6) and K = 6 (97) This analysis was consistent with the calcula

6) and K = 6 (9.7). This analysis was consistent with the calculated phylogenetic tree. When the number of populations was set to K = 2, 114 (44.2%) of the 258 plants showed the estimates of ancestry (q) over 0.95 for one of the putative populations, while 66

plants (25.6%) selleck had q values below 0.75. With respect to horticultural types, a majority of plants in various clades had q values greater than 0.80 at K = 2 (blue or red bars in Fig. 1). These include all crisphead type lines in Clade I, and all stem type lines; 22 (75.9%) of the 29 crisphead type lines in Clade II; 45 (91.8%) of the 49 romaine type lines in Clade III; and 74 (73.3%) of the 101 butterhead type lines in Clade VI. However, 40 (83.3%) of the 48 leaf type lines had q values smaller Talazoparib mw than 0.75. Based on the ΔK and ln P(X|K), K = 6 also shows a high probability of estimating the number of populations ( Fig. 1). Crisphead type lines possessed two different major memberships as indicated by orange and purple bars; whereas butterhead type lines belonged to the groups as indicated by brown and red colors. It seems that the crisphead type lines can be separated by their differences

in origin and head morphology. However, the phenotypic difference between the two groups of the butterhead type lines remains to be determined. The main objective of this study was to detect associations between 10 phenotypic traits and 322 SNP markers analyzed with 258 lettuce lines. Marker-trait association was determined by single factor analysis (SFA), structured association analysis using a general linear model where population membership served as covariates (Q GLM), and a composite approach where the average relationship was estimated

by kinship and implemented in a mixed linear model (Q + K MLM). Table 2 presents the significance levels for P< 0.01 for all markers for each analysis. Using SFA 296 SNPs were significantly associated with all phenotypic traits. PD184352 (CI-1040) A total of 1141 significant marker-trait associations (SMTAs) (P < 0.01) were detected using SFA. CLS_S3_Contig2508-1-OP4 was associated with eight phenotypic traits (leaf anthocyanin, stem anthocyanin, leaf blistering, leaf undulation, leaf color, bolting date, flowering date, and horticultural type), whereas 25 SNPs were associated with one trait each. The lowest P-value (P = 1.31E − 60, R2 = 0.60) using SFA was detected for association of Contig15192-1-OP1 with horticultural type. In the Q GLM analysis, 286 SNP markers were involved in 890 SMTAs from all of the phenotypic traits. RHQGE13G04.yg_3-OP3 was associated with nine traits (all except fasciation), and 63 SNPs were associated with one trait each. The lowest P-value of SMTAs occurred in CLS_S3_Contig8254-1-OP4 (P = 8.22E − 38, R2 = 0.43) associated with seed coat color. According to the Q + K MLM method, 54 SNP markers were involved in 63 SMTAs across all phenotypic traits.

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