) 3000 537, 5613, 6297 2782, 3710, 3711, 5101, (10) 4439 7510 5770 5880, 5677, 2492 629, 628, 6381 5792 5775, 4653, 5710, 4218, (8) 5869 3245, 4613 4085 7353 barc164, 4156, 7078 5711 4507 6157 6221, 6222, 1148, 7131 3305, 3306, 6493 6254, 1467, 7225, 1196, (8) 6223, 5805, 6158, 3304 3018 4721 6492 6104, 6105 7946, 3439 2124 1598, 2399, 2510, 1331 1332, 2361, 3833, 3835 6552, 7870, 8136 8137, 1333, 1334 2204, 3244, 3834, 4457 3046, 3402, 3601 2720, 2721, 2661, 7221 4553 2862, 7889, 2620, 3455, (11) 2167 1682 2063 4906, 6542 1541 1683 7561, 8594 5646 714, 5941, 6375, 6299, (6) 2951, 3592, 1095, 3591, (6) 1731, 3170, 6002, 4498, (10) 3332, 3331 3667 5013, 5014, 5015, 4778, (5) 4600 1094 barc84 7542 784 787, 785, 8628 786 5594, 8058 939 6930 4312, 4311 6273, 8185 26.3 28.8 31.1 31.5 56.2 60.6 60.9 65.0 65.6 78.3 3D 325 5469, 7468, 5695, 1321, (5) 7672 4647 2293 6485 7526, 4081 6777, 4683, 1796 8059, 1715, 7274, 8578, (7) 153, 1624, 4877, 3012, (7) 5230 Fig. 2 continued the consensus map, which resulted in shuffling of locus orders and a reduced rank-order correlation with the consensus map (0.72). The majority of the linkage maps estimated from the breeding populations showed regions with reduced recombination relative to the TCAP consensus maps. These lower estimates of recombination were typically centromeric, which resulted in s-shaped trends when plotted against the consensus map positions (Fig. 3a c). However, the differences in estimated
D 4A 4B 4D 0.5 2.4 6.0 6696 4651 1505 5353, 4858, 7365, 4084, (5) 6457 752 9.4 4859, 7364, 1836, 1835, (5) 13.6 3449, 4030, 7197 20.4 21.5 27.6 29.9 30.2 45.4 46.3 46.9 6690 7765 3864 558 6563 7322 3068 4527, 5968 3061, 3698 17.4 23.8 33.8 34.3 36.0 38.3 39.2 39.8 44.4 46.0 50.1 50.9 5739 8108, 2298, 8107 1768 7268, 1316 7266 3615 8178 2126 4569 3290 wmc710, 1045 4662 28.9 29.9 31.6 37.4 38.9 39.9 1633, 4044 430, 161 3116 3555 3815 410 62.1 64.5 67.1 69.6 76.9 84.5 85.4 86.5 90.5 90.9 92.3 100.2 102.1 102.2 102.4 102.6 104.2 104.7 105.2 110.8 114.4 116.0 117.1 117.4 117.8 121.3 122.4.4 124.0 127.7 128.0 128.6 132.2 132.6 134.2 139.2 140.3 145.6 147.3 148.6 151.8 485, 3188, 5152, 8168, (5) 2505 2761 8209 1521 2719 6906, 2904 4243, 2384, 2383 7058 1692, 1691 5200, 1720 8432 3981, 6883, 4199 6884 6882 6885 2207, 3728, 7535 2582, 2581, 5422 7442 5349 482, 6501 2045 402, 1792 7699, 2585, 2901, 3191, (9) 1727 7521 3584 6100, 1728, 1992, 4252, (5) 4261, 4260, 3902, 4480, (6) 2533 4232 5363 1137 1170 7394 2764 3993 3161 7632 285, 8389, 54 1900 65.8 72.6 73.5 78.0 78.2 78.4 81.6 81.8 81.9 82.2 82.3 82.4 82.5 82.6 82.8 83.0 83.3 83.5 84.8 89.0 91.7 92.0 97.8 98.9 101.0 102.6 105.3 107.9 108.5 113.4 113.8 116.3 128.0 140.7 2313 gwm495, 2963, 3400, 3874, (7) 3325 258 8564 5863 3240 7284, 7767 7688 3392 1910, 7411 6480 86, 8163, 3241, 3736 4347, 4348, 1006 5195, 1007 1344, 2532, 7437, 7168, (8) 2666, 3846, 4070, 4330, (11) 1405 1028, 907, 3074, 7752, (5) 7566 5365, 3041, 3042, 3038, (5) 3040, 6461 3279, 4115 3253 1861 5885, 7202, 3697, 8197 2031, 6465 4490, 5408, 6397, 2595, (5) wmc125 564 5358 3780, 3779, 3781, 6719 7555, 3770 6230 Fig. 2 continued recombination frequencies did not greatly affect the relative ordering of the loci. Discussion The application of mapping algorithms developed for general pedigrees to existing breeding populations facilitated the development of a 3,875 locus linkage map of the wheat genome without the need for extraneous population development. High-throughput SNP genotyping of 18 crosses comprised of a total of 372 four-way F 1 individuals enabled the mapping of over 43 % of the interrogated loci. These results indicate that a collection of breeding populations, derived from crosses among numerous parents, provide a highly polymorphic and informative genetic resource for the development of linkage maps. Comparatively, Cavanagh et al. (2013) were able to map roughly 46 % of the SNP loci from the same 9,000 SNP assay using a four-way cross MAGIC population consisting of 1,579 recombinant inbred lines. Biparental mapping populations used for consensus map individually enabled mapping of
E 1.1 9.9 14.7 15.2 17.1 18.8 20.6 21.2 22.6 23.5 26.2 29.9 32.8 43.7 47.1 61.5 70.2 71.6 82.2 83.1 84.3 86.0 86.3 88.6 90.5 91.5 92.5 96.3 100.4 100.6 102.4 104.4 106.2 106.7 118.1 122.5 122.8.7 130.2 133.7 140.8 143.2 147.2 147.6 150.7 151.5 151.8 152.1 152.5 157.1 160.7 165.6 166.7 167.3 168.4 169.9 170.1 172.6 173.9 179.1 182.6 183.9 184.2 186.4 186.8 187.4 189.7 192.4 193.3 195.4 196.7 197.4 197.7 197.8 198.0 20 200.2 205.3 207.3 208.4 210.1 212.0 215.0 218.5 220.7 221.0 224.0 224.8 227.5 230.2 230.4 235.4 235.6 236.1 236.7 237.4 250.7 250.9 255.5 5A 2642, 2645 2641 2646, 2558, 6988 7509 2947 5002, 5003 2837, 2838, 7491 7789 648, 649 3083 2839, 2840 2802, 1670 6641, 2897 3323, 5154 7568 7009 2857, 2113, 2856, 2858, (10) 2352 3705, 3702, 3704, 3703, (7) 674, 675, 7014, 7043 4394, 7911 4805 4813 5040 4276, 2223 4447 1398 589 7579, 6681, 1439, 2743 1486 2014, 6459 5842, 5623, 6637 4392, 4391, 4390, 5945 4205, 1343, 7833, 7834 5624, 4980 6961 3996, 5668, 12 7665 6456 2364, 2365 2363 1669, 3370 6573, 3369 6522, 6523 6949, 6515 3413 4669, 4670, 4668, 4667, (5) 4914, 1685, 1686 7742 4237, 3283, 3645, 3646 739, 3647 1090, 2445, 6747, 7436, (6) 4047 6126, 8308, 703 2172, 3201, 5726, 6899, (21) 738 6036, 850, 5567 2101, 2926 gwm156, 122, 121 5528, 5529, 3873 5884 6881 5033, 5034, 5032 1630, 5184 5688, 5539, 5689, 6, (7) 291 1253, 1988 114 5735 5107, 7960, 5105 1950, 7961, 7690, 7925, (7) 7130, 7129, 1943 5380 4736 3349 4424 6412, 2463, 2814, 3212, (37) 7777 3099, 3100, 7565, 1301 barc56, 5431, 3445, 1465, (6) 7109, 5496, 2480 5395, 4454, 2120, 2467 6415, 1546 3263 6287, 3190, 8154, 8155 3530, 7061 825 cfa2190 5728, 4465 3365, 3811, 2378, 1062 4069, 5615, 5614 6859 5368 4970 1568 1569 3197, 4325, 7801, 6463, (6) 6227 4932 6226, 7360 7361, 5053 4445, 4446 3566, 3567, 5924, 5923 481, 2142, 480, 2143, (7) 8.8 18.3 22.2 23.5 35.7 38.4 38.7 39.7 40.8 46.1 46.7 48.5 50.2 60.4 62.1 62.2 62.8 63.5 64.2 67.1 73.3 74.3 79.4 81.4 82.0 84.1 84.4 85.0 86.5 99.5 99.7 107.7 108.2 113.8 119.9 121.1 124.6 124.7 124.8 124.9 125.0 125.1 125.2 125.3 125.4 125.5 125.6 125.7 125.8 125.9 126.0 126.1 126.2 126.3 126.4 126.5 126.6 126.7 126.8 126.9 127.1 127.3 127.6 128.3 128.4 129.6 129.8 130.1 130.5 131.0 131.4 134.1 134.5 135.9 136.8 137.1 138.3 138.5 138.9 139.0 139.2 139.5 140.6 141.0 141.3 141.5 143.7 145.6 147.0 147.2 148.5 148.6 148.8 148.9 149.0 149.2 149.5 149.9 150.3 153.0 153.5 156.2 161.3 163.9 173.5 178.9 179.2 184.7 185.5 193.2 212.5 5B 6579, 2682, 2681, 6578, (5) 4903, 2931, 5802, 4329, (5) 2321 3359, 3360, 3358 3658, 1061 1786, 22, 23 3185, 5804 7903, 1658 4635, 5454, 4634, 7708, (5) 37 936 197 1564 3984, 3972, 6393, 3214 4954, 4762, 2659, 4763 7585, 6779, 1433, 6147, (5) 8250 2388, 7965, 7966 1259 4185, 3500 3265, 1441, 1443, 7872 7791, 7668, 7963, 2500 3800 7910, 7989, 4820, 5552, (5) 8395 6718 1774, 2565, 3226, 3432, (9) 4103 8508, 8375, 4211, 7735, (9) 3444 7024, 6894, 4829 6895 6905 3642, 3641, 3640 6721, 6112 1408, 4003 2373, 2335, 2336, 8187, (6) 7485, 7514, 4641, 7776 952 7471 7470 6125 5671 3009 3008 1444 7844 7513 7484 6766 6366 6235 5795 5487 5482 3719 2698 2697 1446 5488 987 3164, 3165 2694, 4632, 3964, 337, (10) 265 4074, 5283, 2453, 2454, (8) 6383, 3025, 1374, 822, (7) 2536, 2934, 2432, 1402 6291, 4622 5217 1380 5218, 7562, 2180, 5620 6638, 3436, 5485, 5486, (8) 6992, 7, 7944, 4533, (5) 1471 2162 721, 301, 1584, 5289, (5) 2791, 5845, 6980, 5743 3633 4422 302, 7127, 6689, 5279, 1777, (7) 5784 8211 2003 5633 2257 396, 1705, 1706, 2071, (20) 5764, 2742, 5497 6846, 7613, 3682, 4526 7953 1057 6030 2320 6065 620, 6429, 1461, 279, (17) 1626 1779, 6521, 6908, 5494, (8) 4377, 4378, 4379, 1176, (9) 1342, 1965, 1084 7608, 7609 7300, 4281, 4282, 5108, (5) 6773, 7227, 6526 303 2597, 3706, 4862, 3106 4300, 4414, 8005, 2596, (6) 2609, 2610 1144, 7209, 7211, 1143, (7) 4355, 7223 421, 332, 3514 7153, 1709, 5176 6251, 3606, 3607 6402, 4416, 4415, 4790, (7) 1719, 7183, 7254, 8126 0.3 20.3 41.3 60.8 75.3 83.6 85.1 103.2 133.0 154.3 156.6 162.9 164.3 166.8 167.7 168.0 169.0 169.3 169.5 185.4 190.1 5D 8360 6289 6052, 5012, 4550, 6268 6439 1681 4087 4274 2771 678 5970 7177 6409 7071 6191, 6190, 6189 7095, 6872, 7147 6059, 6060, 6061, 700 699, 701 7914, 7915, 2276 2919 7383 4113, 4561 1431, 1428, 1427, 1429 Fig. 2 continued
F 6A 6B 6D1 26.2 27.5 27.8 28.3 29.6 37.0 52.6 52.9 61.0 69.3 70.1 70.2 70.4 70.9 73.7 87.3 87.8 89.0 93.4 95.1 98.2 98.7 99.1 99.2 99.3 10 100.5 102.2 103.3 104.2 104.5 104.7 105.0 108.5 115.7 116.2 119.1 121.7 145.9 146.2 147.4 154.0 156.0 156.7 157.0 16 160.6 163.3 168.5 169.1 169.7 170.4 171.1 172.1 172.4 172.7 173.1 176.4 176.5 176.8 7007 6937, 7913, 273 8160 7612, 6711, 2413 2635 272 1205, 6601 8608 4961, 680, 6630, 51 1522 1282 1336 1335 8510, 6013, 612 5401 2235 5930 2018, 2017, 1086 233, 6806, 6807 3207 3670, 3700, 3866, 4738, (11) 1262 5801, 3527, 8110, 6820, (9) 6928, 6560, 6559, 5470 2188, 2186, 2187, 2421, (15) 1423, 1285, 1606, 2033, (7) 416 4059 6986 2812, 3463, 6962, 3483, (7) 7052 664 6724, 8585 224, 1514, 4929, 653, (34) 6938 6550, 3024, 2241, 3023, (18) 259, 260 6775, 4950, 20, 19, (10) 3954 5021 2539, 2538 4809 5398 214 6116, 5704, 504, 503 929, 5964 928, 8438, 8222, 8386 6182, 442 1000 2580 7386 1510, 2639, 7894, 2054 3067, 2055 3918, 5655, 6537, 6316, (10) 2527 5172 5746, 5767, 6305, 6304 2632, 5747, 2603, 5768, (6) 3246 3204, 7497, 3205, 7495, (6) 2795, 4699, 3247, 3203, (5) 1391 4.9 8.1 10.3 10.4 19.9 28.0 36.6 41.5 41.9 47.9 48.3 48.8 49.0 49.4 49.6 50.8 51.2 51.8 52.2 55.0 55.7 55.9 56.1 56.2 56.6 57.3 57.6 58.3 58.5 58.9 59.1 61.2 61.6 62.0 63.1 63.2 63.3 63.4 63.5 63.6 64.0 65.6 65.9 66.0 66.1 66.3 66.5 69.7 71.9 72.1 72.2 72.6 72.7 72.8 72.9 73.0 76.7 81.4 81.6 81.8 82.0 82.7 84.3 84.5 92.2 93.4 95.6 106.3 107.3 109.8 110.5 113.3 121.1 127.7 127.9 133.0 133.7 969 2479, 8477, 1494 921 2495, 1255 4633, 5780 5942, 1901, 5857, 4610, (6) 4290, 7725, 4011 52 1764, 4760, 7320 4761 7257 7240 1721, 3289 7808, 2439, 2888, 5888, (12) 5055 6494, 1905, 5056, 8284 206, 1640 7689 3501, 2937 7979, 2417, 4824, 1655, (16) 3797 4486, 4485, 5625, 1017, (11) 2039, 6660, 4383, 2173 1434, 3234 18, 5045, 5044, 3650 2090, 3869, 4599 683, 7954, 2927, 5197, (13) 3699 2933, 1679 7506 1531, 4202, 5170, 457 8037, 7487, 6904, 657, (6) 4501, 4502, 4503, 755, (13) 7628 3459, 5346, 387, 4440, (5) 1151, 1743, 4086, 6855, (13) 8539 7783, 4515 3167 6293, 3878, 3963, 2653, (5) 450 2342, 5266, 5267 5468 3923, 6466, 6467, 7786 3676 7897 5043, 3677, 5042, 7974, (11) 7929 3967, 283, 3636, 1472, (20) 1838, 5966, 5029 2134, 7574, 5504 4924, 5242, 617, 1840, (62) 6101, 3796 2652, 8464 4065, 2451 6860, 3971, 7401 451, 8129 2219, 7810, 3301, 7618, (6) 7084, 2062 4484, 4436, 4435 800 7111, 4564, 3801, 5722 5530 4959 6428, 221, 3327, 5148, (8) 1629, 3221, 1628 404, 405 2330, 2331, 7056, 3464, (5) 5732 5666 7479 2212, 5709 7116, 8072 4868, 1484, 1485 3268 5605 4245, 8441, 823, 3947, (6) 3225, 4246, 7098, 4244 20.6 20.9 21.1 21.3 23.3 26.4 32.5 32.6 0.4 4.5 6.3 7.0 7.9 3.5 4.6 4.9 6D2 6D3 203 1927, 1926, 6274, 5591 5931, 4918 1406 4056, 5354, 4455, 1925 6181, 600, 4315, 599 6939, 2965, 2966, 3291, (7) 986 1384 5386, 2203 3624, 1317, 1643, 1411 2808 619 7816 7616 4000, 2338, 6673 6625, 1895, 1896, 5576 3461 984 Fig. 2 continued 21 41 % of the SNP loci with population sizes ranging from 96 to 250 fixed lines (Cavanagh et al. 2013). Given the time and resources required for the development of such purpose-built mapping populations, it seems clear that exploiting existing segregating populations in breeding programs provides a cost-efficient alternative for development of dense linkage maps. Furthermore, it should be noted that the breeding populations used in this study were highly interrelated by common founders and the two Wesley-Fhb1 backcross lines were nearly isogenic. A collection of breeding populations derived from a larger number of founders or from a more diverse set of founders would therefore be informative for more loci and thus allow for more extensive linkage mapping than possible in this study.
G 7A 7B 7D1 4.0 5.4 5.9 6.5 6.6 10.7 12.0 15.1 18.2 4558 3978, 6519, 5337 7053 6642 7306 5245 6989 6626, 1735 8032 556, 557 4.1 11.9 24.7 5819 1525, 1526 1181, 783 1089 0.7 7.0 15.1 16.0 17.9 20.1 22.2 6320 2545, 1373 1247 5391, 235 6623 7828, 7827 2523, 2521, 7610, 2522, (5) 1323, 3851, 6822, 266 34.2 48.3 53.8 58.6 63.7 66.5 72.1 72.6 74.0 77.2 79.1 79.9 80.8 81.6 85.1 85.4 85.7 87.6 88.0 88.2 92.2 95.9 96.4 97.3 98.2 99.0 99.6 99.8 10 100.1 101.8 101.9 102.0 102.1 102.2 102.3 102.4 102.5 103.8 105.0 105.9 106.4 107.0 107.8 108.0 108.9 109.1 112.0 117.7 117.8 118.8 119.6 122.7 124.6 126.1 126.3 126.9 128.3 135.5 137.9 141.3 144.2 148.9 153.8 172.8 180.4 185.9 187.5 187.9 191.1 193.3 193.5 200.5 204.0 204.8 205.0 205.4 206.6 7093 834, 930 6088 954 6475, 4614 1751 8390 473, 472 1805, 2513, 7301, 7201, (5) 3760, 7187 7192, 1759 8161, 7121 3832, 3831, 6472, 6473 4426, 6802 2507, 2506, 2735 655 8492, 6331, 3715 6310, 275, 7205, 3674, (6) 7419 7460, 4032, 7282, 3903, (7) 3754, 7731, 2820, 363, (5) 334 3187 6029 1842, 6569, 3318, 4168, (22) 5220, 3, 4082, 1871, (28) 1554, 759, 127, 5867, (14) 3941 3843, 497 6207, 5844, 6208, 208, (6) 4637, 1491 1802, 4063, 1834, 1832, (6) 4639, 7293, 8098, 2302 2301, 3062, 3403 3404, 484 5119, 2082, 3090 5465, 6629, 7976 7682, 6866, 7430, 8113, (6) 7718 5434, 3668, 8073, 1761 7917, 635, 476, 1946, (36) 1110, 1111, 810, 6940 7432, 7140, 4109, 7549, (5) 593, 1581 6004, 2009, 2012, 2011, (5) 6562, 7933 8076, 8077, 4846 614, 5489, 2775 7046 5790 6535, 4910, 4911 5912, 7409, 5913 6670 1032, 1031 3128, 5167 7406, 7407, 2270 4621, 4620 8297 7028, 1363, 7709 7325 3367, 7884 2723 4993, 4991, 4994, 6785 8393 6115, 7185 4594, 4595 4124, 2403, 2402 7184 761, 866, 1223, 865 7964, 2929 4364, 4176, 1271, 4433, (7) 4137, 4173, 1518, 4177, (11) 737, 795, 179, 6833, (6) 6576, 7005, 5904 8312 7592 6736, 7706 502, 501 34.8 37.9 38.8 39.3 39.5 40.6 40.9 41.1 41.3 41.7 42.7 48.8 49.1 56.9 60.1 60.4 61.3 61.7 62.1 62.4 63.9 66.7 68.8 71.5 71.9 72.7 73.1 74.4 85.4 88.4 89.5 89.8 110.8 116.9 119.8.7 124.5 125.7 125.9 135.8 136.2 139.4 140.4 142.8 142.9 148.8 153.3 165.2 165.5 166.1 166.5 166.8 178.9 186.8 gwm400 4977 2105 3958, 2832, 5565 4968, 6901, 1314, 4967, (15) 2894, 2893 7242 3960 3572, 3508, 3506, 3507, (7) 518 7326, 4516 3438, 306, 3437, 3807, (8) 8021, 8022 7233, 7232 1108, 6414, 4873, 2534 3663, 5661, 6788, 5210, (9) 2353, 4727, 6212, 3114, (22) 1642, 2271 gwm46 3063, 8300 gwm297, 3163, 632, 698, (5) gwm333 3691, 3112, 4151 117, 4005 449 636, 3986, 6400, 6857, (7) 1420, 1963, 4190, 4191, (16) 4857, 8550 436, 437 615, 4701, 8570, 1345, (6) 1339, 3928, 3423, 7329, (10) 1340 4305, 7403, 7402 5129 4309 130 2193, 4750, 6246, 4749, (5) 432 431, 5564, 2191 4803, 3387, 7907 5001 4802 5837 5881 7261 3513, 3603, 2825, 7780, (5) 5597 3416, 3415 1651, 1649 182, 180 2149, 3675 1044 8448 1897 31.3 31.4 31.8 32.3 34.1 2.1 7D2 2273 5249, 1257, 5557, 604 688 732 1537 827, 7459 8075 Fig. 2 continued Correct ordering of marker loci during linkage mapping is a critical factor determining the accuracy and power of subsequent QTL mapping applications (Collard et al. 2009). Therefore, an assortment of breeding populations must not only enable the mapping of a large number of marker loci, but also the accurate ordering of those loci from large genotypic data sets. Evaluation of rank-order correlations