Additional file 1: Table S1. of Genetic structure of Mount Huang honey bee (Apis cerana) populations: evidence from microsatellite polymorphism

Allele frequencies, proportion of observed (Ho) and expected (He) heterozygosity of 16 microsatellites loci across seven populations of Mount Huangshan A. cerana, n is the number of individual bees examined. (DOC 218 kb

SNP locus pairs in different linkage stage with significant (P<0.01) and highly significant (p<0.001) linkage disequilibrium (LD) and R² values on genome level in durum wheat.

<p>^a Locus on the same linkage group.</p><p>^b Locus from different linkage groups.</p><p>^c Locus pairs and percentage of all possible locus pairs showing significant LD at P<0.01.</p><p>^d Locus pairs and percentage of all possible locus pairs showing significant LD at P<0.001.</p><p>^e Locus pairs and percentage of all possible locus pairs showing significant LD at R²>0.1; P<0.01 adjusted for locus pairs description.</p><p>^f Locus pairs and percentage of all possible locus pairs showing significant LD at R²>0.1; P<0.001 adjusted for locus pairs description.</p><p>SNP locus pairs in different linkage stage with significant (P<0.01) and highly significant (p<0.001) linkage disequilibrium (LD) and R² values on genome level in durum wheat.</p

Association of Agronomic Traits with SNP Markers in Durum Wheat (<i>Triticum turgidum</i> L. <i>durum</i> (Desf.))

<div><p>Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (<i>Triticum turgidum</i> spp. <i>durum</i>) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.</p></div

Frequency distribution of the 10 examined agronomic traits of durum wheat in four consecutive years.

<p>P value of Kolmogorov-Smirnov test for each year was shown, the hypothesis of normal distribution could be accepted when P>0.05 (significant at P = 0.05), and the trend lines of the accepted normal distribution were shown. PH, plant height (cm); ES, number of effective spikes, LMS, length of main spike (cm); RLMS, rachis internode length of main spike (cm); LFPMS, panicle neck length of main spike (cm); SMS, number of spikelets on main spike; NSPP, number of spikelets per plant; GNP, grain number per plant; GWP, grain weight per plant (g); KGW, 1000-grain weight (g).</p

SNP locus pairs on the same linkage group with significant (P<0.01) and highly significant (p<0.001) linkage disequilibrium (LD) and R² values at levels of chromosome and genome in durum wheat.

<p>^a Number of locus pairs and percentage of all possible locus pairs showing significant LD at P<0.01, P<0.001, R²>0.1 & P<0.01, and R²>0.1 & P<0.001, respectively.</p><p>SNP locus pairs on the same linkage group with significant (P<0.01) and highly significant (p<0.001) linkage disequilibrium (LD) and R² values at levels of chromosome and genome in durum wheat.</p

Chromosome bin map of plausible QTLs anchored by SNP markers in durum wheat.

<p>The relative interval length is indicated on the left of each chromosome and QTLs represented by SNP-based associations and relative R value (%) are shown on the right. The number in front of the symbol means the repeats of the associations anchored in the interval in the corresponding years and without a number in front of the symbol means one repeat of the association anchored in the interval in one corresponding year. Details of the associations are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130854#pone.0130854.s002" target="_blank">S2 Table</a>. The exact bins of some associated EST markers are unknown, and thus are shown below the chromosome.</p

Number of associated SNP markers in different years for the examined traits.

<p>Number of associated SNP markers in different years for the examined traits.</p

Correlation coefficients among the 10 observed agronomic traits.

<p>*, ** significant at the probability level of 0.05 and 0.01, respectively.</p><p>Correlation coefficients among the 10 observed agronomic traits.</p