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Wang F, Xi Z, Wang M, Wang L, Wang J. Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2331-2348. [PMID: 38976378 DOI: 10.1111/tpj.16920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- 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
| | - Linyou Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Crop and Nuclear Technology Utilization, Hangzhou, 310021, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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2
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Wang H, Su B, Zhang Y, Shang M, Li S, Xing D, Wang J, Bern L, Johnson A, Al-Armanazi J, Hasin T, Hettiarachchi D, Paladines Parrales A, Dilawar H, Bruce TJ, Dunham RA, Wang X. From heterosis to outbreeding depression: genotype-by-environment interaction shifts hybrid fitness in opposite directions. Genetics 2024; 227:iyae090. [PMID: 38809057 DOI: 10.1093/genetics/iyae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024] Open
Abstract
In F1 hybrids, phenotypic values are expected to be near the parental means under additive effects or close to one parent under dominance. However, F1 traits can fall outside the parental range, and outbreeding depression occurs when inferior fitness is observed in hybrids. Another possible outcome is heterosis, a phenomenon that interspecific hybrids or intraspecific crossbred F1s exhibit improved fitness compared to both parental species or strains. As an application of heterosis, hybrids between channel catfish females and blue catfish males are superior in feed conversion efficiency, carcass yield, and harvestability. Over 20 years of hybrid catfish production in experimental settings and farming practices generated abundant phenotypic data, making it an ideal system to investigate heterosis. In this study, we characterized fitness in terms of growth and survival longitudinally, revealing environment-dependent heterosis. In ponds, hybrids outgrow both parents due to an extra rapid growth phase of 2-4 months in year 2. This bimodal growth pattern is unique to F1 hybrids in pond culture environments only. In sharp contrast, the same genetic types cultured in tanks display outbreeding depression, where hybrids perform poorly, while channel catfish demonstrate superiority in growth throughout development. Our findings represent the first example, known to the authors, of opposite fitness shifts in response to environmental changes in interspecific vertebrate hybrids, suggesting a broader fitness landscape for F1 hybrids. Future genomic studies based on this experiment will help understand genome-environment interaction in shaping the F1 progeny fitness in the scenario of environment-dependent heterosis and outbreeding depression.
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Affiliation(s)
- Haolong Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
| | - Baofeng Su
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ying Zhang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - De Xing
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Logan Bern
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Andrew Johnson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jacob Al-Armanazi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Tasnuba Hasin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Darshika Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Abel Paladines Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Timothy J Bruce
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rex A Dunham
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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Chen T, Wang Z, Wang J, Liu J, Zhang R, Jia X, Yu C, Yin Y, Creech D. Transcriptomic and metabolomic analyses unveil the growth advantage mechanism conferred by heterosis of Michelia 'Zhongshanhanxiao'. TREE PHYSIOLOGY 2023; 43:1454-1466. [PMID: 37099801 DOI: 10.1093/treephys/tpad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Michelia compressa (Maxim.) Sarg. is one of the important timber trees in Taiwan province, P. R. China. Michelia 'Zhongshanhanxiao' is a group of variants found among the progeny of M. compressa that exhibit higher growth rates compared with normal individuals, with a significantly increased stem diameter and height, as well as enlarged leaves and flowers. However, the molecular mechanisms fostering the growth advantage and morphological variations are unknown and deserve further study. Through analysing the transcriptome, metabolome and physiological processes of leaves, we identified remarkable differences in gene expression and metabolic profiles between Michelia 'Zhongshanhanxiao' and both the maternal M. compressa and its normal progeny. These differences were widely associated with a plant-pathogen interaction, phenylpropanoid biosynthesis, cyanoamino acid metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. Additionally, physiological measurements showed that Michelia 'Zhongshanhanxiao' possesses stronger photosynthetic capacity and higher plant hormone content. These results suggest that the heterosis of Michelia 'Zhongshanhanxiao' is regulated by candidates related to cell division, resistance to pathogens and the accumulation of organic compounds. The findings of this study provide crucial information on the molecular mechanisms underlying the growth advantages conferred by heterosis in trees.
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Affiliation(s)
- Tingting Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Zhiquan Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Junjie Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Jiaqi Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Rui Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Xiaoyu Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Chaoguang Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - Yunlong Yin
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, No. 1, Qianhu Village, Zhongshan Gate, Nanjing 210014, China
| | - David Creech
- Arthur Temple College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA
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Zhang F, Zhang C, Zhao X, Zhu S, Chen K, Zhou G, Wu Z, Li M, Zheng T, Wang W, Yan Z, Fei Q, Li Z, Chen J, Xu J. Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations. RICE (NEW YORK, N.Y.) 2022; 15:49. [PMID: 36181551 PMCID: PMC9526777 DOI: 10.1186/s12284-022-00595-z] [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: 08/12/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM's parents across three environments and gene-based analyses. RESULTS Genome-wide scanning of 13,847 segregating genes between the parents and linkage mapping based on 855 bins across the rice genome and phenotyping experiments across three environments resulted in identification of large numbers of genes, 639 main-effect QTLs (M-QTLs) and 2736 epistatic QTLs with significant additive or heterotic effects on the trait performances of the combined population consisting of RILs and BCF1 hybrids, most of which were environment-specific. The 324 M-QTLs affecting yield components included 32.7% additive QTLs, 38.0% over-dominant or dominant ones with strong and positive effects and 29.3% under-dominant or incomplete recessive ones with significant negative heterotic effects. 63.6% of 1403 genes with allelic introgression from subspecies japonica/Geng in the parents of QYSM may have contributed significantly to the enhanced yield performance of QYSM. CONCLUSIONS The parents of QYSM and related rice hybrids in China carry disproportionally more additive and under-dominant genes/QTLs affecting yield traits. Further focus in indica/Xian rice breeding should shift back to improving inbred varieties, while breaking yield ceiling of Xian hybrids can be achieved by one or combinations of the three strategies: (1) by pyramiding favorable alleles of additive genes, (2) by eliminating or minimizing under-dominant loci, and (3) by pyramiding overdominant/dominant genes polymorphic, particularly those underlying inter-subspecific heterosis.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Conghe Zhang
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuangbing Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China
| | - Guixiang Zhou
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhi Yan
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Qinyong Fei
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, Anhui, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
| | - Jinjie Chen
- Winall Hi-Tech Seed Co., Ltd., Hefei, 230088, Anhui, China.
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou, 518120, China.
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Wang M, Wang J. Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice. FRONTIERS IN PLANT SCIENCE 2022; 13:990656. [PMID: 36226282 PMCID: PMC9549252 DOI: 10.3389/fpls.2022.990656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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Shen G, Hu W, Wang X, Zhou X, Han Z, Sherif A, Ayaad M, Xing Y. Assembly of yield heterosis of an elite rice hybrid is promising by manipulating dominant quantitative trait loci. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:688-701. [PMID: 34995015 DOI: 10.1111/jipb.13220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 05/27/2023]
Abstract
In the past, rice hybrids with strong heterosis have been obtained empirically, by developing and testing thousands of combinations. Here, we aimed to determine whether heterosis of an elite hybrid could be achieved by manipulating major quantitative trait loci. We used 202 chromosome segment substitution lines from the elite hybrid Shanyou 63 to evaluate single segment heterosis (SSH) of yield per plant and identify heterotic loci. All nine detected heterotic loci acted in a dominant fashion, and no SSH exhibited overdominance. Functional alleles of key yield-related genes Ghd7, Ghd7.1, Hd1, and GS3 were dispersed in both parents. No functional alleles of three investigated genes were expressed at higher levels in the hybrids than in the more desirable parents. A hybrid pyramiding eight heterotic loci in the female parent Zhenshan 97 background had a comparable yield to Shanyou 63 and much higher yield than Zhenshan 97. Five hybrids pyramiding eight or nine heterotic loci in the combined parental genome background showed similar yield performance to that of Shanyou 63. These results suggest that dominance underlying functional complementation is an important contributor to yield heterosis and that heterosis assembly might be successfully promised by manipulating several major dominant heterotic loci.
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Affiliation(s)
- Guojing Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Hu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianmeng Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhongming Han
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ahmed Sherif
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal, 13759, Egypt
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Environment-Dependent Heterosis and Transgressive Gene Expression in Reciprocal Hybrids between the Channel Catfish Ictalurus punctatus and the Blue Catfish Ictalurus furcatus. BIOLOGY 2022; 11:biology11010117. [PMID: 35053114 PMCID: PMC8772901 DOI: 10.3390/biology11010117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent heterosis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.
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Wang M, Wang J. Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice. PLANT MOLECULAR BIOLOGY 2022; 108:105-125. [PMID: 34855066 DOI: 10.1007/s11103-021-01228-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to DNA methylation differences between the hybrid and its parents. Inter-subspecific hybrid rice combinations of indica × japonica have great potential to broaden genetic diversity and enhance the heterosis. The genetic and epigenetic molecular mechanism of its heterosis is not completely understood. Here, the dissection of gene expression and epigenetic regulation of an elite inter-subspecific hybrid rice were reported. In the hybrid, plant height, flag leaf area and Pn showed significant heterosis at the heading stage. Chloroplast-related differentially expressed genes (DEGs) and 530 allele-specific expression genes in hybrid were identified. Analysis of the genome-wide distribution of DNA methylation (5-methylcytosine, 5mC) and its association with transcription showed that there were variant DNA methylation maps and that the regulation of gene expression levels was negatively regulated by DNA methylation in the inter-subspecific hybrid rice. Differentially methylated DEGs were significantly enriched in photosynthetic functions. Moreover, distinct 5mC sequence contexts and distinct functional elements (promoter/gene body) may have different influences on heterosis related genes. The data identified heterosis related molecular mechanisms in inter-subspecific hybrid rice and suggested that epigenetic changes could extensively influence the flag leaf gene expression and heterosis.
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Affiliation(s)
- Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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11
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Baertschi C, Cao TV, Bartholomé J, Ospina Y, Quintero C, Frouin J, Bouvet JM, Grenier C. Impact of early genomic prediction for recurrent selection in an upland rice synthetic population. G3 (BETHESDA, MD.) 2021; 11:jkab320. [PMID: 34498036 PMCID: PMC8664429 DOI: 10.1093/g3journal/jkab320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/16/2021] [Indexed: 11/14/2022]
Abstract
Population breeding through recurrent selection is based on the repetition of evaluation and recombination among best-selected individuals. In this type of breeding strategy, early evaluation of selection candidates combined with genomic prediction could substantially shorten the breeding cycle length, thus increasing the rate of genetic gain. The objective of this study was to optimize early genomic prediction in an upland rice (Oryza sativa L.) synthetic population improved through recurrent selection via shuttle breeding in two sites. To this end, we used genomic prediction on 334 S0 genotypes evaluated with early generation progeny testing (S0:2 and S0:3) across two sites. Four traits were measured (plant height, days to flowering, grain yield, and grain zinc concentration) and the predictive ability was assessed for the target site. For days to flowering and plant height, which correlate well among sites (0.51-0.62), an increase of up to 0.4 in predictive ability was observed when the model was trained using the two sites. For grain zinc concentration, adding the phenotype of the predicted lines in the nontarget site to the model improved the predictive ability (0.51 with two-site and 0.31 with single-site model), whereas for grain yield the gain was less (0.42 with two-site and 0.35 with single-site calibration). Through these results, we found a good opportunity to optimize the genomic recurrent selection scheme and maximize the use of resources by performing early progeny testing in two sites for traits with best expression and/or relevance in each specific environment.
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Affiliation(s)
- Cédric Baertschi
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Tuong-Vi Cao
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Jérôme Bartholomé
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Yolima Ospina
- Alliance Bioversity-CIAT, Recta Palmira Cali, Colombia
| | | | - Julien Frouin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Jean-Marc Bouvet
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- CIRAD, Dispositif de Recherche et d’Enseignement en Partenariat “Forêts et Biodiversité à Madagascar”, Antananarivo, Madagascar
| | - Cécile Grenier
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- Alliance Bioversity-CIAT, Recta Palmira Cali, Colombia
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12
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Wei W, Wang P, Li S, Fan G, Zhao F, Zhang X, Shi G, Feng X, Song G, Wang X, Wang F, Wang D, Zhang W, Qiu F, Zhang Y, Li X, Pei J, Zhou X, Zhao Z. Rapid identification of candidate genes controlling male-sterility in Foxtail millet ( Setaria italica). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:73. [PMID: 37309520 PMCID: PMC10236058 DOI: 10.1007/s11032-021-01269-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Photo-(thermo-) sensitive genic male-sterile line is the key component of two-line hybridization system in foxtail millet (Setaria italica), but the genetic basis of male sterility in most male-sterile lines is still unclear. In the present study, a large F2 population was developed derived from a cross between the photo-(thermo-) sensitive male-sterile line A2 and the fertile-line 1484-5. Thirty plants with extreme high and extreme low fertility were selected from the population to construct a sterile DNA pool and a fertile DNA pool, respectively. Sequencing both DNA pools and data analysis revealed that two QTLs conferred male-sterility, qSiMS6.1 with a major effect and qSiMS6.2 with a minor effect, on chromosome 6. Both QTLs exhibited complete dominance. The major QTL, qSiMS6.1, was delimited to a 186-kb interval between the markers SiM20 and SiM9 by the joint analysis of QTL-seq and QTL mapping with SSR and structure variation markers. Millet_GLEAN_10020454 in this region is the most likely candidate gene for qSiMS6.1 since it is predicted to encode a male-sterile 5 like protein. These results lay a solid foundation for qSiMS6.1 cloning and provided gene resources for breeding new male-sterile lines. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01269-2.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Fengcang Qiu
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, 075032 China
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Genetic dissection of heterosis of indica-japonica by introgression line, recombinant inbred line and their testcross populations. Sci Rep 2021; 11:10265. [PMID: 33986411 PMCID: PMC8119717 DOI: 10.1038/s41598-021-89691-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/27/2021] [Indexed: 12/03/2022] Open
Abstract
The successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F1s (TCF1s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF1s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF1s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2, qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.
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14
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Estimation of a New Canopy Structure Parameter for Rice Using Smartphone Photography. SENSORS 2020; 20:s20144011. [PMID: 32707649 PMCID: PMC7412381 DOI: 10.3390/s20144011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/07/2020] [Accepted: 07/15/2020] [Indexed: 12/18/2022]
Abstract
The objective of this study was to develop a low-cost method for rice growth information obtained quickly using digital images taken with smartphone. A new canopy parameter, namely, the canopy volume parameter (CVP), was proposed and developed for rice using the leaf area index (LAI) and plant height (PH). Among these parameters, the CVP was selected as an optimal parameter to characterize rice yields during the growth period. Rice canopy images were acquired with a smartphone. Image feature parameters were extracted, including the canopy cover (CC) and numerous vegetation indices (VIs), before and after image segmentation. A rice CVP prediction model in which the CC and VIs served as independent variables was established using a random forest (RF) regression algorithm. The results revealed the following. The CVP was better than the LAI and PH for predicting the final yield. And a CVP prediction model constructed according to a local modelling method for distinguishing different types of rice varieties was the most accurate (coefficient of determination (R2) = 0.92; root mean square error (RMSE) = 0.44). These findings indicate that digital images can be used to track the growth of crops over time and provide technical support for estimating rice yields.
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15
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A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat. G3-GENES GENOMES GENETICS 2019; 9:675-684. [PMID: 30455184 PMCID: PMC6404624 DOI: 10.1534/g3.118.200646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.
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16
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Dissecting Heterosis During the Ear Inflorescence Development Stage in Maize via a Metabolomics-based Analysis. Sci Rep 2019; 9:212. [PMID: 30659214 PMCID: PMC6338801 DOI: 10.1038/s41598-018-36446-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022] Open
Abstract
Heterosis can increase the yield of many crops and has been extensively applied in agriculture. In maize, female inflorescence architecture directly determines grain yield. Thus, exploring the relationship between early maize ear inflorescence development and heterosis regarding yield-related traits may be helpful for characterizing the molecular mechanisms underlying heterotic performance. In this study, we fine mapped the overdominant heterotic locus (hlEW2b), associated with ear width, in an approximately 1.98-Mb region based on analyses of chromosome segment substitution lines and the corresponding testcross population. Maize ear inflorescences at the floral meristem stage were collected from two inbred lines, one chromosome segment substitution line that carried hlEW2b (sub-CSSL16), the receptor parent lx9801, and the Zheng58 × sub-CSSL16 and Zheng58 × lx9801 hybrid lines. A total of 256 metabolites were identified, including 31 and 24 metabolites that were differentially accumulated between the two hybrid lines and between the two inbred lines, respectively. Most of these metabolites are involved in complex regulatory mechanisms important for maize ear development. For example, nucleotides are basic metabolites affecting cell composition and carbohydrate synthesis. Additionally, nicotinate and nicotinamide metabolism is important for photosynthesis, plant stress responses, and cell expansion. Moreover, flavonoid and phenolic metabolites regulate auxin transport and cell apoptosis. Meanwhile, phytohormone biosynthesis and distribution influence the cell cycle and cell proliferation. Our results revealed that changes in metabolite contents may affect the heterotic performance related to ear width and yield in maize hybrid lines. This study provides new clues in heterosis at the metabolomics level and implies that differentially accumulated metabolites made distinct contributions to the heterosis at an early stage of ear inflorescences development.
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Liu HJ, Yan J. Crop genome-wide association study: a harvest of biological relevance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:8-18. [PMID: 30368955 DOI: 10.1111/tpj.14139] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/13/2018] [Accepted: 10/22/2018] [Indexed: 05/20/2023]
Abstract
With the advent of rapid genotyping and next-generation sequencing technologies, genome-wide association study (GWAS) has become a routine strategy for decoding genotype-phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype-phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many 'hits' obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non-main effects including epistasis, pleiotropy, and phenotypic plasticity. We also discuss how these achievements and the remaining gaps in our knowledge will guide future studies. Synthetic association is highlighted as leading to false causality, which is prevalent but largely underestimated. Furthermore, validation evidence is appealing for future GWAS, especially in the context of emerging genome-editing technologies.
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Affiliation(s)
- Hai-Jun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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18
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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Gao N, Teng J, Ye S, Yuan X, Huang S, Zhang H, Zhang X, Li J, Zhang Z. Genomic Prediction of Complex Phenotypes Using Genic Similarity Based Relatedness Matrix. Front Genet 2018; 9:364. [PMID: 30233646 PMCID: PMC6127733 DOI: 10.3389/fgene.2018.00364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/21/2018] [Indexed: 11/13/2022] Open
Abstract
In the last years, a series of methods for genomic prediction (GP) have been established, and the advantages of GP over pedigree best linear unbiased prediction (BLUP) have been reported. However, the majority of previously proposed GP models are purely based on mathematical considerations while seldom take the abundant biological knowledge into account. Prediction ability of those models largely depends on the consistency between the statistical assumptions and the underlying genetic architectures of traits of interest. In this study, gene annotation information was incorporated into GP models by constructing haplotypes with SNPs mapped to genic regions. Haplotype allele similarity between pairs of individuals was measured through different approaches at single gene level and then converted into whole genome level, which was then treated as a special kernel and used in kernel based GP models. Results shown that the gene annotation guided methods gave higher or at least comparable predictive ability in some traits, especially in the Arabidopsis dataset and the rice breeding population. Compared to SNP models and haplotype models without gene annotation, the gene annotation based models improved the predictive ability by 0.56~26.67% in the Arabidopsis and 1.62~16.53% in the rice breeding population, respectively. However, incorporating gene annotation slightly improved the predictive ability for several traits but did not show any extra gain for the rest traits in a chicken population. In conclusion, integrating gene annotation into GP models could be beneficial for some traits, species, and populations compared to SNP models and haplotype models without gene annotation. However, more studies are yet to be conducted to implicitly investigate the characteristics of these gene annotation guided models.
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Affiliation(s)
- Ning Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shaopan Ye
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shuwen Huang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hao Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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Wang Y, Zhang X, Shi X, Sun C, Jin J, Tian R, Wei X, Xie H, Guo Z, Tang J. Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations. Sci Rep 2018; 8:11101. [PMID: 30038303 PMCID: PMC6056474 DOI: 10.1038/s41598-018-29338-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Heterosis has been widely used to increase grain quality and yield, but its genetic mechanism remains unclear. In this study, the genetic basis of heterosis for four maize kernel traits was examined in two test populations constructed using a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058) in two environments. 63 and 57 different heterotic loci (HL) were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, respectively. Of these, nine HL and six HL were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, at the two locations simultaneously. Comparative analysis of the HL for the four kernel traits identified only 21 HL in the two test populations simultaneously. These results showed that most HL for the four kernel traits differed between the two test populations. The common HL were important loci from the Reid × Tangsipingtou heterotic model, and could be used to predict hybrid performance in maize breeding.
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Xia Shi
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Canran Sun
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiao Jin
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Runmiao Tian
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyi Wei
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453003, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, China.
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Xie F, Zhang J. Shanyou 63: an elite mega rice hybrid in China. RICE (NEW YORK, N.Y.) 2018; 11:17. [PMID: 29629478 PMCID: PMC5890006 DOI: 10.1186/s12284-018-0210-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/18/2018] [Indexed: 05/12/2023]
Abstract
Hybrid rice has been successfully used for commercial rice production for 40 years in China. Shanyou 63, a mega rice hybrid, derived from the parents Zhenshan 97A and Minghui 63, was a milestone for China's hybrid rice development and production because of its high yield and wide adaptability. It was planted in 16 provinces of the country on 17% of the national hybrid rice area annually during the 29 years from 1984 to 2012. The hybrid and its parents have also been widely used for basic and agronomic studies related to rice heterosis, stress tolerance, molecular markers and genomics. We review the development of the hybrid and its parents and their major characteristics for the purpose of learning from the history and guiding future hybrid rice development. The history and development experience show that a successful hybrid rice variety should have multiple traits, including high yield, wide adaptability, resistances to major diseases, and high rice quality that meets the demands of consumers. From the breeding aspect, hybrid rice provides the advantage of combining elite traits or genes from different types of parents, such as those from subspecies of indica and japonica, into a single variety. Farmers prefer not only a variety with high yield potential, but also stable yields and local adaptability.
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Affiliation(s)
- Fangming Xie
- Yuan Longping High-Tech Agriculture Co. Ltd., Changsha, 410001 Hunan China
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018 China
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22
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Wu B, Hu W, Ayaad M, Liu H, Xing Y. Intragenic recombination between two non-functional semi-dwarf 1 alleles produced a functional SD1 allele in a tall recombinant inbred line in rice. PLoS One 2017; 12:e0190116. [PMID: 29281725 PMCID: PMC5744974 DOI: 10.1371/journal.pone.0190116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/10/2017] [Indexed: 02/07/2023] Open
Abstract
Intragenic recombination is one of the most important sources of genetic variability. In our previous study, RI92 a tall line (160 cm of plant height) was observed in the cross progeny between two semi-dwarf indica cultivars Zhenshan 97 and Minghui 63. Genome-wide genotyping and sequencing indicated that the genome constitution of RI92 was completely from both parents. Bulk segregant analysis in a BC3F2 population revealed that “green revolution gene” semi-dwarf 1 (sd1) was most likely the gene controlling the tall plant height in RI92. Sequencing analysis of SD1 revealed that an intragenic recombination occurred between two parental non-functional sd1 alleles and generated a functional SD1 in RI92. Four-fold high recombination rate in SD1 located bins to the genome-wide average was observed in two RIL populations, indicating recombination hotspot in the SD1 region. Intragenic recombination creates new alleles in the progeny distinct from parental alleles and diversifies natural variation.
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Affiliation(s)
- Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wei Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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23
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Xu Q, Xu X, Shi Y, Qi X, Chen X. Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm5.1 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling. BMC Genomics 2017; 18:21. [PMID: 28056792 PMCID: PMC5217421 DOI: 10.1186/s12864-016-3438-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8. RESULTS Whole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers. This led to the identification of a ~6.8 Mb substituted segment predicted to contain 856 genes. RNA-seq was used to study gene expression differences in PM treated (plants harvested 48 h after inoculation) and untreated (control) SSL508-28 and D8 lines. Exactly 1,248 and 1,325 differentially expressed genes (DEGs) were identified in SSL508-28 and D8, respectively. Of those, 88 DEGs were located in the ~6.8 Mb segment interval. Based on expression data and annotation, we identified 8 potential candidate genes that may participate in PM resistance afforded by Pm5.1, including two tandemly arrayed genes encoding receptor protein kinases, two transcription factors, two genes encoding remorin proteins, one gene encoding a P-type ATPase and one gene encoding a 70 kDa heat shock protein. The transcriptome data also revealed a complex regulatory network for Pm5.1-mediated PM resistance that may involve multiple signal regulators and transducers, cell wall modifications and the salicylic acid signaling pathway. CONCLUSION These findings shed light on the cucumber PM defense mechanisms mediated by Pm5.1 and provided valuable information for the fine mapping of Pm5.1 and breeding of cucumber with enhanced resistance to PM.
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Affiliation(s)
- Qiang Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuewen Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Yang Shi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xiaohua Qi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuehao Chen
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
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Detection of QTLs for Yield Heterosis in Rice Using a RIL Population and Its Testcross Population. Int J Genomics 2016; 2016:2587823. [PMID: 28101503 PMCID: PMC5215376 DOI: 10.1155/2016/2587823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/05/2016] [Indexed: 11/17/2022] Open
Abstract
Analysis of the genetic basis of yield heterosis in rice was conducted by quantitative trait locus mapping using a set of 204 recombinant inbred lines (RILs), its testcross population, and mid-parent heterosis dataset (HMP). A total of 39 QTLs for six yield traits were detected, of which three were detected in all the datasets, ten were common to the RIL and testcross populations, six were common to the testcross and HMP, and 17, 2, and 1 were detected for RILs, testcrosses, and HMP, respectively. When a QTL was detected in both the RIL and testcross populations, the difference between TQ and IR24 and that between Zh9A/TQ and Zh9A/IR24 were always in the same direction, providing the potential to increase the yield of hybrids by increasing the yield of parental lines. Genetic action mode of the 39 QTLs was inferred by comparing their performances in RILs, testcrosses, and HMP. The genetic modes were additive for 17 QTLs, dominance for 12 QTLs, and overdominance for 10 QTLs. These results suggest that dominance and overdominance are the most important contributor to yield heterosis in rice, in which the accumulative effects of yield components play an important role.
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Wang H, Zhang X, Yang H, Liu X, Li H, Yuan L, Li W, Fu Z, Tang J, Kang D. Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize. Sci Rep 2016; 6:38205. [PMID: 27917917 PMCID: PMC5137037 DOI: 10.1038/srep38205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 11/07/2016] [Indexed: 11/17/2022] Open
Abstract
Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.
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Affiliation(s)
- Hongqiu Wang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huili Yang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyang Liu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huimin Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liang Yuan
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, China
| | - Dingming Kang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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Exploitation of heterosis loci for yield and yield components in rice using chromosome segment substitution lines. Sci Rep 2016; 6:36802. [PMID: 27833097 PMCID: PMC5105071 DOI: 10.1038/srep36802] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023] Open
Abstract
We constructed 128 chromosome segment substitution lines (CSSLs), derived from a cross between indica rice (Oryza sativa L.) 9311 and japonica rice Nipponbare, to investigate the genetic mechanism of heterosis. Three photo-thermo-sensitive-genic male sterile lines (Guangzhan63-4s, 036s, and Lian99s) were selected to cross with each CSSL to produce testcross populations (TCs). Field experiments were carried out in 2009, 2011, and 2015 to evaluate yield and yield-related traits in the CSSLs and TCs. Four traits (plant height, spikelet per panicle, thousand-grain weight, and grain yield per plant) were significantly related between CSSLs and TCs. In the TCs, plant height, panicle length, seed setting rate, thousand-grain weight, and grain yield per plant showed partial dominance, indicating that dominance largely contributes to heterosis of these five traits. While overdominance may be more important for heterosis of panicles per plant and spikelet per panicle. Based on the bin-maps of CSSLs and TCs, we detected 62 quantitative trait loci (QTLs) and 97 heterotic loci (HLs) using multiple linear regression analyses. Some of these loci were clustered together. The identification of QTLs and HLs for yield and yield-related traits provide useful information for hybrid rice breeding, and help to uncover the genetic basis of rice heterosis.
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Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance. PLoS One 2016; 11:e0164469. [PMID: 27764118 PMCID: PMC5072683 DOI: 10.1371/journal.pone.0164469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels). When compared against the reference genome of the inbred cucumber line 9930, a total of 468,616 SNPs and 67,259 indels were identified in SSL508-28, and 537,352 SNPs and 91,698 indels were identified in D8. Of these, 3,014 non-synonymous SNPs and 226 frameshift indels in SSL508-28, and 3,104 non-synonymous SNPs and 251 frameshift indels in D8, were identified. Bioinformatics analysis of these variations revealed a total of 15,682 SNPs and 6,262 indels between SSL508-28 and D8, among which 120 non-synonymous SNPs and 30 frameshift indels in 94 genes were detected between SSL508-28 and D8. Finally, out of these 94 genes, five resistance genes with nucleotide-binding sites and leucine-rich repeat domains were selected for qRT-PCR analysis. This revealed an upregulation of two transcripts, Csa2M435460.1 and Csa5M579560.1, in SSL508-28. Furthermore, the results of qRT-PCR analysis of these two genes in ten PM resistant and ten PM susceptible cucumber lines showed that when exposed to PM, Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines. This indicates that Csa2M435460.1 and Csa5M579560.1 are candidate genes for PM resistance in cucumber. In addition, the non-synonymous SNPs in Csa2M435460.1 and Csa5M579560.1, identified in SSL508-28 and D8, might be the key to high PM-resistance in SSL508-28.
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Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton. G3-GENES GENOMES GENETICS 2016; 6:3373-3379. [PMID: 27565885 PMCID: PMC5068956 DOI: 10.1534/g3.116.034355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.
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Predicting rice hybrid performance using univariate and multivariate GBLUP models based on North Carolina mating design II. Heredity (Edinb) 2016; 118:302-310. [PMID: 27649618 DOI: 10.1038/hdy.2016.87] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 01/21/2023] Open
Abstract
Genomic selection (GS) is more efficient than traditional phenotype-based methods in hybrid breeding. The present study investigated the predictive ability of genomic best linear unbiased prediction models for rice hybrids based on the North Carolina mating design II, in which a total of 115 inbred rice lines were crossed with 5 male sterile lines. Using 8 traits of the 575 (115 × 5) hybrids from two environments, both univariate (UV) and multivariate (MV) prediction analyses, including additive and dominance effects, were performed. Using UV models, the prediction results of cross-validation indicated that including dominance effects could improve the predictive ability for some traits in rice hybrids. Additionally, we could take advantage of GS even for a low-heritability trait, such as grain yield per plant (GY), because a modest increase in the number of top selection could generate a higher, more stable mean phenotypic value for rice hybrids. Thus this strategy was used to select superior potential crosses between the 115 inbred lines and those between the 5 male sterile lines and other genotyped varieties. In our MV research, an MV model (MV-ADV) was developed utilizing a MV relationship matrix constructed with auxiliary variates. Based on joint analysis with multi-trait (MT) or with multi-environment, the prediction results confirmed the superiority of MV-ADV over an UV model, particularly in the MT scenario for a low-heritability target trait (such as GY), with highly correlated auxiliary traits. For a high-heritability trait (such as thousand-grain weight), MT prediction is unnecessary, and UV prediction is sufficient.
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30
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Biscarini F, Cozzi P, Casella L, Riccardi P, Vattari A, Orasen G, Perrini R, Tacconi G, Tondelli A, Biselli C, Cattivelli L, Spindel J, McCouch S, Abbruscato P, Valé G, Piffanelli P, Greco R. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions. PLoS One 2016; 11:e0155425. [PMID: 27228161 PMCID: PMC4881974 DOI: 10.1371/journal.pone.0155425] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. RESULTS In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). CONCLUSIONS We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.
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Affiliation(s)
| | | | | | | | | | - Gabriele Orasen
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Rosaria Perrini
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Gianni Tacconi
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Alessandro Tondelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Chiara Biselli
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
| | - Jennifer Spindel
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | - Susan McCouch
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America
| | | | - Giampiero Valé
- CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy
- CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d’Arda (Piacenza), Italy
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Xu X, Yu T, Xu R, Shi Y, Lin X, Xu Q, Qi X, Weng Y, Chen X. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:507-16. [PMID: 26660669 DOI: 10.1007/s00122-015-2644-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/24/2015] [Indexed: 05/09/2023]
Abstract
A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ting Yu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ruixue Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yang Shi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaojian Lin
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data. G3-GENES GENOMES GENETICS 2015; 5:2629-37. [PMID: 26438289 PMCID: PMC4683636 DOI: 10.1534/g3.115.019513] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases.
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Li X, Li X, Fridman E, Tesso TT, Yu J. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. Proc Natl Acad Sci U S A 2015; 112:11823-8. [PMID: 26351684 PMCID: PMC4586871 DOI: 10.1073/pnas.1509229112] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.
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Affiliation(s)
- Xin Li
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Eyal Fridman
- Institute of Plant Science, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel
| | - Tesfaye T Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011;
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Shen G, Xing Y. Two Novel QTLs for Heading Date Are Identified Using a Set of Chromosome Segment Substitution Lines in Rice (Oryza sativa L.). J Genet Genomics 2014; 41:659-62. [DOI: 10.1016/j.jgg.2014.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 12/29/2022]
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Renny-Byfield S, Wendel JF. Doubling down on genomes: polyploidy and crop plants. AMERICAN JOURNAL OF BOTANY 2014; 101:1711-25. [PMID: 25090999 DOI: 10.3732/ajb.1400119] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop species are relatively recent allopolyploids, resulting from interspecific hybridization and polyploidy. Thus, an appreciation of the evolutionary consequences of (allo)polyploidy is central to our understanding of crop plant domestication, agricultural improvement, and the evolution of angiosperms in general. Indeed, many recent insights into plant biology have been gleaned from polyploid crops, including, but not limited to wheat, tobacco, sugarcane, apple, and cotton. A multitude of evolutionary processes affect polyploid genomes, including rapid and substantial genome reorganization, transgressive gene expression alterations, gene fractionation, gene conversion, genome downsizing, and sub- and neofunctionalization of duplicate genes. Often these genomic changes are accompanied by heterosis, robustness, and the improvement of crop yield, relative to closely related diploids. Historically, however, the genome-wide analysis of polyploid crops has lagged behind those of diploid crops and other model organisms. This lag is partly due to the difficulties in genome assembly, resulting from the genomic complexities induced by combining two or more evolutionarily diverged genomes into a single nucleus and by the significant size of polyploid genomes. In this review, we explore the role of polyploidy in angiosperm evolution, the domestication process and crop improvement. We focus on the potential of modern technologies, particularly next-generation sequencing, to inform us on the patterns and processes governing polyploid crop improvement and phenotypic change subsequent to domestication.
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Affiliation(s)
- Simon Renny-Byfield
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Jonathan F Wendel
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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