Allelic diversity of newly characterized submergence-tolerant rice (Oryza sativa L.) germplasm from Bangladesh

Allelic diversity of newly characterized submergence-tolerant rice (Oryza sativa L.) germplasm from Bangladesh

A total of 300 germplasm accessions collected from submergence-prone areas of Bangladesh were selected from the genebank of the Bangladesh Rice Research Institute (BRRI) for an allelic diversity study on submergence tolerance during the vegetative stage. Through screening under controlled submergenc...

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Bibliographic Details
Published in:Genetic resources and crop evolution Vol. 63; no. 5; pp. 859 - 867
Main Authors: Iftekharuddaula, Khandakar M., Ghosal, Sharmistha, Gonzaga, Zennia J., Amin, Al, Barman, Hirendra N., Yasmeen, Rumena, Haque, Md. Moinul, Carandang, Jerome, Collard, Bertrand C. Y., Septiningsih, Endang M.
Format: Journal Article
Language:English
Published: Dordrecht Springer Netherlands 01-06-2016
Springer Nature B.V
Subjects:
Agriculture
Alleles
Biomedical and Life Sciences
Chromosome 9
Chromosomes
Clustering
Genetic analysis
Genetic diversity
Germplasm
Life Sciences
Markers
Oryza sativa
Plant Genetics and Genomics
Plant Physiology
Plant Sciences
Plant Systematics/Taxonomy/Biogeography
Polymerase chain reaction
Quantitative trait loci
Research Article
Rice
Subgroups
Submergence
Transcription
Bangladesh
Allelic diversity
SSR
Indel markers
Submergence-tolerant germplasm
region
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Summary:A total of 300 germplasm accessions collected from submergence-prone areas of Bangladesh were selected from the genebank of the Bangladesh Rice Research Institute (BRRI) for an allelic diversity study on submergence tolerance during the vegetative stage. Through screening under controlled submergence for three consecutive years, eight accessions were selected for having submergence tolerance with survival ranging from 71.2 to 95.4 %. A total of 20 SUB1 -region SSR and Indel markers, spanning from 4.5 to 8.6 Mb on chromosome 9, were used to study the allelic diversity of 16 selected rice accessions, including the eight submergence-tolerant accessions and eight sensitive and tolerant checks. A total of 58 alleles were detected at the loci of the 20 markers across the 16 rice accessions. The number of alleles per locus ranged from two to five, with an average of 2.90 alleles across the 20 loci. Genetic similarity analysis using the unweighted pair-group method using arithmetic mean (UPGMA) clustering system generated two major genetic clusters, each of them with three subgroups. DG1-349, Kalojoma, DSL-78-8, Damsi and Putidepa were identified as having higher submergence tolerance but not possessing the same resistance allele as FR13A. Furthermore, RT-PCR analysis of SUB1A , the gene underlying the SUB1 QTL, showed that the transcript abundance in these accessions was significantly less than that of FR13A. Thus, these accessions were selected as potential genetic donors for identifying novel submergence-tolerance QTLs.
ISSN:0925-9864
1573-5109
DOI:10.1007/s10722-015-0289-4