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Gu Z, Han B. Unlocking the mystery of heterosis opens the era of intelligent rice breeding. PLANT PHYSIOLOGY 2024; 196:735-744. [PMID: 39115386 PMCID: PMC11444277 DOI: 10.1093/plphys/kiae385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/02/2024] [Indexed: 10/03/2024]
Abstract
Heterosis refers to the phenomenon where the first filial offspring (F1) from genetically diverse parents displays advantages in growth rate, yield, and adaptability compared with its parents. The exploitation of heterosis in rice breeding has greatly increased the productivity, making a significant contribution to food security in the last half of the century. Conventional hybrid rice breeding highly relies on the breeder's experience on random crossing and comprehensive field selection. This process is time-consuming and labor-intensive. In recent years, rice hybrid breeding has encountered challenges stemming from limited germplasm resource, low breeding efficiency, and high uncertainty, which constrain the progress in yield increase, coupled with difficulties in balancing grain yield, quality, and resistance. Understanding the genetic basis of rice heterosis could lead to significant advancements in breeding concepts and methods. This will fully unleash the advantages of heterosis. In this review, we focus on the research progress of the genetic dissection of crop heterosis and briefly introduce some key advancements in modern intelligent breeding of rice hybrid.
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Affiliation(s)
- Zhoulin Gu
- State Key Laboratory of Plant Molecular Genetics, National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- State Key Laboratory of Plant Molecular Genetics, National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China
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Li M, Heng Q, Hu C, Wang Z, Jiang Y, Wang X, He X, Yong JWH, Dawoud TM, Rahman SU, Fan J, Zhang Y. Phytoremediation efficiency of poplar hybrid varieties with diverse genetic backgrounds in soil contaminated by multiple toxic metals (Cd, Hg, Pb, and As). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116843. [PMID: 39128449 DOI: 10.1016/j.ecoenv.2024.116843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 08/01/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Fifteen poplar varieties were used in a field trial to investigate the phytoremediation efficiency, stress resistance, and wood property of poplar hybrid varieties with diverse genetic backgrounds under the composite pollution of heavy metals. The coefficient of variation and clone repeatability for growth traits and Cd concentration were large. The Cd accumulation of poplar varieties 107 and QHQ reached 1.9 and 1.7 mg, respectively, followed by QHB, Ti, 69, and Pa, in which Cd accumulation reached 1.3 mg. Most of the intra-specific hybrid varieties (69, QH1, SL4, T3, and ZL46) had low Cd concentrations and small biomass, resulting in weak Cd accumulation and low phytoremediation efficiency for Cd-polluted soil. By contrast, the inter-sectional and inter-specific hybrid varieties exhibited better growth performance and accumulated higher concentrations of heavy metals than the intra-specific hybrids. The bioconcentration factor and translocation factor of Hg, As, and Pb were less than 1, indicating that poplars have low phytoremediation efficiency for these heavy metals. The hybrids between section Aigeiros and Tacamahaca (QHQ and QHB) and the inter-specific hybrid 107 within section Aigeiros were more resistant to composite heavy metal stress than the other poplar varieties were partially because of their high levels of free proline that exceeded 93 μg·g-1 FW. According to the correlation analysis of the concentrations of the different heavy metals, the poplar roots absorbed different heavy metals in a cooperative manner, indicating that elite poplar varieties with superior capacity for accumulating diverse heavy metals can be bred feasibly. Compared with the intra-specific hybrid varieties, the inter-sectional (QHQ and QHB) and inter-specific (107) hybrid varieties had higher pollution remediation efficiency, larger biomass, higher cellulose content, and lower lignin content, which is beneficial for pulpwood. Therefore, breeding and extending inter-sectional (QHQ and QHB) and inter-specific hybrid varieties can improve the phytoremediation of composite pollution.
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Affiliation(s)
- Mengge Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qimeng Heng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chaobo Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiyong Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yawei Jiang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xintong Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuelian He
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Science, Alanrp, Sweden.
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. BOX 2455, Riyadh 11451, Saudi Arabia
| | - Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Junfeng Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Yi Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Qi T, Wang M, Wang P, Wang L, Wang J. Insights into heterosis from histone modifications in the flag leaf of inter-subspecific hybrid rice. BMC PLANT BIOLOGY 2024; 24:767. [PMID: 39134930 PMCID: PMC11318154 DOI: 10.1186/s12870-024-05487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Inter-subspecific hybrid rice represents a significant breakthrough in agricultural genetics, offering higher yields and better resilience to various environmental stresses. While the utilization of these hybrids has shed light on the genetic processes underlying hybridization, understanding the molecular mechanisms driving heterosis remains a complex and ongoing challenge. Here, chromatin immunoprecipitation-sequencing (ChIP-seq) was used to analyze genome-wide profiles of H3K4me3 and H3K27me3 modifications in the inter-subspecific hybrid rice ZY19 and its parents, Z04A and ZHF1015, then combined them with the transcriptome and DNA methylation data to uncover the effects of histone modifications on gene expression and the contribution of epigenetic modifications to heterosis. RESULTS In the hybrid, there were 8,126 and 1,610 different peaks for H3K4me3 and H3K27me3 modifications when compared to its parents, respectively, with the majority of them originating from the parental lines. The different modifications between the hybrid and its parents were more frequently observed as higher levels in the hybrid than in the parents. In ZY19, there were 476 and 84 allele-specific genes with H3K4me3 and H3K27me3 modifications identified, representing 7.9% and 12% of the total analyzed genes, respectively. Only a small portion of genes that showed differences in parental H3K4me3 and H3K27me3 modifications which demonstrated allele-specific histone modifications (ASHM) in the hybrid. The H3K4me3 modification level in the hybrid was significantly lower compared to the parents. In the hybrid, DNA methylation occurs more frequently among histone modification target genes. Additionally, over 62.58% of differentially expressed genes (DEGs) were affected by epigenetic variations. Notably, there was a strong correlation observed between variations in H3K4me3 modifications and gene expression levels in the hybrid and its parents. CONCLUSION These findings highlight the substantial impact of histone modifications and DNA methylation on gene expression during hybridization. Epigenetic variations play a crucial role in controlling the differential expression of genes, with potential implications for heterosis.
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Affiliation(s)
- Tianpu Qi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peixuan Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Linyou Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Huang C, Cheng Y, Hu Y, Zhang X, Chen J, Zhao T, Si Z, Cao Y, Li Y, Fang L, Guan X, Zhang T. Impacts of parental genomic divergence in non-syntenic regions on cotton heterosis. J Adv Res 2024:S2090-1232(24)00331-X. [PMID: 39111623 DOI: 10.1016/j.jare.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 08/04/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024] Open
Abstract
INTRODUCTION Heterosis has revolutionized crop breeding, enhancing global agricultural production. However, the mechanisms underlying heterosis remain obscure. Xiangzamian 2# (XZM2), a super hybrid upland cotton (Gossypium hirsutum L.) characterized by high-yield heterosis, has been developed and extensively planted in China. OBJECTIVES We conducted a systematic analysis of CRI12 and J8891, two parents of XZM2. We aimed to reveal the precise genetic information and the role of non-syntenic divergence in shaping heterosis, laying a foundation for advancing understanding of heterosis. METHODS We de novo assembled high-quality genomes of CRI12 and J8891, and further uncovered abundant genetic variations and non-syntenic regions between the parents. Whole-genome comparison, association analysis, transcriptomic analysis and relative identity-by-descent (rIBD) estimation were conducted to identify structural variations (SVs) and introgressions within non-syntenic blocks and to analyze their impacts on promoting heterosis. RESULTS Parental genetic divergence increased in non-syntenic regions. Furthermore, these regions, accounting for only 16.71% of the total genome, contained more loci with significantly higher heterotic effects, far exceeding the syntenic background. SVs covered 97.26% of non-syntenic sequences and caused widespread gene expression differences in these regions, driving dynamic complementation of gene expression in the hybrid. A set of SVs were responsible for trait improvement and had positive effects on heterosis, contributing larger heritability than short variations. We characterized numerous parental-specific introgressions from G. barbadense. Specifically, a functional introgression segment within non-syntenic blocks introduced an elite haplotype, which significantly increased lint yield and enhanced heterosis. CONCLUSION Our study clarified non-syntenic regions to harbor more loci with higher heterotic effects, revealed their importance in promoting heterosis and supported the crucial role of genetic complementation in heterosis. SVs and introgressions were identified as key factors responsible for non-syntenic divergence between the parents. They had important effects on gene expression and trait improvement, positively contributing to heterosis.
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Affiliation(s)
- Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yu Cheng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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Sanchez D, Allier A, Ben Sadoun S, Mary-Huard T, Bauland C, Palaffre C, Lagardère B, Madur D, Combes V, Melkior S, Bettinger L, Murigneux A, Moreau L, Charcosset A. Assessing the potential of genetic resource introduction into elite germplasm: a collaborative multiparental population for flint maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:19. [PMID: 38214870 PMCID: PMC10786986 DOI: 10.1007/s00122-023-04509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/18/2023] [Indexed: 01/13/2024]
Abstract
KEY MESSAGE Implementing a collaborative pre-breeding multi-parental population efficiently identifies promising donor x elite pairs to enrich the flint maize elite germplasm. Genetic diversity is crucial for maintaining genetic gains and ensuring breeding programs' long-term success. In a closed breeding program, selection inevitably leads to a loss of genetic diversity. While managing diversity can delay this loss, introducing external sources of diversity is necessary to bring back favorable genetic variation. Genetic resources exhibit greater diversity than elite materials, but their lower performance levels hinder their use. This is the case for European flint maize, for which elite germplasm has incorporated only a limited portion of the diversity available in landraces. To enrich the diversity of this elite genetic pool, we established an original cooperative maize bridging population that involves crosses between private elite materials and diversity donors to create improved genotypes that will facilitate the incorporation of original favorable variations. Twenty donor × elite BC1S2 families were created and phenotyped for hybrid value for yield related traits. Crosses showed contrasted means and variances and therefore contrasted potential in terms of selection as measured by their usefulness criterion (UC). Average expected mean performance gain over the initial elite material was 5%. The most promising donor for each elite line was identified. Results also suggest that one more generation, i.e., 3 in total, of crossing to the elite is required to fully exploit the potential of a donor. Altogether, our results support the usefulness of incorporating genetic resources into elite flint maize. They call for further effort to create fixed diversity donors and identify those most suitable for each elite program.
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Affiliation(s)
- Dimitri Sanchez
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Antoine Allier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Syngenta, 12 Chemin de L'Hobit, 31790, Saint-Sauveur, France
| | - Sarah Ben Sadoun
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris Saclay, 91120, Palaiseau, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Bernard Lagardère
- UE 0394 SMH, INRAE, 2297 Route de l'INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | | | | | - Alain Murigneux
- Limagrain Europe, 28 Route d'Ennezat, 63720, Chappes, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, 91190, Gif-Sur-Yvette, France.
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Paril J, Reif J, Fournier-Level A, Pourkheirandish M. Heterosis in crop improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:23-32. [PMID: 37971883 DOI: 10.1111/tpj.16488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023]
Abstract
Heterosis, also known as hybrid vigor, is the phenomenon wherein a progeny exhibits superior traits relative to one or both parents. In terms of crop breeding, this usually refers to the yield advantage of F1 hybrids over both inbred parents. The development of high-yielding hybrid cultivars across a wider range of crops is key to meeting future food demands. However, conventional hybrid breeding strategies are proving to be exceptionally challenging to apply commercially in many self-pollinating crops, particularly wheat and barley. Currently in these crops, the relative performance advantage of hybrids over inbred line cultivars does not outweigh the cost of hybrid seed production. Here, we review the genetic basis of heterosis, discuss the challenges in hybrid breeding, and propose a strategy to recruit multiple heterosis-associated genes to develop lines with improved agronomic characteristics. This strategy leverages modern genetic engineering tools to synthesize supergenes by fusing multiple heterotic alleles across multiple heterosis-associated loci. We outline a plan to assess the feasibility of this approach to improve line performance using barley (Hordeum vulgare) as the model self-pollinating crop species, and a few heterosis-associated genes. The proposed method can be applied to all crops for which heterotic gene combinations can be identified.
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Affiliation(s)
- Jefferson Paril
- Faculty of Science, University of Melbourne, Parkville, Melbourne, Victoria, Australia
- AgriBio, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Jochen Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Yadav S, Ross EM, Wei X, Powell O, Hivert V, Hickey LT, Atkin F, Deomano E, Aitken KS, Voss-Fels KP, Hayes BJ. Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies. FRONTIERS IN PLANT SCIENCE 2023; 14:1260517. [PMID: 38023905 PMCID: PMC10667552 DOI: 10.3389/fpls.2023.1260517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Mate-allocation strategies in breeding programs can improve progeny performance by harnessing non-additive genetic effects. These approaches prioritise predicted progeny merit over parental breeding value, making them particularly appealing for clonally propagated crops such as sugarcane. We conducted a comparative analysis of mate-allocation strategies, exploring utilising non-additive and heterozygosity effects to maximise clonal performance with schemes that solely consider additive effects to optimise breeding value. Using phenotypic and genotypic data from a population of 2,909 clones evaluated in final assessment trials of Australian sugarcane breeding programs, we focused on three important traits: tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and Fibre. By simulating families from all possible crosses (1,225) with 50 progenies each, we predicted the breeding and clonal values of progeny using two models: GBLUP (considering additive effects only) and extended-GBLUP (incorporating additive, non-additive, and heterozygosity effects). Integer linear programming was used to identify the optimal mate-allocation among selected parents. Compared to breeding value-based approaches, mate-allocation strategies based on clonal performance yielded substantial improvements, with predicted progeny values increasing by 57% for TCH, 12% for CCS, and 16% for fibre. Our simulation study highlights the effectiveness of mate-allocation approaches that exploit non-additive and heterozygosity effects, resulting in superior clonal performance. However, there was a notable decline in additive gain, particularly for TCH, likely due to significant epistatic effects. When selecting crosses based on clonal performance for TCH, the inbreeding coefficient of progeny was significantly lower compared to random mating, underscoring the advantages of leveraging non-additive and heterozygosity effects in mitigating inbreeding depression. Thus, mate-allocation strategies are recommended in clonally propagated crops to enhance clonal performance and reduce the negative impacts of inbreeding.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth M. Ross
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, Australia
| | - Owen Powell
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Valentin Hivert
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Felicity Atkin
- Sugar Research Australia, Meringa Gordonvale, QLD, Australia
| | - Emily Deomano
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Karen S. Aitken
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QlD, Australia
| | - Kai P. Voss-Fels
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
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Würschum T, Zhu X, Zhao Y, Jiang Y, Reif JC, Maurer HP. Maximization through optimization? On the relationship between hybrid performance and parental genetic distance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:186. [PMID: 37572118 PMCID: PMC10423127 DOI: 10.1007/s00122-023-04436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Heterosis is the improved performance of hybrids compared with their parental components and is widely exploited in agriculture. According to quantitative genetic theory, genetic distance between parents at heterotic quantitative trait loci is required for heterosis, but how heterosis varies with genetic distance has remained elusive, despite intensive research on the topic. Experimental studies have often found a positive association between heterosis and genetic distance that, however, varied in strength. Most importantly, it has remained unclear whether heterosis increases continuously with genetic distance or whether there is an optimum genetic distance after which heterosis declines again. Here, we revisit the relationship between heterosis and genetic distance and provide perspectives on how to maximize heterosis and hybrid performance in breeding, as well as the consequences for the design of heterotic groups and the utilization of more exotic material and genetic resources.
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Affiliation(s)
- Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Xintian Zhu
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Stadt Seeland, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Stadt Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Stadt Seeland, Germany
| | - Hans Peter Maurer
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
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Singh S, Gaurav SS, Vasistha NK, Kumar U, Joshi AK, Mishra VK, Chand R, Gupta PK. Genetics of spot blotch resistance in bread wheat ( Triticum aestivum L.) using five models for GWAS. FRONTIERS IN PLANT SCIENCE 2023; 13:1036064. [PMID: 36743576 PMCID: PMC9891466 DOI: 10.3389/fpls.2022.1036064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.
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Affiliation(s)
- Sahadev Singh
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Shailendra Singh Gaurav
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Arun Kumar Joshi
- The International Maize and Wheat Improvement Center (CIMMYT), Borlaug Institute for South Asia (BISA), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Indian Institute of Agricultural Science, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Indian Institute of Agricultural Science Banaras Hindu University, Varanasi, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- Murdoch’s Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA, Australia
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11
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Zlobin AS, Volkova NA, Zinovieva NA, Iolchiev BS, Bagirov VA, Borodin PM, Axenovich TI, Tsepilov YA. Loci Associated with Negative Heterosis for Viability and Meat Productivity in Interspecific Sheep Hybrids. Animals (Basel) 2023; 13:ani13010184. [PMID: 36611792 PMCID: PMC9817718 DOI: 10.3390/ani13010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Negative heterosis can occur on different economically important traits, but the exact biological mechanisms of this phenomenon are still unknown. The present study focuses on determining the genetic factors associated with negative heterosis in interspecific hybrids between domestic sheep (Ovis aries) and argali (Ovis ammon). One locus (rs417431015) associated with viability and two loci (rs413302370, rs402808951) associated with meat productivity were identified. One gene (ARAP2) was prioritized for viability and three for meat productivity (PDE2A, ARAP1, and PCDH15). The loci associated with meat productivity were demonstrated to fit the overdominant inheritance model and could potentially be involved int negative heterosis mechanisms.
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Affiliation(s)
- Alexander S. Zlobin
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | | | - Baylar S. Iolchiev
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Vugar A. Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | - Yakov A. Tsepilov
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
- Correspondence:
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12
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Schulthess AW, Kale SM, Zhao Y, Gogna A, Rembe M, Philipp N, Liu F, Beukert U, Serfling A, Himmelbach A, Oppermann M, Weise S, Boeven PHG, Schacht J, Longin CFH, Kollers S, Pfeiffer N, Korzun V, Fiebig A, Schüler D, Lange M, Scholz U, Stein N, Mascher M, Reif JC. Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding. Sci Data 2022; 9:784. [PMID: 36572688 PMCID: PMC9792552 DOI: 10.1038/s41597-022-01891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 12/27/2022] Open
Abstract
Plant genetic resources (PGR) stored at genebanks are humanity's crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
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Affiliation(s)
- Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Abhishek Gogna
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maximilian Rembe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Norman Philipp
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Ulrike Beukert
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | | | | | | | | | | | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
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13
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Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 2022; 54:1544-1552. [DOI: 10.1038/s41588-022-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/18/2022] [Indexed: 11/06/2022]
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14
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Sang Z, Wang H, Yang Y, Zhang Z, Liu X, Li Z, Xu Y. Epistasis Activation Contributes Substantially to Heterosis in Temperate by Tropical Maize Hybrids. FRONTIERS IN PLANT SCIENCE 2022; 13:921608. [PMID: 35898210 PMCID: PMC9313604 DOI: 10.3389/fpls.2022.921608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Epistasis strongly affects the performance of superior maize hybrids. In this study, a multiple-hybrid population, consisting of three hybrid maize sets with varied interparental divergence, was generated by crossing 28 temperate and 23 tropical inbred lines with diverse genetic backgrounds. We obtained 1,154 tested hybrids. Among these tested hybrids, heterosis increased steadily as the heterotic genetic distance increased. Mid-parent heterosis was significantly higher in the temperate by tropical hybrids than in the temperate by temperate hybrids. Genome-wide prediction and association mapping was performed for grain weight per plant (GWPP) and days to silking (DTS) using 20K high-quality SNPs, showing that epistatic effects played a more prominent role than dominance effects in temperate by tropical maize hybrids. A total of 33 and 420 epistatic QTL were identified for GWPP and DTS, respectively, in the temperate by tropical hybrids. Protein-protein interaction network and gene-set enrichment analyses showed that epistatic genes were involved in protein interactions, which play an important role in photosynthesis, biological transcription pathways, and protein synthesis. We showed that the interaction of many minor-effect genes in the hybrids could activate the transcription activators of epistatic genes, resulting in a cascade of amplified yield heterosis. The multiple-hybrid population design enhanced our understanding of heterosis in maize, providing an insight into the acceleration of hybrid maize breeding by activating epistatic effects.
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Affiliation(s)
- Zhiqin Sang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hui Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- National Engineering Research Center of Wheat and Maize, Shandong Technology Innovation Center of Wheat, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuxin Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanqin Zhang
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xiaogang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiwei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center, Texcoco, Mexico
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15
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Li T, Wang F, Yasir M, Li K, Qin Y, Zheng J, Luo K, Zhu S, Zhang H, Jiang Y, Zhang Y, Rong J. Expression Patterns Divergence of Reciprocal F 1 Hybrids Between Gossypium hirsutum and Gossypium barbadense Reveals Overdominance Mediating Interspecific Biomass Heterosis. FRONTIERS IN PLANT SCIENCE 2022; 13:892805. [PMID: 35845678 PMCID: PMC9284264 DOI: 10.3389/fpls.2022.892805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Hybrid breeding has provided an impetus to the process and achievement of a higher yield and quality of crops. Interspecific hybridization is critical for resolving parental genetic diversity bottleneck problems. The reciprocal interspecific hybrids and their parents (Gossypium hirsutum and Gossypium barbadense) have been applied in this study to elucidate the transcription regulatory mechanism of early biomass heterosis. Phenotypically, the seed biomass, plant height over parent heterosis, leaf area over parent heterosis, and fresh and dry biomass were found to be significantly higher in hybrids than in parents. Analysis of leaf areas revealed that the one-leaf stage exhibits the most significant performance in initial vegetative growth vigor and larger leaves in hybrids, increasing the synthesis of photosynthesis compounds and enhancing photosynthesis compound synthesis. Comparative transcriptome analysis showed that transgressive down-regulation (TDR) is the main gene expression pattern in the hybrids (G. hirsutum × G. barbadense, HB), and it was found that the genes of photosystem I and Adenosine triphosphate (ATP)-binding may promote early growth vigor. Transgressive up-regulation (TUR) is the major primary gene expression pattern in the hybrids (G. barbadense × G. hirsutum, BH), and photosystem II-related genes mediated the performance of early biomass heterosis. The above results demonstrated that overdominance mediates biomass heterosis in interspecific hybrid cotton and the supervisory mechanism divergence of hybrids with different females. Photosynthesis and other metabolic process are jointly involved in controlling early biomass heterosis in interspecific hybrid cotton. The expression pattern data of transcriptome sequencing were supported using the qRT-PCR analysis. Our findings could be useful in theoretical and practical studies of early interspecific biomass heterosis, and the results provide potential resources for the theoretical and applied research on early interspecific biomass heterosis.
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Affiliation(s)
- Tengyu Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kui Li
- Institute of Food and Nutrition Development, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Kun Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, Zhejiang Agriculture and Forestry University, Hangzhou, China
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16
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Hao M, Zhang L, Huang L, Ning S, Yuan Z, Jiang B, Yan Z, Wu B, Zheng Y, Liu D. 渗入杂交与小麦杂种优势. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Liu W, Zhang Y, He H, He G, Deng XW. From hybrid genomes to heterotic trait output: Challenges and opportunities. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102193. [PMID: 35219140 DOI: 10.1016/j.pbi.2022.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yilin Zhang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China.
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18
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Castillo-Bravo R, Fort A, Cashell R, Brychkova G, McKeown PC, Spillane C. Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:835219. [PMID: 35330872 PMCID: PMC8940307 DOI: 10.3389/fpls.2022.835219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 05/05/2023]
Abstract
Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.
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19
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Malik P, Kumar J, Sharma S, Meher PK, Balyan HS, Gupta PK, Sharma S. GWAS for main effects and epistatic interactions for grain morphology traits in wheat. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:651-668. [PMID: 35465203 PMCID: PMC8986918 DOI: 10.1007/s12298-022-01164-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/05/2023]
Abstract
In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length-width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017-2018, 2018-2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01164-w.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
- Department of Biotechnology, National Agri-Food Biotechnology Institute (NABI), Govt. of India, Sector 81 (Knowledge City), S.A.S. Nagar, Mohali, Punjab 140306 India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P 250 004 India
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20
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Flavell RB. Wheat Breeding, Transcription Factories, and Genetic Interactions: New Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:807884. [PMID: 35283934 PMCID: PMC8905190 DOI: 10.3389/fpls.2022.807884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Epistatic interactions and negative heterosis have been shown to be associated with interchromosomal interactions in wheat. Physical gene-gene interactions between co-regulated genes clustered in "transcription factories" have been documented, and a genome-wide atlas of functionally paired, interacting regulatory elements and genes of wheat recently produced. Integration of these new studies on gene and regulatory element interactions, co-regulation of gene expression in "transcription factories," and epigenetics generates new perspectives for wheat breeding and trait enhancement.
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21
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Creation of winter wheat source material with increased adaptive potential to adverse environmental conditions. EUREKA: LIFE SCIENCES 2021. [DOI: 10.21303/2504-5695.2021.002188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The goal until the last day was to create a new sort with high indicators of productivity, adaptability and quality of grain on the basis of the directed selection process and comprehensive study of hybrid material on field and laboratory estimations.
Creation of initial material with high productivity, adaptability and grain quality by directed selection and hybrid material comprehensive study is described. General scientific, special genetic, field, laboratory methods, morphological analysis and statistical methods were used in the research. Given that the weight of grain from 1 ear is a marker in breeding for high yield (r=0.53), the largest (50 %) positive transgressions were in F1 hybrids using new genetic plasma varieties. Among hybrid populations F2, F3 and F4, selection value is represented by hybrid populations 4971 and 4976, which have the lowest stress resistance (–16.1, –18.6) and variation (16.9, 19.9) and the highest genetic stability (50.0, 50.2) and homeostaticity (19.1, 14.3), respectively. Among Control, Preliminary and Competitive tests, lines UK2621/18 and UK9855/18 have high stress resistance (–4.7, –5.8), homeostaticity (1416.0, 1008.0) and low variability (2.6 %, 3.5 %), respectively. They are the most adaptive and malleable to average and adverse environmental conditions. Line UK1182/17, which in 2020 was submitted for consideration to the State variety testing as "Blahovishchenska" (Kiev, Ukraine), was created using the purposeful method of pedigree in each link of selection. It has high adaptability, resistance to lodging, major diseases, high average yield (90.8 c/ha), and grain quality – it is strong wheat (protein amount 13.5–14.0 %, gluten – 30–35 %). Pedigree is the most effective method of continuous individual selection, which allows creating source material with high productivity, resistance to disease and adverse environmental factors
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22
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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23
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Feng L, Ma A, Song B, Yu S, Qi X. Mapping causal genes and genetic interactions for agronomic traits using a large F2 population in rice. G3 (BETHESDA, MD.) 2021; 11:6369515. [PMID: 34515770 PMCID: PMC8527483 DOI: 10.1093/g3journal/jkab318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022]
Abstract
Dissecting the genetic mechanisms underlying agronomic traits is of great importance for crop breeding. Agronomic traits are usually controlled by multiple quantitative trait loci (QTLs) and genetic interactions, and mapping the underlying causal genes is still labor-intensive and time-consuming. Here, we present a genetic tool for directly targeting the specific causal genes by using a single-gene resolution linkage map that was constructed from 3756 F2 rice plants via targeted sequencing technology and Tukey-Kramer multiple comparisons test. Three large- and moderate-effect QTLs, qHD6-2, qGL3-1, and qGW5-2, were successfully mapped to their specific causal genes, Hd1, GS3, and GW5, respectively. A complex genetic interaction network containing 30 QTL-QTL interactions was constructed, revealing that the alternative allele of hub QTL, qHD6-2, can hide or release the genetic contributions of the alleles at interacting loci. Moreover, arranging genetic interactions in the models lead to more accurate phenotypic predictions. These results provide a community resource and new feasible strategy for deciphering the genetic mechanisms of complex agronomic traits and accelerating crop breeding.
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Affiliation(s)
- Laibao Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Aimin Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100049, China
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24
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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25
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Yadav S, Wei X, Joyce P, Atkin F, Deomano E, Sun Y, Nguyen LT, Ross EM, Cavallaro T, Aitken KS, Hayes BJ, Voss-Fels KP. Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2235-2252. [PMID: 33903985 PMCID: PMC8263546 DOI: 10.1007/s00122-021-03822-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/21/2021] [Indexed: 05/29/2023]
Abstract
Non-additive genetic effects seem to play a substantial role in the expression of complex traits in sugarcane. Including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. In the recent decade, genetic progress has been slow in sugarcane. One reason might be that non-additive genetic effects contribute substantially to complex traits. Dense marker information provides the opportunity to exploit non-additive effects in genomic prediction. In this study, a series of genomic best linear unbiased prediction (GBLUP) models that account for additive and non-additive effects were assessed to improve the accuracy of clonal prediction. The reproducible kernel Hilbert space model, which captures non-additive genetic effects, was also tested. The models were compared using 3,006 genotyped elite clones measured for cane per hectare (TCH), commercial cane sugar (CCS), and Fibre content. Three forward prediction scenarios were considered to investigate the robustness of genomic prediction. By using a pseudo-diploid parameterization, we found significant non-additive effects that accounted for almost two-thirds of the total genetic variance for TCH. Average heterozygosity also had a major impact on TCH, indicating that directional dominance may be an important source of phenotypic variation for this trait. The extended-GBLUP model improved the prediction accuracies by at least 17% for TCH, but no improvement was observed for CCS and Fibre. Our results imply that non-additive genetic variance is important for complex traits in sugarcane, although further work is required to better understand the variance component partitioning in a highly polyploid context. Genomics-based breeding will likely benefit from exploiting non-additive genetic effects, especially in designing crossing schemes. These findings can help to improve clonal prediction, enabling a more accurate identification of variety candidates for the sugarcane industry.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Priya Joyce
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Felicity Atkin
- Sugar Research Australia, Meringa, Gordonvale, QLD, 4865, Australia
| | - Emily Deomano
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Yue Sun
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Loan T Nguyen
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Tony Cavallaro
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Karen S Aitken
- Agriculture and Food, CSIRO, QBP, St. Lucia, QLD, 4067, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, Carmody Rd., St. Lucia, Brisbane, QLD, 3064067, Australia.
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26
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Labroo MR, Ali J, Aslam MU, de Asis EJ, Dela Paz MA, Sevilla MA, Lipka AE, Studer AJ, Rutkoski JE. Genomic Prediction of Yield Traits in Single-Cross Hybrid Rice ( Oryza sativa L.). Front Genet 2021; 12:692870. [PMID: 34276796 PMCID: PMC8278103 DOI: 10.3389/fgene.2021.692870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Hybrid rice varieties can outyield the best inbred varieties by 15 – 30% with appropriate management. However, hybrid rice requires more inputs and management than inbred rice to realize a yield advantage in high-yielding environments. The development of stress-tolerant hybrid rice with lowered input requirements could increase hybrid rice yield relative to production costs. We used genomic prediction to evaluate the combining abilities of 564 stress-tolerant lines used to develop Green Super Rice with 13 male sterile lines of the International Rice Research Institute for yield-related traits. We also evaluated the performance of their F1 hybrids. We identified male sterile lines with good combining ability as well as F1 hybrids with potential further use in product development. For yield per plant, accuracies of genomic predictions of hybrid genetic values ranged from 0.490 to 0.822 in cross-validation if neither parent or up to both parents were included in the training set, and both general and specific combining abilities were modeled. The accuracy of phenotypic selection for hybrid yield per plant was 0.682. The accuracy of genomic predictions of male GCA for yield per plant was 0.241, while the accuracy of phenotypic selection was 0.562. At the observed accuracies, genomic prediction of hybrid genetic value could allow improved identification of high-performing single crosses. In a reciprocal recurrent genomic selection program with an accelerated breeding cycle, observed male GCA genomic prediction accuracies would lead to similar rates of genetic gain as phenotypic selection. It is likely that prediction accuracies of male GCA could be improved further by targeted expansion of the training set. Additionally, we tested the correlation of parental genetic distance with mid-parent heterosis in the phenotyped hybrids. We found the average mid-parent heterosis for yield per plant to be consistent with existing literature values at 32.0%. In the overall population of study, parental genetic distance was significantly negatively correlated with mid-parent heterosis for yield per plant (r = −0.131) and potential yield (r = −0.092), but within female families the correlations were non-significant and near zero. As such, positive parental genetic distance was not reliably associated with positive mid-parent heterosis.
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Affiliation(s)
- Marlee R Labroo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - M Umair Aslam
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Erik Jon de Asis
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Madonna A Dela Paz
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - M Anna Sevilla
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Philippines
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Anthony J Studer
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jessica E Rutkoski
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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27
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Schneider J, Berkner MO, Philipp N, Schulthess AW, Reif JC. Assessing the Suitability of Elite Lines for Hybrid Seed Production and as Testers in Wide Crosses With Wheat Genetic Resources. FRONTIERS IN PLANT SCIENCE 2021; 12:689825. [PMID: 34194460 PMCID: PMC8236896 DOI: 10.3389/fpls.2021.689825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The use of genetic resources in breeding is considered critical to ensure future selection gain, but the absence of important adaptation genes often masks the breeding value of genetic resources for grain yield. Testing genetic resources in a hybrid background has been proposed as a solution to obtain unbiased estimates of breeding values for grain yield. In our study, we evaluated the suitability of European wheat elite lines for implementing this hybrid strategy, focusing on maximizing seed yield in hybrid production and reducing masking effects due to susceptibility to lodging, yellow rust, and leaf rust of genetic resources. Over a 3-year period, 63 wheat elite female lines were crossed with eight male plant genetic resources in a multi-environment field experiment to evaluate seed yield on the female side. Then, the resulting hybrids and their parents were tested for plant height, lodging, and susceptibility to yellow rust and leaf rust in a further field experiment at multiple locations. We found that seed yield was strongly influenced by the elite wheat line choice in addition to environment and observed substantial differences among elite tester lines in their ability to reduce susceptibility to lodging, yellow rust, and leaf rust when the hybrid strategy was implemented. Consequently, breeders can significantly increase the amount of hybrid seed produced in wide crosses through appropriate tester choice and adapt genetic resources of wheat with the hybrid strategy to the modern cropping system.
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28
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Zhao Y, Thorwarth P, Jiang Y, Philipp N, Schulthess AW, Gils M, Boeven PHG, Longin CFH, Schacht J, Ebmeyer E, Korzun V, Mirdita V, Dörnte J, Avenhaus U, Horbach R, Cöster H, Holzapfel J, Ramgraber L, Kühnle S, Varenne P, Starke A, Schürmann F, Beier S, Scholz U, Liu F, Schmidt RH, Reif JC. Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat. SCIENCE ADVANCES 2021; 7:7/24/eabf9106. [PMID: 34117061 PMCID: PMC8195483 DOI: 10.1126/sciadv.abf9106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/28/2021] [Indexed: 05/07/2023]
Abstract
The potential of big data to support businesses has been demonstrated in financial services, manufacturing, and telecommunications. Here, we report on efforts to enter a new data era in plant breeding by collecting genomic and phenotypic information from 12,858 wheat genotypes representing 6575 single-cross hybrids and 6283 inbred lines that were evaluated in six experimental series for yield in field trials encompassing ~125,000 plots. Integrating data resulted in twofold higher prediction ability compared with cases in which hybrid performance was predicted across individual experimental series. Our results suggest that combining data across breeding programs is a particularly appropriate strategy to exploit the potential of big data for predictive plant breeding. This paradigm shift can contribute to increasing yield and resilience, which is needed to feed the growing world population.
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Affiliation(s)
- Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Norman Philipp
- Syngenta Seeds GmbH, Kroppenstedterstr. 4, 39398 Hadmersleben, Germany
| | - Albert W Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Mario Gils
- Nordsaat Saatzucht GmbH, , Böhnshauserstr. 1, 38895 Langenstein, Germany
| | | | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70593 Stuttgart, Germany
| | | | - Erhard Ebmeyer
- KWS LOCHOW GmbH, Ferdinand-von-Lochow-Str. 5, 29303 Bergen, Germany
| | - Viktor Korzun
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574 Einbeck, Germany
- Federal State Budgetary Institution of Science Federal Research Center, "Kazan Scientific Center of Russian Academy of Sciences," ul. Lobachevskogo, 2/31, Kazan, 420111 Tatarstan, Russian Federation
| | - Vilson Mirdita
- BASF Agricultural Solutions Seed GmbH, OT Gatersleben, Am Schwabeplan 8, 06466 Seeland, Germany
| | - Jost Dörnte
- Deutsche Saatveredelung AG, Leutewitz 26, 01665 Käbschütztal, Germany
| | - Ulrike Avenhaus
- W. von Borries-Eckendorf GmbH & Co. KG, Hovedisserstr. 92, 33818 Leopoldshöhe, Germany
| | - Ralf Horbach
- Saatzucht Bauer GmbH & Co. KG, Hofmarkstr.1, 93083 Niederträubling, Germany
| | | | - Josef Holzapfel
- Secobra Saatzucht GmbH, Feldkirchen 3, 85368 Moosburg, Germany
| | - Ludwig Ramgraber
- Saatzucht Josef Breun GmbH & Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Simon Kühnle
- Pflanzenzucht Oberlimpurg, Oberlimpurg 2, 74523 Schwäbisch Hall, Germany
| | - Pierrick Varenne
- Limagrain Europe, Ferme de l'Etang BP3, 77390 Verneuil l'Etang, France
| | - Anne Starke
- Limagrain GmbH, Salderstr. 4, 31226 Peine-Rosenthal, Germany
| | | | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Renate H Schmidt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Stadt Seeland, Germany.
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29
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Li D, Zhou Z, Lu X, Jiang Y, Li G, Li J, Wang H, Chen S, Li X, Würschum T, Reif JC, Xu S, Li M, Liu W. Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:774478. [PMID: 34917109 PMCID: PMC8670227 DOI: 10.3389/fpls.2021.774478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/01/2021] [Indexed: 05/14/2023]
Abstract
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
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Affiliation(s)
- Dongdong Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Guoliang Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junhui Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haoying Wang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaojiang Chen
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Wenxin Liu,
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingshun Li,
| | - Wenxin Liu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Shizhong Xu,
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30
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Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population. G3-GENES GENOMES GENETICS 2020; 10:4565-4577. [PMID: 33051261 PMCID: PMC7718745 DOI: 10.1534/g3.120.401582] [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] [Indexed: 11/18/2022]
Abstract
In sorghum [Sorghum bicolor (L.) Moench], hybrid cultivars for the biofuel industry are desired. Along with selection based on testcross performance, evaluation of the breeding population per se is also important for the success of hybrid breeding. In addition to additive genetic effects, non-additive (i.e., dominance and epistatic) effects are expected to contribute to the performance of early generations. Unfortunately, studies on early generations in sorghum breeding programs are limited. In this study, we analyzed a breeding population for bioenergy sorghum, which was previously developed based on testcross performance, to compare genomic selection models both trained on and evaluated for the per se performance of the 3rd generation S0 individuals. Of over 200 ancestral inbred accessions in the base population, only 13 founders contributed to the 3rd generation as progenitors. Compared to the founders, the performances of the population per se were improved for target traits. The total genetic variance within the S0 generation progenies themselves for all traits was mainly additive, although non-additive variances contributed to each trait to some extent. For genomic selection, linear regression models explicitly considering all genetic components showed a higher predictive ability than other linear and non-linear models. Although the number and effect distribution of underlying loci was different among the traits, the influence of priors for marker effects was relatively small. These results indicate the importance of considering non-additive effects for dissecting the genetic architecture of early breeding generations and predicting the performance per se.
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Beukert U, Liu G, Thorwarth P, Boeven PHG, Longin CFH, Zhao Y, Ganal M, Serfling A, Ordon F, Reif JC. The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2171-2181. [PMID: 32281003 PMCID: PMC7311497 DOI: 10.1007/s00122-020-03588-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/31/2020] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Hybrid wheat breeding is a promising strategy to improve the level of leaf rust and stripe rust resistance in wheat. Leaf rust and stripe rust belong to the most important fungal diseases in wheat production. Due to a dynamic development of new virulent races, epidemics appear in high frequency and causes significant losses in grain yield and quality. Therefore, research is needed to develop strategies to breed wheat varieties carrying highly efficient resistances. Stacking of dominant resistance genes through hybrid breeding is such an approach. Within this study, we investigated the genetic architecture of leaf rust and stripe rust resistance of 1750 wheat hybrids and their 230 parental lines using a genome-wide association study. We observed on average a lower rust susceptibility for hybrids in comparison to their parental inbred lines and some hybrids outperformed their better parent with up to 56%. Marker-trait associations were identified on chromosome 3D and 4A for leaf rust and on chromosome 2A, 2B, and 6A for stripe rust resistance by using a genome-wide association study with a Bonferroni-corrected threshold of P < 0.10. Detected loci on chromosomes 4A and 2A were located within previously reported genomic regions affecting leaf rust and stripe rust resistance, respectively. The degree of dominance was for most associations favorable in the direction of improved resistance. Thus, resistance can be increased in hybrid wheat breeding by fixing complementary leaf rust and stripe rust resistance genes with desired dominance effects in opposite parental pools.
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Affiliation(s)
- Ulrike Beukert
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Guozheng Liu
- BASF Agricultural Solutions Belgium NV, Technologiepark 101, 9052, Zwijnaarde, Ghent, Belgium
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - Philipp H G Boeven
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593, Stuttgart, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute (JKI), Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland OT Gatersleben, Germany.
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