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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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Ansari AA, Akhatar J, Sharma S, Banga SS, Atri C. Integrating multiple statistical indices to measure the stability of photosynthetic pigment content and composition in Brassica juncea (L.) Czern germplasm under varying environmental conditions. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-024-01116-3. [PMID: 39133366 DOI: 10.1007/s11120-024-01116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024]
Abstract
Understanding the stability of photosynthetic pigments is crucial for developing crop cultivars with high productivity and resilience to the environmental stresses. This study leveraged GGE biplot, WAASB, and MTSI indices to assess the stability of content and composition of photosynthetic pigments in leaves and siliques of 286 Brassica juncea (L.) Czern. genotypes across three environments. The GGE biplot analysis identified NRCQR-9901 as the best genotype in terms of chlorophyll 'a' under conditions of high irradiance and long days (E1). For chlorophyll 'b' and total chlorophyll, NC-533728 performed the best. AJ-2 and NPJ-208 had the maximum total carotenoids levels in leaves. RLC-2 was characterized by maximum values for chlorophyll a, chlorophyll b, and total chlorophyll in the siliques. The low irradiance, short days, and moderate to high temperatures (E2) seemed perfect for the synthesis of photosynthetic pigments. NPJ-182 shows the maximum concentrations of chlorophyll 'a', total chlorophyll, and total carotenoids in leaves. Conversely, IC-597869, RE-389, and IC-597894 exhibited the highest concentrations of chlorophyll 'b' under an environment characterized by low light intensity, shorter daylights, and low temperatures (E3) during flowering and siliqua formation stages. The combined analysis found NPJ-182, NC-533728, CN-105233, RLC-2, CN-101846, JA-96, PBR-357, JM-3, and DTM-34 as top performers with high stability. Comparative transcriptome analysis with two stable and high-performing genotypes (PBR-357 and DTM-34) and two average performers revealed upregulation of critical photosynthesis-related genes (ELIP1, CAB3.1, ELIP1.5, and LHCB5) in top performers. This study identified promising trait donors for use in breeding programs aimed at improving the mustard crop's photosynthetic efficiency, productivity, and stability.
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Affiliation(s)
- Aaftab Alam Ansari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder Singh Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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Breeding Canola ( Brassica napus L.) for Protein in Feed and Food. PLANTS 2021; 10:plants10102220. [PMID: 34686029 PMCID: PMC8539702 DOI: 10.3390/plants10102220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 01/12/2023]
Abstract
Interest in canola (Brassica napus L.). In response to this interest, scientists have been tasked with altering and optimizing the protein production chain to ensure canola proteins are safe for consumption and economical to produce. Specifically, the role of plant breeders in developing suitable varieties with the necessary protein profiles is crucial to this interdisciplinary endeavour. In this article, we aim to provide an overarching review of the canola protein chain from the perspective of a plant breeder, spanning from the genetic regulation of seed storage proteins in the crop to advancements of novel breeding technologies and their application in improving protein quality in canola. A review on the current uses of canola meal in animal husbandry is presented to underscore potential limitations for the consumption of canola meal in mammals. General discussions on the allergenic potential of canola proteins and the regulation of novel food products are provided to highlight some of the challenges that will be encountered on the road to commercialization and general acceptance of canola protein as a dietary protein source.
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Hu D, Jing J, Snowdon RJ, Mason AS, Shen J, Meng J, Zou J. Exploring the gene pool of Brassica napus by genomics-based approaches. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1693-1712. [PMID: 34031989 PMCID: PMC8428838 DOI: 10.1111/pbi.13636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 05/08/2023]
Abstract
De novo allopolyploidization in Brassica provides a very successful model for reconstructing polyploid genomes using progenitor species and relatives to broaden crop gene pools and understand genome evolution after polyploidy, interspecific hybridization and exotic introgression. B. napus (AACC), the major cultivated rapeseed species and the third largest oilseed crop in the world, is a young Brassica species with a limited genetic base resulting from its short history of domestication, cultivation, and intensive selection during breeding for target economic traits. However, the gene pool of B. napus has been significantly enriched in recent decades that has been benefit from worldwide effects by the successful introduction of abundant subgenomic variation and novel genomic variation via intraspecific, interspecific and intergeneric crosses. An important question in this respect is how to utilize such variation to breed crops adapted to the changing global climate. Here, we review the genetic diversity, genome structure, and population-level differentiation of the B. napus gene pool in relation to known exotic introgressions from various species of the Brassicaceae, especially those elucidated by recent genome-sequencing projects. We also summarize progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection and genome-wide prediction, and describe the challenges and opportunities of these techniques as molecular platforms to exploit novel genomic variation and their value in the rapeseed gene pool. Future progress will accelerate the creation and manipulation of genetic diversity with genomic-based improvement, as well as provide novel insights into the neo-domestication of polyploid crops with novel genetic diversity from reconstructed genomes.
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Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinjie Jing
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for Biosystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
- Plant Breeding DepartmentINRESThe University of BonnBonnGermany
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
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Hu X, Zuo J. The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genomics 2021; 22:511. [PMID: 34233625 PMCID: PMC8261996 DOI: 10.1186/s12864-021-07787-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. RESULTS In this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication. CONCLUSIONS This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Xin S, Dong H, Yang L, Huang D, Zheng F, Cui Y, Wu S, Liao J, He Y, Wan H, Liu Z, Li X, Qian W. Both overlapping and independent loci underlie seed number per pod and seed weight in Brassica napus by comparative quantitative trait loci analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:41. [PMID: 37309442 PMCID: PMC10236046 DOI: 10.1007/s11032-021-01232-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/10/2021] [Indexed: 06/14/2023]
Abstract
Seed number per pod (SNPP) and seed weight (SW) are two components of seed yield in rapeseed (Brassica napus). Here, a natural population of rapeseed was employed for genome-wide association analysis for SNPP and SW across multi-years. A total of 101 and 77 SNPs significantly associated with SNPP and SW with the phenotypic variances (R2) ranging from 1.35 to 29.47% and from 0.78 to 34.58%, respectively. And 43 and 33 homologs of known genes from model plants were located in the 65 and 49 haplotype blocks (HBs) for SNPP and SW, respectively. Notably, we found 5 overlapping loci and 3 sets of loci with collinearity for both SNPP and SW, of which 4 overlapping loci harbored the haplotypes with the same direction of genetic effects on SNPP and SW, indicating high possibility to simultaneously improve SNPP and SW in rapeseed. Our findings revealed both overlapping and independent loci controlling seed number per pod and seed weight in rapeseed. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01232-1.
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Affiliation(s)
- Shuangshuang Xin
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Lei Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Dengwen Huang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Fajing Zheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Shuang Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Jinghang Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaorong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715 China
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Wani GA, Shah MA, Tekeu H, Reshi ZA, Atangana AR, Khasa DP. Phenotypic Variability and Genetic Diversity of Phragmites australis in Quebec and Kashmir Reveal Contrasting Population Structure. PLANTS 2020; 9:plants9101392. [PMID: 33092113 PMCID: PMC7589717 DOI: 10.3390/plants9101392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 11/23/2022]
Abstract
The origin of differences in traits influencing competitive success between invasive and native wild populations of alien species is subject of debate. Herbarium-based information sources from 2005 onwards about nativity and distributional range of Phragmites australis were used to survey putative native populations of the species in Quebec, and chloroplast DNA (cpDNA) PCR-RFLP analyses identified only one native population, whereas the same analyses revealed that the Kashmir populations are invasive. We compared the native population of P. australis in Quebec (QN), ten populations invasive to Quebec (QE), and five populations invasive in Kashmir, India (KE) using morphometric traits. Using nine cpDNA microsatellite loci, we also compared nine KE populations, ten QE populations, and the QN population. Phenotypic variation was observed among and within populations. Only dry mass of flowers varied across regions. Characterization of morphotypes defined three distinct haplotypes. A bimodal distribution of stem diameter (SD), internode length (IL), leaf length (LL), and leaf width (LW) suggests that a major gene may control growth traits or occurrence of co-selection. High genetic differentiation was observed between populations (RST = 0.353) and haplotypes (RST = 0.133 to 0.418), indicating limited gene flow and probable local adaptation. Principal coordinates analysis and the neighbor-joining phylogenetic tree clearly distinguished the three haplotypes. Among-populations phenotypic difference (PST) was lower than overall RST for plant height, SD, and fresh and dry mass of flowers and seeds, whereas PST estimates for LL and LW exceeded among-populations RST, suggesting divergent selection, while local adaptation might have occurred in IL, LL, and flower masses. Genetic drift probably influenced among-populations IL differences.
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Affiliation(s)
- Gowher A. Wani
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- Correspondence: ; Tel.: +91-700-601-1834
| | - Manzoor A. Shah
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
| | - Honoré Tekeu
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- Department of Plant Biology, Faculty of Science, University of Yaoundé, IPO Box 812 Yaoundé, Cameroon
| | - Zafar A. Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
| | - Alain R. Atangana
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- World Agroforestry, West and Central Africa Region, Cocody, Angré 7ème Tranche B.P. 2823, Abidjan 08 BP 2823, Cote D’Ivoire
| | - Damase P. Khasa
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
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Yao M, Guan M, Zhang Z, Zhang Q, Cui Y, Chen H, Liu W, Jan HU, Voss-Fels KP, Werner CR, He X, Liu Z, Guan C, Snowdon RJ, Hua W, Qian L. GWAS and co-expression network combination uncovers multigenes with close linkage effects on the oleic acid content accumulation in Brassica napus. BMC Genomics 2020; 21:320. [PMID: 32326904 PMCID: PMC7181522 DOI: 10.1186/s12864-020-6711-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 03/31/2020] [Indexed: 11/19/2022] Open
Abstract
Background Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed.
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Affiliation(s)
- Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Zhenqian Zhang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Qiuping Zhang
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Yixin Cui
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Hao Chen
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Habib U Jan
- Precision Medicine Lab, Rehman Medical Institute (RMI), Phase 5, Hayatabad, Peshawar, 25000, Pakistan
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Christian R Werner
- The Roslin Institute University of Edinburgh Easter Bush Research Centre Midlothian, Edinburgh, EH25 9RG, UK
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Zhongsong Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Wei Hua
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China. .,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062, China.
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, 410128, China.
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Jan HU, Guan M, Yao M, Liu W, Wei D, Abbadi A, Zheng M, He X, Chen H, Guan C, Nichols RA, Snowdon RJ, Hua W, Qian L. Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:157-164. [PMID: 31128685 DOI: 10.1016/j.plantsci.2019.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/01/2019] [Accepted: 02/09/2019] [Indexed: 05/05/2023]
Abstract
Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.
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Affiliation(s)
- Habib U Jan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China; Department of Microbiology and Biotechnology, Abasyn University Peshawar, Khyber Pakhtunkhwa, 25000, Pakistan; Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Mei Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Min Yao
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Wei Liu
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363, Holtsee, Germany
| | - Ming Zheng
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Xin He
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Hao Chen
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Chunyun Guan
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Wei Hua
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China.
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha, China; Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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11
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Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
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12
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Yuan Y, Peng D, Gu X, Gong Y, Sheng Z, Hu X. Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight -A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds. Front Genet 2018; 9:229. [PMID: 30013594 PMCID: PMC6036123 DOI: 10.3389/fgene.2018.00229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype–genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role of other factors in its genetic architecture, including their frequencies in the population and their interactions, have been largely overlooked. To comprehensively characterized the genetic architecture of BW, we performed a genome-wide association study (GWAS) both at the single-marker and haplotype level on birds from four indigenous Chinese chicken breeds (Chahua, Silkie, Langshan, and Beard), rather than studying crosses between two founder lines. Additionally, samples from two more breeds (Red Junglefowl and Recessive White) were included to better reflect variable genetic characteristics across populations. Six loci were mapped in this study, revealing the polygenic basis underlying BW. Moreover, by further examining the frequencies of the significantly associated haplotypes in each subpopulation and their effect sizes, most of the loci were found to affect BW in the Beard chicken breed alone. Two loci in GGA9 and GGA27, however, had a common effect on BW across subpopulations, showing that different underlying genetic mechanisms contribute to the phenotypic variability. These findings, particularly the variable genetic architectures found in different loci, improve our understanding of the overall genetic contributions to the large variability in BW among Chinese indigenous chicken breeds. These findings thus will have important implications for future chicken breeding.
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Affiliation(s)
- Yangyang Yuan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dezhi Peng
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Xiaorong Gu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
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13
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Qian L, Hickey LT, Stahl A, Werner CR, Hayes B, Snowdon RJ, Voss-Fels KP. Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1534. [PMID: 28928764 PMCID: PMC5591830 DOI: 10.3389/fpls.2017.01534] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/22/2017] [Indexed: 05/19/2023]
Abstract
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.
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Affiliation(s)
- Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural UniversityChangsha, China
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Christian R. Werner
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Ben Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Kai P. Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St LuciaQLD, Australia
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14
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Mason AS, Higgins EE, Snowdon RJ, Batley J, Stein A, Werner C, Parkin IAP. A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:621-633. [PMID: 28220206 DOI: 10.1007/s00122-016-2849-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.
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Affiliation(s)
- Annaliese S Mason
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jacqueline Batley
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia
- School of Plant Biology and The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia
| | - Anna Stein
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Christian Werner
- Department of Plant Breeding, IFZ for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada
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15
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Qian L, Voss-Fels K, Cui Y, Jan HU, Samans B, Obermeier C, Qian W, Snowdon RJ. Deletion of a Stay-Green Gene Associates with Adaptive Selection in Brassica napus. MOLECULAR PLANT 2016; 9:1559-1569. [PMID: 27825945 DOI: 10.1016/j.molp.2016.10.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 05/02/2023]
Abstract
Chlorophyll levels provide important information about plant growth and physiological plasticity in response to changing environments. The stay-green gene NON-YELLOWING 1 (NYE1) is believed to regulate chlorophyll degradation during senescence, concomitantly affecting the disassembly of the light-harvesting complex and hence indirectly influencing photosynthesis. We identified Brassica napus accessions carrying an NYE1 deletion associated with increased chlorophyll content, and with upregulated expression of light-harvesting complex and photosynthetic reaction center (PSI and PSII) genes. Comparative analysis of the seed oil content of accessions with related genetic backgrounds revealed that the B. napus NYE1 gene deletion (bnnye1) affected oil accumulation, and linkage disequilibrium signatures suggested that the locus has been subject to artificial selection by breeding in oilseed B. napus forms. Comparative analysis of haplotype diversity groups (haplogroups) between three different ecotypes of the allopolyploid B. napus and its A-subgenome diploid progenitor, Brassica rapa, indicated that introgression of the bnnye1 deletion from Asian B. rapa into winter-type B. napus may have simultaneously improved its adaptation to cooler environments experienced by autumn-sown rapeseed.
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Affiliation(s)
- Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Kai Voss-Fels
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, 400716 Chongqing, China
| | - Habib U Jan
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, 400716 Chongqing, China
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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