M. Z. Islam
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh,
M. Khalequzzaman
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh,
M. F. R. K. Prince
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh,
M. A. Siddique
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh,
E. S. M. H. Rashid
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh,
M. S. U. Ahmed
Genetic Resources and Seed Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
B. R. Pittendrigh
Department of Entomology, Michigan State University, East Lansing, MI, United States of America
M. P. Ali
Entomology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
Diversity, Red rice, Germplasm, Bangladesh
Bangladesh Rice Research Institute in Gazipur, Bangladesh
Conservation and Biodiversity
Plant materials Rice germplasm, including Aus, Aman and Boro rice cultivated throughout Bangladesh, have been collected and conserved by the Bangladesh Rice Research Institute (BRRI) genebank. To date, approximately 8,200 germplasm have been preserved by the BRRI genebank, of which 1,500 are Aus rice, with more than 30% of those considered red rice. For this study, we cultivated fifty red rice germplasm—collected by BRRI from the sites noted and designated as red due to their red-colored pericarp in upland conditions during the Aus growing season in Bangladesh. Agro-morphological characterization All experiments described here were conducted at the Bangladesh Rice Research Institute in Gazipur, Bangladesh during the March to June Aus rice growing season in 2015. Fifty red rice germplasm were seeded directly under upland conditions in two 5 m x 3 m plot replicated trials. Production practices, including fertilizers, intercultural operations, pest control, and grain harvesting, were conducted according to standard methods. Fifteen agro-morphological traits—leaf area index, culm diameter, effective tiller number, days to flowering, plant height, days to maturity, five panicles weight, filled grains per panicle, unfilled grains per panicle, grain length, grain breadth, 1000 grain weight, length-breadth ratio, and yield per hill—were recorded. Genetic diversity was worked out for the principal component analysis and Mahalanobis’ generalized distance (D2 ) analysis [48]. All multivariate analyses were performed using the GENSTAT 5.5 program. Molecular characterization We used fifty well-distributed SSRs for the diversity analysis; position (cM), repeat motifs, and chromosomal positions for the SSR markers can be found in the rice genome database. Most of these markers were obtained from a panel of fifty standard SSR markers, which has been proposed by CGIAR for rice diversity analysis. DNA was extracted from the young leaves of 14-day-old plants using the miniscale method [51]. The total PCR reaction was performed using the standard procedure. The 10 μL of each PCR product, with 2μL of a loading dye, were analyzed using 8% polyacrylamide gel electrophoresis in a 1 × TBE buffer, run at 75 V for between 2.0–2.5 h depending upon the allele size. The gels were then stained, using ethidium bromide solution (0.5 mg/mL), for 25 min and exposed to UV light using a molecular imager gel documentation unit (XR System, Uvitec Cambridge, France) for visualization. Data analysis The band-size for each of the markers was scored using the AlphaEaseFC 4.0 software. Using PowerMarker version 3.25, summary statistics included the following: the number of alleles, the major allele size and its frequency, gene diversity, and the polymorphism information content (PIC) value. For the unrooted phylogenic tree, the genetic distance was calculated using MEGA 6 based on Nei’s unbiased pairwise. Binary form for allele frequency was prepared using PowerMarker software and used for dendrogram construction by NTSYS-pc software. The unweighted pair grouping method using arithmetic average (UPGMA) was used to determine a similarity matrix following the Dice coefficient with the SAHN subprogram. Population STRUCTURE for germplasm was determined using STRUCTURE, (version 2.3.4). The number of clusters (K) investigated, in this study, ranged from one to fifteen, with five replications for analysis of each K value. The model following admixture and correlated allele frequency with a 5,000 burn period and a run length of 50,000 were used for conducting model-based structure analysis. Output of analysis was collected using the STRUCTURE harvester [56] and identified 4 as the best K value based on the LnP(D) and Evanno’s ΔK. Principal components analysis (PCA) analysis was conducted also using the STRUCTURE software. In order to summarize the major patterns of variation within the multi-locus dataset, an analysis of molecular variance (AMOVA) using GenAlEx V6.5 was also performed.
PLoS ONE 13 (5): e0196096. https://doi.org/10.1371/journal. pone.0196096
Journal