TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data

Kumagai, Masahiko; Nishikawa, Daiki; Kawahara, Yoshihiro; Wakimoto, Hironobu; Itoh, Ryutaro; Tabei, Norio; Tanaka, Tsuyoshi; Itoh, Takeshi

doi:10.1093/dnares/dsz022

Cited by 26 publications

(23 citation statements)

References 43 publications

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“…‘Takanari’ has A-type in the G / A polymorphism and TT-type in the GC / TT polymorphism of the Alk gene based on genotyping by the DNA marker of Bao et al ( 2006 ) and Hiratsuka et al ( 2010 ). It was different with other weak functional alleles of the japonica -type alk ( Alk a ) in ‘Koshihikari’, Alk ( Alk c ) in typical indica type and Alk b in the previous study (Chen et al 2020 ), but the same weak functional allele as other japonica rice cultivars such as ‘Asahi’ and ‘Akebono’ according to the RAP-DB and Rice-TASUKE database ( https://ricegenomes.dna.affrc.go.jp/ , Sakai et al 2013 ; Kawahara et al 2013 ; Kumagai et al 2019 ). Therefore, ‘Koshihikari’ and ‘Takanari’ have the two weak functional alleles of both the Wx and Alk genes.…”

Section: Discussionmentioning

confidence: 66%

“…Here, we detected one eating quality QTL, qST3–1 , also on the short arm of chromosome 3, and the ‘Koshihikari’ allele of this QTL was also associated with high eating quality score and strong stickiness of cooked grains. The ‘Takanari’ allele of qOE3 would be the same as the ‘Nipponbare’ allele because of consistent haplotypes between these cultivars according to the RAP-DB and TASUKE databases (Sakai et al 2013 ; Kawahara et al 2013 ; Kumagai et al 2019 ). Therefore, qST3–1 is likely identical to qOE3 .…”

Section: Discussionmentioning

confidence: 99%

“…The centromere side is on the left, and the distal end of the long arm is on the right. White bars, homozygous for the 'Koshihikari'-type allele; black bars, homozygous for the 'Takanari'-type allele (Chen et al 2020), but the same weak functional allele as other japonica rice cultivars such as 'Asahi' and 'Akebono' according to the RAP-DB and Rice-TASUKE database (https://ricegenomes.dna.affrc.go.jp/, Sakai et al 2013;Kawahara et al 2013;Kumagai et al 2019). Therefore, 'Koshihikari' and 'Takanari' have the two weak functional alleles of both the Wx and Alk genes.…”

Section: Discussionmentioning

confidence: 99%

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Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Hori

Suzuki

Ishikawa

et al. 2021

Rice

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Background In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar ‘Koshihikari’ and an indica rice cultivar ‘Takanari’. Results We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of ‘Koshihikari’ chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1–5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2–4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1–5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the ‘Koshihikari’ genetic background. Conclusion The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.

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Section: Discussionmentioning

confidence: 66%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Hori

Suzuki

Ishikawa

et al. 2021

Rice

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“…To clarify the functional diversity of the flowering time genes in JRC, we exhibited sequence variation in JRC using a multiple genome browser, TASUKE+ ( Kumagai et�al. 2013 , Kumagai et�al. 2019 ), and performed haplotype analysis for flowering genes ( Fig.�2 , Table�1 ).…”

Section: Resultsmentioning

confidence: 99%

Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing

Tanaka

Shenton

Kawahara

et al. 2020

Plant and Cell Physiology

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The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole genome re-sequencing of these 50 accessions, and obtained a total of 2,145,095 SNPs and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+ to examine haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed GWAS for agronomical traits using the JRC and another core collection, the world rice core collection (WRC), comprising of 69 accessions also provided by the NARO genebank. In leaf blade width a strong peak close to NAL1, a key gene for the regulation of leaf width, and in heading date, a peak near HESO1, involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC+WRC. Thus, JRC and JRC+WRC are suitable populations for GWAS in particular traits.

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“…We exported the consensus sequences covering the coding region and the flanking regions of OsSh1 in wild and cultivated rice from TASUKE + 64 . The variant filter was set as follows: quality > =20 and depth > =4.…”

Section: Methodsmentioning

confidence: 99%

Direct identification of a mutation in OsSh1 causing non-shattering in a rice (Oryza sativa L.) mutant cultivar using whole-genome resequencing

Komatsu

Ohtake

et al. 2020

Sci Rep

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Loss of seed shattering has been regarded as a key step during crop domestication. Mutagenesis contributes to the development of novel crop cultivars with a desired seed-shattering habit in a relatively short period of time, but also to uncovering the genetic architecture of seed shattering. ‘Minamiyutaka’, a non-shattering indica rice cultivar, was developed from the easy-shattering cultivar ‘Moretsu’ by mutation breeding via gamma-ray irradiation. In present study, we observed significant differences in shattering habit, breaking tensile strength, and abscission zone structure between ‘Moretsu’ and ‘Minamiyutaka’. Whole-genome mutation analysis of ‘Minamiyutaka’ newly identified a 13-bp deletion causing defective splicing in exon 3 of the OsSh1 gene which has previously been referred to as a candidate for controlling seed shattering. Using CRISPR/Cas9 gene editing, we demonstrated that loss-of-function mutation in OsSh1 causes non-shattering in rice. Furthermore, gene expression analysis suggests that OsSh1 may function downstream of qSH1, a known key gene involved in abscission zone differentiation. Nucleotide diversity analysis of OsSh1 in wild rice accessions and cultivars revealed that OsSh1 has been under strong selection during rice domestication, and a missense mutation might have contributed to the reduction of seed shattering from the wild progenitors to cultivated rice.

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TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data

Cited by 26 publications

References 43 publications

Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing

Direct identification of a mutation in OsSh1 causing non-shattering in a rice (Oryza sativa L.) mutant cultivar using whole-genome resequencing

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