Appearance and disappearance of alleles over decadal periods.

<p>Appearance and disappearance of alleles over decadal periods.</p

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

<div><p>Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (<i>Na</i>), allelic richness (<i>Rs</i>), Nei’s genetic diversity index (<i>He</i>), observed heterozygosity (<i>Ho</i>) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (<i>Fst</i>) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.</p></div

Rice varieties used in the present study.

<p>Rice varieties used in the present study.</p

Distribution of number of alleles (<i>Na</i>) (A), polymorphism information content (PIC) (B) and genetic diversity (<i>He</i>) (C) estimated from 100 rice varieties using 52 hypervariable microsatellite loci.

<p>Distribution of number of alleles (<i>Na</i>) (A), polymorphism information content (PIC) (B) and genetic diversity (<i>He</i>) (C) estimated from 100 rice varieties using 52 hypervariable microsatellite loci.</p

Molecular diversity parameters of the microsatellite markers used in the study.

<p>Chr.- Chromosome; <i>Na</i>-Number of alleles; PIC-Polymorphism Information Content; <i>Rs</i>: Allelic richness; <i>Ho</i>- Observed heterozygosity; <i>He</i>- Nei’s genetic diversity; <i>I</i>- Shannon Index; SD-Standard Deviation.</p

Nei’s Unbiased measures of genetic distance among decadal periods of major Indian rice cultivars.

<p>Lower diagonal: Year of releasewise; Upper diagonal: Longevitywise.</p

Analysis of molecular variance (AMOVA) of major Indian rice cultivars.

<p>df: degrees of freedom; p>0.001-*** : p>0.01-**.</p

UPGMA dendrogram based on Nei’s genetic distances using POPGENE v 1.31 showing the genetic relationship of rice genotypes among decadal periods.

<p>The genetic distances between different groups are as follows. Year of releasewise: 4 and Landraces - 10.96, 4 and 3–5.01, 3 and 2–0.97, 2 and 1970s - 4.97, 2 and 1980s- 4.97, 3 and 1–1.41, 1 and 1990s-4.52 and 1 and 2000s-4.52. Longevitywise: 4 and Landraces −9.55, 4 and 3–6.76, 3 and 1970s - 2.78, 3 and 2 -0.93, 2 and 1 - 0.66, 1 and 1980s - 1.18, 1 and 2000s - 1.18, 1 and 1990s - 1.85.</p

Genetic relationship among 100 rice varieties estimated using Unbiased Neighbour-Joining dendrogram of 52 hypervariable microsatellite loci.

<p>Landraces- green colored;1970s-pink colored;1980-red colored;1990s-dark blue colored;2000s-sky blue colored. Rice varieties were represented in numbers. For full details of the varieties refer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066197#pone.0066197.s003" target="_blank">Table S1</a>.</p

A representative gel picture of screening of rice varieties with RM562.

<p>For decoding of the numbers refer Table S1.</p