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Lewandowicz J, Le Thanh-Blicharz J, Szwengiel A. Insight into Rheological Properties and Structure of Native Waxy Starches: Cluster Analysis Grouping. Molecules 2024; 29:2669. [PMID: 38893543 PMCID: PMC11173837 DOI: 10.3390/molecules29112669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
Recent interest in the use of waxy starches in food production is due to the possibility of replacing chemically modified starches as texture-forming agents with native starch analogues. However, there is a lack of a coherent research comparing different varieties of commercially available waxy starches with respect to their molecular and functional properties. Therefore, the objective of this study was to compare native waxy starches from potatoes, corn, and rice, with particular attention to rheological characteristics in relation to molecular structure. The investigated potato, corn, and rice starch preparations were characterized by significantly different molecular properties due to both botanical origin of starch and variety. The molecular weights of waxy starches were significantly higher than those of their normal counterparts. This phenomenon was accompanied by a more loose conformation of the waxy starch macromolecule in solution. The presence of amylose confers the ability to coagulate starch sol into gel, resulting in substantial changes in the rheological properties of starch paste, and waxy starch pastes being characterized by more viscous flow and smoother texture. Hierarchical cluster analysis indicated that differences between functional properties are more notable for normal than for waxy preparations, in which potato starch, regardless of its variety, was characterized by the most unique characteristics.
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Affiliation(s)
- Jacek Lewandowicz
- Department of Food Concentrates and Starch Products, Prof. Wacław Dąbrowski Institute of Agriculture and Food Biotechnology—State Research Institute, Starołęcka 40, 61-361 Poznan, Poland;
| | - Joanna Le Thanh-Blicharz
- Department of Food Concentrates and Starch Products, Prof. Wacław Dąbrowski Institute of Agriculture and Food Biotechnology—State Research Institute, Starołęcka 40, 61-361 Poznan, Poland;
| | - Artur Szwengiel
- Department of Food Technology of Plant Origin, Faculty of Food Science and Nutrition, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624 Poznan, Poland;
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2
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Gaur VS, Sood S, Guzmán C, Olsen KM. Molecular insights on the origin and development of waxy genotypes in major crop plants. Brief Funct Genomics 2024; 23:193-213. [PMID: 38751352 DOI: 10.1093/bfgp/elad035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 06/14/2024] Open
Abstract
Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.
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Affiliation(s)
- Vikram S Gaur
- Raja Bhoj College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla- 171001, Himachal Pradesh, India
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, CeiA3, ES-14071, Córdoba, Spain
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3
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Fukunaga K, Kawase M. Crop Evolution of Foxtail Millet. PLANTS (BASEL, SWITZERLAND) 2024; 13:218. [PMID: 38256771 PMCID: PMC10819197 DOI: 10.3390/plants13020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Studies on the domestication, genetic differentiation, and crop evolution of foxtail millet are reviewed in this paper. Several genetic studies were carried out to elucidate the genetic relationships among foxtail millet accessions originating mainly from Eurasia based on intraspecific hybrid pollen semi-sterility, isozymes, DNA markers, and single-nucleotide polymorphisms. Most studies suggest that China is the center of diversity of foxtail millet, and landraces were categorized into geographical groups. These results indicate that this millet was domesticated in China and spread over Eurasia, but independent origin in other regions cannot be ruled out. Furthermore, the evolution of genes was reviewed (i.e., the Waxy gene conferring amylose content in the endosperm, the Si7PPO gene controlling polyphenol oxidase, the HD1 and SiPRR37 genes controlling heading time, the Sh1 and SvLes1 genes involved in grain shattering, and the C gene controlling leaf sheath pigmentation), and the variation and distribution of these genes suggested complex patterns of evolution under human and/or natural selection.
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Affiliation(s)
- Kenji Fukunaga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara 727-0023, Japan
| | - Makoto Kawase
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi 243-0034, Japan
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4
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Tian S, Yang J, Fu Y, Zhang X, Zhang J, Zhao H, Hu Q, Liu P, He W, Han X, Wen C. McAPRR2: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd. PLANTS (BASEL, SWITZERLAND) 2023; 12:3585. [PMID: 37896048 PMCID: PMC10610206 DOI: 10.3390/plants12203585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (McAPRR2) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the McAPRR2 gene and its promoter. High πwild/SEA and πSA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Changlong Wen
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China (J.Y.); (J.Z.); (H.Z.)
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5
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Somers J, Nelms B. The sporophyte-to-gametophyte transition: The haploid generation comes of age. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102416. [PMID: 37441836 DOI: 10.1016/j.pbi.2023.102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Flowering plants alternate between two multicellular generations: the diploid sporophyte and haploid gametophyte. Despite its small size, the gametophyte has significant impacts on plant genetics, evolution, and breeding. Each male pollen grain and female embryo sac is a multicellular organism with independent gene expression, a functioning metabolism, and specialized cell types. In this review, we describe recent progress in understanding the process in which the haploid genome takes over expression from its diploid parent - the sporophyte-to-gametophyte transition. The focus is on pollen, but similar concepts may also apply to the female gametophyte. Technological advances in single-cell genomics offer the opportunity to characterize haploid gene expression in unprecedented detail, positioning the field to make rapid progress.
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Affiliation(s)
- Julian Somers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Brad Nelms
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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6
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Liang C, Guan Z, Wei K, Yu W, Wang L, Chen X, Wang Y. Characteristics of antioxidant capacity and metabolomics analysis of flavonoids in the bran layer of green glutinous rice (Oryza sativa L. var. Glutinosa Matsum). Sci Rep 2023; 13:16372. [PMID: 37773271 PMCID: PMC10541414 DOI: 10.1038/s41598-023-43466-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023] Open
Abstract
Green glutinous rice is a unique genetic germplasm that has yet to be adequately studied. This study investigated antioxidant capacity and flavonoid metabolites in the bran layer of green glutinous rice (LvH) compared to purple (HeiH), red (HongH) and white (GJG) varieties. The results showed that LvH bran had significantly higher content of total flavonoids and anthocyanin than that of HongH (1.91-fold and 4.34-fold) and GJG (2.45-fold and 13.30-fold). LvH bran also showed significantly higher levels of vitamin B1 and vitamin E than that of HeiH (1.94-fold and 1.15-fold) and HongH (1.22-fold and 1.13-fold), indicating that green glutinous rice bran was rich in bioactive components. LvH bran showed significantly lower IC50 values for scavenging DPPH and ATBS radicals than GJG and even significantly lower IC50 value for scavenging DPPH radicals than HongH, highlighting its potential as an effective source of antioxidants. LvH bran had significantly different downstream metabolite synthesis in the flavonoid pathway compared to HeiH, HongH, and GJG, with 40, 26, and 22 different metabolites, 23, 20, and 33 up-regulated differentially expressed metabolites (DEMs), and 73, 50, and 13 down-regulated DEMs, respectively. Of the 139 flavonoid metabolites identified in colored rice bran, 26 metabolites showed significant positive correlation with both ABTS and DPPH radical scavenging capacity. Typically, quercetin derivatives showed potential for evaluating the antioxidant capacity of colored rice bran. These findings offer valuable insights into the antioxidant properties of green glutinous rice bran and provide references for better understanding of flavonoid metabolites in different colored rice bran.
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Affiliation(s)
- Chenggang Liang
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China
| | - Zhixiu Guan
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China
| | - Kesu Wei
- Guizhou Academy of Tobacco Science, Guiyang, 550003, China.
| | - Wujuan Yu
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China
| | - Li Wang
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China
| | - Xuling Chen
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China
| | - Yan Wang
- Institution of Plant Genetics and Breeding, Guizhou Normal University, Guiyang, 550001, China.
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7
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Zhang C, Yun P, Xia J, Zhou K, Wang L, Zhang J, Zhao B, Yin D, Fu Z, Wang Y, Ma T, Li Z, Wu D. CRISPR/Cas9-mediated editing of Wx and BADH2 genes created glutinous and aromatic two-line hybrid rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:24. [PMID: 37313522 PMCID: PMC10248662 DOI: 10.1007/s11032-023-01368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/02/2023] [Indexed: 06/15/2023]
Abstract
Amylose content (AC) is one of the physicochemical indexes of rice quality, which is largely determined by the Waxy (Wx) gene. Fragrance in rice is favored because it adds good flavor and a faint scent. Loss of function of the BADH2 (FGR) gene promotes the biosynthesis of 2-acetyl-1-pyrroline (2AP), which is the main compound responsible for aroma in rice. Here, we used a CRISPR/Cas9 system to simultaneously knock out Wx and FGR genes in 1892S and M858, which are the parents of an indica two-line hybrid rice, Huiliangyou 858 (HLY858). Four T-DNA-free homozygous mutants (1892Swxfgr-1, 1892Swxfgr-2, M858wxfgr-1, and M858wxfgr-2) were obtained. The 1892Swxfgr and M858wxfgr were crossed to generate double mutant hybrid lines HLY858wxfgr-1 and HLY858wxfgr-2. Size-exclusion chromatography (SEC) data indicated that true AC of the wx mutant starches ranged from 0.22 to 1.63%, much lower than those of the wild types (12.93 to 13.76%). However, the gelatinization temperature (GT) of the wx mutants in backgrounds of 1892S, M858, and HLY858 were still high, and showed no significant differences with the wild type controls. The aroma compounds 2AP content in grains of HLY858wxfgr-1 and HLY858wxfgr-2 were 153.0 μg/kg and 151.0 μg/kg, respectively. In contrast, 2AP was not detected in grains of HLY858. There were no significant differences in major agronomic traits between the mutants and HLY858. This study provides guidelines for cultivation of ideal glutinous and aromatic hybrid rice by gene editing.
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Affiliation(s)
- Caijuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Peng Yun
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Jiafa Xia
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Kunneng Zhou
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Lili Wang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Jingwen Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Bo Zhao
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Daokun Yin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Zhe Fu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yuanlei Wang
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Tingchen Ma
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zefu Li
- Rice Research Institute/Key Laboratory of Rice Genetics and Breeding of Anhui Province, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Dexiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
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8
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Burešová I, Červenka L, Šebestíková R, Augustová M, Jarošová A. Applicability of Flours from Pigmented and Glutinous Rice in Gluten-Free Bread Baking. Foods 2023; 12:foods12061324. [PMID: 36981251 PMCID: PMC10048109 DOI: 10.3390/foods12061324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The flours from pigmented and glutinous rice have a great potential to increase the nutritional quality of gluten-free breads. The characteristics of whole-meal fine flours, slurries, doughs, and breads prepared from black, red, and white glutinous rice were, therefore, compared with commercially used refined fine and semi-coarse white rice flours. The pasting properties of different flours were strongly influenced by the type of rice they were made from. Slurries with red and glutinous flours exhibited a shift to a lower pasting temperature T0, lower values of ηPeak and ηFinal, as well as higher values of the breakdown and setback region than the slurries with refined flours. The slurry with black flour exhibited high values of viscosity η0 and breakdown, together with low values of ηFinal, setback region and total setback. Bread characteristics were strongly correlated with the pasting properties. The presence of bran particles did not negatively impact loaf volume, crumb hardness, springiness, and chewiness. Some defects were observed in glutinous and red rice bread. Fine flour exhibited better baking performance than semi-coarse flour. Glutinous flour has the potential to become an ingredient in gluten-free baking. The applicability of various black and red rice flours may be limited by the flavor and the taste.
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Affiliation(s)
- Iva Burešová
- Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic
| | - Libor Červenka
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 532 10 Pardubice, Czech Republic
| | - Romana Šebestíková
- Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic
| | - Monika Augustová
- Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic
| | - Alžbeta Jarošová
- Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
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9
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Feng X, Rahman MM, Hu Q, Wang B, Karim H, Guzmán C, Harwood W, Xu Q, Zhang Y, Tang H, Jiang Y, Qi P, Deng M, Ma J, Lan J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. HvGBSSI mutation at the splicing receptor site affected RNA splicing and decreased amylose content in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:1003333. [PMID: 36212333 PMCID: PMC9538149 DOI: 10.3389/fpls.2022.1003333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Granule-bound starch synthase I (HvGBSSI) is encoded by the barley waxy (Wx-1) gene and is the sole enzyme in the synthesis of amylose. Here, a Wx-1 mutant was identified from an ethyl methane sulfonate (EMS)-mutagenized barley population. There were two single-base mutations G1086A and A2424G in Wx-1 in the mutant (M2-1105). The G1086A mutation is located at the 3' splicing receptor (AG) site of the fourth intron, resulting in an abnormal RNA splicing. The A2424G mutation was a synonymous mutation in the ninth intron. The pre-mRNA of Wx-1 was incorrectly spliced and transcribed into two abnormal transcripts. The type I transcript had a 6 bp deletion in the 5' of fifth exon, leading to a translated HvGBSSI protein lacking two amino acids with a decreased starch-binding capacity. In the type II transcript, the fourth intron was incorrectly cleaved and retained, resulting in the premature termination of the barley Wx-1 gene. The mutations in the Wx-1 decreased the enzymatic activity of the HvGBSSI enzyme and resulted in a decreased level in amylose content. This work sheds light on a new Wx-1 gene inaction mechanism.
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Affiliation(s)
- Xiuqin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Md. Mostafijur Rahman
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qian Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hassan Karim
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Cordoba, Spain
| | - Wendy Harwood
- John Innes Center, Norwich Research Park, Norwich, United Kingdom
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jingyu Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
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10
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Wang M, Chen J, Zhou F, Yuan J, Chen L, Wu R, Liu Y, Zhang Q. The ties of brotherhood between japonica and indica rice for regional adaptation. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1369-1379. [PMID: 34902099 DOI: 10.1007/s11427-021-2019-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.
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Affiliation(s)
- Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiehu Chen
- Science Corporation of Gene, Guangzhou, 510000, China
| | - Feng Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianming Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Libin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
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11
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Fu Y, Luo T, Hua Y, Yan X, Liu X, Liu Y, Liu Y, Zhang B, Liu R, Zhu Z, Zhu J. Assessment of the Characteristics of Waxy Rice Mutants Generated by CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:881964. [PMID: 35755680 PMCID: PMC9226628 DOI: 10.3389/fpls.2022.881964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The cooking and eating quality of rice grains is a major focus from a consumer's perspective and is mainly determined by the apparent amylose content (AAC) of the starch. Waxy rice, a type of rice with an AAC of less than 2%, is an important goal for the breeding of high-quality rice. In recent years, the cloning of the Waxy (Wx) gene has revealed the molecular mechanism of the formation of waxy traits in rice. However, there have been limited studies on the physicochemical properties, such as gelatinization temperature, rapid viscosity analyzer profile, and amylopectin fine structure of wx mutants. In the current study, a rapid and highly efficient strategy was developed through the CRISPR/Cas9 gene-editing system for generating wx mutants in the background of five different rice varieties. The wx mutation significantly reduced the AAC and starch viscosity but did not affect the major agronomic traits (such as plant height, panicle number per plant, grain number per panicle, and seed-setting frequency). Incorporation of the wx mutation into varieties with low initial AAC levels resulted in further reduction in AAC, but without significantly affecting the original, desirable gelatinization traits and amylopectin structure types, suggesting that parents with low initial AAC should be preferred in breeding programs.
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Affiliation(s)
- Yuhao Fu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tingting Luo
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Yonghuan Hua
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Xuehai Yan
- Leshan Municipal Bureau of Agriculture and Rural Affairs, Leshan, China
| | - Xu Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Ying Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Baoli Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Rui Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Zizhong Zhu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Jun Zhu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
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12
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Jiang C, Rashid MAR, Zhang Y, Zhao Y, Pan Y. Genome wide association study on development and evolution of glutinous rice. BMC Genom Data 2022; 23:33. [PMID: 35508973 PMCID: PMC9066796 DOI: 10.1186/s12863-022-01033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers' preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous. RESULTS Here, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR. CONCLUSIONS The cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.
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Affiliation(s)
- Conghui Jiang
- Shandong Rice Engineering Technology Research Center, Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yanhong Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China.
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
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13
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Zi Y, Cheng D, Li H, Guo J, Ju W, Wang C, Humphreys DG, Liu A, Cao X, Liu C, Liu J, Zhao Z, Song J. Effects of the different waxy proteins on starch biosynthesis, starch physicochemical properties and Chinese noodle quality in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:23. [PMID: 37309456 PMCID: PMC10248619 DOI: 10.1007/s11032-022-01292-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Noodles are an important food in Asia. Wheat starch is the most important component in Chinese noodles. Loss of the waxy genes leads to lower activity of starch synthesis enzymes and decreased amylose content that further affects starch properties and noodle quality. To study the effects of different waxy (Wx) protein subunits on starch biosynthesis and processing quality, the high-yielding wheat cultivar Jimai 22 was treated with the mutagen ethyl methane sulfonate (EMS) to produce a population of Wx lines and chosen 7 Wx protein combinations. The amylose content increased but swelling power decreased as the number of Wx proteins increased. Both GBSS activity and gene expression were the lowest for the waxy mutant, followed by the mutants with 1 Wx protein. The combinations of these mutant alleles lead to reductions in both RNA expression and protein levels. Noodles made from materials with 2 Wx protein subunits had the highest score, which agreed with peak viscosity. The influence of the Wx-B1 protein on amylose synthesis and noodle quality was the highest, whereas the influence of Wx-A1 protein was the lowest. Mutants with lower amylose content caused by the absence of 1 subunit, especially the Wx-B1 subunit, had superior noodle quality. Additionally, the identified mutant lines can be used as intermediate materials to improve wheat quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01292-x.
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Affiliation(s)
- Yan Zi
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Dungong Cheng
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Haosheng Li
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jun Guo
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Wei Ju
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Canguo Wang
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - D. G. Humphreys
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, K.W. Neatby Building, 960 Carling Avenue, Ottawa, K1A 06C ON UK
| | - Aifeng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Xinyou Cao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Cheng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianjun Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Zhendong Zhao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianmin Song
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
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14
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Zhang G, Wang R, Ma J, Gao H, Deng L, Wang N, Wang Y, Zhang J, Li K, Zhang W, Mu F, Liu H, Wang Y. Genome-wide association studies of yield-related traits in high-latitude japonica rice. BMC Genom Data 2021; 22:39. [PMID: 34610789 PMCID: PMC8493688 DOI: 10.1186/s12863-021-00995-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. However, yield is a complex quantitative trait composed of many factors. The purpose of this study was to determine how many genetic loci are associated with yield-related traits. Genome-wide association studies (GWAS) were performed on 450 accessions collected from northeast Asia, including Russia, Korea, Japan and Heilongjiang Province of China. These accessions consist of elite varieties and landraces introduced into Heilongjiang Province decade ago. RESULTS After resequencing of the 450 accessions, 189,019 single nucleotide polymorphisms (SNPs) were used for association studies by two different models, a general linear model (GLM) and a mixed linear model (MLM), examining four traits: days to heading (DH), plant height (PH), panicle weight (PW) and tiller number (TI). Over 25 SNPs were found to be associated with each trait. Among them, 22 SNPs were selected to identify candidate genes, and 2, 8, 1 and 11 SNPs were found to be located in 3' UTR region, intron region, coding region and intergenic region, respectively. CONCLUSIONS All SNPs detected in this research may become candidates for further fine mapping and may be used in the molecular breeding of high-latitude rice.
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Affiliation(s)
- Guomin Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Rongsheng Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Juntao Ma
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Hongru Gao
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Lingwei Deng
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Nanbo Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Yongli Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Jun Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Kun Li
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Wei Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Fengchen Mu
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Hui Liu
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China
| | - Ying Wang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China.
- Northern Japonica Rice Molecular Breeding Joint Research Center, Chinese Academy of Sciences, Harbin, China.
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15
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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16
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Maung TZ, Yoo JM, Chu SH, Kim KW, Chung IM, Park YJ. Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:707237. [PMID: 34504507 PMCID: PMC8421862 DOI: 10.3389/fpls.2021.707237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Ill-Min Chung
- Department of Applied Life Science, Konkuk University, Seoul, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
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17
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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18
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Seung D. Amylose in starch: towards an understanding of biosynthesis, structure and function. THE NEW PHYTOLOGIST 2020; 228:1490-1504. [PMID: 32767769 DOI: 10.1111/nph.16858] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/13/2020] [Indexed: 05/20/2023]
Abstract
Starch granules are composed of two distinct glucose polymers - amylose and amylopectin. Amylose constitutes 5-35% of most natural starches and has a major influence over starch properties in foods. Its synthesis and storage occurs within the semicrystalline amylopectin matrix of starch granules, this poses a great challenge for biochemical and structural analyses. However, the last two decades have seen vast progress in understanding amylose synthesis, including new insights into the action of GRANULE BOUND STARCH SYNTHASE (GBSS), the major glucosyltransferase that synthesises amylose, and the discovery of PROTEIN TARGETING TO STARCH1 (PTST1) that targets GBSS to starch granules. Advances in analytical techniques have resolved the fine structure of amylose, raising new questions on how structure is determined during biosynthesis. Furthermore, the discovery of wild plants that do not produce amylose revives a long-standing question of why starch granules contain amylose, rather than amylopectin alone. Overall, these findings contribute towards a full understanding of amylose biosynthesis, structure and function that will be essential for future approaches to improve starch quality in crops.
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Affiliation(s)
- David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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19
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Sequence polymorphism of the waxy gene in waxy maize accessions and characterization of a new waxy allele. Sci Rep 2020; 10:15851. [PMID: 32985558 PMCID: PMC7522969 DOI: 10.1038/s41598-020-72764-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/07/2020] [Indexed: 01/05/2023] Open
Abstract
Waxy maize has many excellent characteristics in terms of its nutritional and economic value. In recent decades, the waxy maize germplasm has increased dramatically as a result of different selection methods. We collected 200 waxy maize inbred accessions from different origins to study their genetic diversity and phylogenetic relationships, and to identify new waxy mutations. A simple sequence repeat (SSR) analysis revealed wide genetic diversity among the 200 waxy maize accessions. The maize accessions were clustered into three groups. We sequenced the waxy gene from the first to the 14th exon. Nucleotide variation analysis of 167 waxy maize and 14 flint maize lines revealed some nucleotide differences in the waxy gene among different waxy maize groups, and much narrower nucleotide diversity in waxy maize than in flint maize. In a phylogenetic analysis, waxy maize carrying the same mutation allele clustered together, and waxy maize carrying different mutation alleles distributed in different groups; waxy maize was intermixed with flint maize in each branch, and wx-D7 waxy maize separated significantly from waxy maize lines carrying wx-D10, wx-124 and wx-hAT mutant alleles. The wx-hAT was a new waxy mutation identified in this study. It consisted of a 2286-bp transposon inserted into the middle of exon three of the waxy gene. A PCR marker specific for the wx-hAT allele was developed. These results will be useful for the utilization and preservation of the waxy maize germplasm, and the PCR marker has potential uses in waxy maize breeding programs.
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20
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Abstract
Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.
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Affiliation(s)
- Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place New York University, New York, NY, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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21
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Roy S, Banerjee A, Basak N, Bagchi TB, Mandal NP, Patra BC, Misra AK, Singh SK, Rathi RS, Pattanayak A. Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity. J Biosci 2020. [DOI: 10.1007/s12038-020-00059-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Seung D, Echevarría-Poza A, Steuernagel B, Smith AM. Natural Polymorphisms in Arabidopsis Result in Wide Variation or Loss of the Amylose Component of Starch. PLANT PHYSIOLOGY 2020; 182:870-881. [PMID: 31694903 PMCID: PMC6997676 DOI: 10.1104/pp.19.01062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/25/2019] [Indexed: 05/04/2023]
Abstract
Starch granules contain two Glc polymers, amylopectin and amylose. Amylose makes up approximately 10% to 30% (w/w) of all natural starches thus far examined, but mutants of crop and model plants that produce amylose-free starch are generally indistinguishable from their wild-type counterparts with respect to growth, starch content, and granule morphology. Since the function and adaptive significance of amylose are unknown, we asked whether there is natural genetic variation in amylose synthesis within a wild, uncultivated species. We examined polymorphisms among the 1,135 sequenced accessions of Arabidopsis (Arabidopsis thaliana) in GRANULE-BOUND STARCH SYNTHASE (GBSS), encoding the enzyme responsible for amylose synthesis. We identified 18 accessions that are predicted to have polymorphisms in GBSS that affect protein function, and five of these accessions produced starch with no or extremely low amylose (< 0.5% [w/w]). Eight further accessions had amylose contents that were significantly lower or higher than that of Col-0 (9% [w/w]), ranging from 5% to 12% (w/w). We examined the effect of the polymorphisms on GBSS function and uncovered three mechanisms by which GBSS sequence variation led to different amylose contents: (1) altered GBSS abundance, (2) altered GBSS activity, and (3) altered affinity of GBSS for binding PROTEIN TARGETING TO STARCH1-a protein that targets GBSS to starch granules. These findings demonstrate that amylose in leaves is not essential for the viability of some naturally occurring Arabidopsis genotypes, at least over short timescales and under some environmental conditions and open an opportunity to explore the adaptive significance of amylose.
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Affiliation(s)
- David Seung
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | | | | | - Alison M Smith
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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23
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Page A, Gibson J, Meyer RS, Chapman MA. Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence. Mol Biol Evol 2020; 36:1359-1372. [PMID: 31039581 DOI: 10.1093/molbev/msz062] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.
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Affiliation(s)
- Anna Page
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jane Gibson
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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25
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Zhang C, Zhu J, Chen S, Fan X, Li Q, Lu Y, Wang M, Yu H, Yi C, Tang S, Gu M, Liu Q. Wx lv, the Ancestral Allele of Rice Waxy Gene. MOLECULAR PLANT 2019; 12:1157-1166. [PMID: 31181338 DOI: 10.1016/j.molp.2019.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/28/2019] [Indexed: 05/07/2023]
Abstract
In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wxlv, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.
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Affiliation(s)
- Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jihui Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Shengjie Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiaolei Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yan Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Min Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Chuandeng Yi
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuzhu Tang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
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26
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Abstract
Rice is a staple crop for half the world's population, which is expected to grow by 3 billion over the next 30 years. It is also a key model for studying the genomics of agroecosystems. This dual role places rice at the centre of an enormous challenge facing agriculture: how to leverage genomics to produce enough food to feed an expanding global population. Scientists worldwide are investigating the genetic variation among domesticated rice species and their wild relatives with the aim of identifying loci that can be exploited to breed a new generation of sustainable crops known as Green Super Rice.
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27
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Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Burgarella C, Barnaud A, Kane NA, Jankowski F, Scarcelli N, Billot C, Vigouroux Y, Berthouly-Salazar C. Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation. FRONTIERS IN PLANT SCIENCE 2019; 10:4. [PMID: 30774638 PMCID: PMC6367218 DOI: 10.3389/fpls.2019.00004] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/04/2019] [Indexed: 05/18/2023]
Abstract
Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.
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Affiliation(s)
- Concetta Burgarella
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
| | - Adeline Barnaud
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Ndjido Ardo Kane
- Laboratoire National de Recherches sur les Productions Végétales, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
| | - Frédérique Jankowski
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UPR GREEN, Montpellier, France
- GREEN, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Université de Montpellier, Montpellier, France
- Bureau d’Analyses Macro-Economiques, Institut Sénégalais de Recherches Agricoles, Dakar, Senegal
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Claire Billot
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
| | - Cécile Berthouly-Salazar
- Institut de Recherche pour le Développement, UMR DIADE, Montpellier, France
- DIADE, Université de Montpellier, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Dakar, Senegal
- *Correspondence: Concetta Burgarella, Cécile Berthouly-Salazar,
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29
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Wang Y, Jiao A, Chen H, Ma X, Cui D, Han B, Ruan R, Xue D, Han L. Status and factors influencing on-farm conservation of Kam Sweet Rice (Oryza sativa L.) genetic resources in southeast Guizhou Province, China. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2018; 14:76. [PMID: 30497534 PMCID: PMC6267802 DOI: 10.1186/s13002-018-0256-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/15/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Kam Sweet Rice (KSR) is a special kind of rice landrace that has been cultivated for thousands of years in the borders of Guizhou, Hunan, and Guangxi Provinces of China, and is mainly distributed in southeast Guizhou Province of China currently. KSR has many unique qualities, including strong resistance to diseases, pests, and adverse abiotic conditions, difficulty of threshing, and well glutinous features. KSR germplasm resources are an indispensable material and cultural symbol in the production and daily life and customs of the Dong people. Related studies showed that numerous traditional KSR varieties and cultivation area of KSR decreased sharply from the Qing dynasty to 2015, but many KSR varieties are still conserved in Dong villages of southeast Guizhou Province compared to other areas. However, the number of KSR varieties that are conserved on farms in southeast Guizhou Province and factors influencing the erosion and conservation of KSR genetic resources is unclear. Therefore, this study was an on-farm conservation investigation of KSR genetic resource in China's major KSR producing areas-Liping, Congjiang, and Rongjiang counties in Guizhou Province and influencing factors analysis of KSR abandonment and conservation. METHODS The information of KSR conservation status and variety characteristics, typical villages, Dong's cultural customs, and factors influencing KSR abandonment and conservation was obtained using ethno-biology methods, mainly through field research interviews, including participatory observation, semi-structured interviews, key informant interviews, focus group discussions, and cultural anthropology. The altitude, plant height, awn color and length, hull color, and rice color of 156 KSR accessions in 28 villages were recorded. The variety quantity and cultivation area of KSR were investigated in 33 ethnic villages. Questionnaire surveys were conducted in typical Dong villages to obtain local farmers' attitudes toward cultivation and protection of KSR. We randomly selected 26 farmers from Sizhai village and 30 farmers from Huanggang village and chose 3 social characteristics including age, gender, and education levels of farmers, and adopted the method of face-to-face interviewing to complete the questionnaires. Then, we analyzed the correlation and determined the significance between farmers with different social characteristics and farmers' attitudes to KSR development and protection using SPSS 17.0 software. RESULTS (1) On-farm conservation status of KSR: a total of 156 KSR varieties were collected from 28 ethnic minority villages from 13 townships (accounting for 21% of three counties) in Liping, Congjiang, and Rongjiang counties. KSR accessions accounted for more than 90% of local rice varieties in each village. According to local farmers, although the quantity of KSR varieties decreased more than 50% in the investigated villages compared to the past 10-20 years, some Dong villages have still cultivated KSR, accounting for more than 50% of the rice field area in 10 villages. This result showed that many KSR varieties are still conserved by in Dong villages, and these KSR varieties have a high genetic diversity of phenotypes. (2) Typical villages investigation: the cultivation area of KSR in Congjiang was the highest, 6.7 times larger than Liping and eight times larger than Rongjiang. In addition, the cultivation area of KSR in Dong villages was larger than that in other ethnic villages, and villages that had a higher planting area of KSR had more KSR accessions. (3) Farmers' attitude toward the development and conservation of KSR: Dong farmers hold the negative attitudes concerning the development of KSR resources, but they thought it is necessary to protect KSR landraces. Especially, a high level of education and female, young, and old farmers played more important roles in the cultivation and protection of KSR. CONCLUSIONS Until now, some Dong ethnic villages have still cultivated KSR for thousands of years in Qiandongnan area, although the number of varieties and the planting area of KSR have been greatly reduced. In addition, ethnic traditional culture and social customs were the main influencing factors of KSR conservation; economic, management, and policy factors were the main influencing factors of KSR abandonment. Through the analysis of the correlation between farmers with different social characteristics and their attitudes toward the cultivation, reasons for conservation and abandonment, development tendency, and protection of KSR, we found that a high level of education and female, young, and old farmers play more important role in the cultivation and protection of KSR. Therefore, in order to promote the protection and sustainable utilization of KSR, it is necessary to build on-farm conservation of KSR and improve the position of female farmers and the education level of young people, and encourage the old people to educate the middle-aged to conserve and protect KSR as well as Dong's traditional culture and social customs. This study is of great significance to promote better protection and optimal utilization of KSR and enable the public, government, and related researchers pay more attention to conserving ethnic traditional cultures.
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Affiliation(s)
- Yanjie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Aixia Jiao
- Institute of Crop Germplasm Resources, Guizhou Academy of Agriculture Sciences, Guiyang, 550006 China
| | - Huicha Chen
- Institute of Crop Germplasm Resources, Guizhou Academy of Agriculture Sciences, Guiyang, 550006 China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Renchao Ruan
- Institute of Horticultural Research, Guizhou Academy of Agriculture Sciences, Guiyang, 550006 China
| | - Dayuan Xue
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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30
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Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S, Lin T, Tang J, Wang Y, Wang H, Lin H, Zhu B, Chen M, Kong F, Liu B, Zeng D, Jackson SA, Chu C, Tian Z. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet 2018; 50:1435-1441. [PMID: 30250128 DOI: 10.1038/s41588-018-0229-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 08/07/2018] [Indexed: 12/27/2022]
Abstract
Domesticated species often exhibit convergent phenotypic evolution, termed the domestication syndrome, of which loss of seed dormancy is a component. To date, dormancy genes that contribute to parallel domestication across different families have not been reported. Here, we cloned the classical stay-green G gene from soybean and found that it controls seed dormancy and showed evidence of selection during soybean domestication. Moreover, orthologs in rice and tomato also showed evidence of selection during domestication. Analysis of transgenic plants confirmed that orthologs of G had conserved functions in controlling seed dormancy in soybean, rice, and Arabidopsis. Functional investigation demonstrated that G affected seed dormancy through interactions with NCED3 and PSY and in turn modulated abscisic acid synthesis. Therefore, we identified a gene responsible for seed dormancy that has been subject to parallel selection in multiple crop families. This may help facilitate the domestication of new crops.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhen Li
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Xu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Lu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Tao Lin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongru Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
| | - Chengcai Chu
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers. Genes (Basel) 2018; 9:genes9090433. [PMID: 30158460 PMCID: PMC6162735 DOI: 10.3390/genes9090433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.
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Nakaew N, Sungthong R. Seed phytochemicals shape the community structures of cultivable actinobacteria-inhabiting plant interiors of Thai pigmented rice. Microbiologyopen 2018; 7:e00591. [PMID: 29575814 PMCID: PMC6079165 DOI: 10.1002/mbo3.591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 12/02/2022] Open
Abstract
We examined abundance, bioactivity, and endophytism of cultivable actinobacteria isolated from plant interiors of two Thai pigmented rice cultivars: Hom Nin (HN) rice and Luem Pua (LP) glutinous rice. Both rice cultivars housed the same amount of endophytic actinobacteria (33 isolates each). Microbispora (76%) and Streptomyces (73%) were the predominant endophytic actinobacteria of LP glutinous rice and HN rice, respectively. Sphaerisporangium (9%) was found only in LP glutinous rice. Twelve percent of endophytic actinobacteria was the possibility of discovering novel species from both rice cultivars. Most endophytic actinobacteria exhibited plant growth‐promoting potentials, including antimicrobial activity against test bacteria and phytopathogenic fungi, solubilization of phosphate, and production of biostimulants (i.e., ammonia, indole‐3‐acetic acid, and siderophore) and biocatalysts (i.e., amylase, cellulase, chitinase, lipase, and protease). Our findings revealed that seed phytochemicals of pigmented rice (e.g., anthocyanin, γ‐oryzanol, phytate, antioxidants, and content of amylose) were effectors, shaping the community structures and biofunctions of endophytic actinobacteria. We conclude that pigmented rice is yet a challenging source for discovery of bioactive and novel actinobacteria. This study also provides new insights into the plant‐endophyte interactions by which seed phytochemicals act as a primary checkpoint in the natural selection for establishing unique plant endophytomes.
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Affiliation(s)
- Nareeluk Nakaew
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Rungroch Sungthong
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
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33
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Kates HR, Soltis PS, Soltis DE. Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci. Mol Phylogenet Evol 2017; 111:98-109. [PMID: 28288944 DOI: 10.1016/j.ympev.2017.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/28/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
Abstract
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.
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Affiliation(s)
- Heather R Kates
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA.
| | - Pamela S Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Univ Florida, Genet Inst, Gainesville, FL 32611, USA; Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611, USA; Univ Florida, Dept Biol, Gainesville, FL 32611, USA
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Wei X, Jiao G, Lin H, Sheng Z, Shao G, Xie L, Tang S, Xu Q, Hu P. GRAIN INCOMPLETE FILLING 2 regulates grain filling and starch synthesis during rice caryopsis development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:134-153. [PMID: 27957808 DOI: 10.1111/jipb.12510] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/12/2016] [Indexed: 05/26/2023]
Abstract
Rice grain filling determines grain weight, final yield and grain quality. Here, a rice defective grain filling mutant, gif2, was identified. Grains of gif2 showed a slower filling rate and a significant lower final grain weight and yield compared to wild-type. The starch content in gif2 was noticeably decreased and its physicochemical properties were also altered. Moreover, gif2 endosperm cells showed obvious defects in compound granule formation. Positional cloning identified GIF2 to encode an ADP-glucose pyrophosphorylase (AGP) large subunit, AGPL2; consequently, AGP enzyme activity in gif2 endosperms was remarkably decreased. GIF2 is mainly expressed in developing grains and the coded protein localizes in the cytosol. Yeast two hybrid assay showed that GIF2 interacted with AGP small subunits OsAGPS1, OsAGPS2a and OsAGPS2b. Transcript levels for granule-bound starch synthase, starch synthase, starch branching enzyme and starch debranching enzyme were distinctly elevated in gif2 grains. In addition, the level of nucleotide diversity of the GIF2 locus was extremely low in both cultivated and wild rice. All of these results suggest that GIF2 plays important roles in the regulation of grain filling and starch biosynthesis during caryopsis development, and that it has been preserved during selection throughout domestication of modern rice.
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Affiliation(s)
- Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
| | - Qingguo Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou 310006, China
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Hebelstrup KH, Nielsen MM, Carciofi M, Andrzejczak O, Shaik SS, Blennow A, Palcic MM. Waxy and non-waxy barley cultivars exhibit differences in the targeting and catalytic activity of GBSS1a. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:931-941. [PMID: 28199682 PMCID: PMC5441850 DOI: 10.1093/jxb/erw503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Amylose synthesis is strictly associated with activity of granule-bound starch synthase (GBSS) enzymes. Among several crops there are cultivars containing starch types with either little or no amylose known as near-waxy or waxy. This (near) amylose-free phenotype is associated with a single locus (waxy) which has been mapped to GBSS-type genes in different crops. Most waxy varieties are a result of either low or no expression of a GBSS gene. However, there are some waxy cultivars where the GBSS enzymes are expressed normally. For these types, single nucleotide polymorphisms have been hypothesized to represent amino-acid substitutions leading to loss of catalytic activity. We here confirm that the HvGBSSIa enzyme from one such waxy barley variety, CDC_Alamo, has a 90% reduction in catalytic activity. We also engineered plants with expression of transgenic C-terminal green fluorescent protein-tagged HvGBSSIa of both the non-waxy type and of the CDC_Alamo type to monitor their subcellular localization patterns in grain endosperm. HvGBSSIa from non-waxy cultivars was found to localize in discrete concentric spheres strictly within starch granules. In contrast, HvGBSSIa from waxy CDC_Alamo showed deficient starch targeting mostly into unknown subcellular bodies of 0.5-3 µm in size, indicating that the waxy phenotype of CDC_Alamo is associated with deficient targeting of HvGBSSIa into starch granules.
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Affiliation(s)
- Kim H Hebelstrup
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | | | - Massimiliano Carciofi
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 København V, Denmark
| | - Olga Andrzejczak
- Department of Molecular Biology and Genetics, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Shahnoor Sultana Shaik
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Monica M Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 København V, Denmark
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Wu M, Lewis J, Moore RC. A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya). AMERICAN JOURNAL OF BOTANY 2017; 104:116-126. [PMID: 28082282 DOI: 10.3732/ajb.1600301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya. METHODS We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region. KEY RESULTS Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates. CONCLUSIONS Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.
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Affiliation(s)
- Meng Wu
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Jamicia Lewis
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104 USA
| | - Richard C Moore
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
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37
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Chin HS, Wu YP, Hour AL, Hong CY, Lin YR. Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice. RICE (NEW YORK, N.Y.) 2016; 9:8. [PMID: 26922355 PMCID: PMC4769704 DOI: 10.1186/s12284-016-0080-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/19/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND Anthocyanin accumulates in many plant tissues or organs, in rice for example leading to red, purple red and purple phenotypes for protection from damage by biotic and abiotic stresses and for reproduction. Purple leaf, leaf sheath, stigma, pericarp, and apiculus are common in wild rice and landraces and occasionally found in modern cultivars. No gene directly conferring anthocyanin deposited in a purple leaf sheath has yet been isolated by using natural variants. An F2 population derived from ssp. japonica cv. Tainung 72 (TNG72) with purple leaf sheath (PSH) crossed with ssp. indica cv. Taichung Sen 17 (TCS17) with green leaf sheath (GSH) was utilized to isolate a gene conferring leaf sheath color. RESULTS By positional cloning, 10-and 3-bp deletions in the R2R3 Myb domain of OsC1 were uncovered in GSH varieties TCS17 and Nipponbare, respectively. Allelic diversity, rather than gene expression levels of OsC1, might be responsible for anthocyanin accumulation. Parsimony-based analysis of genetic diversity in 50 accessions, including cultivars, landraces, and A-genome wild rice, suggests that independent mutation occurred in Asian, African, South American, and Australian species, while O. meridionalis had a divergent sequence. OsC1 was thought of as a domestication related gene, with up to 90 % reduction of genetic diversity in GSH; however, no values from three tests showed significant differences from neutral expectations, implying that OsC1 had not been subjected to recent selection. Haplotype network analysis revealed that species from different continents formed unique haplotypes with no gene flow. Two major groups of haplotypes corresponding to 10-bp deletion and other sequences were formed in Asian rice, including O. rufipogon, O. nivara and O. sativa. Introgressions of OsC1 between subspecies through natural and artificial hybridization were not rare. Because artificial and natural selection imposed admixture on rice germplasm in Taiwan, the genealogy of OsC1 might not be congruent with the current distribution of alleles through lineage diversification. CONCLUSION OsC1 is responsible for purple leaf sheath, and much new information about OsC1 is provided e.g., new alleles, non-domestication syndrome, and incongruence of genealogy with geographic distribution.
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Affiliation(s)
- Han-shiuan Chin
- />Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yong-pei Wu
- />Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Ai-ling Hour
- />Department of Life Science, Fu-Jen Catholic University, Xinbei, Taiwan
| | - Chwan-yang Hong
- />Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yann-rong Lin
- />Department of Agronomy, National Taiwan University, Taipei, Taiwan
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38
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Shahid S, Begum R, Razzaque S, Jesmin, Seraj ZI. Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele. J Cereal Sci 2016. [DOI: 10.1016/j.jcs.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. BREEDING SCIENCE 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
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40
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Zhang P, Zhong K, Shahid MQ, Tong H. Association Analysis in Rice: From Application to Utilization. FRONTIERS IN PLANT SCIENCE 2016; 7:1202. [PMID: 27582745 PMCID: PMC4987372 DOI: 10.3389/fpls.2016.01202] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/28/2016] [Indexed: 05/03/2023]
Abstract
Association analysis based on linkage disequilibrium (LD) is an efficient way to dissect complex traits and to identify gene functions in rice. Although association analysis is an effective way to construct fine maps for quantitative traits, there are a few issues which need to be addressed. In this review, we will first summarize type, structure, and LD level of populations used for association analysis of rice, and then discuss the genotyping methods and statistical approaches used for association analysis in rice. Moreover, we will review current shortcomings and benefits of association analysis as well as specific types of future research to overcome these shortcomings. Furthermore, we will analyze the reasons for the underutilization of the results within association analysis in rice breeding.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- *Correspondence: Peng Zhang
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- Hanhua Tong
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41
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Guzmán C, Alvarez JB. Wheat waxy proteins: polymorphism, molecular characterization and effects on starch properties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1-16. [PMID: 26276148 DOI: 10.1007/s00122-015-2595-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/05/2015] [Indexed: 05/21/2023]
Abstract
The starch fraction, comprising about 70% of the total dry matter in the wheat grain, can greatly affect the end-use quality of products made from wheat kernels, especially Asian noodles. Starch is associated with the shelf life and nutritional value (glycaemic index) of different wheat products. Starch quality is closely associated with the ratio of amylose to amylopectin, the two main macromolecules forming starch. In this review, we briefly summarise the discovery of waxy proteins-shown to be the sole enzymes responsible for amylose synthesis in wheat. The review particularly focuses on the different variants of these proteins, together with their molecular characterisation and evaluation of their effects on starch composition. There have been 19 different waxy protein variants described using protein electrophoresis; and at a molecular level 19, 15 and seven alleles described for Wx-A1, Wx-B1 and Wx-D1, respectively. This large variability, found in modern wheat and genetic resources such as wheat ancestors and wild relatives, is in some cases not properly ordered. The proper ordering of all the data generated is the key to enhancing use in breeding programmes of the current variability described, and thus generating wheat with novel starch properties to satisfy the demand of industry and consumers for novel high-quality processed food.
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Affiliation(s)
- Carlos Guzmán
- CIMMYT. Global Wheat Program, Km 45 Carretera México-Veracruz, El Batán, C.P. 56237, Texcoco, Estado De México, Mexico.
| | - Juan B Alvarez
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
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Mascagni F, Barghini E, Giordani T, Rieseberg LH, Cavallini A, Natali L. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes. Genome Biol Evol 2015; 7:3368-82. [PMID: 26608057 PMCID: PMC4700961 DOI: 10.1093/gbe/evv230] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.
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Affiliation(s)
- Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Loren H Rieseberg
- The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa, Italy
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Pathak N, Bhaduri A, Bhat KV, Rai AK. Tracking sesamin synthase gene expression through seed maturity in wild and cultivated sesame species--a domestication footprint. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1039-46. [PMID: 25754459 DOI: 10.1111/plb.12327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/02/2015] [Indexed: 05/24/2023]
Abstract
Sesamin and sesamolin are the major oil-soluble lignans present in sesame seed, having a wide range of biological functions beneficial to human health. Understanding sesame domestication history using sesamin synthase gene expression could enable delineation of the sesame putative progenitor. This report examined the functional expression of sesamin synthase (CYP81Q1) during capsule maturation (0-40 days after flowering) in three wild Sesamum species and four sesame cultivars. Among the cultivated accessions, only S. indicum (CO-1) exhibited transcript abundance of sesamin synthase along with high sesamin content similar to S. malabaricum, while the other cultivated sesame showed low expression. The sesamin synthase expression analysis, coupled with quantification of sesamin level, indicates that sesamin synthase was not positively favoured during domestication. The sesamin synthase expression pattern and lignan content, along with phylogenetic analysis suggested a close relationship of cultivated sesame and the wild species S. malabaricum. The high genetic identity between the two species S. indicum and S. malabaricum points towards the role of the putative progenitor S. malabaricum in sesame breeding programmes to broaden the genetic base of sesame cultivars. This study emphasises the need to investigate intraspecific and interspecific variation in the primary, secondary and tertiary gene pools to develop superior sesame genotypes.
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Affiliation(s)
- N Pathak
- Centre for Advanced Study in Botany, Banaras Hindu University, Varanasi, India
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, India
| | - A Bhaduri
- Cluster Innovation Centre, University of Delhi, New Delhi, India
| | - K V Bhat
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, India
| | - A K Rai
- Centre for Advanced Study in Botany, Banaras Hindu University, Varanasi, India
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Klein RR, Miller FR, Dugas DV, Brown PJ, Burrell AM, Klein PE. Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1669-83. [PMID: 25982128 DOI: 10.1007/s00122-015-2523-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/17/2015] [Indexed: 05/16/2023]
Abstract
Allele phylogenetic analysis of the sorghum flowering-time gene PRR37 provided new insight into the human-mediated selection of a key adaptive gene that occurred during sorghum's diversification and worldwide dispersal. The domestication and spread of the tropical cereal sorghum is associated with the historic movement of humans. We show that an allelic series at PRR37 (pseudo-response regulator 37), a circadian clock-associated transcription factor, was selected in long-day ecosystems worldwide to permit floral initiation and grain production. We identified a series of loss-of-function (photoperiod-insensitive) alleles encoding truncated PRR37 proteins, alleles with key amino acid substitutions in the pseudo-receiver domain, and a novel splice variant in which the pseudo-receiver domain is truncated. Each PRR37 allelic variant was traced to a specific geographic location or specialized agronomic type. We present a graphical model that shows evidence of human selection and gene flow of the PRR37 allelic variants during the global dispersal and agronomic diversification of sorghum. With the recent identification of the Ghd7 gene as an important regulator of flowering date in sorghum, we briefly examine whether loss-of-function Ghd7 allelic variants were selected prior to the human-mediated movement of sorghum from its equatorial center of origin to temperate climates worldwide.
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Affiliation(s)
- Robert R Klein
- United States Department of Agriculture-Agricultural Research Service, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA
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Rao ES, Kadirvel P, Symonds RC, Geethanjali S, Thontadarya RN, Ebert AW. Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium). PLoS One 2015; 10:e0132535. [PMID: 26161546 PMCID: PMC4498769 DOI: 10.1371/journal.pone.0132535] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/15/2015] [Indexed: 12/23/2022] Open
Abstract
Association analysis was conducted in a core collection of 94 genotypes of Solanum pimpinellifolium to identify variations linked to salt tolerance traits (physiological and yield traits under salt stress) in four candidate genes viz., DREB1A, VP1.1, NHX1, and TIP. The candidate gene analysis covered a concatenated length of 4594 bp per individual and identified five SNP/Indels in DREB1A and VP1.1 genes explaining 17.0% to 25.8% phenotypic variation for various salt tolerance traits. Out of these five alleles, one at 297 bp in DREB1A had in-frame deletion of 6 bp (CTGCAT) or 12 bp (CTGCATCTGCAT), resulting in two alleles, viz., SpDREB1A_297_6 and SpDREB1A_297_12. These alleles individually or as haplotypes accounted for maximum phenotypic variance of about 25% for various salt tolerance traits. Design of markers for selection of the favorable alleles/haplotypes will hasten marker-assisted introgression of salt tolerance from S. pimpinellifolium into cultivated tomato.
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Affiliation(s)
- Eguru Sreenivasa Rao
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
- Genetic Resources and Seed Unit, AVRDC–The World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Palchamy Kadirvel
- Crop Improvement Section, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, India
- Genetic Resources and Seed Unit, AVRDC–The World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Rachael C. Symonds
- School of Biosciences, The University of Nottingham Malaysia Campus, Jalan Broga, Semenyih, Selangor, Darul Ehsan, Malaysia
- Genetic Resources and Seed Unit, AVRDC–The World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Subramaniam Geethanjali
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
- Genetic Resources and Seed Unit, AVRDC–The World Vegetable Center, Shanhua, Tainan, Taiwan
| | | | - Andreas W. Ebert
- Genetic Resources and Seed Unit, AVRDC–The World Vegetable Center, Shanhua, Tainan, Taiwan
- * E-mail: (AWE)
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Hong L, Zhuo J, Lei Q, Zhou J, Ahmed S, Wang C, Long Y, Li F, Long C. Ethnobotany of wild plants used for starting fermented beverages in Shui communities of southwest China. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2015; 11:42. [PMID: 26017691 PMCID: PMC4458060 DOI: 10.1186/s13002-015-0028-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/01/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Shui communities of southwest China have an extensive history of using wild plants as starters (Xiaoqu) to prepare fermented beverages that serve important roles in interpersonal relationships and cultural events. While the practice of using wild plants as starters for the preparation of fermented beverages was once prevalent throughout China, this tradition has seen a decline nationally since the 1930s. The traditional technique of preparing fermented beverages from wild plant starters remains well preserved in the Shui communities in southwest China and provides insight on local human-environment interactions and conservation of plant biodiversity for cultural purposes. The present study sought to examine the ethnobotany of wild plants used as starters for the preparation of fermented beverages including an inventory of plants used as a starter in liquor fermentation and associated knowledge and practices. METHODS Field surveys were carried out that consisted of semi-structured surveys and plant species inventories. One hundred forty-nine informants in twenty Shui villages were interviewed between July 2012 and October 2014 to document knowledge associated with wild plants used as a liquor fermentation starter. The inventories involved plant voucher specimens and taxonomic identification of plant collections. RESULTS A total of 103 species in 57 botanical families of wild plants were inventoried and documented that are traditionally used as starters for preparing fermented beverages by Shui communities. The majority of the species (93.2%) have multiple uses in addition to being used as a starter with medicinal purposes being the most prevalent. Shui women are the major harvesters and users of wild plants used as starters for preparing fermented beverages and transfer knowledge orally from mother to daughter. CONCLUSIONS Findings from this study can serve as a basis for future investigation on fermented beverages and foods and associated knowledge and cultural practices. However, with rapid development, utilization of wild plants and the cultural systems that support them are at risk of erosion. Cultural preservation practices are necessary in Shui communities for the continued use and transmission of this ethnobiological knowledge as well as associated biodiversity.
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Affiliation(s)
- Liya Hong
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, People's Republic of China.
| | - Jingxian Zhuo
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China.
- School of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, People's Republic of China.
| | - Qiyi Lei
- School of Environment & Life Science, Kaili University, Guizhou, 556011, People's Republic of China.
| | - Jiangju Zhou
- School of Environment & Life Science, Kaili University, Guizhou, 556011, People's Republic of China.
| | - Selena Ahmed
- Department of Health & Human Development, Montana State University, Bozeman, MT, 59717, USA.
| | - Chaoying Wang
- School of Chemistry and Life Science, Guizhou Normal College, Guiyang, 550018, People's Republic of China.
| | - Yuxiao Long
- Guizhou Institute for Advanced Study in Anthropology & Ethnology, Guizhou Normal College, Guiyang, 550018, People's Republic of China.
| | - Feifei Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, People's Republic of China.
| | - Chunlin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, People's Republic of China.
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China.
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Eslami Farouji A, Khodayari H, Saeidi H, Rahiminejad MR. Genetic diversity of diploid Triticum species in Iran assessed using inter-retroelement amplified polymorphisms (IRAP) markers. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Choudhury BI, Khan ML, Dayanandan S. Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene. BMC Res Notes 2014; 7:953. [PMID: 25547027 PMCID: PMC4320456 DOI: 10.1186/1756-0500-7-953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 12/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. FINDINGS The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. CONCLUSION The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.
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Affiliation(s)
- Baharul I Choudhury
- Biology Department, Forest and Evolutionary Genomics Laboratory, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St, West, Montreal, Quebec H4B 1R6, Canada.
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Phung NTP, Mai CD, Mournet P, Frouin J, Droc G, Ta NK, Jouannic S, Lê LT, Do VN, Gantet P, Courtois B. Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC PLANT BIOLOGY 2014; 14:371. [PMID: 25524444 PMCID: PMC4279583 DOI: 10.1186/s12870-014-0371-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/08/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes. RESULTS The panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel. CONCLUSIONS This publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits.
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Affiliation(s)
- Nhung Thi Phuong Phung
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
| | - Chung Duc Mai
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | | | | | - Gaëtan Droc
- />Cirad, UMR-AGAP, 34398 Montpellier, France
| | - Nhung Kim Ta
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
- />IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, 34095 Montpellier, France
| | | | | | - Vinh Nang Do
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, Hanoi, Vietnam
| | - Pascal Gantet
- />IRD, UMR-DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, 34095 Montpellier, France
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
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Ootsuka K, Takahashi I, Tanaka K, Itani T, Tabuchi H, Yoshihashi T, Tonouchi A, Ishikawa R. Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan. BREEDING SCIENCE 2014; 64:115-124. [PMID: 24987297 PMCID: PMC4065318 DOI: 10.1270/jsbbs.64.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 02/07/2014] [Indexed: 05/30/2023]
Abstract
Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.
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Affiliation(s)
- Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ikuya Takahashi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Katsunori Tanaka
- Faculty of Humanity, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Tomio Itani
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima,
Shobara, Hiroshima 727-0023,
Japan
| | - Hiroaki Tabuchi
- Upland Farming Research Division, Miyakonojo Research Station, NARO Kyushu Okinawa Agricultural Research Center,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
| | - Tadashi Yoshihashi
- Post harvest Science and Technology Division, Japan International Research Center for Agricultural Sciences,
Tsukuba, Ibaraki 305-8686,
Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
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