Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"

Kim, Backki; Kim, Dong-Gwan; Lee, Gileung; Seo, Jeonghwan; Choi, Ik‐Young; Choi, Beom-Soon; Yang, Tae-Jin; Kim, Kwang S.; Lee, Joohyun; Chin, Joong Hyoun; Koh, Hee‐Jong

doi:10.1186/s12284-014-0022-5

Cited by 26 publications

(31 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of the genes assigned to the three GO categories were mainly involved in metabolic process, cellular process, binding, catalytic activity, cell, and cell part. This functional annotation of genes is consistent with previous findings in rice (Kim et al, 2014;Liu et al, 2017). Additionally, our data showed that the metabolic process involved in the cellular aromatic compound was associated with the common mutated gene cluster ( Figure 5A) and further analyses revealed that nine genes including Badh2 gene having alternative allele's among aromatic group of rice varieties with more than 80% of frequency ( Supplementary Table 8).…”

Section: Discussionsupporting

confidence: 91%

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

et al. 2020

Self Cite

View full text Add to dashboard Cite

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 found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, aromatic (22 varieties), aus (four varieties), and indica (four varieties), based on genome-wide SNPs. All 22 aromatic Basmati varieties harbored the fragrant-inducing Badh2 allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant (P < 0.05 and P < 0.01) differences between the aromatic and indica/aus groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will

show abstract

Section: Discussionsupporting

confidence: 91%

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

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…These indica varieties have a remarkably higher αT content compared to other indica varieties. Genetic backgrounds of the nine special varieties were investigated, and two were tongli-type varieties obtained using a three-way cross of indica/japonica varieties (Chung and Heu 1991;Kim et al 2014). Thus, the japonica alleles in those indica varieties were introduced from the japonica parents via artificial crossing.…”

Section: Discussionmentioning

confidence: 99%

Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice

Wang

Yoon

et al. 2015

Mol Genet Genomics

View full text Add to dashboard Cite

Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, α-tocopherol (αΤ) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of αΤ content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (OsγTMT) was identified as the major factor responsible for the αΤ content among rice accessions. Nucleotide variations in the coding region of OsγTMT were significantly associated with the αΤ content variations, while nucleotide polymorphisms in the promoter region of OsγTMT also could partly demonstrate the correlation with αΤ content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying αΤ content variations in rice, which will significantly contribute the research on αΤ biosynthesis mechanisms and αΤ improvement of rice.

show abstract

“…ricediversity.org/data/), the HapRice world SNP data (Yonemaru et al 2014) of the Q-TARO database (http://qtaro.abr.affrc.go.jp/), and the resequencing data of 40 rice cultivars from CMB lab. Seoul National University generated using Illumina platform based on methods described by Kim et al (2014). SNPs showing only substitution polymorphism between indica and japonica varieties and no other SNP in at least 60 bp on either side were selected.…”

Section: Snp Selection and Fluidigm Genotype Assay Designmentioning

confidence: 99%

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

et al. 2020

Self Cite

View full text Add to dashboard Cite

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indicajaponica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4-5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F 2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

show abstract

Defining the genome structure of `Tongil' rice, an important cultivar in the Korean "Green Revolution"

Cited by 26 publications

References 32 publications

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

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

Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice

Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Contact Info

Product

Resources

About