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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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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. Multi-model genome-wide association studies for appearance quality in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1304388. [PMID: 38273959 PMCID: PMC10808671 DOI: 10.3389/fpls.2023.1304388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024]
Abstract
Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, International Crop Reseach Institute for Semi Arid Tropics (ICRISAT), Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
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Gan Z, Zhang M, Xu S, Li T, Zhang X, Wang J, Wang L. Comparison of quinoa and highland barley derived dietary fibers influence on the physicochemical properties and digestion of rice starch. Food Res Int 2023; 174:113549. [PMID: 37986428 DOI: 10.1016/j.foodres.2023.113549] [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: 07/23/2023] [Revised: 09/26/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
This study investigated the potential of highland barley and quinoa dietary fibers, rich in β-glucan and pectin respectively, as cost-effective and nutritionally valuable physical modifiers for rice starch (RS). HPAEC revealed differences between the monosaccharide composition of soluble and insoluble dietary fibers sourced from highland barley and quinoa (HSDF, HIDF, QSDF and QIDF). Results from both RVA and DSC analysis revealed that the addition of low amounts of dietary fiber significantly modified the pasting properties of RS. Notably, the addition of quinoa soluble dietary fiber (QSDF) significantly inhibits the formation of a stable gel network in rice starch, even at low concentrations (0.1 %), as confirmed by rheological measurements. Furthermore, the incorporation of QSDF effectively reduces the content of rapidly digestible starch in rice starch by 15.6 % and increases the content of slowly digestible starch, from 23.36 % ± 3.02 % to 31.07 % ± 3.98 %. By leveraging the compositional richness of these fibers, this research opens up novel opportunities for developing functional food products with improved nutritional profiles, as well as for improving texture and reducing glycemic index (GI) in starch-based foods.
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Affiliation(s)
- Zhicong Gan
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Ming Zhang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Shunqian Xu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Ting Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Xinxia Zhang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Junren Wang
- Institute of Modern Agriculture, Jiangsu Provincial Agricultural Reclamation and Development Co., Ltd., Nanjing 211800, China
| | - Li Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Lihu Road 1800, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.
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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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Kumar A, Thomas J, Gill N, Dwiningsih Y, Ruiz C, Famoso A, Pereira A. Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress. Sci Rep 2023; 13:4880. [PMID: 36966148 PMCID: PMC10039871 DOI: 10.1038/s41598-023-31399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from - 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from - 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.
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Affiliation(s)
- Anuj Kumar
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Julie Thomas
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yheni Dwiningsih
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Charles Ruiz
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Rayne, LA, 70578, USA
| | - Andy Pereira
- Departemnt of Crop, Soil, & Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Wu M, Cai M, Zhai R, Ye J, Zhu G, Yu F, Ye S, Zhang X. A mitochondrion-associated PPR protein, WBG1, regulates grain chalkiness in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1136849. [PMID: 36968383 PMCID: PMC10033517 DOI: 10.3389/fpls.2023.1136849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Rice kernel quality has vital commercial value. Grain chalkiness deteriorates rice's appearance and palatability. However, the molecular mechanisms that govern grain chalkiness remain unclear and may be regulated by many factors. In this study, we identified a stable hereditary mutant, white belly grain 1 (wbg1), which has a white belly in its mature grains. The grain filling rate of wbg1 was lower than that of the wild type across the whole filling period, and the starch granules in the chalky part were oval or round and loosely arranged. Map-based cloning showed that wbg1 was an allelic mutant of FLO10, which encodes a mitochondrion-targeted P-type pentatricopeptide repeat protein. Amino acid sequence analysis found that two PPR motifs present in the C-terminal of WBG1 were lost in wbg1. This deletion reduced the splicing efficiency of nad1 intron 1 to approximately 50% in wbg1, thereby partially reducing the activity of complex I and affecting ATP production in wbg1 grains. Furthermore, haplotype analysis showed that WBG1 was associated with grain width between indica and japonica rice varieties. These results suggested that WBG1 influences rice grain chalkiness and grain width by regulating the splicing efficiency of nad1 intron 1. This deepens understanding of the molecular mechanisms governing rice grain quality and provides theoretical support for molecular breeding to improve rice quality.
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Affiliation(s)
- Mingming Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maohong Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jing Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guofu Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Faming Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoming Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Itagi H, Sartagoda KJD, Pratap V, Roy P, Tiozon RN, Regina A, Sreenivasulu N. Popped rice with distinct nutraceutical properties. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Abhijith KP, Gopala Krishnan S, Ravikiran KT, Dhawan G, Kumar P, Vinod KK, Bhowmick PK, Nagarajan M, Seth R, Sharma R, Badhran SK, Bollinedi H, Ellur RK, Singh AK. Genome-wide association study reveals novel genomic regions governing agronomic and grain quality traits and superior allelic combinations for Basmati rice improvement. FRONTIERS IN PLANT SCIENCE 2022; 13:994447. [PMID: 36544876 PMCID: PMC9760805 DOI: 10.3389/fpls.2022.994447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Basmati is a speciality segment in the rice genepool characterised by explicit grain quality. For the want of suitable populations, genome-wide association study (GWAS) in Basmati rice has not been attempted. MATERIALS To address this gap, we have performed a GWAS on a panel of 172 elite Basmati multiparent population comprising of potential restorers and maintainers. Phenotypic data was generated for various agronomic and grain quality traits across seven different environments during two consecutive crop seasons. Based on the observed phenotypic variation, three agronomic traits namely, days to fifty per cent flowering, plant height and panicle length, and three grain quality traits namely, kernel length before cooking, length breadth ratio and kernel length after cooking were subjected to GWAS. Genotyped with 80K SNP array, the population was subjected to principal component analysis to stratify the underlying substructure and subjected to the association analysis using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. RESULTS We identified 32 unique MTAs including 11 robust MTAs for the agronomic traits and 25 unique MTAs including two robust MTAs for the grain quality traits. Six out of 13 robust MTAs were novel. By genome annotation, six candidate genes associated with the robust MTAs were identified. Further analysis of the allelic combinations of the robust MTAs enabled the identification of superior allelic combinations in the population. This information was utilized in selecting 77 elite Basmati rice genotypes from the panel. CONCLUSION This is the first ever GWAS study in Basmati rice which could generate valuable information usable for further breeding through marker assisted selection, including enhancing of heterosis.
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Affiliation(s)
- Krishnan P. Abhijith
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S. Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Gaurav Dhawan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pankaj Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, Tamil Nadu, India
| | - Rakesh Seth
- Regional Station, ICAR-Indian Agricultural Research Institute, Karnal, Haryana, India
| | - Ritesh Sharma
- Basmati Export Development Foundation (BEDF), Meerut, Uttar Pradesh, India
| | | | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Deng Z, Liu Y, Gong C, Chen B, Wang T. Waxy is an important factor for grain fissure resistance and head rice yield as revealed by a genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6942-6954. [PMID: 36052968 PMCID: PMC9629786 DOI: 10.1093/jxb/erac330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Head rice yield (HRY) is an essential quality trait, and is sensitive to environmental stresses during the grain-filling, harvest, and postharvest stages. It is therefore important for rice production and global food security to select for superior HRY traits; however, the molecular basis of this trait remains unknown. Using diverse rice germplasm material, we performed a genome-wide association study of grain fissure resistance (GFR), the phenotype most associated with HRY, and found that the granule-bound starch synthase I gene Waxy is an important gene controlling GFR. Analysis of near-isogenic lines demonstrated that genetic variations in Waxy conferred different levels of tolerance to fissuring in grains. The null allele wx resulted in the highest GFR, while alleles that increased amylose synthesis reduced GFR. Increases in amylose content led to increases in the ratio of the widths of the amorphous layer to the semi-crystalline layer of the starch granules, and also to increased occurrence of chalkiness. The layer structure determined GFR by affecting the degree of swelling of granules in response to moisture, and chalkiness acted as an accelerator of moisture infiltration to rapidly increase the number of swelling granules. Our study reveals the molecular basis of GFR and HRY, thus opening the door for further understanding of the molecular networks of GFR and HRY.
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Affiliation(s)
| | | | - Chunyan Gong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bingtang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Chandran AKN, Sandhu J, Irvin L, Paul P, Dhatt BK, Hussain W, Gao T, Staswick P, Yu H, Morota G, Walia H. Rice Chalky Grain 5 regulates natural variation for grain quality under heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1026472. [PMID: 36304400 PMCID: PMC9593041 DOI: 10.3389/fpls.2022.1026472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature grain images to be effective in distinguishing chalky grains from translucent grains derived from control (28/24°C) and heat stressed (36/32°C) plants. Our analysis yielded a novel gene, rice Chalky Grain 5 (OsCG5) that regulates natural variation for grain chalkiness under heat stress. OsCG5 encodes a grain-specific, expressed protein of unknown function. Accessions with lower transcript abundance of OsCG5 exhibit higher chalkiness, which correlates with higher RG values under stress. These findings are supported by increased chalkiness of OsCG5 knock-out (KO) mutants relative to wildtype (WT) under heat stress. Grains from plants overexpressing OsCG5 are less chalky than KOs but comparable to WT under heat stress. Compared to WT and OE, KO mutants exhibit greater heat sensitivity for grain size and weight relative to controls. Collectively, these results show that the natural variation at OsCG5 may contribute towards rice grain quality under heat stress.
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Affiliation(s)
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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Low Light Stress Increases Chalkiness by Disturbing Starch Synthesis and Grain Filling of Rice. Int J Mol Sci 2022; 23:ijms23169153. [PMID: 36012414 PMCID: PMC9408977 DOI: 10.3390/ijms23169153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Low light stress increases the chalkiness of rice; however, this effect has not been fully characterized. In this study, we demonstrated that low light resulted in markedly decreased activity of ADP-glucose pyrophosphorylase in the grains and those of sucrose synthase and soluble starch synthase in the early period of grain filling. Furthermore, low light also resulted in decreased activities of granule-bound starch synthase and starch branching enzyme in the late period of grain filling. Therefore, the maximum and mean grain filling rates were reduced but the time to reach the maximum grain filling rates and effective grain filling period were increased by low light. Thus, it significantly decreased the grain weight at the maximum grain filling rate and grain weight and retarded the endosperm growth and development, leading to a loose arrangement of the amyloplasts and an increase in the chalkiness of the rice grains. Compared to the grains at the top panicle part, low light led to a greater decrease in the grain weight at the maximum grain filling rate and time to reach the grain weight at the maximum grain filling rate at the bottom panicle part, which contributed to an increase in chalkiness by increasing the rates of different chalky types at the bottom panicle part. In conclusion, low light disturbed starch synthesis in grains, thereby impeding the grain filling progress and increasing chalkiness, particularly for grains at the bottom panicle part.
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12
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Yang W, Hao Q, Liang J, Tan Q, Luan X, Lin S, Zhu H, Bu S, Liu Z, Liu G, Wang S, Zhang G. Fine Mapping of Two Major Quantitative Trait Loci for Rice Chalkiness With High Temperature-Enhanced Additive Effects. FRONTIERS IN PLANT SCIENCE 2022; 13:957863. [PMID: 35845647 PMCID: PMC9280674 DOI: 10.3389/fpls.2022.957863] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 05/31/2023]
Abstract
Chalkiness is a crucial determinant of rice quality. During seed filling period, high temperature usually increases grain chalkiness, resulting in poor grain quality. Rice chalkiness was controlled by quantitative trait loci (QTLs) and influenced by environmental conditions. In this study, we identified two single-segment substitution lines (SSSLs) 22-05 and 15-06 with significantly lower percentage of grain chalkiness (PGC) than recipient Huajingxian 74 (HJX74) over 6 cropping seasons. Two major QTLs for chalkiness, qPGC5 and qPGC6, were located by substitution mapping of SSSLs 22-05 and 15-06, respectively. qPGC5 was located in the 876.5 kb interval of chromosome 5 and qPGC6 was located in the 269.1 kb interval of chromosome 6. Interestingly, the PGC of HJX74 was significantly different between the two cropping seasons per year, with 25.8% in the first cropping season (FCS) and 16.6% in the second cropping season (SCS), while the PGC of SSSLs 22-05 and 15-06 did not significantly differ between FCS and SCS. The additive effects of qPGC5 and qPGC6 on chalkiness in the SSSLs were significantly greater in FCS than in SCS. These results showed that qPGC5 and qPGC6 had major effects on chalkiness and the SSSL alleles were more effective in reducing chalkiness under high temperature condition in FCS. The fine-mapping of the two QTLs will facilitate the cloning of genes for chalkiness and provide new genetic resources to develop new cultivars with low chalkiness even under high temperature condition.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jiayan Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Shaojun Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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13
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Ravikiran KT, Gopala Krishnan S, Abhijith KP, Bollinedi H, Nagarajan M, Vinod KK, Bhowmick PK, Pal M, Ellur RK, Singh AK. Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice. Front Genet 2022; 13:876522. [PMID: 35734422 PMCID: PMC9208292 DOI: 10.3389/fgene.2022.876522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/25/2022] [Indexed: 11/14/2022] Open
Abstract
Temperature rise predicted for the future will severely affect rice productivity because the crop is highly sensitive to heat stress at the reproductive stage. Breeding tolerant varieties is an economically viable option to combat heat stress, for which the knowledge of target genomic regions associated with the reproductive stage heat stress tolerance (RSHT) is essential. A set of 192 rice genotypes of diverse origins were evaluated under natural field conditions through staggered sowings for RSHT using two surrogate traits, spikelet fertility and grain yield, which showed significant reduction under heat stress. These genotypes were genotyped using a 50 k SNP array, and the association analysis identified 10 quantitative trait nucleotides (QTNs) for grain yield, of which one QTN (qHTGY8.1) was consistent across the different models used. Only two out of 10 MTAs coincided with the previously reported QTLs, making the remaing eight novel. A total of 22 QTNs were observed for spikelet fertility, among which qHTSF5.1 was consistently found across three models. Of the QTNs identified, seven coincided with previous reports, while the remaining QTNs were new. The genes near the QTNs were found associated with the protein–protein interaction, protein ubiquitination, stress signal transduction, and so forth, qualifying them to be putative for RSHT. An in silico expression analysis revealed the predominant expression of genes identified for spikelet fertility in reproductive organs. Further validation of the biological relevance of QTNs in conferring heat stress tolerance will enable their utilization in improving the reproductive stage heat stress tolerance in rice.
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Affiliation(s)
- K T Ravikiran
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K P Abhijith
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - H Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-IARI, Aduthurai, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - P K Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - R K Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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14
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Yu P, Ye C, Li L, Yin H, Zhao J, Wang Y, Zhang Z, Li W, Long Y, Hu X, Xiao J, Jia G, Tian B. Genome-wide association study and genomic prediction for yield and grain quality traits of hybrid rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:16. [PMID: 37309463 PMCID: PMC10248665 DOI: 10.1007/s11032-022-01289-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Genomic selection is an efficient tool for breeding selection, especially for quantitative traits controlled by multiples genes with low heritability. To validate the application of genomic selection in hybrid rice breeding, the yield and grain quality traits of 404 hybrid rice breeding lines were investigated, and the same accessions were genotyped by using a 56 K SNP chip. There were wide variances among the tested accessions for all the measured traits, and most of the traits were correlated. A total of 67 significant loci were identified for the yield-related traits, and 123 significant loci were identified for the grain quality traits by GWAS. Two of these loci associated with increasing grain yield but decreasing grain quality. The GEBVs of all the yield and grain quality traits were calculated by using 15 different prediction algorithms. The plant height, panicle length, thousand grain weight, grain length and width ratio, amylose content, and alkali value have higher predictability than other traits. However, the predictive accuracy of different GS models is different for different traits. This study provided useful information for genomic selection of specific trait using proper markers and prediction models. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01289-6.
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Affiliation(s)
- Peiyi Yu
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Changrong Ye
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Le Li
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Hexing Yin
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Jian Zhao
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Yongka Wang
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Zhe Zhang
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Weiguo Li
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Yu Long
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Xueyi Hu
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Jinhua Xiao
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Gaofeng Jia
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
| | - Bingchuan Tian
- Huazhi Biotechnology Co. Ltd, Changsha, 410125 Hunan China
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15
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Hu X, Zhang W, Lu L, Shao Y, Chen M, Zhu Z, Mou R. Comparison of quality of appearance, cooking quality, and protein content of green‐labeled rice and conventional rice. Cereal Chem 2022. [DOI: 10.1002/cche.10543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xianqiao Hu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Weixing Zhang
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Lin Lu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Yafang Shao
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Mingxue Chen
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Zhiwei Zhu
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
| | - Renxiang Mou
- Rice Product Quality Supervision and Inspection Center, Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou China
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16
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OsbZIP60-mediated unfolded protein response regulates grain chalkiness in rice. J Genet Genomics 2022; 49:414-426. [DOI: 10.1016/j.jgg.2022.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 12/21/2022]
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17
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Tiozon RJN, Bonto AP, Sreenivasulu N. Enhancing the functional properties of rice starch through biopolymer blending for industrial applications: A review. Int J Biol Macromol 2021; 192:100-117. [PMID: 34619270 DOI: 10.1016/j.ijbiomac.2021.09.194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023]
Abstract
Rice starch has been used in various agri-food products due to its hypoallergenic properties. However, rice starch has poor solubility, lower resistant starch content with reduced retrogradation and poor functional properties. Hence, its industrial applications are rather limited. The lack of comprehensive information and a holistic understanding of the interaction between rice starch and endo/exogenous constituents to improve physico-chemical properties is a prerequisite in designing industrial products with enhanced functional attributes. In this comprehensive review, we highlight the potentials of physically mixing of biopolymers in upgrading the functional characteristics of rice starch as a raw material for industrial applications. Specifically, this review tackles rice starch modifications by adding natural/synthetic polymers and plasticizers, leading to functional blends or composites in developing sustainable packaging materials, pharma- and nutraceutical products. Moreover, a brief discussion on rice starch chemical and genetic modifications to alter starch quality for the deployment of rice starch industrial application is also highlighted.
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Affiliation(s)
- Rhowell Jr N Tiozon
- Consumer driven Grain Quality and Nutrition unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines; Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Aldrin P Bonto
- Chemistry Department, De La Salle University, 2401 Taft, Avenue, Manila 0922, Philippines; Department of Chemistry, College of Science, University of Santo Tomas, España Blvd, Sampaloc, Manila, 1008, Metro Manila, Philippines.
| | - Nese Sreenivasulu
- Consumer driven Grain Quality and Nutrition unit, Rice Breeding and Innovation Platform, International Rice Research Institute, Los Baños 4030, Philippines.
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18
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Wu B, Xia D, Zhou H, Cheng S, Wang Y, Li M, Gao G, Zhang Q, Li X, He Y. Fine mapping of qWCR7, a grain chalkiness QTL in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:68. [PMID: 37309362 PMCID: PMC10236040 DOI: 10.1007/s11032-021-01260-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
Chalkiness is one of the key determinants of rice quality and is a highly undesirable trait for breeding and marketing. In this study, qWCR7, a major quantitative trait locus (QTL) of white-core rate (WCR), was genetically validated using a BC3F2 segregation population and further fine mapped using a near isogenic line (NIL) population, of which both were derived from a cross between the donor parent DL208 and the recurrent parent ZS97. qWCR7 was finally narrowed to a genomic interval of ~ 68 kb, containing seven annotated genes. Among those, two genes displayed markedly different expression levels in endosperm of NILs. Transcriptome analysis showed that the synthesis and accumulation of metabolites played a key role in chalkiness formation. The contents of storage components and expression levels of related genes were detected, suggesting that starch and storage protein were closely related to white-core trait. Our findings have laid the foundation of map-based cloning of qWCR7, which may have potential value in quality improvement during rice breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01260-x.
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Affiliation(s)
- Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Shiyuan Cheng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yipei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070 Hubei China
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19
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Yang W, Xiong L, Liang J, Hao Q, Luan X, Tan Q, Lin S, Zhu H, Liu G, Liu Z, Bu S, Wang S, Zhang G. Substitution Mapping of Two Closely Linked QTLs on Chromosome 8 Controlling Grain Chalkiness in Rice. RICE (NEW YORK, N.Y.) 2021; 14:85. [PMID: 34601659 PMCID: PMC8487414 DOI: 10.1186/s12284-021-00526-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/18/2021] [Indexed: 05/27/2023]
Abstract
Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness, grain length and width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by higher temperature. Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to higher temperature.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jiayan Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shiwan Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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20
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Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
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Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
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21
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Misra G, Badoni S, Parween S, Singh RK, Leung H, Ladejobi O, Mott R, Sreenivasulu N. Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:910-925. [PMID: 33220119 PMCID: PMC8131057 DOI: 10.1111/pbi.13516] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/07/2020] [Accepted: 11/12/2020] [Indexed: 05/11/2023]
Abstract
Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome-wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high-value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi-parent advanced generation intercrosses and several low-chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high-yielding potentials.
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Affiliation(s)
- Gopal Misra
- International Rice Research InstituteLos BañosPhilippines
| | - Saurabh Badoni
- International Rice Research InstituteLos BañosPhilippines
| | - Sabiha Parween
- International Rice Research InstituteLos BañosPhilippines
| | - Rakesh Kumar Singh
- International Rice Research InstituteLos BañosPhilippines
- Present address:
International Center for Biosaline AgricultureAcademic CityDubaiUnited Arab Emirates
| | - Hei Leung
- International Rice Research InstituteLos BañosPhilippines
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NH787 EMS mutant of rice variety Nagina22 exhibits higher phosphate use efficiency. Sci Rep 2021; 11:9156. [PMID: 33911118 PMCID: PMC8080636 DOI: 10.1038/s41598-021-88419-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Rice (Oryza sativa L.), a major dietary source, is often cultivated in soils poor in available inorganic orthophosphate (Pi), which is a key nutrient for growth and development. Poor soils are amended by phosphorus (P) fertilizer, which is derived from the non-renewable rock phosphate reserves. Therefore, there is a need for developing rice varieties with high productivity under low P conditions. At the ICAR-IIRR, ethyl methanesulfonate (EMS) mutagenized rice genotype Nagina22 (N22) were screened for high grain yield in Pi-deprived soil, which led to the identification of ~ 10 gain-of-function mutants including NH787. Here, detailed comparative morphophysiological, biochemical, and molecular analyses of N22 and NH787 were carried out in hydroponics and potting soil under different Pi regimes. Under Pi-deprived condition, compared with N22, NH787 exhibited higher root and vegetative biomass, the number of tillers, and grain yield. The augmented agronomic traits of NH787 were corroborated with significantly higher photosynthetic rate, pollen fertility, stigma receptivity, and the activities of antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT). Further, several genes involved in the maintenance of Pi homeostasis (GPH) were differentially regulated. The study thus revealed a wide-spectrum influence of the mutation in NH787 that contributed towards its higher Pi use efficiency (PUE).
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Yang W, Liang J, Hao Q, Luan X, Tan Q, Lin S, Zhu H, Liu G, Liu Z, Bu S, Wang S, Zhang G. Fine mapping of two grain chalkiness QTLs sensitive to high temperature in rice. RICE (NEW YORK, N.Y.) 2021; 14:33. [PMID: 33792792 PMCID: PMC8017073 DOI: 10.1186/s12284-021-00476-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/23/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grain chalkiness is one of important factors affected rice grain quality. It is known that chalkiness is affected by the high temperature during the seed filling period. Although a larger of QTLs for chalkiness were reported across all 12 chromosomes, only a few of the QTLs were fine mapped or cloned up to now. Here, we fine map two QTLs for chalkiness in two single-segment substitution lines (SSSLs), 11-09 with substitution segment from O. sativa and HP67-11 with substitution segment from O. glaberrima. RESULTS The grain chalkiness of SSSLs 11-09 and HP67-11 was significantly lower than that in the recipient Huajingxian 74 (HJX74) in consecutive 8 cropping seasons. The regression correlation analysis showed that percentage of chalky grain (PCG) and percentage of chalky area (PCA) were significantly and positively correlated with percentage of grain chalkiness (PGC). Two QTLs for grain chalkiness were located on two chromosomes by substitution mapping. qPGC9 was mapped on chromosome 9 with an estimated interval of 345.6 kb. qPGC11 was located on chromosome 11 and delimited to a 432.1 kb interval in the O. sativa genome and a 332.9 kb interval in the O. glaberrima genome. qPGC11 is a QTL for grain chalkiness from O. glaberrima and was mapped in a new region of chromosome 11. The effect of two QTLs was incomplete dominance. The additive effects of two QTLs on chalkiness in second cropping season (SCS) were significantly greater than that in first cropping season (FCS). CONCLUSIONS qPGC11 is a new QTL for grain chalkiness. The two QTLs were fine mapped. The donor alleles of qPGC9 and qPGC11 were sensitive to the high temperature of FCS.
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Affiliation(s)
- Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jiayan Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qingwen Hao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shiwan Lin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
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24
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Rapid prediction of head rice yield and grain shape for genome-wide association study in indica rice. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.103091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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