Diversity and population structure of red rice germplasm in Bangladesh

PLOS ONE, Nov 2019

While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

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Diversity and population structure of red rice germplasm in Bangladesh

May Diversity and population structure of red rice germplasm in Bangladesh M. Z. Islam 2 3 M. Khalequzzaman 2 3 M. F. R. K. Prince 2 3 M. A. Siddique 2 3 E. S. M. H. Rashid 2 3 M. S. U. Ahmed 2 3 B. R. Pittendrigh 1 3 M. P. Ali 0 3 0 Entomology Division, Bangladesh Rice Research Institute , Gazipur , Bangladesh 1 Department of Entomology, Michigan State University , East Lansing, MI , United States of America 2 Genetic Resources and Seed Division, Bangladesh Rice Research Institute , Gazipur , Bangladesh 3 Editor: Tzen-Yuh Chiang, National Cheng Kung University , TAIWAN While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: The authors are grateful for the financial support provided by the Bangladesh Rice Research Institute (BRRI) through the Ministry of Agriculture, Bangladesh. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. Introduction Rice is the main food for more than half of the world's population and is the staple food for the people of Bangladesh, constituting over 91% of the food grain production, and providing 62% of the caloric as well 46% of the protein intake in the average daily diet [ 1 ]. The rice production area in Bangladesh is approximately 11.4 million hectares (ha) producing 51.64 million tons of rice annually [ 2 ]. Bangladesh has three major rice crops, Aman, Aus, and Boro, which are grown during three overlapping seasons and with a large number of varieties suitable for various agro-ecological and climatic niches [ 3 ]. The Aus growing season usually starts in March-April, is harvested in July-August, and has an average yield of 2.00 t/ha, which is lower than the other two crops. More than 30% of Aus rice in Bangladesh are a red variety, which characteristically has limited yield. In Bangladesh, high temperatures during the Aus growing season increase plant height but decrease growth duration in rice. Solar radiation is also lower in Aus versus Boro growing seasons, resulting in lower Aus yields. Traditional red rice varieties also typically have weak stems, low tillering ability, long droopy leaves, turn yellow during grain development, and become logged at maturity. However, farmers still plant them widely because they can be grown under low inputs and produce a reasonable yield under the seasonal environmental conditions to which modern varieties are not adapted. Nonetheless, this limited yield makes farmers less interested in cultivating red rice despite its high medicinal value and use as a functional food. Modern breeding techniques could improve the yield of red rice to overcome this problem. Successful breeding for crop improvement, however, depends on genetic variability in the parents [ 4 ], such that a lack of genetic variability would have the potential to significantly lim (...truncated)


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M. Z. Islam, M. Khalequzzaman, M. F. R. K. Prince, M. A. Siddique, E. S. M. H. Rashid, M. S. U. Ahmed, B. R. Pittendrigh, M. P. Ali. Diversity and population structure of red rice germplasm in Bangladesh, PLOS ONE, 2018, Volume 13, Issue 5, DOI: 10.1371/journal.pone.0196096