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Huggins TD, Chen MH, Fjellstrom RG, Jackson AK, McClung AM, Edwards JD. Association Analysis of Three Diverse Rice ( Oryza sativa L.) Germplasm Collections for Loci Regulating Grain Quality Traits. THE PLANT GENOME 2019; 12:170085. [PMID: 30951092 DOI: 10.3835/plantgenome2017.09.0085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice ( L.) end-use cooking quality is vital for producers and billions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality provides essential information for improved breeding strategies to enhance desirable traits that are stable across variable climatic and environmental conditions. In this study, genome-wide association (GWA) analysis of three rice diversity panels, the USDA rice core subset (1364 accessions), the minicore (MC) (173 accessions after removing non-), and the high density rice array-MC (HDMC) (383 accessions), with simple sequence repeats, single nucleotide polymorphic markers, or both, revealed large- and small-effect loci associated with known genes and previously uncharacterized genomic regions. Clustering of the significant regions in the GWA results suggests that multiple grain quality traits are inherited together. The 11 novel candidate loci for grain quality traits and the seven candidates for grain chalk identified are involved in the starch biosynthesis pathway. This study highlights the intricate pleiotropic relationships that exist in complex genotype-phenotypic associations and gives a greater insight into effective breeding strategies for grain quality improvement.
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Muraya MM, Chu J, Zhao Y, Junker A, Klukas C, Reif JC, Altmann T. Genetic variation of growth dynamics in maize (Zea mays L.) revealed through automated non-invasive phenotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:366-380. [PMID: 27714888 DOI: 10.1111/tpj.13390] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 05/02/2023]
Abstract
Hitherto, most quantitative trait loci of maize growth and biomass yield have been identified for a single time point, usually the final harvest stage. Through this approach cumulative effects are detected, without considering genetic factors causing phase-specific differences in growth rates. To assess the genetics of growth dynamics, we employed automated non-invasive phenotyping to monitor the plant sizes of 252 diverse maize inbred lines at 11 different developmental time points; 50 k SNP array genotype data were used for genome-wide association mapping and genomic selection. The heritability of biomass was estimated to be over 71%, and the average prediction accuracy amounted to 0.39. Using the individual time point data, 12 main effect marker-trait associations (MTAs) and six pairs of epistatic interactions were detected that displayed different patterns of expression at various developmental time points. A subset of them also showed significant effects on relative growth rates in different intervals. The detected MTAs jointly explained up to 12% of the total phenotypic variation, decreasing with developmental progression. Using non-parametric functional mapping and multivariate mapping approaches, four additional marker loci affecting growth dynamics were detected. Our results demonstrate that plant biomass accumulation is a complex trait governed by many small effect loci, most of which act at certain restricted developmental phases. This highlights the need for investigation of stage-specific growth affecting genes to elucidate important processes operating at different developmental phases.
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Affiliation(s)
- Moses M Muraya
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
- Department of Plant Sciences, Chuka University, P.O. Box 109 - 60400, Chuka, Kenya
| | - Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Christian Klukas
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Seeland, Germany
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Gao Y, Liu C, Li Y, Zhang A, Dong G, Xie L, Zhang B, Ruan B, Hong K, Xue D, Zeng D, Guo L, Qian Q, Gao Z. QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9. RICE (NEW YORK, N.Y.) 2016; 9:41. [PMID: 27549111 PMCID: PMC4993740 DOI: 10.1186/s12284-016-0114-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/12/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far. RESULTS In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis. CONCLUSIONS OsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Kai Hong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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