Genetic Diversity and Population Structure of Basmati Rice (<i>Oryza sativa</i> L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers

<div><p>One hundred forty one basmati rice genotypes collected from different geographic regions of North Western Himalayas were characterized using 40 traits linked microsatellite markers. Number of alleles detected by the abovementioned primers were 112 with a maximum and minimum frequency of 5 and 2 alleles, respectively. The maximum and minimum polymorphic information content values were found to be 0.63 and 0.17 for the primers RM206 and RM213, respectively. The genetic similarity coefficient for the most number of pairs ranged between of 0.2-0.9 with the average value of 0.60 for all possible combinations, indicating moderate genetic diversity among the chosen genotypes. Phylogenetic cluster analysis of the SSR data based on distance divided all genotypes into four groups (I, II, III and IV), whereas model based clustering method divided these genotypes into five groups (A, B, C, D and E). However, the result from both the analysis are in well agreement with each other for clustering on the basis of place of collection and geographic region, except the local basmati genotypes which clustered into three subpopulations in structure analysis comparison to two clusters in distance based clustering. The diverse genotypes and polymorphic trait linked microsatellites markers in the present study will be used for the identification of quantitative trait loci/genes for different economically important traits to be utilized in molecular breeding programme of rice in the future.</p></div

UPGMA dendrogram of five subpopulations.

<p>A (pop1), B (pop2), C (pop3), D (pop4) and E (pop5) of basmati rice genotypes showing two clusters Z and X based on Nei’s genetic distances using POPGENE version 1.31.</p

UPGMA dendrogram showing four clusters (I, II, III and IV) of all 141 basmati genotypes of rice.

<p>UPGMA dendrogram showing four clusters (I, II, III and IV) of all 141 basmati genotypes of rice.</p

Pairwise population differentiation according to groups of populations as measured by Fst using Arlequin.

<p>*Significance at P<0.05 at 1,000 permutations</p><p>**Significance at P<0.01 at 1,000 permutations</p><p>Pairwise population differentiation according to groups of populations as measured by Fst using Arlequin.</p

Gel picture of marker RM212 showing banding pattern in 141 basmati rice genotypes.

<p>Gel picture of marker RM212 showing banding pattern in 141 basmati rice genotypes.</p

Assignment of 141 basmati rice genotypes to five subpopulations (A, B, C, D and E) using STRUCTURE 2.3.4 software.

<p>Assignment of 141 basmati rice genotypes to five subpopulations (A, B, C, D and E) using STRUCTURE 2.3.4 software.</p

Percentage of distribution of the genetic similarity coefficient calculated between a 9870 pair of genotypes.

<p>Percentage of distribution of the genetic similarity coefficient calculated between a 9870 pair of genotypes.</p

List of markers used, chromosome number, functional gene, associated trait, number of alleles, major allele frequency, PIC values, marker index (MI), resolving power (RP), and discrimination power (DP).

<p>Functional genes as modified from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131858#pone.0131858.ref025" target="_blank">25</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131858#pone.0131858.ref036" target="_blank">36</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131858#pone.0131858.ref037" target="_blank">37</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131858#pone.0131858.ref038" target="_blank">38</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131858#pone.0131858.ref039" target="_blank">39</a>].</p><p>List of markers used, chromosome number, functional gene, associated trait, number of alleles, major allele frequency, PIC values, marker index (MI), resolving power (RP), and discrimination power (DP).</p

Basmati rice growing areas in NW Himalaya.

<p>(a) Political map of India showing the states (encircled) from which basmati rice genotypes were collected. (b) Enlarged view of basmati rice growing states of NW Himalaya. (c) Map of Jammu region showing areas from which local basmati rice (<i>Oryza sativa</i> L.) genotypes were collected.</p

Major allele frequency of polymorphic SSR markers.

<p>Major allele frequency of polymorphic SSR markers.</p