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Fu Y, Yao M, Qiu P, Song M, Ni X, Niu E, Shi J, Wang T, Zhang Y, Yu H, Qian L. Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:243. [PMID: 39352575 DOI: 10.1007/s00122-024-04733-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/24/2024] [Indexed: 10/03/2024]
Abstract
KEY MESSAGE We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Min Yao
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Ping Qiu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Maolin Song
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Xiyuan Ni
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Erli Niu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jianghua Shi
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tanliu Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Lunwen Qian
- College of Agronomy, Hunan Agricultural University, Changsha, China.
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Baker RL, Brock GL, Newsome EL, Zhao M. Polyploidy and the evolution of phenotypic integration: Network analysis reveals relationships among anatomy, morphology, and physiology. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11605. [PMID: 39184197 PMCID: PMC11342231 DOI: 10.1002/aps3.11605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 08/27/2024]
Abstract
Premise Most traits are polygenic and most genes are pleiotropic, resulting in complex, integrated phenotypes. Polyploidy presents an excellent opportunity to explore the evolution of phenotypic integration as entire genomes are duplicated, allowing for new associations among traits and potentially leading to enhanced or reduced phenotypic integration. Despite the multivariate nature of phenotypic evolution, studies often rely on simplistic bivariate correlations that cannot accurately represent complex phenotypes or data reduction techniques that can obscure specific trait relationships. Methods We apply network modeling, a common gene co-expression analysis, to the study of phenotypic integration to identify multivariate patterns of phenotypic evolution, including anatomy and morphology (structural) and physiology (functional) traits in response to whole genome duplication in the genus Brassica. Results We identify four key structural traits that are overrepresented in the evolution of phenotypic integration. Seeding networks with key traits allowed us to identify structure-function relationships not apparent from bivariate analyses. In general, allopolyploids exhibited larger, more robust networks indicative of increased phenotypic integration compared to diploids. Discussion Phenotypic network analysis may provide important insights into the effects of selection on non-target traits, even when they lack direct correlations with the target traits. Network analysis may allow for more nuanced predictions of both natural and artificial selection.
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Affiliation(s)
- Robert L. Baker
- Inventory and Monitoring DivisionNational Park ServiceFort Collins80525ColoradoUSA
| | | | - Eastyn L. Newsome
- Department of Botany and Plant PathologyPurdue UniversityWest Lafayette47907IndianaUSA
| | - Meixia Zhao
- Department of Microbiology and Cell ScienceUniversity of FloridaGainesville32611FloridaUSA
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Salami M, Heidari B, Alizadeh B, Batley J, Wang J, Tan XL, Dadkhodaie A, Richards C. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2024; 15:1342359. [PMID: 38567131 PMCID: PMC10985355 DOI: 10.3389/fpls.2024.1342359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction An important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security. Methods In this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season. Results The results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation. Discussion The results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
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Affiliation(s)
- Maryam Salami
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Alizadeh
- Oil Crops Research Department, Seed and Plant Improvement Institute, Agricultural Research Education and Extension, Organization, (AREEO), Karaj, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher Richards
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Laboratory for Genetic Resources Preservation, Fort Collins, CO, United States
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Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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Raman H, Shamaya N, Pirathiban R, McVittie B, Raman R, Cullis B, Easton A. Quantitative Trait Loci for Genotype and Genotype by Environment Interaction Effects for Seed Yield Plasticity to Terminal Water-Deficit Conditions in Canola ( Brassica napus L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040720. [PMID: 36840067 PMCID: PMC9964187 DOI: 10.3390/plants12040720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/12/2023]
Abstract
Canola plants suffer severe crop yield and oil content reductions when exposed to water-deficit conditions, especially during the reproductive stages of plant development. There is a pressing need to develop canola cultivars that can perform better under increased water-deficit conditions with changing weather patterns. In this study, we analysed genetic determinants for the main effects of quantitative trait loci (QTL), (Q), and the interaction effects of QTL and Environment (QE) underlying seed yield and related traits utilising 223 doubled haploid (DH) lines of canola in well-watered and water-deficit conditions under a rainout shelter. Moderate water-deficit at the pre-flowering stage reduced the seed yield to 40.8%. Multi-environmental QTL analysis revealed 23 genomic regions associated with days to flower (DTF), plant height (PH) and seed yield (SY) under well-watered and water-deficit conditions. Three seed yield QTL for main effects were identified on chromosomes A09, C03, and C09, while two were related to QE interactions on A02 and C09. Two QTL regions were co-localised to similar genomic regions for flowering time and seed yield (A09) and the second for plant height and chlorophyll content. The A09 QTL was co-located with a previously mapped QTL for carbon isotope discrimination (Δ13C) that showed a positive relationship with seed yield in the same population. Opposite allelic effects for plasticity in seed yield were identified due to QE interactions in response to water stress on chromosomes A02 and C09. Our results showed that QTL's allelic effects for DTF, PH, and SY and their correlation with Δ13C are stable across environments (field conditions, previous study) and contrasting water regimes (this study). The QTL and DH lines that showed high yield under well-watered and water-deficit conditions could be used to manipulate water-use efficiency for breeding improved canola cultivars.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Nawar Shamaya
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Ramethaa Pirathiban
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Brett McVittie
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Rosy Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Brian Cullis
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Andrew Easton
- Advanta Seeds Pty Ltd., 268 Anzac Avenue, Toowoomba, QLD 4350, Australia
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Ahmad A, Li W, Zhang H, Wang H, Wang P, Jiao Y, Zhao C, Yang G, Hong D. Linkage and association mapping of ovule number per ovary (ON) in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:11. [PMID: 37313129 PMCID: PMC10248604 DOI: 10.1007/s11032-023-01355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/11/2023] [Indexed: 06/15/2023]
Abstract
Ovule number (ON) produced during flower development determines the maximum number of seeds per silique and thereby affects crop productivity; however, the genetic basis of ON remains poorly understood in oilseed rape (Brassica napus). In this study, we genetically dissected the ON variations in a double haploid (DH) population and in natural population (NP) by linkage mapping and genome-wide association analysis. Phenotypic analysis showed that ON displayed normal distribution in both populations with the broad-sense heritability of 0.861 (DH population) and 0.930 (natural population). Linkage mapping identified 5 QTLs related to ON, including qON-A03, qON-A07, qON-A07-2, qON-A10, and qON-C06. Genome-wide association studies (GWAS) revealed 214, 48, and 40 significant single-nucleotide polymorphisms (SNPs) by individually using the single-locus model GLM and the multiple-locus model MrMLM and FASTMrMLM. The phenotypic variation explained (PVE) by these QTLs and SNPs ranged from 2.00-17.40% to 5.03-7.33%, respectively. Integration of the results from both strategies identified four consensus genomic regions associated with ON from the chromosomes A03, A07, and A10. Our results preliminarily resolved the genetic basis of ON and provides useful molecular markers for plant yield improvement in B. napus. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01355-7.
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Affiliation(s)
- Ali Ahmad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wenhui Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yushun Jiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Chenqi Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Zhao C, Xie M, Liang L, Yang L, Han H, Qin X, Zhao J, Hou Y, Dai W, Du C, Xiang Y, Liu S, Huang X. Genome-Wide Association Analysis Combined With Quantitative Trait Loci Mapping and Dynamic Transcriptome Unveil the Genetic Control of Seed Oil Content in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2022; 13:929197. [PMID: 35845656 PMCID: PMC9283957 DOI: 10.3389/fpls.2022.929197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed, an allotetraploid oil crop, provides vegetable oil for human consumption. The growing demand for oilseeds has necessitated the development of rapeseed varieties with improved quality. Therefore, a clear understanding of the genetic basis underlying the seed oil content (SOC) is required. In this study, a natural population comprising 204 diverse accessions and recombinant inbred lines (RILs) derived from Brassica napus and Sinapis alba via distant hybridization were collected for genome-wide association analysis (GWAS) and quantitative trait loci (QTL) mapping of the SOC trait, respectively. The variable coefficient of the RIL and natural populations ranged from 7.43 to 10.43% and 8.40 to 10.91%. Then, a high-density linkage map was constructed based on whole genome re-sequencing (WGS); the map harbored 2,799 bin markers and covered a total distance of 1,835.21 cM, with an average marker interval of 0.66 cM. The QTLs for SOC on chromosome A07 were stably detected in both single and multiple environments. Finally, a novel locus qA07.SOC was identified as the major QTL for SOC based on the GWAS and RIL populations. In addition, the RNA-seq results showed that photosynthesis, lipid biosynthesis proteins, fatty acid metabolism, and unsaturated fatty acid biosynthesis were significantly different between the developed seeds of the two parents of the RIL population. By comparing the variation information and expression levels of the syntenic genes within qA07.SOC and its syntenic genomic regions, as well as through haplotype analysis via GWAS, BnaA07.STR18, BnaA07.NRT1, and BnaA07g12880D were predicted as candidate genes in the qA07.SOC interval. These stable QTLs containing candidate genes and haplotypes can potentially provide a reliable basis for marker-assisted selection in B. napus breeding for SOC.
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Affiliation(s)
- Chuanji Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Longbing Liang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Hongshi Han
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xinrong Qin
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jixian Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yan Hou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wendong Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Caifu Du
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianqun Huang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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Fine mapping of qDB.A03, a QTL for rapeseed branching, and identification of the candidate gene. Mol Genet Genomics 2022; 297:699-710. [DOI: 10.1007/s00438-022-01881-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [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: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Suri GK, Braich S, Noy DM, Rosewarne GM, Cogan NOI, Kaur S. Advances in lentil production through heterosis: Evaluating generations and breeding systems. PLoS One 2022; 17:e0262857. [PMID: 35180225 PMCID: PMC8856536 DOI: 10.1371/journal.pone.0262857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/06/2022] [Indexed: 11/19/2022] Open
Abstract
Heterosis is defined as increased performance of the F1 hybrid relative to its parents. In the current study, a cohort of populations and parents were created to evaluate and understand heterosis across generations (i.e., F1 to F3) in lentil, a self-pollinated annual diploid (2n = 2× = 14) crop species. Lentil plants were evaluated for heterotic traits in terms of plant height, biomass fresh weight, seed number, yield per plant and 100 grain weight. A total of 47 selected lentil genotypes were cross hybridized to generate 72 F1 hybrids. The F1 hybrids from the top five crosses exhibited between 31%-62% heterosis for seed number with reference to the better parent. The five best performing heterotic crosses were selected with a negative control for evaluation at the subsequent F2 generation and only the tails of the distribution taken forward to be assessed in the F3 generation as a sub selection. Overall, heterosis decreases across the subsequent generations for all traits studied. However, some individual genotypes were identified at the F2 and sub-selected F3 generations with higher levels of heterosis than the best F1 mean value (hybrid mimics). The phenotypic data for the selected F2 and sub selected F3 hybrids were analysed, and the study suggested that 100 grain weight was the biggest driver of yield followed by seed number. A genetic diversity analysis of all the F1 parents failed to correlate genetic distance and divergence among parents with heterotic F1's. Therefore, genetic distance was not a key factor to determine heterosis in lentil. The study highlights the challenges associated with different breeding systems for heterosis (i.e., F1 hybrid-based breeding systems and/or via hybrid mimics) but demonstrates the potential significant gains that could be achieved in lentil productivity.
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Affiliation(s)
- Gurpreet Kaur Suri
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Shivraj Braich
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Dianne M. Noy
- Agriculture Victoria, Grains Innovation Park, Horsham
| | | | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, Victoria, Australia
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11
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Aakanksha, Yadava SK, Yadav BG, Gupta V, Mukhopadhyay A, Pental D, Pradhan AK. Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies. FRONTIERS IN PLANT SCIENCE 2021; 12:721631. [PMID: 34603351 PMCID: PMC8481694 DOI: 10.3389/fpls.2021.721631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/16/2021] [Indexed: 01/07/2024]
Abstract
The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.
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Affiliation(s)
- Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Bal Govind Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Akshay K. Pradhan
- Department of Genetics, University of Delhi South Campus, New Delhi, India
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
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12
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Guo X, Ma BL, McLaughlin NB, Wu X, Chen B, Gao Y. Nitrogen utilisation-efficient oilseed rape (Brassica napus) genotypes exhibit stronger growth attributes from flowering stage onwards. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:755-765. [PMID: 33715767 DOI: 10.1071/fp20263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Preliminary studies observed a lower growth activity during the vegetative stage with higher growth attributes at the pod-filling stage among the high nitrogen (N) utilisation efficiency (NUtE) oilseed rape (Brassica napus L.) genotypes, compared with the low NUtE genotypes. Therefore, we hypothesised that there would exist a critical growth stage when distinctive phenotypic traits are exhibited to regulate yield formation and NUE. A field experiment and a hydroponic culture were conducted to characterise the differences in shoot and root physiological indicators of the high and low NUtE oilseed rape genotypes at seedling, bud, bolting, flowering and pod-filling stages. We found that flowering was the critical period when the reverse growth habit occurred between high and low NUtE genotypes. The high NUtE genotypes displayed larger values of root traits, stronger N uptake kinetics parameters, higher activity of leaf glutamine synthetase (GS) and glutamate synthetase (GOGAT), larger SPAD values and net photosynthetic rate, ultimately leading to higher seed yield and NUE. Our results indicate that flowering is the critical growth stage to distinguish the high from low NUtE oilseed rape genotypes, and plant breeders may focus on selecting root and shoot phenotypic traits from flowering stage onwards to achieve both high yields and NUE for oilseed rape genotypes.
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Affiliation(s)
- Xiao Guo
- College of Natural Resource and Environment, Northwest A and F University, 712100 Yangling, Shaanxi, China; and Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K1A 0C6 Ottawa, Ontario, Canada
| | - Bao-Luo Ma
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K1A 0C6 Ottawa, Ontario, Canada
| | - Neil B McLaughlin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K1A 0C6 Ottawa, Ontario, Canada
| | - Xiaoming Wu
- Institute of Oil Crop Research, Chinese Academy of Agricultural Sciences, 430062 Wuhan, Hubei, China
| | - Biyun Chen
- Institute of Oil Crop Research, Chinese Academy of Agricultural Sciences, 430062 Wuhan, Hubei, China
| | - Yajun Gao
- College of Natural Resource and Environment, Northwest A and F University, 712100 Yangling, Shaanxi, China; and Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, 712100 Yangling, Shaanxi, China; and Corresponding author.
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13
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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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14
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Knoch D, Werner CR, Meyer RC, Riewe D, Abbadi A, Lücke S, Snowdon RJ, Altmann T. Multi-omics-based prediction of hybrid performance in canola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1147-1165. [PMID: 33523261 PMCID: PMC7973648 DOI: 10.1007/s00122-020-03759-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/19/2020] [Indexed: 05/05/2023]
Abstract
Complementing or replacing genetic markers with transcriptomic data and use of reproducing kernel Hilbert space regression based on Gaussian kernels increases hybrid prediction accuracies for complex agronomic traits in canola. In plant breeding, hybrids gained particular importance due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new top performing hybrids requires labour-intensive and costly breeding programmes, including testing of large numbers of experimental hybrids, the prediction of hybrid performance is of utmost interest to plant breeders. In this study, we tested the effectiveness of hybrid prediction models in spring-type oilseed rape (Brassica napus L./canola) employing different omics profiles, individually and in combination. To this end, a population of 950 F1 hybrids was evaluated for seed yield and six other agronomically relevant traits in commercial field trials at several locations throughout Europe. A subset of these hybrids was also evaluated in a climatized glasshouse regarding early biomass production. For each of the 477 parental rapeseed lines, 13,201 single nucleotide polymorphisms (SNPs), 154 primary metabolites, and 19,479 transcripts were determined and used as predictive variables. Both, SNP markers and transcripts, effectively predict hybrid performance using (genomic) best linear unbiased prediction models (gBLUP). Compared to models using pure genetic markers, models incorporating transcriptome data resulted in significantly higher prediction accuracies for five out of seven agronomic traits, indicating that transcripts carry important information beyond genomic data. Notably, reproducing kernel Hilbert space regression based on Gaussian kernels significantly exceeded the predictive abilities of gBLUP models for six of the seven agronomic traits, demonstrating its potential for implementation in future canola breeding programmes.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - Christian R. Werner
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Rhonda C. Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 14195 Berlin, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363 Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Sophie Lücke
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - 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
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
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15
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Cui Y, Zeng X, Xiong Q, Wei D, Liao J, Xu Y, Chen G, Zhou Y, Dong H, Wan H, Liu Z, Li J, Guo L, Jung C, He Y, Qian W. Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1649-1660. [PMID: 33249500 DOI: 10.1093/jxb/eraa563] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
In crops there are quantitative trait loci (QTLs) in which some of the causal quantitative trait genes (QTGs) have not been functionally characterized even in the model plant Arabidopsis. We propose an approach to delineate QTGs in rapeseed by coordinating expression of genes located within QTLs and known orthologs related to traits from Arabidopsis. Using this method in developing siliques 15 d after pollination in 71 lines of rapeseed, we established an acyl-lipid metabolism co-expression network with 21 modules composed of 270 known acyl-lipid genes and 3503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein processes, seed maturation, and phytohormone metabolism. Moreover, the core module closely associated with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analysed using Arabidopsis knockout and overexpression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 overexpression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping, this study provides new insights into the detection of QTGs and into acyl-lipid metabolism in rapeseed.
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Affiliation(s)
- Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiao Zeng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Jinghang Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Yonghong Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Zhi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr., Kiel, Germany
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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16
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Wang H, Yan M, Xiong M, Wang P, Liu Y, Xin Q, Wan L, Yang G, Hong D. Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1321-1335. [PMID: 32002584 DOI: 10.1007/s00122-020-03553-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE: cqSW.A03-2, one of the six identified quantitative trait loci associated with thousand-seed weight in rapeseed, is mapped to a 61.6-kb region on chromosome A03 and corresponds to the candidate gene BnaA03G37960D. Seed weight is an important factor that determines the seed yield of oilseed rape (Brassica napus L.). To elucidate the genetic mechanism of thousand-seed weight (TSW), quantitative trait locus (QTL) mapping was conducted using a double haploid population derived from the cross between an elite line ZY50 and a pol cytoplasmic male sterility restorer line 7-5. The genetic basis of TSW was dissected into six major QTLs. One major QTL denoted as cqSW.A03-2, which explained 8.46-13.70% of the phenotypic variation, was detected across multiple environments. To uncover the genetic basis of cqSW.A03-2, a set of near-isogenic lines were developed. Based on the test of self-pollinated progenies, cqSW.A03-2 was identified as a single Mendelian factor and the ZY50 allele at cqSW.A03-2 showed a positive effect on TSW. Fine mapping delimited the cqSW.A03-2 locus into a 61.6-kb region, and 18 genes within this region were predicted. Candidate gene association analysis and expression analysis indicated that a histidine kinase gene (BnaA03G37960D) is likely to be the candidate gene for the cqSW.A03-2 locus. Our results may contribute to a better understanding of the molecular mechanism of seed weight regulation and promote the breeding program for yield improvement in rapeseed.
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Affiliation(s)
- Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Min Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mei Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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17
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Tang M, Tong C, Liang L, Du C, Zhao J, Xiao L, Tong J, Dai X, Helal M, Dai W, Xiang Y. A recessive high-density pod mutant resource of Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110411. [PMID: 32081260 DOI: 10.1016/j.plantsci.2020.110411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/28/2023]
Abstract
In Brassica napus, pod number and pod density are critical factors to determine seed yield. Although the pod density is an essential yield trait, the regulation of yield formation in oil crops, as well as the genetic and molecular mechanisms, are poorly understood. In this study, we characterized a rapeseed high-density pod mutant (dpt247) from composite hybridization. To shed some light on the nature of this mutation, it was investigated morphologically, anatomically, physiologically, genetically and transcriptomically. The mutant plant showed noticeable phenotypic differences in comparison with the control plant, including reduced plant height and primary branch length, decreased number of primary branches, significantly increased number of pod on the main inflorescence, and more compact pod distribution. Besides, the mutant had higher levels of indole-3-acetic acid (IAA) and zeatin riboside (ZR) in the shoot apical meristem (SAM). The dense pod trait was controlled by two major recessive genes identified in the segregating genetic populations of GRE501 and dpt247. RNA sequencing indicated genes participated in auxin, cytokinin and WUS/CLV signalling pathway in dpt247 were more active in the mutant. These results provide important information for understanding the regulation of yield formation and high yield breeding in rapeseed.
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Affiliation(s)
- Minqiang Tang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR 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 and Rural Affairs, Wuhan 430062, PR China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, PR China
| | - Longbin Liang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Caifu Du
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Jixian Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, PR China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, PR China
| | - Xianglai Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Mmu Helal
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, PR China
| | - Wendong Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China.
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18
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Zhu Y, Ye J, Zhan J, Zheng X, Zhang J, Shi J, Wang X, Liu G, Wang H. Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2020; 11:68. [PMID: 32153604 PMCID: PMC7047150 DOI: 10.3389/fpls.2020.00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.
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Affiliation(s)
| | | | | | | | | | - Jiaqin Shi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministryof Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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19
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Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Heterotic patterns of primary and secondary metabolites in the oilseed crop Brassica juncea. Heredity (Edinb) 2019; 123:318-336. [PMID: 30911141 DOI: 10.1038/s41437-019-0213-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
Heterosis refers to the superior performance of F1 hybrids over their respective parental inbred lines. Although the genetic and expression basis of heterosis have been previously investigated, the metabolic basis for this phenomenon is poorly understood. In a preliminary morphological study in Brassica juncea, we observed significant heterosis at the 50% flowering stage, wherein both the growth and reproduction of F1 reciprocal hybrids were greater than that of their parents. To identify the possible metabolic causes or consequences of this heterosis, we carried out targeted LC-MS analysis of 48 primary (amino acids and sugars) and secondary metabolites (phytohormones, glucosinolates, flavonoids, and phenolic esters) in five developmental tissues at 50% flowering in hybrids and inbred parents. Principal component analysis (PCA) of metabolites clearly separated inbred lines from their hybrids, particularly in the bud tissues. In general, secondary metabolites displayed more negative heterosis values in comparison to primary metabolites. The tested primary and secondary metabolites displayed both additive and non-additive modes of inheritance in F1 hybrids, wherein the number of metabolites showing an additive mode of inheritance were higher in buds and siliques (52.77-97.14%) compared to leaf tissues (47.37-80%). Partial least regression (PLS) analysis further showed that primary metabolites, in general, displayed higher association with morphological parameters in F1 hybrids. Overall, our results are consistent with a resource-cost model for heterosis in B. juncea, where metabolite allocation in hybrids appears to favor growth, at the expense of secondary metabolism.
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Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:508. [PMID: 29725344 PMCID: PMC5917405 DOI: 10.3389/fpls.2018.00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
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Affiliation(s)
- M. Michelle Malmberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Fan Shi
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
| | - German C. Spangenberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Noel O. I. Cogan,
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Zhou Q, Han D, Mason AS, Zhou C, Zheng W, Li Y, Wu C, Fu D, Huang Y. Earliness traits in rapeseed (Brassica napus): SNP loci and candidate genes identified by genome-wide association analysis. DNA Res 2017; 25:229-244. [PMID: 29236947 PMCID: PMC6014513 DOI: 10.1093/dnares/dsx052] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/14/2017] [Indexed: 11/29/2022] Open
Abstract
Life cycle timing is critical for yield and productivity of Brassica napus (rapeseed) cultivars grown in different environments. To facilitate breeding for earliness traits in rapeseed, SNP loci and underlying candidate genes associated with the timing of initial flowering, maturity and final flowering, as well as flowering period (FP) were investigated in two environments in a diversity panel comprising 300 B. napus inbred lines. Genome-wide association studies (GWAS) using 201,817 SNP markers previously developed from SLAF-seq (specific locus amplified fragment sequencing) revealed a total of 131 SNPs strongly linked (P < 4.96E-07) to the investigated traits. Of these 131 SNPs, 40 fell into confidence intervals or were physically adjacent to previously published flowering time QTL or SNPs. Phenotypic effect analysis detected 35 elite allelic variants for early maturing, and 90 for long FP. Candidate genes present in the same linkage disequilibrium blocks (r2>0.6) or in 100 kb regions around significant trait-associated SNPs were screened, revealing 57 B. napus genes (33 SNPs) orthologous to 39 Arabidopsis thaliana flowering time genes. These results support the practical and scientific value of novel large-scale SNP data generation in uncovering the genetic control of agronomic traits in B. napus, and also provide a theoretical basis for molecular marker-assisted selection of earliness breeding in rapeseed.
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Affiliation(s)
- Qinghong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Depeng Han
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen 35392, Germany
| | - Can Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wei Zheng
- Jiangxi Institute of Red Soil, Jinxian, 331717, China
| | - Yazhen Li
- Jiangxi Institute of Red Soil, Jinxian, 331717, China
| | - Caijun Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
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23
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Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4791-4801. [PMID: 28992309 PMCID: PMC5853444 DOI: 10.1093/jxb/erx311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
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Affiliation(s)
- Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Correspondence:
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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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25
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Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Sci Rep 2017; 7:439. [PMID: 28348403 PMCID: PMC5428490 DOI: 10.1038/s41598-017-00438-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/22/2017] [Indexed: 01/09/2023] Open
Abstract
Oil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.
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26
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Luo X, Ding Y, Zhang L, Yue Y, Snyder JH, Ma C, Zhu J. Genomic Prediction of Genotypic Effects with Epistasis and Environment Interactions for Yield-Related Traits of Rapeseed ( Brassica napus L.). Front Genet 2017; 8:15. [PMID: 28270831 PMCID: PMC5318398 DOI: 10.3389/fgene.2017.00015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 02/03/2017] [Indexed: 11/16/2022] Open
Abstract
Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects. As a result, 17 quantitative trait SNPs (QTSs) were identified significantly for target traits with total heritability varied from 58.47 to 87.98%, most of which were contributed by dominance, epistasis, and environment-specific effects. The results indicated that non-additive effects were large contributions to heritability and epistasis, and also noted that environment interactions were important variants for oilseed breeding. Our study facilitates the understanding of genetic basis of rapeseed yield trait, helps to accelerate rapeseed breading, and also offers a roadmap for precision plant breeding via marker-assisted selection.
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Affiliation(s)
- Xiang Luo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - Yi Ding
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
| | - Linzhong Zhang
- Economic and Technical College, Anhui Agricultural University Hefei, China
| | - Yao Yue
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - John H Snyder
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - Jun Zhu
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
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27
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Liu P, Zhao Y, Liu G, Wang M, Hu D, Hu J, Meng J, Reif JC, Zou J. Hybrid Performance of an Immortalized F 2 Rapeseed Population Is Driven by Additive, Dominance, and Epistatic Effects. FRONTIERS IN PLANT SCIENCE 2017; 8:815. [PMID: 28572809 PMCID: PMC5435766 DOI: 10.3389/fpls.2017.00815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/01/2017] [Indexed: 05/19/2023]
Abstract
Genomics-based prediction of hybrid performance promises to boost selection gain. The main goal of our study was to investigate the relevance of additive, dominance, and epistatic effects for determining hybrid seed yield in a biparental rapeseed population. We re-analyzed 60,000 SNP array and seed yield data points from an immortalized F2 population comprised of 318 hybrids and 180 parental lines by performing genome-wide QTL mapping and predictions in combination with five-fold cross-validation. Moreover, an additional set of 37 hybrids were genotyped and phenotyped in an independent environment. The decomposition of the phenotypic variance components and the cross-validated results of the QTL mapping and genome-wide predictions revealed that the hybrid performance in rapeseed was driven by a mix of additive, dominance, and epistatic effects. Interestingly, the genome-wide prediction accuracy in the additional 37 hybrids remained high when modeling exclusively additive effects but was severely reduced when dominance or epistatic effects were also included. This loss in accuracy was most likely caused by more pronounced interactions of environments with dominance and epistatic effects than with additive effects. Consequently, the development of robust hybrid prediction models, including dominance and epistatic effects, required much deeper phenotyping in multi-environmental trials.
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Affiliation(s)
- Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Guozheng Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Jun Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt Seeland, Germany
- *Correspondence: Jochen C. Reif
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- Jun Zou
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28
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Yang Y, Shen Y, Li S, Ge X, Li Z. High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population. FRONTIERS IN PLANT SCIENCE 2017; 8:1512. [PMID: 28932230 PMCID: PMC5592274 DOI: 10.3389/fpls.2017.01512] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.
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29
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Zheng M, Peng C, Liu H, Tang M, Yang H, Li X, Liu J, Sun X, Wang X, Xu J, Hua W, Wang H. Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1246. [PMID: 28769955 PMCID: PMC5513965 DOI: 10.3389/fpls.2017.01246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 05/13/2023]
Abstract
Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.
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Affiliation(s)
- Ming Zheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongfang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Min Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xiaokang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jinglin Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xingchao Sun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Hanzhong Wang
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30
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A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus. Sci Rep 2016; 6:36452. [PMID: 27811979 PMCID: PMC5095561 DOI: 10.1038/srep36452] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/14/2016] [Indexed: 01/02/2023] Open
Abstract
Harvest index (HI), the ratio of seed mass to total biomass of the aboveground plant parts, is an important trait for harvestable yield of crops. Unfortunately, HI of Brassica napus is lower than that of other economically important crops. To identify candidate genes associated with high HI, a genome-wide association study of HI and four HI-related traits was conducted with 520 B. napus accessions cultivated in both Yunnan and Chongqing. We detected 294 single nucleotide polymorphisms significantly associated with the abovementioned traits, including 79 SNPs that affected two or more traits. Differentially expressed genes between extremely high- and low-HI accessions were identified in 8 tissues at two cultivated regions. Combination of linkage disequilibrium and transcriptome analyses revealed 33 functional candidate genes located within the confidence intervals of significant SNPs associated with more than one trait, such as SHOOT GRAVITROPISM 5 (Bna.SGR5), ATP-CITRATE LYASE A-3 (Bna.ACLA-3) and CAROTENOID CLEAVAGE DIOXYGENASE 1 (Bna.CCD1), their orthologs in the Arabidopsis thaliana have been shown to play key roles in photosynthesis, inflorescence, and silique development. Our results provide insight into the molecular mechanisms underlying establishment of high-HI B. napus and lay a foundation for characterization of candidate genes aimed at developing high-HI B. napus varieties.
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31
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Wang X, Chen L, Wang A, Wang H, Tian J, Zhao X, Chao H, Zhao Y, Zhao W, Xiang J, Gan J, Li M. Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus. BMC PLANT BIOLOGY 2016; 16:71. [PMID: 27000872 PMCID: PMC4802616 DOI: 10.1186/s12870-016-0759-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Yield of rapeseed is determined by three components: silique number, seed number per silique and thousand seed weight. Seed number per silique and thousand seed weight are influenced by silique length, seed density, silique breadth, silique thickness and silique volume. Some QTLs for silique traits have been reported in B. napus, however, no studies have focused on the six agronomic traits (seed number per silique, silique length, silique breadth, silique thickness, seed density and silique volume) simultaneously, and the genetic determinism of such complex traits have not been fully elucidated. RESULTS In this study, the six silique traits were evaluated using 348 lines of a doubled haploid population, the KN population. The results showed that 2, 4, 1, 1 and 2 QTLs explaining > 10 % of phenotypic variation were obtained for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively. Notably, three major effect QTLs (cqSB-C6-1, cqSB-C6-2 and cqSV-C6-3) were identified in at least three environments, and 17 unique QTLs controlling at least two traits were obtained. A high-density consensus map containing 1225 markers was constructed for QTL comparison by combining the KN map with other five published maps. The comparative results revealed that 14, 13 and 11 QTLs for silique breadth, silique thickness and silique volume might be the potential new QTLs because few QTLs for these traits were reported in B. napus. In addition, potential new QTLs for silique length (11), seed number per silique (6) and seed density (5) were also identified. Twenty-five candidate genes underlying 27 QTLs for silique related traits were obtained. CONCLUSIONS This study constructed QTL analysis in B. napus, and obtained 60 consensus QTLs for six silique related traits. The potential new QTLs will enhance our understanding of the genetic control of silique traits, and the stable QTLs provided the targets for improving seed yield in future. These findings provided comprehensive insights into the genetic network affecting silique traits at QTL level in B. napus.
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Affiliation(s)
- Xiaodong Wang
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Provincial Key Laboratory of Agrobiology, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Li Chen
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Aina Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hao Wang
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jianhua Tian
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Xiaoping Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Hongbo Chao
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Yajun Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Weiguo Zhao
- />Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100 China
| | - Jun Xiang
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Jianping Gan
- />Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000 China
| | - Maoteng Li
- />Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
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Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R. Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC PLANT BIOLOGY 2016; 16:45. [PMID: 26882898 PMCID: PMC4756405 DOI: 10.1186/s12870-016-0734-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior performance compared to their parental inbred lines. Most commercial Chinese cabbage cultivars are F1 hybrids and their level of hybrid vigour is of critical importance and is a key selection criterion in the breeding system. RESULTS We have characterized the heterotic phenotype of one F1 hybrid cultivar of Chinese cabbage and its parental lines from early- to late-developmental stages of the plants. Hybrid cotyledons are larger than those of the parents at 4 days after sowing and biomass in the hybrid, determined by the fresh weight of leaves, is greater than that of the larger parent line by approximately 20% at 14 days after sowing. The final yield of the hybrid harvested at 63 days after sowing is 25% greater than the yield of the better parent. The larger leaves of the hybrid are a consequence of increased cell size and number of the photosynthetic palisade mesophyll cells and other leaf cells. The accumulation of plant hormones in the F1 was within the range of the parental levels at both 2 and 10 days after sowing. Two days after sowing, the expression levels of chloroplast-targeted genes in the cotyledon cells were upregulated in the F1 hybrid relative to their mid parent values. Shutdown of chlorophyll biosynthesis in the cotyledon by norflurazon prevented the increased leaf area in the F1 hybrid. CONCLUSIONS In the cotyledons of F1 hybrids, chloroplast-targeted genes were upregulated at 2 days after sowing. The increased activity levels of this group of genes suggested that their differential transcription levels could be important for establishing early heterosis but the increased transcription levels were transient. Inhibition of the photosynthetic process in the cotyledon reduced heterosis in later seedling stages. These observations suggest early developmental events in the germinating seedling of the hybrid may be important for later developmental vigour and yield advantage.
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Affiliation(s)
- Natsumi Saeki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Hua Ying
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
| | - Motoki Shimizu
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Mikiko Kojima
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - Hiroshi Abe
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, 305-0074, Japan.
| | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, Niigata, 950-2181, Japan.
| | - Makoto Kaji
- Watanabe Seed Co., Ltd, Machiyashiki, Misato-cho, Miyagi, 987-0003, Japan.
| | | | - Hitoshi Sakakibara
- Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia.
- University of Technology, Broadway, Sydney, PO Box 123, NSW, 2007, Australia.
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
- Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, 332-0012, Japan.
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Bertazzini M, Forlani G. Intraspecific Variability of Floral Nectar Volume and Composition in Rapeseed (Brassica napus L. var. oleifera). FRONTIERS IN PLANT SCIENCE 2016; 7:288. [PMID: 27014311 PMCID: PMC4792878 DOI: 10.3389/fpls.2016.00288] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/23/2016] [Indexed: 05/08/2023]
Abstract
Numerous angiosperms rely on pollinators to ensure efficient flower fertilization, offering a reward consisting of nourishing nectars produced by specialized floral cells, known as nectaries. Nectar components are believed to derive from phloem sap that is enzymatically processed and transformed within nectaries. An increasing body of evidence suggests that nectar composition, mainly amino acids, may influence pollinator attraction and fidelity. This notwithstanding, little is known about the range of natural variability in nectar content for crop species. Sugar and amino acid composition of nectar harvested from field-grown plants at the 63-65 phenological stage was determined for a set of 44 winter genotypes of rapeseed, a bee-pollinated crop. Significant differences were found for solute concentrations, and an even higher variability was evident for nectar volumes, resulting in striking differences when results were expressed on a single flower basis. The comparison of nectar and phloem sap from a subset of eight varieties pointed out qualitative and quantitative diversities with respect to both sugars and amino acids. Notably, amino acid concentration in phloem sap was up to 100 times higher than in nectar. Phloem sap showed a much more uniform composition, suggesting that nectar variability depends mainly on nectary metabolism. A better understanding of the basis of nectar production would allow an improvement of seed set efficiency, as well as hive management and honey production.
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Dan Z, Hu J, Zhou W, Yao G, Zhu R, Huang W, Zhu Y. Hierarchical additive effects on heterosis in rice (Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:738. [PMID: 26442051 PMCID: PMC4566041 DOI: 10.3389/fpls.2015.00738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/31/2015] [Indexed: 05/21/2023]
Abstract
Exploitation of heterosis in crops has contributed greatly to improvement in global food and energy production. In spite of the pervasive importance of heterosis, a complete understanding of its mechanisms has remained elusive. In this study, a small test-crossed rice population was constructed to investigate the formation mechanism of heterosis for 13 traits. The results of the relative mid-parent heterosis and modes of inheritance of all investigated traits demonstrated that additive effects were the foundation of heterosis for complex traits in a hierarchical structure, and multiplicative interactions among the component traits were the framework of heterosis in complex traits. Furthermore, new balances between unit traits and related component traits provided hybrids with the opportunity to achieve an optimal degree of heterosis for complex traits. This study dissected heterosis of both reproductive and vegetative traits from the perspective of hierarchical structure for the first time. Additive multiplicative interactions of component traits were proven to be the origin of heterosis in complex traits. Meanwhile, more attention should be paid to component traits, rather than complex traits, in the process of revealing the mechanism of heterosis.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Guoxin Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, China, ;
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan UniversityWuhan, China
- Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, Wuhan UniversityWuhan, China
- The Yangzte River Valley Hybrid Rice Collaboration Innovation Center, Wuhan UniversityWuhan, China
- *Correspondence: Wenchao Huang and Yingguo Zhu, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Bayi Road, Wuhan 430072, China, ;
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Xing N, Fan C, Zhou Y. Parental selection of hybrid breeding based on maternal and paternal inheritance of traits in rapeseed (Brassica napus L.). PLoS One 2014; 9:e103165. [PMID: 25061995 PMCID: PMC4111582 DOI: 10.1371/journal.pone.0103165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 12/01/2022] Open
Abstract
Parental selection is crucial for hybrid breeding, but the methods available for such a selection are not very effective. In this study, a 6×6 incomplete diallel cross was designed using 12 rapeseed germplasms, and a total of 36 hybrids together with their parental lines were planted in 4 environments. Four yield-related traits and seed oil content (OC) were evaluated. Genetic distance (GD) was estimated with 359 simple sequence repeats (SSRs) markers. Heterosis levels, general combining ability (GCA) and specific combining ability (SCA) were evaluated. GD was found to have a significant correlation with better-parent heterosis (BPH) of thousand seed weight (TSW), SCA of seeds per silique (SS), TSW, and seed yield per plant (SY), while SCA showed a statistically significant correlation with heterosis levels of all traits at 1% significance level. Statistically significant correlations were also observed between GCA of maternal or paternal parents and heterosis levels of different traits except for SS. Interestingly, maternal (TSW, SS, and OC) and paternal (siliques per plant (SP) and SY) inheritance of traits was detected using contribution ratio of maternal and paternal GCA variance as well as correlations between GCA and heterosis levels. Phenotype and heterosis levels of all the traits except TSW of hybrids were significantly correlated with the average performance of parents. The correlations between SS and SP, SP and OC, and SY and OC were statistically significant in hybrids but not in parents. Potential applications of parental selection in hybrid breeding were discussed.
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Affiliation(s)
- Nailin Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Jiang C, Shi J, Li R, Long Y, Wang H, Li D, Zhao J, Meng J. Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:957-68. [PMID: 24504552 DOI: 10.1007/s00122-014-2271-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/16/2014] [Indexed: 05/20/2023]
Abstract
This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.
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Affiliation(s)
- Congcong Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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Xing N, Fan C, Zhou Y. Parental selection of hybrid breeding based on maternal and paternal inheritance of traits in rapeseed (Brassica napus L.). PLoS One 2014. [PMID: 25061995 DOI: 10.1371/journal.pone.010316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Parental selection is crucial for hybrid breeding, but the methods available for such a selection are not very effective. In this study, a 6×6 incomplete diallel cross was designed using 12 rapeseed germplasms, and a total of 36 hybrids together with their parental lines were planted in 4 environments. Four yield-related traits and seed oil content (OC) were evaluated. Genetic distance (GD) was estimated with 359 simple sequence repeats (SSRs) markers. Heterosis levels, general combining ability (GCA) and specific combining ability (SCA) were evaluated. GD was found to have a significant correlation with better-parent heterosis (BPH) of thousand seed weight (TSW), SCA of seeds per silique (SS), TSW, and seed yield per plant (SY), while SCA showed a statistically significant correlation with heterosis levels of all traits at 1% significance level. Statistically significant correlations were also observed between GCA of maternal or paternal parents and heterosis levels of different traits except for SS. Interestingly, maternal (TSW, SS, and OC) and paternal (siliques per plant (SP) and SY) inheritance of traits was detected using contribution ratio of maternal and paternal GCA variance as well as correlations between GCA and heterosis levels. Phenotype and heterosis levels of all the traits except TSW of hybrids were significantly correlated with the average performance of parents. The correlations between SS and SP, SP and OC, and SY and OC were statistically significant in hybrids but not in parents. Potential applications of parental selection in hybrid breeding were discussed.
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Affiliation(s)
- Nailin Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Cai D, Xiao Y, Yang W, Ye W, Wang B, Younas M, Wu J, Liu K. Association mapping of six yield‑related traits in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:85-96. [PMID: 24121524 DOI: 10.1007/s00122-013-2203-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/22/2013] [Indexed: 05/18/2023]
Abstract
Yield is one of the most important traits for rapeseed (Brassica napus L.) breeding, but its genetic basis remains largely ambiguous. Association mapping has provided a robust approach to understand the genetic basis of complex agronomic traits in crops. In this study, a panel of 192 inbred lines of B. napus from all over the world was genotyped using 451 single-locus microsatellite markers and 740 amplified fragment length polymorphism markers. Six yield-related traits of these inbred lines were investigated in three consecutive years with three replications, and genome-wide association studies were conducted for these six traits. Using the model controlling both population structure and relative kinship (Q + K), a total of 43 associations (P < 0.001) were detected using the means of the six yield-related traits across 3 years, with two to fourteen markers associated with individual traits. Among these, 18 markers were repeatedly detected in at least 2 years, and 12 markers were located within or close to QTLs identified in previous studies. Six markers commonly associated with correlated traits. Conditional association analysis indicated that five of the associations between markers and correlated traits are caused by one QTL with pleiotropic effects, and the remaining association is caused by linked but independent QTLs. The combination of favorable alleles of multiple associated markers significantly enhances trait performance, illustrating a great potential of utilization of the associations in rapeseed breeding programs.
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Schnable PS, Springer NM. Progress toward understanding heterosis in crop plants. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:71-88. [PMID: 23394499 DOI: 10.1146/annurev-arplant-042110-103827] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description of its molecular underpinnings has remained elusive despite extensive investigation. It appears that there is not a single, simple explanation for heterosis. Instead, it is likely that heterosis arises in crosses between genetically distinct individuals as a result of a diversity of mechanisms. Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids. Hence, multigene models are likely to prove most informative for understanding heterosis. Complementation of allelic variation, as well as complementation of variation in gene content and gene expression patterns, is likely to be an important contributor to heterosis. Epigenetic variation has the potential to interact in hybrid genotypes via novel mechanisms. Several other intriguing hypotheses are also under investigation. In crops, heterosis must be considered within the context of the genomic impacts of prior selection for agronomic traits.
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Affiliation(s)
- Patrick S Schnable
- Center for Plant Genomics and Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA.
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Li Y, Zhang X, Ma C, Shen J, Chen Q, Wang T, Fu T, Tu J. QTL and epistatic analyses of heterosis for seed yield and three yield component traits using molecular markers in rapeseed (Brassica napus L.). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412050146] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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