Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis

M Z Islam,M Khalequzzaman,M A K Mian,M K Bashar,N A Ivy,M M Haque,B R Pittendrigh,M P Ali

doi:10.1038/s41598-018-28001-z

M Z Islam, M Khalequzzaman + Show 6 more

Open Access

https://doi.org/10.1038/s41598-018-28001-z

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Abstract

While the pleasant scent of aromatic rice is making it more popular, with demand for aromatic rice expected to rise in future, varieties of this have low yield potential. Genetic diversity and population structure of aromatic germplasm provide valuable information for yield improvement which has potential market value and farm profit. Here, we show diversity and population structure of 113 rice germplasm based on phenotypic and genotypic traits. Phenotypic traits showed that considerable variation existed across the germplasm. Based on Shannon–Weaver index, the most variable phenotypic trait was lemma-palea color. Detecting 140 alleles, 11 were unique and suitable as a germplasm diagnostic tool. Phylogenetic cluster analysis using genotypic traits classified germplasm into three major groups. Moreover, model-based population structure analysis divided all germplasm into three groups, confirmed by principal component and neighbors joining tree analyses. An analysis of molecular variance (AMOVA) and pairwise FST test showed significant differentiation among all population pairs, ranging from 0.023 to 0.068, suggesting that all three groups differed. Significant correlation coefficient was detected between phenotypic and genotypic traits which could be valuable to select further improvement of germplasm. Findings from this study have the potential for future use in aromatic rice molecular breeding programs.

Highlights

Thousands of local rice varieties have been cultivated across Bangladesh[4] and local landraces, including aromatic ones, which have often been cultivated in less than favorable ecosystems that cover 12.16% of the total rice growing areas[1]
The analysis showed genetic variation among the aromatic rice germplasm tested, with similarity coefficient values ranging from 0.39 to 0.93, demonstrating a moderate degree of genetic diversity among the germplasm used in this study
By Nei distance ranking, StrawTAPL-500 and Desi Katari stood first and last rank, respectively; by D2 distance ranking, Kalobakri and Tilkapur ranked first and last, respectively. These results indicated that a statistical association between groups, phenotypic and genotypic traits existed

Summary

Introduction

Thousands of local rice varieties have been cultivated across Bangladesh[4] and local landraces, including aromatic ones, which have often been cultivated in less than favorable ecosystems that cover 12.16% of the total rice growing areas[1] Some of these local varieties have desirable characteristics around aroma, better taste, and higher cooking quality, all of which potentiate value-added parameters to the rice both socially and economically. The advent of PCR-based molecular marker technology, provides highly effective and reliable tools both for measuring genetic diversity in crop germplasm and evaluating evolutionary relationships within and between plant populations, varieties, and species[14]. SSRs have been used for genetic diversity analysis, genetic characterization of genotypes, cultivar identification, marker-assisted selection breeding, and population structure assessment in multiple previously published rice genetic studies[23,24,25,26,27,28,29,30,31]

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