TY - JOUR
T1 - Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryza sativa ‘Nipponbare’
AU - Tsujimura, Yuki
AU - Sugiyama, Shohei
AU - Otsuka, Kotaro
AU - Htun, Than Myint
AU - Numaguchi, Koji
AU - Castillo, Cristina
AU - Akagi, Takashi
AU - Ishii, Takashige
AU - Ishikawa, Ryo
N1 - Funding Information:
was provided by the National Institute of Genetics supported by the National Bioresource Project, MEXT, Japan. We thank Satoshi Nat-sume (Iwate Biotechnology Research Center), Kentaro Yoshida (Kobe University), Soichiro Nishiyama and Takuya Morimoto (Kyoto University) for their useful advices on our QTL-seq analysis. This study was supported in part by Grants-in-Aid from the Japan Society for the Promotion of Science (JSPS) to R.I. (Nos. 15KK0280 and 18K05594) and by the JSPS Bilateral Open Partnership Joint Research Project to R.I.
Funding Information:
The wild rice accession, O. rufipogon W630, was provided by the National Institute of Genetics supported by the National Bioresource Project, MEXT, Japan. We thank Satoshi Natsume (Iwate Biotechnology Research Center), Kentaro Yoshida (Kobe University), Soichiro Nishiyama and Takuya Morimoto (Kyoto University) for their useful advices on our QTL-seq analysis. This study was supported in part by Grants-in-Aid from the Japan Society for the Promotion of Science (JSPS) to R.I. (Nos. 15KK0280 and 18K05594) and by the JSPS Bilateral Open Partnership Joint Research Project to R.I.
Publisher Copyright:
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
PY - 2019/9/1
Y1 - 2019/9/1
N2 - Key message: A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, ‘Nipponbare’, was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci. Abstract: Asian cultivated rice, Oryzasativa, was domesticated from its wild ancestor, O.rufipogon. Loss of seed shattering is one of the most recognisable traits selected during rice domestication. Three quantitative trait loci (QTLs), qSH1, qSH3, and sh4, were previously reported to be involved in the loss of seed shattering of Japonica cultivated rice, O.sativa ‘Nipponbare’.However, the introgression line (IL) carrying ‘Nipponbare’ alleles at these three loci in the genetic background of wild rice, O.rufipogon W630, showed a lower value for detaching a grain from the pedicel than ‘Nipponbare’. Here, we investigated abscission layer formation in the IL and found a partially formed abscission layer in the central region between the epidermis and vascular bundles. Based on QTL-seq analysis using the F2 population obtained from a cross between ‘Nipponbare’ and the IL, we detected two novel loci qCSS3 and qCSS9 (QTL for the Control of Seed Shattering in rice on chromosomes 3 and 9), which were found to be involved in the difference in seed-shattering degree between ‘Nipponbare’ and W630. Then, we further focused on qCSS3 in order to understand its potential role on the loss of seed shattering. The candidate region of qCSS3 was found to be located within a 526-kb region using substitution mapping analysis. Interestingly, the qCSS3 candidate region partially overlaps the selective sweep detected for Japonica but not for Indica rice cultivars, suggesting that this region harbours the mutation at a novel seed-shattering locus specifically selected for non-seed-shattering behaviour in Japonica cultivars.
AB - Key message: A novel locus, qCSS3, involved in the non-seed-shattering behaviour of Japonica rice cultivar, ‘Nipponbare’, was detected by QTL-seq analysis using the segregating population with the fixed known seed-shattering loci. Abstract: Asian cultivated rice, Oryzasativa, was domesticated from its wild ancestor, O.rufipogon. Loss of seed shattering is one of the most recognisable traits selected during rice domestication. Three quantitative trait loci (QTLs), qSH1, qSH3, and sh4, were previously reported to be involved in the loss of seed shattering of Japonica cultivated rice, O.sativa ‘Nipponbare’.However, the introgression line (IL) carrying ‘Nipponbare’ alleles at these three loci in the genetic background of wild rice, O.rufipogon W630, showed a lower value for detaching a grain from the pedicel than ‘Nipponbare’. Here, we investigated abscission layer formation in the IL and found a partially formed abscission layer in the central region between the epidermis and vascular bundles. Based on QTL-seq analysis using the F2 population obtained from a cross between ‘Nipponbare’ and the IL, we detected two novel loci qCSS3 and qCSS9 (QTL for the Control of Seed Shattering in rice on chromosomes 3 and 9), which were found to be involved in the difference in seed-shattering degree between ‘Nipponbare’ and W630. Then, we further focused on qCSS3 in order to understand its potential role on the loss of seed shattering. The candidate region of qCSS3 was found to be located within a 526-kb region using substitution mapping analysis. Interestingly, the qCSS3 candidate region partially overlaps the selective sweep detected for Japonica but not for Indica rice cultivars, suggesting that this region harbours the mutation at a novel seed-shattering locus specifically selected for non-seed-shattering behaviour in Japonica cultivars.
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U2 - 10.1007/s00122-019-03376-3
DO - 10.1007/s00122-019-03376-3
M3 - Article
C2 - 31222437
AN - SCOPUS:85067848346
VL - 132
SP - 2615
EP - 2623
JO - Theoretical And Applied Genetics
JF - Theoretical And Applied Genetics
SN - 0040-5752
IS - 9
ER -