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Nawade B, Shim SH, Chu SH, Zhao W, Lee SK, Somsri A, Maung TZ, Kang KK, Kim JY, Lee CY, Kim MS, Baik MY, Jeon JS, Park YJ. Integrative transcriptogenomic analyses reveal the regulatory network underlying rice eating and cooking quality and identify a role for alpha-globulin in modulating starch and sucrose metabolism. PLANT COMMUNICATIONS 2025; 6:101287. [PMID: 39980198 DOI: 10.1016/j.xplc.2025.101287] [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: 03/28/2024] [Revised: 12/03/2024] [Accepted: 02/18/2025] [Indexed: 02/22/2025]
Abstract
Rice eating and cooking quality (ECQ) is significantly influenced by the physicochemical properties of rice starch. This study integrates whole-genome resequencing, transcriptomic data, and phenotypic analysis to identify the genetic factors that regulate transcript expression levels and contribute to phenotypic variation in rice ECQ traits. A TWAS (transcriptome-wide association study) identified 285 transcripts linked to 6 ECQ traits. Genome-wide mapping of these transcripts revealed 21 747 local eQTLs (expression quantitative trait loci) and 45 158 distal eQTLs. TWAS and eQTL analysis detected several known and novel genes, including starch synthesis-related genes, heat shock proteins, transcription factors, genes related to ATP accumulation, and UDP-glucosyltransferases, showcasing the complex genetic regulation of rice ECQ. WGCNA (weighted gene co-expression network analysis) uncovered key co-expression networks, including a module that links alpha-globulin1 (GLB1) to starch and sucrose metabolism. Genetic diversity analysis of the GLB1 gene across a Korean rice collection identified 26 haplotypes, with indica and aus forming 7 and 3 haplotypes, respectively, which showed significant phenotypic effects on ECQ traits. CRISPR-Cas9-created knockout lines validated these findings, demonstrating that loss of GLB1 function caused significant changes in seed storage proteins, reduced amylose content, altered starch granules, and modified pasting properties without affecting plant phenotypes. By integrating TWAS, eQTL mapping, haplotype analysis, gene expression networks, and CRISPR validation, this study establishes GLB1 as a regulator of ECQ, linking starch biosynthesis and protein accumulation pathways. This transcriptogenomic convergence approach provides novel insights into the genetic regulation of ECQ in rice, demonstrating its effectiveness for characterizing complex traits and enabling precision breeding.
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Affiliation(s)
- Bhagwat Nawade
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea
| | - Su-Hyeon Shim
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Sang-Ho Chu
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea
| | - Weiguo Zhao
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea; School of Biotechnology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang, Jiangsu 212100, P.R. China
| | - Sang-Kyu Lee
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Anseong 17579, Republic of Korea
| | - Jae Yoon Kim
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, Kongju National University, Cheonan 31080, Republic of Korea
| | - Min-Seok Kim
- Department of Food Science and Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Moo-Yeol Baik
- Department of Food Science and Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Yong-Jin Park
- Department of Plant Resources, Kongju National University, Yesan 32439, Republic of Korea.
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Li X, Yang X, Yang L, Muhu-Din Ahmed HG, Yao C, Yang J, Wang L, Yang T, Pu X, Zeng Y. Evolution and association analysis of SSIIIa in rice landraces of Yunnan Province. Biologia (Bratisl) 2024; 79:2203-2211. [DOI: 10.1007/s11756-024-01705-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/03/2024] [Indexed: 11/07/2024]
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3
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Shi S, Ma Y, Zhao D, Li L, Cao C, Jiang Y. The differences in metabolites, starch structure, and physicochemical properties of rice were related to the decrease in taste quality under high nitrogen fertilizer application. Int J Biol Macromol 2023; 253:126546. [PMID: 37643670 DOI: 10.1016/j.ijbiomac.2023.126546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/30/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Nitrogen fertilizer application is one of the key cultivation practices to improve rice yields. However, the application of high nitrogen fertilizers often leads to a reduction in the stickiness of the rice after cooking, thus reducing the taste quality of rice. Moreover, there are differences in taste quality among rice varieties, and the mechanism has not been studied in depth. In this study, two rice varieties (Meixiangzhan2hao and Exiang2hao) were planted under two nitrogen fertilizer levels. The physicochemical properties and taste quality of the rice were determined after maturity. Our results showed that high nitrogen fertilizer level alters tryptophan metabolism in rice, increasing most amino acid content and protein content in rice. The high content of protein and the higher short-range ordered structure of starch inhibited the gelatinization characteristics of starch and reduced the taste quality of rice. Under high nitrogen fertilizer application, Exiang2hao showed smaller increases in protein content, lower level of amylose and relative crystallinity, and higher content of lipid metabolites. These differences in chemical substances resulted in a less pronounced reduction in the taste quality of Exiang2hao. In this study, the taste quality of different rice varieties under different levels of nitrogen fertilizer application was analyzed, providing new ideas for future improvement of rice taste quality.
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Affiliation(s)
- Shijie Shi
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Yingying Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Dan Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Lina Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cougui Cao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan 430070, China.
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4
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Gann PJI, Dharwadker D, Cherati SR, Vinzant K, Khodakovskaya M, Srivastava V. Targeted mutagenesis of the vacuolar H + translocating pyrophosphatase gene reduces grain chalkiness in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1261-1276. [PMID: 37256847 DOI: 10.1111/tpj.16317] [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: 12/16/2022] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
Grain chalkiness is a major concern in rice production because it impacts milling yield and cooking quality, eventually reducing market value of the rice. A gene encoding vacuolar H+ translocating pyrophosphatase (V-PPase) is a major quantitative trait locus in indica rice, controlling grain chalkiness. Higher transcriptional activity of this gene is associated with increased chalk content. However, whether the suppression of V-PPase could reduce chalkiness is not clear. Furthermore, natural variation in the chalkiness of japonica rice has not been linked with V-PPase. Here, we describe promoter targeting of the japonica V-PPase allele that led to reduced grain chalkiness and the development of more translucent grains. Disruption of a putative GATA element by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 suppressed V-PPase activity, reduced grain chalkiness and impacted post-germination growth that could be rescued by the exogenous supply of sucrose. The mature grains of the targeted lines showed a much lower percentage of large or medium chalk. Interestingly, the targeted lines developed a significantly lower chalk under heat stress, a major inducer of grain chalk. Metabolomic analysis showed that pathways related to starch and sugar metabolism were affected in the developing grains of the targeted lines that correlated with higher inorganic pyrophosphate and starch contents and upregulation of starch biosynthesis genes. In summary, we show a biotechnology approach of reducing grain chalkiness in rice by downregulating the transcriptional activity of V-PPase that presumably leads to altered metabolic rates, including starch biosynthesis, resulting in more compact packing of starch granules and formation of translucent rice grains.
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Affiliation(s)
- Peter James Icalia Gann
- Cell and Molecular Biology Program, University of Arkansas, 115 Plant Science Building, Fayetteville, AR, 72701, USA
- Department of Crop, Soil and Environmental Sciences, University of Arkansas Division of Agriculture, 115 Plant Science Building, Fayetteville, AR, 72701, USA
| | - Dominic Dharwadker
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, West Maple Street, AR, 72701, USA
| | - Sajedeh Rezaei Cherati
- Department of Biology, University of Arkansas Little Rock, 2801 S University Avenue, Little Rock, AR, 727704, USA
| | - Kari Vinzant
- Department of Biology, University of Arkansas Little Rock, 2801 S University Avenue, Little Rock, AR, 727704, USA
| | - Mariya Khodakovskaya
- Department of Biology, University of Arkansas Little Rock, 2801 S University Avenue, Little Rock, AR, 727704, USA
| | - Vibha Srivastava
- Cell and Molecular Biology Program, University of Arkansas, 115 Plant Science Building, Fayetteville, AR, 72701, USA
- Department of Crop, Soil and Environmental Sciences, University of Arkansas Division of Agriculture, 115 Plant Science Building, Fayetteville, AR, 72701, USA
- Department of Horticulture, University of Arkansas Division of Agriculture, 315 Plant Science Building, Fayetteville, AR, 72701, USA
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Zhou J, Li W, Yang Y, Xie X, Liu J, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, He Y, Ren Y, Tang L, Gou L, Zheng Y, Wei Y, Ma J. A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for the number of spikelets per spike of wheat shows no adverse effects on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:181. [PMID: 37550493 DOI: 10.1007/s00122-023-04429-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023]
Abstract
KEY MESSAGE A likely new locus QSns.sau-MC-3D.1 associated with SNS showing no negative effect on yield-related traits compared to WAPO1 was identified and validated in various genetic populations under multiple environments. The number of spikelets per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop wheat varieties with higher yield. In this study, a recombinant inbred line (RIL) population (MC) containing 198 lines derived from a cross between msf and Chuannong 16 (CN16) was used to construct a genetic linkage map using the GenoBaits Wheat 16 K Panel. The genetic map contained 5,991 polymorphic SNP markers spanning 2,813.25 cM. A total of twelve QTL for SNS were detected, and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one, and two kompetitive allele-specific PCR (KASP) markers were further developed. The positive effect of QSns.sau-MC-3D.1 was also validated in three biparental populations and a diverse panel containing 388 Chinese wheat accessions. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. Pyramiding of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. Correlation analysis suggested that QSns.sau-MC-3D.1 was likely independent of effective tiller number, plant height, spike length, anthesis date, and thousand kernel weight. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. These results indicated that utilization of QSns.sau-MC-3D.1 should be given priority for wheat breeding. Geographical distribution analysis showed that the positive allele of QSns.nsau-MC-3D.1 was dominant in most wheat-producing regions of China, and it has been positively selected among modern cultivars released in China since the 1940s. Gene prediction, qRT-PCR analysis, and sequence alignment suggested that TraesCS3D03G0216800 may be the candidate gene of QSns.nsau-MC-3D.1. Taken together, these results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of the gene underlying QSns.sau-MC-3D.1.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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6
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Sharma V, Jahan K, Kumar P, Puri A, Sharma VK, Mishra A, Bharatam PV, Sharma D, Rishi V, Roy J. Mechanistic insights into granule-bound starch synthase I (GBSSI.L539P) allele in high amylose starch biosynthesis in wheat (Triticum aestivum L.). Funct Integr Genomics 2022; 23:20. [PMID: 36564499 DOI: 10.1007/s10142-022-00923-y] [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: 07/18/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Amylose fraction of grain starch is correlated with a type of resistant starch with better nutritional quality. Granule-bound starch synthase I (GBSSI) is the known starch synthase, responsible for elongation of linear amylose chains. GBSSI expression, activity, and binding to starch and other proteins are the key factors that can affect amylose content. Previously, a QTL, qhams7A.1 carrying GBSSI mutant allele, was identified through QTL mapping using F2 population of the high amylose mutant line, 'TAC 75'. This high amylose mutant line has >2-fold higher amylose content than wild variety 'C 306'. In this study, we characterized this novel mutant allele, GBSSI.L539P. In vitro starch synthase activity of GBSSI.L539P showed improved activity than the wild type (GBSSI-wt). When expressed in yeast glycogen synthase mutants (Δgsy1gsy2), GBSSI-wt and GBSSI.L539P partially complemented the glycogen synthase (gsy1gsy2) activity in yeast. Structural analysis by circular dichroism (CD) and homology modelling showed no significant structural distortion in the mutant enzyme. Molecular docking studies suggested that the residue Leu539 is distant from the catalytic active site (ADP binding pocket) and had no detectable conformational changes in active site. Both wild and mutant enzymes were assayed for starch binding in vitro, and demonstrating higher affinity of the GBSSI.L539P mutant for starch than the wild type. The present study indicated that distant residue (L539P) influenced GBSSI activity by affecting its starch-binding ability. Therefore, it may be a potential molecular target for enhanced amylose content in grain.
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Affiliation(s)
- Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education & Research (IISER) Mohali, SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Prashant Kumar
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Anuradhika Puri
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vishnu K Sharma
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - P V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Deepak Sharma
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), SAS Nagar, Sector-81, Mohali, 140306, Punjab, India.
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7
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Rahim MS, Kumar V, Roy J. Genetic dissection of quantitative traits loci identifies new genes for gelatinization parameters of starch and amylose-lipid complex (Resistant starch 5) in bread wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111452. [PMID: 36087884 DOI: 10.1016/j.plantsci.2022.111452] [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: 06/13/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Starch is a major component of cereal grains such as wheat. Physicochemical and functional properties of starch affect end-use food quality and nutrients. To improve cultivars that preserve superior starch quality, the genetic foundation of the wheat starch and amylose-lipid complex (ALc, Resistant starch type 5) gelatinization are needed. This genome-wide association (GWA) mapping used 192 wheat genotypes (previously reported) to generate SNPs using an enhanced version of sequencing termed ddRAD on the Illumina Hi-seq X platform and 3696 high-quality influential SNPs were filtered out. The heterozygosity and Fst ranges in five subpopulations were 0.31-0.40 and 0.18-0.30 respectively. Nucleotide diversity and PIC ranged from 0.21 (6A) to 0.32 (2A) and 0.29 (6A) to 0.39 (4D) respectively. The Shannon waiver index was 1.7 and the whole-genome LD decay was 22 Mb at r2 = 0.38. Following FDR, 23 and 8 SNPs showed association with starch properties in the year 2017 and 2018, respectively while 93 and 20 SNPs were associated with ALc gelatinization in the year 2017 and 2018 respectively. The identified potential new genes (GSK3-alpha, RING-type domain-containing protein, Tetratricopeptide repeat, Hexosyltransferase, GLP, SNF1, and WRKY transcription factor) within LD range (∼16 Kb to ∼15 Mb), BLUP value, and cis and trans-position of SNPs network provide valuable information for the future wheat breeding strategy for the improvement of the starch quality trait.
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Affiliation(s)
- Mohammed Saba Rahim
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Vinay Kumar
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda.
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali-140 306, Punjab, India.
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Zhou Y, Cheng Z, Jiang S, Cen J, Wu D, Shu X. High temperature boosts resistant starch content by altering starch structure and lipid content in rice ssIIIa mutants. FRONTIERS IN PLANT SCIENCE 2022; 13:1059749. [PMID: 36466223 PMCID: PMC9715984 DOI: 10.3389/fpls.2022.1059749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/21/2022] [Indexed: 06/12/2023]
Abstract
High temperature (HT) during grain filling had adverse influences on starch synthesis. In this study, the influences of HT on resistant starch (RS) formation in rice were investigated. Most genes in ssIIIa mutants especially in RS4 were upregulated under Normal Temperature (NT) while downregulated under HT when compared with those of wild parent R7954. ssIIIa mutants had higher RS content, more lipid accumulation, higher proportion of short chains of DP 9-15, and less long chains of DP ≥37. ssIIIa mutation exacerbated the influences of HT on starch metabolite and caused larger declines in the expression of BEI, BEIIa, BEIIb, and SSIVb when exposed to HT. HT reduced the contents of total starch and apparent amylose significantly in wild type but not in mutants. Meanwhile, lipids were enriched in all varieties, but the amounts of starch-lipid complexes and the RS content were only heightened in mutants under HT. HT led to greatest declines in the amount of DP 9-15 and increases in the proportion of fb3 (DP ≥37); the declines and increases were all larger in mutants, which resulted in varied starch crystallinity. The increased long-chain amylopectin and lipids may be the major contributor for the elevated RS content in mutants under HT through forming more starch-lipid complexes (RSV).
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Affiliation(s)
- Yufeng Zhou
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Zhenfeng Cheng
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Shuo Jiang
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Jinxi Cen
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
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9
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Lee SK, Lee J, Jo M, Jeon JS. Exploration of Sugar and Starch Metabolic Pathway Crucial for Pollen Fertility in Rice. Int J Mol Sci 2022; 23:ijms232214091. [PMID: 36430574 PMCID: PMC9695277 DOI: 10.3390/ijms232214091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Starch is the primary storage carbohydrate in mature pollen grains in many crop plants, including rice. Impaired starch accumulation causes male sterility because of the shortage of energy and building blocks for pollen germination and pollen tube growth. Thus, starch-defective pollen is applicable for inducing male sterility and hybrid rice production. Despite the importance of pollen starch, the details of the starch biosynthesis and breakdown pathway in pollen are still largely unknown. As pollen is isolated from the maternal tissue, photoassimilate transported from leaves must pass through the apoplastic space from the anther to the filial pollen, where it is stored as starch. Several sugar transporters and enzymes are involved in this process, but many are still unknown. Thus, the current review provides possible scenarios for sucrose transport and metabolic pathways that lead to starch biosynthesis and breakdown in rice pollen.
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Affiliation(s)
- Sang-Kyu Lee
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
- Correspondence: (S.-K.L.); (J.-S.J.)
| | - Juho Lee
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Mingyu Jo
- Division of Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Correspondence: (S.-K.L.); (J.-S.J.)
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10
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Zhou H, Wang B, Liu Y, Ouyang L, Zhou D, He H, Liu J, Hu J, He X. Effects of Four Non‐synonymous SNPs of
SSIIa
Gene on Amylopectin Structure and Gelatinization Characteristics in Rice. STARCH-STARKE 2022. [DOI: 10.1002/star.202100198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Huiying Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences / Jiangxi Provincial Crop Germplasm Resources Research Center Nanchang 330200 China
| | - Bingqing Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
| | - Yantong Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences / Jiangxi Provincial Crop Germplasm Resources Research Center Nanchang 330200 China
| | - Jiaxiao Hu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences / Jiangxi Provincial Crop Germplasm Resources Research Center Nanchang 330200 China
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy Jiangxi Agricultural University Nanchang 330045 China
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11
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Wang S, Gao S, Nie J, Tan X, Xie J, Bi X, Sun Y, Luo S, Zhu Q, Geng J, Liu W, Lin Q, Cui P, Hu S, Wu S. Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics. FRONTIERS IN PLANT SCIENCE 2022; 12:769700. [PMID: 35126409 PMCID: PMC8813773 DOI: 10.3389/fpls.2021.769700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 05/28/2023]
Abstract
In 2002, the first crop genome was published using the rice cultivar 93-11, which is the progenitor of the first super-hybrid rice. The genome sequence has served as a reference genome for the indica cultivars, but the assembly has not been updated. In this study, we update the 93-11 genome assembly to a gap-less sequence using ultra-depth single molecule real-time (SMRT) reads, Hi-C sequencing, reference-guided, and gap-closing approach. The differences in the genome collinearity and gene content between the 93-11 and the Nipponbare reference genomes confirmed to map the indica cultivar sequencing data to the 93-11 genome, instead of the reference. Furthermore, time-course transcriptome data showed that the expression pattern was consistently correlated with the stages of seed development. Alternative splicing of starch synthesis-related genes and genomic variations of waxy make it a novel resource for targeted breeding. Collectively, the updated high quality 93-11 genome assembly can improve the understanding of the genome structures and functions of Oryza groups in molecular breeding programs.
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Affiliation(s)
- Sen Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jingyi Nie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junhua Xie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaochun Bi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianing Geng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
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12
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Adegoke TV, Wang Y, Chen L, Wang H, Liu W, Liu X, Cheng YC, Tong X, Ying J, Zhang J. Posttranslational Modification of Waxy to Genetically Improve Starch Quality in Rice Grain. Int J Mol Sci 2021; 22:4845. [PMID: 34063649 PMCID: PMC8124582 DOI: 10.3390/ijms22094845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 01/07/2023] Open
Abstract
The waxy (Wx) gene, encoding the granule-bound starch synthase (GBSS), is responsible for amylose biosynthesis and plays a crucial role in defining eating and cooking quality. The waxy locus controls both the non-waxy and waxy rice phenotypes. Rice starch can be altered into various forms by either reducing or increasing the amylose content, depending on consumer preference and region. Low-amylose rice is preferred by consumers because of its softness and sticky appearance. A better way of improving crops other than downregulation and overexpression of a gene or genes may be achieved through the posttranslational modification of sites or regulatory enzymes that regulate them because of their significance. The impact of posttranslational GBSSI modifications on extra-long unit chains (ELCs) remains largely unknown. Numerous studies have been reported on different crops, such as wheat, maize, and barley, but the rice starch granule proteome remains largely unknown. There is a need to improve the yield of low-amylose rice by employing posttranslational modification of Wx, since the market demand is increasing every day in order to meet the market demand for low-amylose rice in the regional area that prefers low-amylose rice, particularly in China. In this review, we have conducted an in-depth review of waxy rice, starch properties, starch biosynthesis, and posttranslational modification of waxy protein to genetically improve starch quality in rice grains.
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Affiliation(s)
- Tosin Victor Adegoke
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Lijuan Chen
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Huimei Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Wanning Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xingyong Liu
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Yi-Chen Cheng
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jiezheng Ying
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China; (T.V.A.); (Y.W.); (L.C.); (H.W.); (W.L.); (X.L.); (Y.-C.C.); (X.T.); (J.Y.)
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13
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Kim MS, Yang JY, Yu JK, Lee Y, Park YJ, Kang KK, Cho YG. Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers. PLANTS 2021; 10:plants10040804. [PMID: 33921910 PMCID: PMC8073074 DOI: 10.3390/plants10040804] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/03/2022]
Abstract
The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.
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Affiliation(s)
- Me-Sun Kim
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Young Yang
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Ju-Kyung Yu
- Syngenta Crop Protection LLC, Seeds Research, 9 Davis Dr. Research Triangle Park, Durham, NC 27709, USA;
| | - Yi Lee
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
| | - Yong-Jin Park
- College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea
- Correspondence: (K.-K.K.); (Y.-G.C.)
| | - Yong-Gu Cho
- College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Korea; (M.-S.K.); (J.-Y.Y.); (Y.L.)
- Correspondence: (K.-K.K.); (Y.-G.C.)
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14
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Xia Y, Sun Y, Yuan J, Xing C. Grain quality evaluation of japonica rice effected by cultivars, environment, and their interactions based on appearance and processing characteristics. Food Sci Nutr 2021; 9:2129-2138. [PMID: 33841829 PMCID: PMC8020948 DOI: 10.1002/fsn3.2181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022] Open
Abstract
Appearance and processing characteristics of 45 japonica rice samples, collected from different regions in Jiangsu province, were investigated and evaluated in this study. Specifically, the chalkiness degree had been presented significant differences among different cultivars and regions. The average chalkiness degree varied from 6.81% to 15.34% for different regions and from 1.93% to 28.31% for different cultivars. The minimum head rice rate of cultivars from four regions, NJ9108 (HA), was 80.5%. The AC of CNG10, HD5, and PJ surpassed 13.68% and lower than 11.33% for the others. The protein content ranged from 6.1% to 11%, and the taste value was significantly different among cultivars. In addition, the RVA curves of the samples were similar, but the peak viscosities of NG8 and NJ5055 were higher than others, and there were significant differences in RVA traits among regions. Cultivars were the main reasons for the difference in appearance and processing quality of japonica rice, while environmental factors had leaded to the change of rice composition, texture, and gelatinization.
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Affiliation(s)
- Yujie Xia
- College of Food Science and EngineeringCollaborative Innovation Center for Modern Grain Circulation and SafetyKey Laboratory of Grains and Oils Quality Control and ProcessingNanjing University of Finance and EconomicsNanjingChina
| | - Yuying Sun
- College of Food Science and EngineeringCollaborative Innovation Center for Modern Grain Circulation and SafetyKey Laboratory of Grains and Oils Quality Control and ProcessingNanjing University of Finance and EconomicsNanjingChina
| | - Jian Yuan
- College of Food Science and EngineeringCollaborative Innovation Center for Modern Grain Circulation and SafetyKey Laboratory of Grains and Oils Quality Control and ProcessingNanjing University of Finance and EconomicsNanjingChina
| | - Changrui Xing
- College of Food Science and EngineeringCollaborative Innovation Center for Modern Grain Circulation and SafetyKey Laboratory of Grains and Oils Quality Control and ProcessingNanjing University of Finance and EconomicsNanjingChina
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15
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Pan Z, Deng X, Li Q, Xie R, Zhai H, Zeng X, Luobu Z, Tashi N, Li Z. Effects of Two Starch Synthase IIa Isoforms on Grain Components and Other Grain Traits in Barley. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1206-1213. [PMID: 33481586 DOI: 10.1021/acs.jafc.0c05445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Starch biosynthesis in cereal crops is a complex pathway regulated by multiple starch synthetic enzymes. Starch synthase IIa (SSIIa) is well-known to be one of the major starch synthases and is very important in amylopectin biosynthesis. It has significant effects on grain composition and kernel traits. However, there are few reports on the association of natural variation of SSIIa in barley and grain composition and characteristics. In this work, two SSIIa isoforms were first identified as SSIIaH and SSIIaL by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis, mass spectrometry, and Western blotting. Sequence analysis of the SSIIa gene demonstrated that a 33 bp insertion coding a peptide of APPSSVVPAKK caused different SSIIa, e.g., SSIIaH and SSIIaL. Based on this molecular difference, a polymerase chain reaction marker was developed, which could be used to screen different SSIIa genotypes easily. Kernel hardness of SSIIaL genotypes was significantly higher than that of SSIIaH Chinese barley cultivars. The proportion of SSIIaL genotypes was extremely low in Australian barley cultivars (5/24) and much higher in Tibetan hull-less barley cultivars (46/74), consistent with the end-use requirements of barley grain. This study provided new information in barley endosperm starch synthesis and indicated that it is valuable for choosing the preferred SSIIa genotype according to the end-use requirements.
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Affiliation(s)
- Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, People's Republic of China
| | - Xiaoqing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, People's Republic of China
- University of the Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100039, People's Republic of China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, People's Republic of China
| | - Rong Xie
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, People's Republic of China
- University of the Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100039, People's Republic of China
| | - Huisheng Zhai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, People's Republic of China
| | - Xingquan Zeng
- Tibet Academy of Agriculture and Animal Sciences, No. 130 Jinzhu West Road, Lhasa 850002, People's Republic of China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, People's Republic of China
| | - Zhaxi Luobu
- Tibet Academy of Agriculture and Animal Sciences, No. 130 Jinzhu West Road, Lhasa 850002, People's Republic of China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, People's Republic of China
| | - Nyima Tashi
- Tibet Academy of Agriculture and Animal Sciences, No. 130 Jinzhu West Road, Lhasa 850002, People's Republic of China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, People's Republic of China
| | - Zhongyi Li
- CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia, retired
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16
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do Carmo CD, Sousa MBE, Dos Santos Silva PP, Oliveira GAF, Ceballos H, de Oliveira EJ. Identification and validation of mutation points associated with waxy phenotype in cassava. BMC PLANT BIOLOGY 2020; 20:164. [PMID: 32293293 PMCID: PMC7160975 DOI: 10.1186/s12870-020-02379-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The granule-bound starch synthase I (GBSSI) enzyme is responsible for the synthesis of amylose, and therefore, its absence results in individuals with a waxy starch phenotype in various amylaceous crops. The validation of mutation points previously associated with the waxy starch phenotype in cassava, as well as the identification of alternative mutant alleles in the GBSSI gene, can allow the development of molecular-assisted selection to introgress the waxy starch mutation into cassava breeding populations. RESULTS A waxy cassava allele has been identified previously, associated with several SNPs. A particular SNP (intron 11) was used to develop SNAP markers for screening heterozygote types in cassava germplasm. Although the molecular segregation corresponds to the expected segregation at 3:1 ratio (dominant gene for the presence of amylose), the homozygotes containing the SNP associated with the waxy mutation did not show waxy phenotypes. To identify more markers, we sequenced the GBSS gene from 89 genotypes, including some that were segregated from a cross with a line carrying the known waxy allele. As a result, 17 mutations in the GBSSI gene were identified, in which only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype. The evaluation of mutation points by discriminant analysis of principal component analysis (DAPC) also did not completely discriminate the waxy individuals. Therefore, we developed Kompetitive Allele Specific PCR (KASP) markers that allowed discrimination between WX and wx alleles. The results demonstrated the non-existence of heterozygous individuals of the MeWxEx6-del-C deletion in the analyzed germplasm. Therefore, the deletion MeWxEx6-del-C should not be used for assisted selection in genetic backgrounds different from the original source of waxy starch. Also, the alternative SNPs identified in this study were not associated with the waxy phenotype when compared to a panel of accessions with high genetic diversity. CONCLUSION Although the GBSSI gene can exhibit several mutations in cassava, only the deletion in exon 6 (MeWxEx6-del-C) was correlated with the waxy phenotype in the original AM206-5 source.
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Affiliation(s)
- Cátia Dias do Carmo
- Universidade Federal do Recôncavo da Bahia, Campus Cruz das Almas, CEP, Cruz das Almas, BA, 44380-000, Brazil
| | - Massaine Bandeira E Sousa
- Universidade Federal do Recôncavo da Bahia, Campus Cruz das Almas, CEP, Cruz das Almas, BA, 44380-000, Brazil
| | | | | | - Hernán Ceballos
- International Center for Tropical Agriculture (CIAT), A.A 6713, Cali, Colombia
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, CEP, Cruz das Almas, BA, 44380-000, Brazil.
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17
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Anacleto R, Badoni S, Parween S, Butardo VM, Misra G, Cuevas RP, Kuhlmann M, Trinidad TP, Mallillin AC, Acuin C, Bird AR, Morell MK, Sreenivasulu N. Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1261-1275. [PMID: 30549178 PMCID: PMC6575982 DOI: 10.1111/pbi.13051] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 11/15/2018] [Accepted: 11/25/2018] [Indexed: 05/19/2023]
Abstract
Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.
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Affiliation(s)
| | - Saurabh Badoni
- International Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- International Rice Research InstituteLos BañosPhilippines
| | - Vito M. Butardo
- International Rice Research InstituteLos BañosPhilippines
- Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVic.Australia
| | - Gopal Misra
- International Rice Research InstituteLos BañosPhilippines
| | | | - Markus Kuhlmann
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | | | - Cecilia Acuin
- International Rice Research InstituteLos BañosPhilippines
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18
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New clues into the mechanisms of rice domestication. J Biosci 2019. [DOI: 10.1007/s12038-019-9844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Shivaprasad PV. New clues into the mechanisms of rice domestication. J Biosci 2019; 44:28. [PMID: 31180041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Domestication of rice involved incorporation of specific yield-related changes in wild species of rice. This agricultural process has been of significant interest for plant biologists. The recent advance in genomics has provided new tools to investigate the genetic basis and consequences of domestication. Several genes involved in domestication and diversification process have been characterized, and as expected, this list is over-represented by transcription factors and their cofactors. Most often the modification orchestrated expression levels of genes such as those coding for transcription factors. It has been proposed that transcriptional regulators and their regulation is likely a major theme controlling morphological differences between crops and their progenitors. However, recent data indicate that single amino acid changes in genes coding for key proteins as well as epigenetic and small RNA-mediated pathways also contributed towards domesticationassociated phenotypes.
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Affiliation(s)
- Padubidri V Shivaprasad
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bengaluru 560 065, India,
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20
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Li M, Yang S, Xu W, Pu Z, Feng J, Wang Z, Zhang C, Peng M, Du C, Lin F, Wei C, Qiao S, Zou H, Zhang L, Li Y, Yang H, Liao A, Song W, Zhang Z, Li J, Wang K, Zhang Y, Lin H, Zhang J, Tan W. The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. BMC PLANT BIOLOGY 2019; 19:119. [PMID: 30935381 PMCID: PMC6444543 DOI: 10.1186/s12870-019-1708-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/11/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.
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Affiliation(s)
- Ming Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Songtao Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Zhigang Pu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Junyan Feng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Cong Zhang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Meifang Peng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ 07043 USA
| | - Feng Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Changhe Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Shuai Qiao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Hongda Zou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Lei Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Huan Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Anzhong Liao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Song
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yizheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Wenfang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
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Uthup TK, Rajamani A, Ravindran M, Saha T. Distinguishing CPT gene family members and vetting the sequence structure of a putative rubber synthesizing variant in Hevea brasiliensis. Gene 2019; 689:183-193. [PMID: 30528269 DOI: 10.1016/j.gene.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/21/2018] [Accepted: 12/01/2018] [Indexed: 11/19/2022]
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze the cis-1,4-polymerization of isoprene units to generate isoprenoids with carbon skeletons varying from C10 (neryl pyrophosphate) to C > 10,000 (natural rubber). Though the previously reported CPTs in Hevea are designated based on sequence variations, their classification was done mostly by phylogenetic analysis using a mixture of partial as well as full length sequences often excluding the UTRs. In this context an attempt was made to reclassify the CPTs strictly based on their sequence similarity and distinguish the members putatively associated with rubber biosynthesis from the others. Extensive computational analysis was carried out on CPT sequences obtained from public resources and whole genome assemblies of Hevea. Based on the results from BLAST analysis, multiple sequence alignments of protein, nucleotide and untranslated regions, open reading frame analysis, gene prediction analysis and sequence length variations, we conclude that there exists mainly three CPTs namely RubCPT1, RubCPT2 and RubCPT3 putatively associated with rubber biosynthesis in Hevea brasiliensis. The rest were categorised as variants of dehydrodolichyl diphosphate synthase (DHDDS) involved in the synthesis of dolichols having short chain isoprenoids. Analysis of the sequence structure of the most highly expressed RubCPT1 in latex revealed the allele richness and diversity of this important variant prevailing in the popular rubber clones. Haplotypes consisting of SNPs with high degree of heterozygosity were also identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor towards the generation of allelic diversity rather than point mutations. Alternatively, gene expression analysis indicated the possibility of association between specific haplotypes and RubCPT1 expression in Hevea clones which may have downstream impact up to the level of rubber production. The conclusions from this study may pave way for the identification and better understanding of CPTs directly involved with natural rubber biosynthesis in Hevea and the SNP data generated may aid in the development of molecular markers putatively associated with yield in rubber.
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Affiliation(s)
- Thomas Kadampanattu Uthup
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India.
| | - Anantharamanan Rajamani
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Minimol Ravindran
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
| | - Thakurdas Saha
- Genome Analysis Laboratory, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala PIN-686009, India
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22
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Butardo VM, Sreenivasulu N, Juliano BO. Improving Rice Grain Quality: State-of-the-Art and Future Prospects. Methods Mol Biol 2019; 1892:19-55. [PMID: 30397798 DOI: 10.1007/978-1-4939-8914-0_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rice grain quality encompasses complex interrelated traits that cover biochemical composition, cooking, eating, nutritional, and sensory properties. Because rice endosperm is composed mainly of starch, rice grain quality is traditionally defined by characterizing starch structure and composition, which is then subsequently correlated with functional properties of the grain. The current proxy tests routinely used to describe rice grain quality preferences are rather limited to the estimation of apparent amylose content, gelatinization temperature, and gel consistency. Additional tests that characterize starch property, viscoelasticity, grain texture, and aroma are also employed in more advanced laboratories. However, these tests are not routinely applied in breeding programs to distinguish cooking quality classes to reflect evolving consumer preference and market demand. As consumer preferences in Asia and all over the world are diverse due to varied demographics and culture, defining uniform attributes to capture regional grain quality preferences becomes more challenging. Hence, novel and innovative proxy tests are needed to characterize rice grain quality to meet the demand for consumer preferences of commercially-released cultivars. In this chapter, the current methods employed in rice grain quality monitoring are succinctly reviewed. Future prospects for improvement are identified, introducing cutting edge technologies that can facilitate high-throughput screening of rice diversity panels and breeding lines. Aside from addressing the requirements for quality improvement in the traditional inbred rice breeding programs, we also tackled the need to enhance grain quality in the hybrid rice sector.
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Affiliation(s)
- Vito M Butardo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Nese Sreenivasulu
- International Rice Research Institute, Los Baños, Laguna, Philippines.
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23
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Re-sequencing Resources to Improve Starch and Grain Quality in Rice. Methods Mol Biol 2018. [PMID: 30397808 DOI: 10.1007/978-1-4939-8914-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.
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Swetha C, Basu D, Pachamuthu K, Tirumalai V, Nair A, Prasad M, Shivaprasad PV. Major Domestication-Related Phenotypes in Indica Rice Are Due to Loss of miRNA-Mediated Laccase Silencing. THE PLANT CELL 2018; 30:2649-2662. [PMID: 30341147 PMCID: PMC6305975 DOI: 10.1105/tpc.18.00472] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/11/2018] [Accepted: 10/15/2018] [Indexed: 05/20/2023]
Abstract
Domestication of rice (Oryza sativa) included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key proteins such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA-mediated regulation. Analysis of small (s) RNA data sets from cultivated indica rice lines, a few landraces, and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 was expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs encoding laccases that decayed and induced robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, overexpression of miR397 induced de-domestication phenotypes. At least 26 uncharacterized QTLs previously implicated in rice yield overlapped with laccases and miR397 genes. These results suggest that miRNAs contribute to rice domestication-associated phenotypes.
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Affiliation(s)
- Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Debjani Basu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Melvin Prasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
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Quero G, Gutiérrez L, Monteverde E, Blanco P, Pérez de Vida F, Rosas J, Fernández S, Garaycochea S, McCouch S, Berberian N, Simondi S, Bonnecarrère V. Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice. THE PLANT GENOME 2018; 11:170076. [PMID: 30512035 DOI: 10.3835/plantgenome2017.08.0076] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection. We used two locally adapted rice breeding populations and historical phenotypic data for three rice quality traits: yield after milling, percentage of head rice recovery, and percentage of chalky grain. We detected 22 putative quantitative trait loci (QTL) in the same genomic regions as starch synthesis, starch metabolism, and cell wall synthesis-related genes are found. Additionally, we found a genomic region on chromosome 6 in the population that was associated with all quality traits and we identified favorable haplotypes. Furthermore, this region is linked to the gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In , we also found two putative QTL linked to , , and . Our study provides an insight into the genetic basis of rice grain chalkiness, yield after milling, and head rice, identifying favorable haplotypes and molecular markers for selection in breeding programs.
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26
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Pang Y, Zhou X, Chen Y, Bao J. Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice ( Oryza sativa L.) Cultivars with Different Starch Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3030-3037. [PMID: 29486119 DOI: 10.1021/acs.jafc.8b00074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.
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Affiliation(s)
- Yuehan Pang
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Xin Zhou
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
| | - Yaling Chen
- College of Life Sciences , Jiangxi Normal University , Nanchang , 330022 , China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology , Zhejiang University , Huajiachi Campus, Hangzhou , 310029 , China
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Balindong JL, Ward RM, Liu L, Rose TJ, Pallas LA, Ovenden BW, Snell PJ, Waters DL. Rice grain protein composition influences instrumental measures of rice cooking and eating quality. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2017.09.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Ponce KS, Ye G, Zhao X. QTL Identification for Cooking and Eating Quality in indica Rice Using Multi-Parent Advanced Generation Intercross (MAGIC) Population. FRONTIERS IN PLANT SCIENCE 2018; 9:868. [PMID: 30042770 PMCID: PMC6048290 DOI: 10.3389/fpls.2018.00868] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/04/2018] [Indexed: 05/17/2023]
Abstract
Association mapping using a multi-parent advanced generation intercross (MAGIC) population provides a promising tool in genetic dissection of rice cooking and eating quality (CEQ). In this study, QTLs were identified for ten physicochemical properties related to CEQ using 508 F6 MAGIC lines. The whole population and eight founder lines were genotyped with 6K Illumina Infinium HD Assay. All traits had high heritability estimates and showed a large genetic variation in the MAGIC population. Highly significant phenotypic correlations were present between traits. AC was significantly positively correlated with PKT, TV, FV, SBV, PKT, and RT but significantly negatively correlated with GC and BDV. Seventeen QTLs were identified for all traits. GBSSI locus was hosted or closely to nine QTLs, qAC6, qGC6.1, qPKT6.1, qPKV6, qBDV6.1, qTV6.1, qFV6, qSBV6, and qRT6, suggesting that GBSSI impacts the overall CEQ. Another locus closed to SSIIa, located at 6.99 Mb, affects five traits, GC, PKT, BDV, SBV, and PT. The identified QTLs revealed small to modest effects where the highest percentage of phenotypic variance explained was 17.18%. These QTLs are directly relevant and useful in breeding for CEQ in indica rice. These results also confirmed that QTL mapping via association mapping using a MAGIC population is a powerful method in genetic analysis of complex traits.
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Affiliation(s)
- Kimberly S. Ponce
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Guoyou Ye
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute, Shenzhen, China
| | - Xiangqian Zhao
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
- *Correspondence: Xiangqian Zhao,
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30
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Wang X, Pang Y, Zhang J, Wu Z, Chen K, Ali J, Ye G, Xu J, Li Z. Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content. Sci Rep 2017; 7:17203. [PMID: 29222496 PMCID: PMC5722854 DOI: 10.1038/s41598-017-17347-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/19/2017] [Indexed: 01/12/2023] Open
Abstract
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.
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Affiliation(s)
- Xiaoqian Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunlong Pang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018, China
| | - Jian Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kai Chen
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 777, Metro Manila, Philippines
| | - Guoyou Ye
- International Rice Research Institute, DAPO Box 777, Metro Manila, Philippines
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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Jiang S, Sun S, Bai L, Ding G, Wang T, Xia T, Jiang H, Zhang X, Zhang F. Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield. PLoS One 2017; 12:e0181037. [PMID: 28715430 PMCID: PMC5513431 DOI: 10.1371/journal.pone.0181037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 06/26/2017] [Indexed: 01/04/2023] Open
Abstract
Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.
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Affiliation(s)
- Shukun Jiang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
- * E-mail:
| | - Shichen Sun
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Liangming Bai
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Guohua Ding
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Tongtong Wang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Tianshu Xia
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Hui Jiang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Xijuan Zhang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
| | - Fengming Zhang
- Cultivation and Farming Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, P.R.China
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Maddison AL, Camargo-Rodriguez A, Scott IM, Jones CM, Elias DMO, Hawkins S, Massey A, Clifton-Brown J, McNamara NP, Donnison IS, Purdy SJ. Predicting future biomass yield in Miscanthus using the carbohydrate metabolic profile as a biomarker. GLOBAL CHANGE BIOLOGY. BIOENERGY 2017; 9:1264-1278. [PMID: 28713439 PMCID: PMC5488626 DOI: 10.1111/gcbb.12418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/23/2016] [Indexed: 05/08/2023]
Abstract
In perennial energy crop breeding programmes, it can take several years before a mature yield is reached when potential new varieties can be scored. Modern plant breeding technologies have focussed on molecular markers, but for many crop species, this technology is unavailable. Therefore, prematurity predictors of harvestable yield would accelerate the release of new varieties. Metabolic biomarkers are routinely used in medicine, but they have been largely overlooked as predictive tools in plant science. We aimed to identify biomarkers of productivity in the bioenergy crop, Miscanthus, that could be used prognostically to predict future yields. This study identified a metabolic profile reflecting productivity in Miscanthus by correlating the summer carbohydrate composition of multiple genotypes with final yield 6 months later. Consistent and strong, significant correlations were observed between carbohydrate metrics and biomass traits at two separate field sites over 2 years. Machine-learning feature selection was used to optimize carbohydrate metrics for support vector regression models, which were able to predict interyear biomass traits with a correlation (R) of >0.67 between predicted and actual values. To identify a causal basis for the relationships between the glycome profile and biomass, a 13C-labelling experiment compared carbohydrate partitioning between high- and low-yielding genotypes. A lower yielding and slower growing genotype partitioned a greater percentage of the 13C pulse into starch compared to a faster growing genotype where a greater percentage was located in the structural biomass. These results supported a link between plant performance and carbon flow through two rival pathways (starch vs. sucrose), with higher yielding plants exhibiting greater partitioning into structural biomass, via sucrose metabolism, rather than starch. Our results demonstrate that the plant metabolome can be used prognostically to anticipate future yields and this is a method that could be used to accelerate selection in perennial energy crop breeding programmes.
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Affiliation(s)
- Anne L Maddison
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Anyela Camargo-Rodriguez
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Ian M Scott
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Charlotte M Jones
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Dafydd M O Elias
- Centre for Ecology and Hydrology Lancaster Environment Centre Library Avenue Bailrigg Lancaster LA1 4AP UK
| | - Sarah Hawkins
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Alice Massey
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - John Clifton-Brown
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Niall P McNamara
- Centre for Ecology and Hydrology Lancaster Environment Centre Library Avenue Bailrigg Lancaster LA1 4AP UK
| | - Iain S Donnison
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
| | - Sarah J Purdy
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University Plas Gogerddan SY23 3EB UK
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Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:765-774. [PMID: 27889940 PMCID: PMC5425390 DOI: 10.1111/pbi.12674] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 05/04/2023]
Abstract
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityCairnsQLDAustralia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandToowoombaQLDAustralia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
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Review: Amylopectin synthesis and hydrolysis – Understanding isoamylase and limit dextrinase and their impact on starch structure on barley ( Hordeum vulgare ) quality. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2016.11.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Butardo VM, Anacleto R, Parween S, Samson I, de Guzman K, Alhambra CM, Misra G, Sreenivasulu N. Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis. PLANT PHYSIOLOGY 2017; 173:887-906. [PMID: 27881726 PMCID: PMC5210722 DOI: 10.1104/pp.16.01248] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/21/2016] [Indexed: 05/20/2023]
Abstract
A deeper understanding of the regulation of starch biosynthesis in rice (Oryza sativa) endosperm is crucial in tailoring digestibility without sacrificing grain quality. In this study, significant association peaks on chromosomes 6 and 7 were identified through a genomewide association study (GWAS) of debranched starch structure from grains of a 320 indica rice diversity panel using genotyping data from the high-density rice array. A systems genetics approach that interrelates starch structure data from GWAS to functional pathways from a gene regulatory network identified known genes with high correlation to the proportion of amylose and amylopectin. An SNP in the promoter region of Granule Bound Starch Synthase I was identified along with seven other SNPs to form haplotypes that discriminate samples into different phenotypic ranges of amylose. A GWAS peak on chromosome 7 between LOC_Os07g11020 and LOC_Os07g11520 indexed by a nonsynonymous SNP mutation on exon 5 of a bHLH transcription factor was found to elevate the proportion of amylose at the expense of reduced short-chain amylopectin. Linking starch structure with starch digestibility by determining the kinetics of cooked grain amylolysis of selected haplotypes revealed strong association of starch structure with estimated digestibility kinetics. Combining all results from grain quality genomics, systems genetics, and digestibility phenotyping, we propose target haplotypes for fine-tuning starch structure in rice through marker-assisted breeding that can be used to alter the digestibility of rice grain, thus offering rice consumers a new diet-based intervention to mitigate the impact of nutrition-related noncommunicable diseases.
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Affiliation(s)
- Vito M Butardo
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Roslen Anacleto
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sabiha Parween
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Irene Samson
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Krishna de Guzman
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Crisline Mae Alhambra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Gopal Misra
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Nese Sreenivasulu
- Grain Quality and Nutrition Center, Plant Breeding Division, International Rice Research Institute, Los Baños, Laguna, Philippines
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Mahender A, Anandan A, Pradhan SK, Pandit E. Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. SPRINGERPLUS 2016; 5:2086. [PMID: 28018794 PMCID: PMC5148756 DOI: 10.1186/s40064-016-3744-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. RESULTS Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation. CONCLUSION Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.
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Affiliation(s)
- Anumalla Mahender
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
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Se CH, Chuah KA, Mishra A, Wickneswari R, Karupaiah T. Evaluating Crossbred Red Rice Variants for Postprandial Glucometabolic Responses: A Comparison with Commercial Varieties. Nutrients 2016; 8:nu8050308. [PMID: 27213446 PMCID: PMC4882720 DOI: 10.3390/nu8050308] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/17/2022] Open
Abstract
Consumption of white rice predisposes some Asian populations to increased risk of type 2 diabetes. We compared the postprandial glucometabolic responses to three newly-developed crossbred red rice variants (UKMRC9, UKMRC10, UKMRC11) against three selected commercial rice types (Thai red, Basmati white, Jasmine white) using 50-g carbohydrate equivalents provided to 12 normoglycaemic adults in a crossover design. Venous blood was drawn fasted and postprandially for three hours. Glycaemic (GI) and insulin (II) indices, incremental areas-under-the-curves for glucose and insulin (IAUCins), indices of insulin sensitivity and secretion, lactate and peptide hormones (motilin, neuropeptide-Y, orexin-A) were analyzed. The lowest to highest trends for GI and II were similar i.e., UKMRC9 < Basmati < Thai red < UKMRC10 < UKMRC11 < Jasmine. Postprandial insulinaemia and IAUCins of only UKMRC9 were significantly the lowest compared to Jasmine. Crude protein and fiber content correlated negatively with the GI values of the test rice. Although peptide hormones were not associated with GI and II characteristics of test rice, early and late phases of prandial neuropeptide-Y changes were negatively correlated with postprandial insulinaemia. This study indicated that only UKMRC9 among the new rice crossbreeds could serve as an alternative cereal option to improve diet quality of Asians with its lowest glycaemic and insulinaemic burden.
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Affiliation(s)
- Chee-Hee Se
- School of Healthcare Sciences, Faculty of Health Sciences, National University of Malaysia (UKM), Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia.
| | - Khun-Aik Chuah
- School of Healthcare Sciences, Faculty of Health Sciences, National University of Malaysia (UKM), Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia.
| | - Ankitta Mishra
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, National University of Malaysia (UKM), Bangi, Selangor 43600, Malaysia.
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, National University of Malaysia (UKM), Bangi, Selangor 43600, Malaysia.
| | - Tilakavati Karupaiah
- School of Healthcare Sciences, Faculty of Health Sciences, National University of Malaysia (UKM), Jalan Raja Muda Abdul Aziz, Kuala Lumpur 50300, Malaysia.
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38
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Upadhyaya HD, Bajaj D, Das S, Kumar V, Gowda CLL, Sharma S, Tyagi AK, Parida SK. Genetic dissection of seed-iron and zinc concentrations in chickpea. Sci Rep 2016; 6:24050. [PMID: 27063651 PMCID: PMC4827059 DOI: 10.1038/srep24050] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/18/2016] [Indexed: 02/07/2023] Open
Abstract
The SNP-based high-resolution QTL mapping mapped eight major genomic regions harbouring robust QTLs governing seed-Fe and Zn concentrations (39.4% combined phenotypic variation explained/PVE) on six chromosomes of an intra-specific high-density genetic linkage map (1.56 cM map-density). 24620 SNPs discovered from genome-wide GBS (genotyping-by-sequencing) and 13 known cloned Fe and Zn contents-related chickpea gene-orthologs were genotyped in a structured population of 92 sequenced desi and kabuli accessions. The large-scale 16591 SNP genotyping- and phenotyping-based GWAS (genome-wide association study) identified 16 genomic loci/genes associated (29% combined PVE) with seed-Fe and Zn concentrations. Of these, 11 trait-associated SNPs in the genes linked tightly with eight QTLs were validated by QTL mapping. The seed-specific expression, including pronounced differential-regulation of 16 trait-associated genes particularly in accessions/mapping individuals with contrasting level of seed-Fe and Zn contents was apparent. Collectively, the aforementioned rapid integrated genomic strategy led to delineate novel functional non-synonymous and regulatory SNP allelic-variants from 16 known/candidate genes, including three strong trait-associated genes (encoding late embryogenesis abundant and yellow stripe-like 1 protein, and vacuolar protein sorting-associated protein) and eight major QTLs regulating seed-Fe and Zn concentrations in chickpea. These essential inputs thus have potential to be deployed in marker-assisted genetic enhancement for developing nutritionally-rich iron/zinc-biofortified chickpea cultivars.
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Affiliation(s)
- Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 PMCID: PMC11389173 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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Henry RJ, Rangan P, Furtado A. Functional cereals for production in new and variable climates. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:11-18. [PMID: 26828379 DOI: 10.1016/j.pbi.2015.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/14/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Adaptation of cereal crops to variable or changing climates requires that essential quality attributes are maintained to deliver food that will be acceptable to human consumers. Advances in cereal genomics are delivering insights into the molecular basis of nutritional and functional quality traits in cereals and defining new genetic resources. Understanding the influence of the environment on expression of these traits will support the retention of these essential functional properties during climate adaptation. New cereals for use as whole grain or ground to flour for other food products may be based upon the traditional species such as rice and wheat currently used in these food applications but may also include new options exploiting genomics tools to allow accelerated domestication of new species.
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Affiliation(s)
- Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Parimalan Rangan
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
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Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice. Sci Rep 2016; 6:23765. [PMID: 27032371 PMCID: PMC4817136 DOI: 10.1038/srep23765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/11/2016] [Indexed: 12/13/2022] Open
Abstract
We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17-79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9-21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, "Oryza ISM-ILP marker" database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice.
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Huq A, Akter S, Nou IS, Kim HT, Jung YJ, Kang KK. Identification of functional SNPs in genes and their effects on plant phenotypes. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.1.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amdadul Huq
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Shahina Akter
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Hoy Taek Kim
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Yu Jin Jung
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
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43
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Chen Y, Bao J. Underlying Mechanisms of Zymographic Diversity in Starch Synthase I and Pullulanase in Rice-Developing Endosperm. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2030-7. [PMID: 26860852 DOI: 10.1021/acs.jafc.5b06030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Amylopectin is synthesized by the coordinated actions of many (iso)enzymes, including ADP-glucose pyrophosphorylase (AGPase), starch synthases (SSs), branching enzymes (BEs), and debranching enzymes (DBEs). Here, two polymorphic forms of starch synthase I (SSI) and pullulanase (PUL) in rice-developing seeds, designated as SSI-1/SSI-2 and PUL-1/PUL-2, were discovered for the first time by zymographic analysis. The SSI and PUL polymorphisms were strongly associated with the SSI microsatellite marker (p = 3.6 × 10(-37)) and PUL insertion/deletion (InDel) markers (p < 3.6 × 10(-51)). Western blotting and mass spectrometric analysis confirmed that the polymorphic bands were truly the SSI and PUL enzymes. Only one non-synonymous variation in SSI DNA sequence (the SNP A/G) causing the change of the amino acid K438 to E438 was observed, which coincided well with the polymorphic forms of SSI. Nine non-synonymous variations were found between PUL-1 and PUL-2. Two non-synonymous variations of PUL (F316L and D770E) were identified by mass spectrometric analysis, but all of the variations did not change the structure of PUL. The co-immunoprecipitation results revealed the differences in protein-protein interaction patterns, i.e., strong or weaker signals of SSI-BEI and SSI-BEIIb, between the two forms of SSI. The results will enhance our understanding of SSI and PUL properties and provide helpful information to understand their functions in starch biosynthesis in rice endosperm.
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Affiliation(s)
- Yaling Chen
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou, Zhejiang 310029, People's Republic of China
| | - Jinsong Bao
- Institute of Nuclear Agricultural Science, College of Agriculture and Biotechnology, Zhejiang University , Huajiachi Campus, Hangzhou, Zhejiang 310029, People's Republic of China
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44
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Zhao X, Zhou L, Ponce K, Ye G. The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis. RICE (NEW YORK, N.Y.) 2015; 8:29. [PMID: 26391157 PMCID: PMC4577492 DOI: 10.1186/s12284-015-0064-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/05/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND A number of studies reported major genes/QTLs for rice grain shapes, chalkiness and starch physicochemical properties. For these finely mapped QTLs or cloned genes to make an impact in practical breeding, it is necessary to test their effects in different genetic backgrounds. In this study, two hundred nineteen markers for 20 starch synthesis genes, 41 fine mapped grain shape and related traits QTLs/genes, and 54 chalkiness QTLs/genes plus 15 additional markers and a large indica population of 375 advanced lines were used to identify marker-trait associations under 6 environments that can be used directly in breeding for grain quality traits. RESULTS The significant associations detected by the QK model were used to declare the usefulness of the targeted genes/QTLs. A total of 65 markers were detected associations with grain quality trait at least in one environment. More phenotypic variations could be explained by haplotype than single marker, as exemplified by the starch biosynthesising genes. GBSSI was the major gene for AC and explained up to 55 % of the phenotypic variation, which also affected GC and accounted up to 11.31 % of the phenotypic variation. SSIIa was the major gene for chalkiness and explained up to 17 and 21 % of variation of DEC and PGWC, respectively. In addition, RMw513 and RM18068 were associated with DEC in 6 environments as well. Four markers (RGS1, RM15206, RMw513 and Indel1) tightly linked to GS3, gw5, and qGL7-2 were the most important ones for grain shapes. Allelic combinations between SSIIa and RMw513 revealed more variations in DEC. CONCLUSIONS The validated markers for genes/QTLs with major effects could be directly used in breeding for grain quality via marker-assisted selection. Creating desirable allelic combinations by gene pyramiding might be an effective approach for the development of high quality breeding lines in rice.
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Affiliation(s)
- Xiangqian Zhao
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Lijie Zhou
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- Present address: Longping Branch, Graduate School of Central South University, Changsha, 410125, Hunan, China
| | - Kimberley Ponce
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Guoyou Ye
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
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Bajaj D, Das S, Upadhyaya HD, Ranjan R, Badoni S, Kumar V, Tripathi S, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea. FRONTIERS IN PLANT SCIENCE 2015; 6:979. [PMID: 26635822 PMCID: PMC4647070 DOI: 10.3389/fpls.2015.00979] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 10/26/2015] [Indexed: 05/29/2023]
Abstract
The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Shouvik Das
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
| | - Rajeev Ranjan
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome ResearchNew Delhi, India
| | - Vinod Kumar
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid TropicsTelangana, India
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Anacleto R, Cuevas RP, Jimenez R, Llorente C, Nissila E, Henry R, Sreenivasulu N. Prospects of breeding high-quality rice using post-genomic tools. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1449-66. [PMID: 25993897 DOI: 10.1007/s00122-015-2537-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 05/08/2015] [Indexed: 05/15/2023]
Abstract
The holistic understanding derived from integrating grain quality and sensory research outcomes in breeding high-quality rice in the light of post-genomics resources has been synthesized. Acceptance of new rice genotypes by producers and consumers hinges not only on their potential for higher yield but recent emphasis has also been on premium-value genotypes that have the ability to satisfy consumer preferences for grain quality. This review article provides insights into how to link grain quality attributes and sensory perception to support breeding superior rice varieties. Recent advances in quality profiling and omics technologies have provided efficient approaches to identify the key genes and biochemical markers involved in rice quality traits. Emphasis has been given to the upcoming area of holistic understanding of grain quality and attributes derived from sensory evaluation to leverage integrative gene discovery strategies that enable breeding programs to efficiently tap the huge genetic diversity in rice for novel genes that enhance rice food quality.
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Affiliation(s)
- Roslen Anacleto
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines,
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Rathinasabapathi P, Purushothaman N, Ramprasad VL, Parani M. Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index. Sci Rep 2015; 5:11303. [PMID: 26068787 PMCID: PMC4464077 DOI: 10.1038/srep11303] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/18/2015] [Indexed: 12/13/2022] Open
Abstract
Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina’s paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, ‘A’ at position 2,386, and ‘C’ at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors.
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Affiliation(s)
- Pasupathi Rathinasabapathi
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
| | - Natarajan Purushothaman
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
| | | | - Madasamy Parani
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu- 603 203, India
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The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima). Carbohydr Polym 2015; 129:92-100. [PMID: 26050893 DOI: 10.1016/j.carbpol.2015.04.035] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
Abstract
The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes.
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Roles of GBSSI and SSIIa in determining amylose fine structure. Carbohydr Polym 2015; 127:264-74. [PMID: 25965483 DOI: 10.1016/j.carbpol.2015.03.081] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 03/27/2015] [Accepted: 03/28/2015] [Indexed: 11/23/2022]
Abstract
This study examines the relationships between genetics (single nucleotide polymorphisms (SNPs) in GBSSI and SSIIa genes), starch structure (amylose and amylopectin fine structures), and starch properties (relating to gelatinization). GBSSI and SSIIa SNPs did not alter the starch content of rice grains. GBSSI SNPs can affect the amylose content, but they are incapable of altering the chain-lengths of amylopectin and amylose. The amounts of both long and short amylose branches changed with the same trend as amylose content, and they appeared to affect starch gelatinization properties. SSIIa synthesizes intermediate single-lamella amylopectin chains (DP 16-21), and consequently impacts the gelatinization temperature. Mathematical modelling suggests that the reduction in SSIIa activity significantly increases the activity of SBEII, resulting in a decreased activity ratio of SS to SBE in the enzyme set governing an appropriate chain-length distribution range. This application of the genetics-structure-property paradigm provides selection strategies to produce rice varieties with improved qualities.
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50
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Luo J, Jobling SA, Millar A, Morell MK, Li Z. Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population. RICE (NEW YORK, N.Y.) 2015; 8:15. [PMID: 25844120 PMCID: PMC4385112 DOI: 10.1186/s12284-015-0046-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/28/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes. RESULTS The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules. CONCLUSIONS Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.
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Affiliation(s)
- Jixun Luo
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
- />College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Stephen A Jobling
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
| | - Anthony Millar
- />College of Medicine, Biology and Environment, Australian National University, Canberra, ACT 0200 Australia
| | - Matthew K Morell
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
- />International Rice Research Institute, Maligaya, Muñoz, Nueva Ecija Philippines
| | - Zhongyi Li
- />CSIRO Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601 Australia
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