Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species
Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution o...
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MDPI AG
2021-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/4/725 |
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| author | Kanako Bessho-Uehara Yoshiyuki Yamagata Tomonori Takashi Takashi Makino Hideshi Yasui Atsushi Yoshimura Motoyuki Ashikari |
| author_facet | Kanako Bessho-Uehara Yoshiyuki Yamagata Tomonori Takashi Takashi Makino Hideshi Yasui Atsushi Yoshimura Motoyuki Ashikari |
| author_sort | Kanako Bessho-Uehara |
| collection | DOAJ |
| description | Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species <i>Oryza sativa</i> ssp. <i>japonica</i>. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, <i>REGULATOR OF AWN ELONGATION 1</i> (<i>RAE1</i>) and <i>RAE2</i>. To understand the conserveness of <i>RAE1</i> and <i>RAE2</i> in wild rice relatives, we analyzed <i>RAE1</i> and <i>RAE2</i> sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional <i>RAE1</i> and <i>RAE2</i>, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of <i>RAE1</i> and <i>RAE2</i> were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of <i>RAE1</i> and <i>RAE2</i> were selected after the speciation of <i>O</i>. <i>sativa</i>, and that two-step loss of function in <i>RAE1</i> and <i>RAE2</i> contributed to awnlessness in Asian cultivated rice. |
| first_indexed | 2024-03-10T12:29:56Z |
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| publishDate | 2021-04-01 |
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| spelling | doaj.art-6cdd6fa9440240ceb11e1077354fa3792023-11-21T14:44:11ZengMDPI AGPlants2223-77472021-04-0110472510.3390/plants10040725Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome SpeciesKanako Bessho-Uehara0Yoshiyuki Yamagata1Tomonori Takashi2Takashi Makino3Hideshi Yasui4Atsushi Yoshimura5Motoyuki Ashikari6Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, JapanFaculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, JapanSTAY GREEN Co., Ltd., 2-1-5 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, JapanGraduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, JapanFaculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, JapanFaculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, JapanBioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, JapanWild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species <i>Oryza sativa</i> ssp. <i>japonica</i>. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, <i>REGULATOR OF AWN ELONGATION 1</i> (<i>RAE1</i>) and <i>RAE2</i>. To understand the conserveness of <i>RAE1</i> and <i>RAE2</i> in wild rice relatives, we analyzed <i>RAE1</i> and <i>RAE2</i> sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional <i>RAE1</i> and <i>RAE2</i>, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of <i>RAE1</i> and <i>RAE2</i> were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of <i>RAE1</i> and <i>RAE2</i> were selected after the speciation of <i>O</i>. <i>sativa</i>, and that two-step loss of function in <i>RAE1</i> and <i>RAE2</i> contributed to awnlessness in Asian cultivated rice.https://www.mdpi.com/2223-7747/10/4/725AA genomeawnchromosome segment substitution linesricewild species |
| spellingShingle | Kanako Bessho-Uehara Yoshiyuki Yamagata Tomonori Takashi Takashi Makino Hideshi Yasui Atsushi Yoshimura Motoyuki Ashikari Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species Plants AA genome awn chromosome segment substitution lines rice wild species |
| title | Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species |
| title_full | Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species |
| title_fullStr | Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species |
| title_full_unstemmed | Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species |
| title_short | Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species |
| title_sort | exploring the loci responsible for awn development in rice through comparative analysis of all aa genome species |
| topic | AA genome awn chromosome segment substitution lines rice wild species |
| url | https://www.mdpi.com/2223-7747/10/4/725 |
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