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Nie S, Chen L, Zheng M, Dong J, Ma Y, Zhou L, Wang J, Chen J, Hu H, Yang T, Zhao J, Zhang S, Yang W. GWAS and Transcriptomic Analysis Identify OsRING315 as a New Candidate Gene Controlling Amylose Content and Gel Consistency in Rice. RICE (NEW YORK, N.Y.) 2024; 17:38. [PMID: 38849622 PMCID: PMC11161452 DOI: 10.1186/s12284-024-00718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/26/2024] [Indexed: 06/09/2024]
Abstract
Cooking quality is the main factor determining the market value of rice. Although several major genes and a certain number of QTLs controlling cooking quality have been identified, the genetic complexity and environmental susceptibility limit the further improvement for cooking quality by molecular breeding. This research conducted a genome-wide association study to elucidate the QTLs related to cooking quality including amylose content (AC), gel consistency (GC) and alkali spreading value (ASV) by using 450 rice accessions consisting of 300 indica and 150 japonica accessions in two distinct environments. A total of 54 QTLs were identified, including 25 QTLs for AC, 12 QTLs for GC and 17 QTLs for ASV. Among them, 10 QTLs were consistently observed by the same population in both environments. Six QTLs were co-localized with the reported QTLs or cloned genes. The Wx gene for AC and GC, and the ALK gene for ASV were identified in every population across the two environments. The qAC9-2 for AC and the qGC9-2 for GC were defined to the same interval. The OsRING315 gene, encoding an E3 ubiquitin ligase, was considered as the candidate gene for both qAC9-2 and qGC9-2. The higher expression of OsRING315 corresponded to the lower AC and higher GC. Three haplotypes of OsRING315 were identified. The Hap 1 mainly existed in the japonica accessions and had lower AC. The Hap 2 and Hap 3 were predominantly present in the indica accessions, associated with higher AC. Meanwhile, the GC of accessions harboring Hap 1 was higher than that of accessions harboring Hap 3. In addition, the distribution of the three haplotypes in several rice-growing regions was unbalanced. The three traits of cooking quality are controlled by both major and minor genes and susceptible to environmental factors. The expression level of OsRING315 is related to both AC and GC, and this gene can be a promising target in quality improvement by using the gene editing method. Moreover, the haplotypes of OsRING315 differentiate between indica and japonica, and reveal the differences in GC and AC between indica and japonica rice.
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Affiliation(s)
- Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Minhua Zheng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou, 510640, P.R. China.
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Yang X, Pan Y, Xia X, Qing D, Chen W, Nong B, Zhang Z, Zhou W, Li J, Li D, Dai G, Deng G. Molecular basis of genetic improvement for key rice quality traits in Southern China. Genomics 2023; 115:110745. [PMID: 37977332 DOI: 10.1016/j.ygeno.2023.110745] [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: 07/11/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.
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Affiliation(s)
- Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Dongjin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiwei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Weiyong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Jingcheng Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Gaoxing Dai
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
| | - Guofu Deng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
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Sudan J, Urwat U, Farooq A, Pakhtoon MM, Zaffar A, Naik ZA, Batool A, Bashir S, Mansoor M, Sofi PA, Sofi NUR, Shikari AB, Khan MK, Hossain MA, Henry RJ, Zargar SM. Explicating genetic architecture governing nutritional quality in pigmented rice. PeerJ 2023; 11:e15901. [PMID: 37719119 PMCID: PMC10501373 DOI: 10.7717/peerj.15901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023] Open
Abstract
Rice is one of the most important staple plant foods that provide a major source of calories and nutrients for tackling the global hunger index especially in developing countries. In terms of nutritional profile, pigmented rice grains are favoured for their nutritional and health benefits. The pigmented rice varieties are rich sources of flavonoids, anthocyanin and proanthocyanidin that can be readily incorporated into diets to help address various lifestyle diseases. However, the cultivation of pigmented rice is limited due to low productivity and unfavourable cooking qualities. With the advances in genome sequencing, molecular breeding, gene expression analysis and multi-omics approaches, various attempts have been made to explore the genetic architecture of rice grain pigmentation. In this review, we have compiled the current state of knowledge of the genetic architecture and nutritional value of pigmentation in rice based upon the available experimental evidence. Future research areas that can help to deepen our understanding and help in harnessing the economic and health benefits of pigmented rice are also explored.
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Affiliation(s)
- Jebi Sudan
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Uneeb Urwat
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Asmat Farooq
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Aaqif Zaffar
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Zafir Ahmad Naik
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Aneesa Batool
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Saika Bashir
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Madeeha Mansoor
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Najeebul Ul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Jammu and Kashmir, India
| | - Asif B. Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (J&K), Srinagar, Jammu and Kashmir, India
| | - Mohd. Kamran Khan
- Department of Soil Sciences and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, Queensland University, Brisbane, Australia
| | - Sajad Majeed Zargar
- Proteomics Lab, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
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4
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Liao Z, Xia X, Zhang Z, Nong B, Guo H, Feng R, Chen C, Xiong F, Qiu Y, Li D, Yang X. Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1126254. [PMID: 37521918 PMCID: PMC10375723 DOI: 10.3389/fpls.2023.1126254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/28/2023] [Indexed: 08/01/2023]
Abstract
Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.
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Affiliation(s)
- Zuyu Liao
- College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiuzhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hui Guo
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Feng
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Can Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Faqian Xiong
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongfu Qiu
- College of Agriculture, Guangxi University, Nanning, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xinghai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Yang W, Chen L, Zhao J, Wang J, Li W, Yang T, Dong J, Ma Y, Zhou L, Chen J, Wu W, Zhang S, Liu B. Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures. FRONTIERS IN PLANT SCIENCE 2022; 13:841191. [PMID: 35356125 PMCID: PMC8959774 DOI: 10.3389/fpls.2022.841191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.
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Affiliation(s)
- Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wei Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- *Correspondence: Shaohong Zhang,
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Bin Liu,
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Genotypic diversity of quality traits in Chinese foxtail millet (Setaria italica L.) and the establishment of a quality evaluation system. Food Chem 2021; 353:129421. [PMID: 33714791 DOI: 10.1016/j.foodchem.2021.129421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 11/21/2022]
Abstract
Foxtail millet (Setaria italica L.) is an important reserve cereal crop, and its nutritional and medicinal properties have seen its demand increase in recent years. Therefore, it is important to establish an evaluation system for the comprehensive assessment of its quality. We assessed 90 accessions of foxtail millet from China for 23 quality traits. The results showed that the 23 quality traits had diverse coefficients of variation, with the greatest variation in a*, phosphorus content, and potassium contents, at 37.71, 28.81, and 20.18%, respectively. Cluster analysis defined five categories that were consistent with the geographical origins of the accessions. Seven principal components were also extracted from the 23 traits using principal component analysis. A comprehensive quality evaluation system was established, and 8 high-quality accessions were identified. The findings of the present study could facilitate the breeding of high-quality foxtail millet and enhance quality evaluation activities.
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Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) as High-Throughput SNP Genotyping Methods. Methods Mol Biol 2021; 2264:75-87. [PMID: 33263904 DOI: 10.1007/978-1-0716-1201-9_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Most plant agronomic traits are quantitatively inherited. Identification of quantitative trait loci (QTL) is a challenging target for most scientists and crop breeders as large-scale genotyping is difficult. Molecular marker technology has continuously evolved from hybridization-based technology to PCR-based technology, and finally, sequencing-based high-throughput single-nucleotide polymorphisms (SNPs). High-throughput sequencing technologies can provide strategies for sequence-based SNP genotyping. Here we describe the SLAF-seq that can be applied as the SNP genotyping approach. The high-throughput SNP genotyping methods will prove useful for the construction of high-density genetic maps and identification of QTLs for their deployment in plant breeding and facilitate genome-wide selection (GWS) and genome-wide association studies (GWAS).
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8
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Pan Y, Chen L, Zhao Y, Guo H, Li J, Rashid MAR, Lu C, Zhou W, Yang X, Liang Y, Wu H, Qing D, Gao L, Dai G, Li D, Deng G. Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:784037. [PMID: 34899812 PMCID: PMC8655879 DOI: 10.3389/fpls.2021.784037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 05/17/2023]
Abstract
Rice (Oryza sativa L.) is an important staple food crop for more than half of the world's population. Enhancing the grain quality and yield of rice to meet growing demand remains a major challenge. Here, we show that OsMKK3 encode a MAP kinase kinase that controls grain size and chalkiness by affecting cell proliferation in spikelet hulls. We showed that OsSPL16, GS5, and GIF1 have a substantial effect on the OsMKK3-regulated grain size pathway. OsMKK3 has experienced strong directional selection in indica and japonica. Wild rice accessions contained four OsMKK3 haplotypes, suggesting that the OsMKK3 haplotypes present in cultivated rice likely originated from different wild rice accessions during rice domestication. OsMKK3-Hap1, gs3, and gw8 were polymerized to enhance the grain length. Polymerization of beneficial alleles, such as OsMKK3-Hap1, gs3, gw8, fgr, alk, chalk5, and wx, also improved the quality of hybrid rice. Overall, the results indicated that beneficial OsMKK3 alleles could be used for genomic-assisted breeding for rice cultivar improvement and be polymerized with other beneficial alleles.
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Affiliation(s)
- Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Haifeng Guo
- Beijing Key Laboratory of Crop Genetic Improvement, State Key Laboratory of Agrobiotechnology, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jingcheng Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | | | - Chunju Lu
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weiyong Zhou
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xingka Yang
- Guangxi Lvhai Seed Co., Ltd., Nanning, China
| | - Yuntao Liang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hao Wu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dongjing Qing
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- *Correspondence: Lijun Gao,
| | - Gaoxing Dai
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Gaoxing Dai,
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Danting Li,
| | - Guofu Deng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guofu Deng,
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9
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Zhang A, Gao Y, Li Y, Ruan B, Yang S, Liu C, Zhang B, Jiang H, Fang G, Ding S, Jahan N, Xie L, Dong G, Xu Z, Gao Z, Guo L, Qian Q. Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency. FRONTIERS IN PLANT SCIENCE 2020; 11:342. [PMID: 32265976 PMCID: PMC7105826 DOI: 10.3389/fpls.2020.00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/06/2020] [Indexed: 05/27/2023]
Abstract
Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC4F2 population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.
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Affiliation(s)
- Anpeng Zhang
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shenglong Yang
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guonan Fang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Noushin Jahan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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10
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Mbanjo EGN, Kretzschmar T, Jones H, Ereful N, Blanchard C, Boyd LA, Sreenivasulu N. The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain. Front Genet 2020; 11:229. [PMID: 32231689 PMCID: PMC7083195 DOI: 10.3389/fgene.2020.00229] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
Improving the nutritional quality of rice grains through modulation of bioactive compounds and micronutrients represents an efficient means of addressing nutritional security in societies which depend heavily on rice as a staple food. White rice makes a major contribution to the calorific intake of Asian and African populations, but its nutritional quality is poor compared to that of pigmented (black, purple, red orange, or brown) variants. The compounds responsible for these color variations are the flavonoids anthocyanin and proanthocyanidin, which are known to have nutritional value. The rapid progress made in the technologies underlying genome sequencing, the analysis of gene expression and the acquisition of global 'omics data, genetics of grain pigmentation has created novel opportunities for applying molecular breeding to improve the nutritional value and productivity of pigmented rice. This review provides an update on the nutritional value and health benefits of pigmented rice grain, taking advantage of both indigenous and modern knowledge, while also describing the current approaches taken to deciphering the genetic basis of pigmentation.
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Affiliation(s)
- Edwige Gaby Nkouaya Mbanjo
- International Rice Research Institute, Los Baños, Philippines
- International Institute for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Huw Jones
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Nelzo Ereful
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Christopher Blanchard
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Lesley Ann Boyd
- National Institute of Agricultural Botany, Cambridge, United Kingdom
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11
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Wen Y, Fang Y, Hu P, Tan Y, Wang Y, Hou L, Deng X, Wu H, Zhu L, Zhu L, Chen G, Zeng D, Guo L, Zhang G, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Xue D, Qian Q, Hu J. Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1143. [PMID: 32849702 PMCID: PMC7411225 DOI: 10.3389/fpls.2020.01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 05/02/2023]
Abstract
Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.
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Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Peng Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiqing Tan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yueying Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xuemei Deng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hao Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- *Correspondence: Qian Qian, ; Jiang Hu,
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Qian Qian, ; Jiang Hu,
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12
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Wang RJ, Gao XF, Yang J, Kong XR. Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea ( Camellia sinensis) Using SLAF-seq. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10380-10391. [PMID: 31464444 DOI: 10.1021/acs.jafc.9b03330] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The timing of spring bud flush (TBF) is of economic importance for tea plant (Camellia sinensis) breeding. We employed a genome-wide association study (GWAS) to identify favorable single nucleotide polymorphism (SNP) allelic variations as well as candidate genes that control TBF of C. sinensis using specific-locus-amplified fragment sequencing (SLAF-seq) in a diversity panel comprising 151 tea plant germplasm resources. GWAS analysis revealed 26 SNPs associated with TBF in three years, and we eventually identified a final significant SNP for TBF. To identify candidate genes possibly related to TBF, we screened seven candidate genes within 100 kb regions surrounding the trait-related SNP loci. Furthermore, the favorable allelic variation, the "TT" genotype in the SNP loci, was discovered, and a derived cleaved amplified polymorphism (dCAPS) marker was designed that cosegregated with TBF, which could be used for marker-assisted selection (MAS) breeding in C. sinensis. The results obtained from this study can provide a theoretical and applied basis for the MAS of early breeding in tea plants in the future.
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Affiliation(s)
- Rang Jian Wang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Feng Gao
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Jun Yang
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
| | - Xiang Rui Kong
- Institute of Tea , Fujian Academy of Agricultural Sciences , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
- Fujian Branch , National Center for Tea Improvement , 1 Hutouyang Road, Shekou , Fu'an , Fujian 355015 , China
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13
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Sun D, Cen H, Weng H, Wan L, Abdalla A, El-Manawy AI, Zhu Y, Zhao N, Fu H, Tang J, Li X, Zheng H, Shu Q, Liu F, He Y. Using hyperspectral analysis as a potential high throughput phenotyping tool in GWAS for protein content of rice quality. PLANT METHODS 2019; 15:54. [PMID: 31139243 PMCID: PMC6532189 DOI: 10.1186/s13007-019-0432-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/02/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The advances of hyperspectral technology provide a new analytic means to decrease the gap of phenomics and genomics caused by the fast development of plant genomics with the next generation sequencing technology. Through hyperspectral technology, it is possible to phenotype the biochemical attributes of rice seeds and use the data for GWAS. RESULTS The results of correlation analysis indicated that Normalized Difference Spectral Index (NDSI) had high correlation with protein content (PC) with RNDSI 2 = 0.68. Based on GWAS analysis using all the traits, NDSI was able to identify the same SNP loci as rice protein content that was measured by traditional methods. In total, hyperspectral trait NDSI identified all the 43 genes that were identified by biochemical trait PC. NDSI identified 1 extra SNP marker on chromosome 1, which annotated extra 22 genes that were not identified by PC. Kegg annotation results showed that traits NDSI annotated 3 pathways that are exactly the same as PC. The cysteine and methionine metabolic pathway identified by both NDSI and PC was reported important for biosynthesis and metabolism of some of amino acids/protein in rice seeds. CONCLUSION This study combined hyperspectral technology and GWAS analysis to dissect PC of rice seeds, which was high throughput and proven to be able to apply to GWAS as a new phenotyping tool. It provided a new means to phenotype one of the important biochemical traits for the determination of rice quality that could be used for genetic studies.
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Affiliation(s)
- Dawei Sun
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Haiyan Cen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Haiyong Weng
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Liang Wan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Alwaseela Abdalla
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Ahmed Islam El-Manawy
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Yueming Zhu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Nan Zhao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Haowei Fu
- Jiaxing Academy of Agricultural Sciences, Jiaxing, 314016 China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing, 101300 China
| | - Xiaolong Li
- Biomarker Technologies Corporation, Beijing, 101300 China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing, 101300 China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institution of Crop Science, Zhejiang University, Hangzhou, 310058 China
| | - Fei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People’s Republic of China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, 310058 People’s Republic of China
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou, 310058 People’s Republic of China
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