Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Frontiers in Genetics
D S KishorHee-Jong Koh

Abstract

Basmati is considered a unique varietal group of rice (Oryza sativa L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the aromatic group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 (indica rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the aus group than with the japonica and indica groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was ...Continue Reading

References

Jan 18, 2005·Genetics·Amanda J GarrisSusan McCouch
Feb 12, 2005·Bioinformatics·Kejun Liu, Spencer V Muse
Oct 12, 2005·Plant Molecular Biology·Yonghong Wang, Jiayang Li
Nov 30, 2006·Plant Biotechnology Journal·Louis M T BradburyDaniel L E Waters
Oct 30, 2007·Trends in Genetics : TIG·Michael J KovachSusan R McCouch
Nov 9, 2007·Current Opinion in Genetics & Development·Tao Sang, Song Ge
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Aug 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael J KovachSusan R McCouch
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Zhixi TianJiayang Li
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Apr 16, 2011·Bioinformatics·Derek W BarnettGabor T Marth
Dec 7, 2011·PLoS Computational Biology·Christopher J CreeveyPeer Bork
Oct 15, 2013·Molecular Plant·Haodong ChenQifa Zhang
Dec 1, 1988·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·S R McCouchS D Tanksley
May 1, 1987·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·J C Glaszmann
Mar 1, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hiroaki SakaiJianzhong Wu
Aug 22, 2015·BMC Plant Biology·Lakshminarayana R VemireddyJavaregowda Nagaraju
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jan 1, 2015·Nature Plants·Peter CiváňTerence A Brown
Jan 15, 2017·Molecular Biology and Evolution·Jae Young ChoiMichael D Purugganan
Aug 20, 2017·Scientific Reports·Venea Dara DaygonMelissa A Fitzgerald
Feb 23, 2019·Genome Biology and Evolution·Peter CiváňTerence A Brown
May 1, 2019·Annual Review of Plant Biology·Erwang ChenBin Han
Oct 6, 2020·The Plant Genome·Desalegn D SerbaElfadil Bashir

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Methods Mentioned

BETA
DNA-Seq
genotyping
electrophoresis
PCR

Software Mentioned

Orthovenn
STRUCTURE HARVESTER
Circos
Fluidigm SNP Genotyping Analysis
Molecular Evolutionary Genetics Analysis 7 ( MEGA7 )
Genesys
GATK
BLAST2GO
SPSS
STRUCTURE

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