1
|
Seong GU, Kim JY, Kim JS, Jeong SU, Cho JH, Lee JY, Lee SB, Kabange NR, Park DS, Moon KD, Kang JW. Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents. Foods 2023; 12:foods12071518. [PMID: 37048338 PMCID: PMC10094488 DOI: 10.3390/foods12071518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Ice cream consumption has increased over the years. In this study, we investigated the potential of using rice varieties with varying amylose contents for ice cream production. We analyzed the physical and chemical properties and sensory quality characteristics (appearance, taste, texture, chewiness, aroma, and rice flavor) of rice-based ice cream made from five varieties with low and high amylose levels. To make the ice cream, we ground rice into a fine powder and combined it with skim milk powder, butter, sugar, glycerin esters of fatty acids, locust bean gum, and water to form a gelatinized mixture. This mixture was then aged, frozen, and hardened. The ice cream’s key quality characteristics, such as viscosity (2170–25,030 cP), hardness (4.27–49.55 N cm−2), and overrun (17.95–46.99%), showed a wide range. Ice cream made from Saemimyeon (high amylose content rice variety) exhibited the highest hardness value (49.55 N cm−2) among the varieties tested, but had relatively low viscosity (4030 cP), overrun (17.95%), and drip-through (0.75 g/min) values. These findings suggest that rice varieties with different amylose contents are suitable for making ice cream and have the potential to expand the rice processing market and increase its value.
Collapse
Affiliation(s)
- Gi-Un Seong
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Ji-Yoon Kim
- School of Food Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Soo Kim
- School of Food Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sae-Ul Jeong
- School of Food Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Hyeon Cho
- National Institute of Crop Science, Rural Development Administration, Sangju 37139, Republic of Korea
| | - Ji-Yoon Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Sais-Beul Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Nkulu-Rolly Kabange
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Dong-Soo Park
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Kwang-Deog Moon
- School of Food Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ju-Won Kang
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| |
Collapse
|
2
|
Identification of quantitative trait loci for tillering, root, and shoot biomass at the maximum tillering stage in rice. Sci Rep 2022; 12:13304. [PMID: 35922462 PMCID: PMC9349274 DOI: 10.1038/s41598-022-17109-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Tillering and plant biomass are key determinants of rice crop productivity. Tillering at the vegetative stage is associated with weed competition, nutrient uptake, and methane emissions. However, little information is available on quantitative trait loci (QTLs) associated with tiller number (qTN), root biomass (qRB), and shoot biomass (qSB) at the active tillering stage which occurs approximately 6 weeks after planting. Here, we mapped tiller and biomass QTLs with ~ 250 recombinant inbred lines derived from a ‘Francis’ by ‘Rondo’ cross using data collected at the maximum tillering stage from two years of greenhouse study, and further compared these QTLs with those mapped at the harvest stage from a field study. Across these three studies, we discovered six qTNs, two qRBs, and three qSBs. Multiple linear regression further indicated that qTN1-2, qTN3-3, qTN4-1, qRB3-1, and qRB5-1 were significant at the maximum tillering stage while qTN3-2 was detected only at the harvest stage. Moreover, qTN3-1 was consistently significant across different developmental stages and growing environments. The genes identified from the peak target qTN regions included a carotenoid metabolism enzyme, a MYB transcription factor, a CBS domain-containing protein, a SAC3/GANP family protein, a TIFY motif containing protein, and an ABC transporter protein. Two genes in the qRB peak target regions included an expressed protein and a WRKY gene. This knowledge of the QTLs, associated markers, candidate genes, and germplasm resources with high TN, RB and SB is of value to rice cultivar improvement programs.
Collapse
|
3
|
Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MYJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics 2021; 113:2656-2674. [PMID: 34111524 DOI: 10.1016/j.ygeno.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 "miracle rice". We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.
Collapse
Affiliation(s)
- Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultutral Sciences, National Chiayi University, Chiayi 60004, Taiwan; School of Biological Sciences, Washington State University, Pullman 99164, WA, USA
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
4
|
Jeon YA, Lee HS, Kim SH, Shim KC, Kang JW, Kim HJ, Tai TH, Ahn SN. Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4254-4268. [PMID: 33831183 PMCID: PMC8163052 DOI: 10.1093/jxb/erab155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 05/08/2023]
Abstract
We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.
Collapse
Affiliation(s)
- Yun-A Jeon
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyun-Sook Lee
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sun-Ha Kim
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyu-Chan Shim
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ju-Won Kang
- Department of Southern Area Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | | | - Thomas H Tai
- USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA 95616, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Sang-Nag Ahn
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
- Correspondence:
| |
Collapse
|
5
|
Tanaka K, Zhao C, Wang N, Kubota S, Kanehara M, Kamijo N, Ishikawa R, Tasaki H, Kanehara M, Liu B, Chen M, Nakamura SI, Udatsu T, Wang C. Classification of archaic rice grains excavated at the Mojiaoshan site within the Liangzhu site complex reveals an Indica and Japonica chloroplast complex. FOOD PRODUCTION, PROCESSING AND NUTRITION 2020. [DOI: 10.1186/s43014-020-00028-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
To understand rice types that were utilized during postdomestication and in the modern age and the potential of genetic research in aged rice materials, archaeogenetic analysis was conducted for two populations of archaic rice grains from the Mojiaoshan site during the Liangzhu Period in China (2940 to 2840 BC). Sequencing after the PCR amplification of three regions of the chloroplast genome and one region of the nuclear genome showed recovery rates that were comparable to those in previous studies except for one chloroplast genome region, suggesting that the materials used in this work were appropriate for recovering genetic information related to domestication traits by using advanced technology. Classification after sequencing in these regions proved the existence of Japonica and Indica chloroplasts in archaic grains from the west trench, which were subsequently classified into eight plastid groups (type I–VIII), and indicated that these rice grains derived from different maternal lineages were stored together in storage houses at the Mojiaohsan site. Among these plastid groups, type V exhibited the same sequences as two modern Indica accessions that are utilized in basic studies and rice breeding. It was inferred that part of the chloroplast genome of archaic rice has been preserved in modern genetic resources in these two modern Indica accessions, and the results indicated that rice related to their maternal ancestor was present at the Mojiaoshan site during the Liangzhu Period in China. The usefulness of archaeogenetic analysis can be demonstrated by our research data as well as previous studies, providing encouragement for the possibility that archaeogenetic analysis can be applied to older rice materials that were utilized in the rice-domesticated period.
Graphical abstract
Collapse
|
6
|
Seo J, Lee SM, Han JH, Shin NH, Lee YK, Kim B, Chin JH, Koh HJ. Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11050562. [PMID: 32443496 PMCID: PMC7290844 DOI: 10.3390/genes11050562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/18/2023] Open
Abstract
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
Collapse
Affiliation(s)
- Jeonghwan Seo
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - So-Myeong Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
| | - Yoon Kyung Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Backki Kim
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea; (J.-H.H.); (N.-H.S.)
- Correspondence: (J.H.C.); (H.-J.K.)
| | - Hee-Jong Koh
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; (J.S.); (S.-M.L.); (Y.K.L.); (B.K.)
- Correspondence: (J.H.C.); (H.-J.K.)
| |
Collapse
|
7
|
Kishor D, Seo J, Chin JH, Koh HJ. Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice ( Oryza sativa L.). Front Genet 2020; 11:86. [PMID: 32153645 PMCID: PMC7046879 DOI: 10.3389/fgene.2020.00086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
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 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 serve as an important resource for molecular breeding and genetic analysis of Basmati varieties.
Collapse
Affiliation(s)
- D.S. Kishor
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Jeonghwan Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| | - Joong Hyoun Chin
- Department of Integrative Bio-industrial Engineering, Sejong University, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea
| |
Collapse
|
8
|
Ferrero-Serrano Á, Cantos C, Assmann SM. The Role of Dwarfing Traits in Historical and Modern Agriculture with a Focus on Rice. Cold Spring Harb Perspect Biol 2019; 11:a034645. [PMID: 31358515 PMCID: PMC6824242 DOI: 10.1101/cshperspect.a034645] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Semidwarf stature is a valuable agronomic trait in grain crops that reduces lodging and increases harvest index. A fundamental advance during the 1960s Green Revolution was the introduction of semidwarf cultivars of rice and wheat. Essentially, all semidwarf varieties of rice under cultivation today owe their diminished stature to a specific null mutation in the gibberellic acid (GA) biosynthesis gene, SD1 However, it is now well-established that, in addition to GAs, brassinosteroids and strigolactones also control plant height. In this review, we describe the synthesis and signaling pathways of these three hormones as understood in rice and discuss the mutants and transgenics in these pathways that confer semidwarfism and other valuable architectural traits. We propose that such genes offer underexploited opportunities for broadening the genetic basis and germplasm in semidwarf rice breeding.
Collapse
Affiliation(s)
| | - Christian Cantos
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
9
|
Kim SR, Ramos JM, Hizon RJM, Ashikari M, Virk PS, Torres EA, Nissila E, Jena KK. Introgression of a functional epigenetic OsSPL14 WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield. Sci Rep 2018; 8:3833. [PMID: 29497052 PMCID: PMC5832747 DOI: 10.1038/s41598-018-21355-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 12/20/2022] Open
Abstract
Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6–59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4–83.5% (7.87–12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.
Collapse
Affiliation(s)
- Sung-Ryul Kim
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Joie M Ramos
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Rona Joy M Hizon
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Parminder S Virk
- International Center for Tropical Agriculture (CIAT), A.A, 6713, Cali, Colombia
| | | | - Eero Nissila
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Strategic Innovation Platform, International Rice Research Institute (IRRI), DAPO Box, 7777, Metro Manila, Philippines.
| |
Collapse
|
10
|
Morphological and starch characteristics of the Japonica rice mutant variety Seolgaeng for dry-milled flour. Food Sci Biotechnol 2017; 26:43-48. [PMID: 30263508 DOI: 10.1007/s10068-017-0006-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/06/2016] [Accepted: 12/04/2016] [Indexed: 10/20/2022] Open
Abstract
Producing good-quality, fine rice flour is more difficult than wheat flour because the rice grain is harder. The non-glutinous Japonica-type variety Seolgaeng, derived from N-methyl-N-nitrosourea (MNU) mutagenesis, and four other varieties, representing a range of amylose contents, were evaluated in this study. Dry-milled Seolgaeng rice flour exhibited an average particle size that is <70 μm, a more uniform particle-size proportion than other varieties. Moreover, we noted significant differences in the damaged starch content in flour from Seolgaeng compared to the other varieties (p<0.05). Seolgaeng flour showed a round starch structure, which would lead to better friability, finer particle size, and less damage to the endosperm during dry milling. Indeed, among all varieties evaluated in this study, dry-milled Seolgaeng flour had the finest particle size (averaging <70 μm) and exhibited less damaged starch. With its round starch granules, Seolgaeng is a suitable candidate for drymilled rice flour.
Collapse
|
11
|
Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep 2015; 5:15655. [PMID: 26506948 PMCID: PMC4623524 DOI: 10.1038/srep15655] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/15/2022] Open
Abstract
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
Collapse
Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.,Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Kiwoung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyeon Ju Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Backki Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon, Kangwon-do, 200-702, Republic of Korea
| | - Jungho Lee
- Green Plant Institute, #2-202 Biovalley, 89 Seoho-ro, Kwonseon-gu, Suwon, Republic of Korea
| | - Kwang-Su Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang-gun, Kangwon-do, 232-955, Republic of Korea
| | - Beom-Seok Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| |
Collapse
|