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Wang L, Wang W, Huang Z, Zhen S, Wang R. Discrimination of internal crack for rice seeds using near infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124578. [PMID: 38833887 DOI: 10.1016/j.saa.2024.124578] [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: 06/02/2023] [Revised: 04/16/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
It is an important thing to identify internal crack in seeds from normal seeds for evaluating the quality of rice seeds (Oryza sativa L.). In this study, non-destructive discrimination of internal crack in rice seeds using near infrared spectroscopy and chemometrics is proposed. Principal component analysis (PCA) was used to analyze the rice seeds spectra. Four supervised classification techniques(partial least squares discriminate analysis (PLS-DA), support vector machines (SVM), k-nearest neighbors (KNN) and random forest (RF)) with four different pre-processing techniques (standard normal variate (SNV), multiplicative scatter correction (MSC), first and second derivative with Savitzky-Golay (SG) smoothing) were applied. The best results (Sn = 0.8824, Sp = 0.9429, Acc = 0.913) were achieved by PLS-DA with the raw spectral data. The performance of the best SVM model was inferior to that of PLS-DA, but superior to that of RF and KNN. Except for PLS-DA, four different preprocessing techniques were improved the performance of the developed models. The important variables for discriminating internal cracks in rice seeds were related to the amylose. Overall, the all results demonstrated the feasibility of non-destructive discrimination of internal crack for rice seeds (Oryza sativa L.) using near infrared spectroscopy and chemometrics.
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Affiliation(s)
- Liusan Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
| | - Weisheng Wang
- Institute of Nuclear Energy Safety Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; University of Science and Technology of China, Hefei 230026, China
| | - Ziliang Huang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; University of Science and Technology of China, Hefei 230026, China
| | - Shijian Zhen
- Southwest University of Science and Technology, Mianyang 621010, China
| | - Rujing Wang
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; University of Science and Technology of China, Hefei 230026, China
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Zhu M, Liu Y, Jiao G, Yu J, Zhao R, Lu A, Zhou W, Cao N, Wu J, Hu S, Sheng Z, Wei X, Zhao F, Xie L, Ahmad S, Lin Y, Shao G, Tang S, Hu P. The elite eating quality alleles Wx b and ALK b are regulated by OsDOF18 and coordinately improve head rice yield. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1582-1595. [PMID: 38245899 PMCID: PMC11123401 DOI: 10.1111/pbi.14288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq-1 and qMq-2, represent allelic variants of Waxylv/Waxyb (hereafter Wx) encoding Granule-Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc/ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc. Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY.
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Affiliation(s)
- Maodi Zhu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yongqiang Liu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Junming Yu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Rumeng Zhao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Ao Lu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Wei Zhou
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Ni Cao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Jiamin Wu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Shikai Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Fengli Zhao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Lihong Xie
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & AgricultureRiyadhSaudi Arabia
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Zhejiang LabHangzhouChina
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
| | - Peisong Hu
- State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhouChina
- Zhejiang LabHangzhouChina
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Sanchez DL, Samonte SOPB, Wilson LT. Genetic architecture of head rice and rice chalky grain percentages using genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2023; 14:1274823. [PMID: 38046607 PMCID: PMC10691675 DOI: 10.3389/fpls.2023.1274823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
High head rice and low chalky grain percentages are key grain quality traits selected in developing rice cultivars. The objectives of this research were to characterize the phenotypic variation of head rice and chalky grain percentages in a diverse collection of rice accessions, identify single nucleotide polymorphism (SNP) markers associated with each of these traits using genome-wide association studies (GWAS), and identify putative candidate genes linked to the SNPs identified by GWAS. Diverse rice varieties, landraces, and breeding lines were grown at the Texas A&M AgriLife Research Center in Beaumont. Head rice percentages (HRP) and chalky grain percentages (CGP) of 195 and 199 non-waxy accessions were estimated in 2018 and 2019, respectively. Phenotypic data were analyzed along with 854,832 SNPs using three statistical models: mixed linear model (MLM), multi-locus mixed model (MLMM), and fixed and random model circulating probability unification (FarmCPU). Significant variations in HRP and CGP were observed between rice accessions. Two significant marker-trait associations (MTAs) were detected on chromosomes 1 and 2, respectively, based on best linear unbiased prediction (BLUP) values in 2018, while in 2019, one SNP was significantly associated with HRP in each of chromosomes 6, 8, 9, and 11, and two in chromosome 7. CGP was significantly associated with five SNPs located in chromosomes 2, 4, 6, and 8 in the 2018 study and ten SNPs in chromosomes 1, 2, 3, 4, 7, 8, 11, and 12 in the 2019 study. The SNPs are located within or linked to putative candidate genes involved in HRP and CGP. This study reports five and ten novel MTAs for HRP and CGP, respectively, while three and five MTAs co-located with previously reported quantitative trait loci for HRP and CGP, respectively. The validation of candidate genes for their roles in determining HRP and CGP is necessary to design functional molecular markers that can be used to effectively develop rice cultivars with desirable grain quality.
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Praphasanobol P, Purnama PR, Junbuathong S, Chotechuen S, Moung-Ngam P, Kasettranan W, Paliyavuth C, Comai L, Pongpanich M, Buaboocha T, Chadchawan S. Genome-Wide Association Study of Starch Properties in Local Thai Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3290. [PMID: 37765454 PMCID: PMC10535886 DOI: 10.3390/plants12183290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Rice (Oryza sativa L.) is the main source of energy for humans and a staple food of high cultural significance for much of the world's population. Rice with highly resistant starch (RS) is beneficial for health and can reduce the risk of disease, especially type II diabetes. The identification of loci affecting starch properties will facilitate breeding of high-quality and health-supportive rice. A genome-wide association study (GWAS) of 230 rice cultivars was used to identify candidate loci affecting starch properties. The apparent amylose content (AAC) among rice cultivars ranged from 7.04 to 33.06%, and the AAC was positively correlated with RS (R2 = 0.94) and negatively correlated with rapidly available glucose (RAG) (R2 = -0.73). Three loci responsible for starch properties were detected on chromosomes 1, 6, and 11. On chromosome 6, the most significant SNP corresponded to LOC_Os06g04200 which encodes granule-bound starch synthase I (GBSSI) or starch synthase. Two novel loci associated with starch traits were LOC_Os01g65810 and LOC_Os11g01580, which encode an unknown protein and a sodium/calcium exchanger, respectively. The markers associated with GBSSI and LOC_Os11g01580 were tested in two independent sets of rice populations to confirm their effect on starch properties. The identification of genes associated with starch traits will further the understanding of the molecular mechanisms affecting starch in rice and may be useful in the selection of rice varieties with improved starch.
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Affiliation(s)
- Parama Praphasanobol
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Putut Rakhmad Purnama
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Bioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supaporn Junbuathong
- Pathum Thani Rice Research Center, Ministry of Agriculture and Cooperatives, Thanyaburi, Pathum Thani 12110, Thailand; (S.J.); (P.M.-N.)
| | - Somsong Chotechuen
- Division of Rice Research and Development, Rice Department, Ministry of Agriculture and Cooperatives, Bangkok 10900, Thailand;
| | - Peerapon Moung-Ngam
- Pathum Thani Rice Research Center, Ministry of Agriculture and Cooperatives, Thanyaburi, Pathum Thani 12110, Thailand; (S.J.); (P.M.-N.)
| | - Waraluk Kasettranan
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.K.); (C.P.)
| | - Chanita Paliyavuth
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (W.K.); (C.P.)
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA;
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Teerapong Buaboocha
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supachitra Chadchawan
- Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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