# Genetic Variation of a Lentil (_Lens culinaris_) Landrace during Three Generations of Breeding
## 3 Results

Table 3: SSRs’ parameters obtained after statistical analysis of data from 15 SSR loci of 40 lines: Na (number of different alleles), Ne (Number of effective alleles), I (Shannon’s information index), PIC (Polymorphic Information Content), h (diversity), and uh (unbiased diversity). Figure 2: **(a)** Allele frequencies: Histogram depicting the allele frequency per locus varying from 0.025 for unique alleles to as high as 0.90 for the major alleles of SSR154 and SSR317; **(b)** Allelic patterns across GSLs: histogram depicting the mean and standard errors across loci by breeding generation for the following statistics: Mean numbers of alleles (Na), alleles with a frequency higher than 5% (Na Freq. \(\geq\) 5%) effective alleles (Ne), information index (I), number of private alleles (No. Pr. Al), and haploid diversity (h). 1.97 while Shannon information index (I) got values between 0.60 (1 GSLs) and 0.73 (2 GSLs). Diversity (h) and unbiased diversity (uh) indicators took values from 0.33 (1 GSLs) to 0.45 (2 GSLs, 3 GSLs) and from 0.35 (1 GSLs) to 0.49 (2 GSLs), respectively (Table 4). AMOVA (Table 5) showed that diversity within populations (88%) was much greater than between them (12%). The highest percentage of polymorphic loci was observed in 2 GSLs and 3 GSLs (100%) followed by 1 GSLs with 93.33%. The observed private alleles were 0.6 in 1 GSLs, 0.2 in 2 GSLs, and 0.067 in 3 GSLs. A distance matrix based on \(\varphi\)PT between GSLs showed that the genetic distance between 1 GSLs and 2 GSLs was lower (2.5%) than the observed between 2 GSLs and 3 GSLs (7.7%) while the highest difference (26.7%) was recorded between the 1 GSLs and 3 GSLs (Table 6). The UPGMA dendrogram of 40 lines based on the dissimilarity distance matrix is depicted in Figure 3. Lines of family 8 form a separate branch in a bifurcated tree, indicating their close genetic relationships. The second branch of the tree is divided into a clade solely comprising the family 5 while the rest of the families are mixed in a separate clade. Principal Coordinates Analysis (PCoA) was employed to find and plot the major patterns between the families based on their distance matrix (Figure 4). The first two PCoA axes explained the 69.81% of total variation within lentil families. Samples were separated into three major groups along the first axis with family 8 and its progeny to form a cluster, family 5 alone, and the rest of the samples to form a second group. No specific grouping was detected for samples derived from family 2 or family 15. \begin{table}
\begin{tabular}{c c c c} \hline \hline  & **1 GSLs** & **2 GSLs** \\ \hline
**2 GSLs** & 0.025 & \\
**3 GSLs** & 0.267 & 0.077 \\ \hline \hline \end{tabular}
\end{table} 
Table 6: Pairwise Population \(\varphi\)PT Genetic Distance between GSLs. \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Populations** & **Na** & **Ne** & **I** & **h** & **uh** \\ \hline
**1 GSLs** & 2.87 \(\pm\) 0.24 & 1.65 \(\pm\) 0.16 & 0.60 \(\pm\) 0.09 & 0.33 \(\pm\) 0.05 & 0.35 \(\pm\) 0.06 \\
**2 GSLs** & 2.60 \(\pm\) 0.21 & 1.97 \(\pm\) 0.17 & 0.73 \(\pm\) 0.07 & 0.45 \(\pm\) 0.04 & 0.49 \(\pm\) 0.04 \\
**3 GSLs** & 2.13 \(\pm\) 0.09 & 1.81 \(\pm\) 0.08 & 0.64 \(\pm\) 0.04 & 0.45 \(\pm\) 0.03 & 0.48 \(\pm\) 0.03 \\
**Mean** & 2.53 \(\pm\) 0.12 & 1.81 \(\pm\) 0.08 & 0.66 \(\pm\) 0.04 & 0.41 \(\pm\) 0.03 & 0.44 \(\pm\) 0.03 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Genetic diversity parameters at population level (1 GSLs, 2 GSLs, 3 GSLs) for the 15 SSR loci. Na (number of different alleles), Ne (number of effective alleles), I (Shannon information index), h (diversity), uh (unbiased diversity).