1
|
Guo J, Wang H, Guan W, Guo Q, Wang J, Yang J, Peng Y, Shan J, Gao M, Shi S, Shangguan X, Liu B, Jing S, Zhang J, Xu C, Huang J, Rao W, Zheng X, Wu D, Zhou C, Du B, Chen R, Zhu L, Zhu Y, Walling LL, Zhang Q, He G. A tripartite rheostat controls self-regulated host plant resistance to insects. Nature 2023:10.1038/s41586-023-06197-z. [PMID: 37316670 DOI: 10.1038/s41586-023-06197-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
Plants deploy receptor-like kinases and nucleotide-binding leucine-rich repeat receptors to confer host plant resistance (HPR) to herbivores1. These gene-for-gene interactions between insects and their hosts have been proposed for more than 50 years2. However, the molecular and cellular mechanisms that underlie HPR have been elusive, as the identity and sensing mechanisms of insect avirulence effectors have remained unknown. Here we identify an insect salivary protein perceived by a plant immune receptor. The BPH14-interacting salivary protein (BISP) from the brown planthopper (Nilaparvata lugens Stål) is secreted into rice (Oryza sativa) during feeding. In susceptible plants, BISP targets O. satvia RLCK185 (OsRLCK185; hereafter Os is used to denote O. satvia-related proteins or genes) to suppress basal defences. In resistant plants, the nucleotide-binding leucine-rich repeat receptor BPH14 directly binds BISP to activate HPR. Constitutive activation of Bph14-mediated immunity is detrimental to plant growth and productivity. The fine-tuning of Bph14-mediated HPR is achieved through direct binding of BISP and BPH14 to the selective autophagy cargo receptor OsNBR1, which delivers BISP to OsATG8 for degradation. Autophagy therefore controls BISP levels. In Bph14 plants, autophagy restores cellular homeostasis by downregulating HPR when feeding by brown planthoppers ceases. We identify an insect saliva protein sensed by a plant immune receptor and discover a three-way interaction system that offers opportunities for developing high-yield, insect-resistant crops.
Collapse
Affiliation(s)
- Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huiying Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Guan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qin Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaxin Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junhan Shan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mingyang Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaojie Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinxin Shangguan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bingfang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shengli Jing
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunxue Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jin Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiwei Rao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaohong Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Cong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuxian Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Qifa Zhang
- Hubei Hongshan Laboratory, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| |
Collapse
|
2
|
Aloryi KD, Okpala NE, Amo A, Bello SF, Akaba S, Tian X. A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1035851. [PMID: 36466247 PMCID: PMC9709451 DOI: 10.3389/fpls.2022.1035851] [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: 09/03/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Improving grain yield potential in rice is an important step toward addressing global food security challenges. The meta-QTL analysis offers stable and robust QTLs irrespective of the genetic background of mapping populations and phenotype environment and effectively narrows confidence intervals (CI) for candidate gene (CG) mining and marker-assisted selection improvement. To achieve these aims, a comprehensive bibliographic search for grain yield traits (spikelet fertility, number of grains per panicle, panicles number per plant, and 1000-grain weight) QTLs was conducted, and 462 QTLs were retrieved from 47 independent QTL research published between 2002 and 2022. QTL projection was performed using a reference map with a cumulative length of 2,945.67 cM, and MQTL analysis was conducted on 313 QTLs. Consequently, a total of 62 MQTLs were identified with reduced mean CI (up to 3.40 fold) compared to the mean CI of original QTLs. However, 10 of these MQTLs harbored at least six of the initial QTLs from diverse genetic backgrounds and environments and were considered the most stable and robust MQTLs. Also, MQTLs were compared with GWAS studies and resulted in the identification of 16 common significant loci modulating the evaluated traits. Gene annotation, gene ontology (GO) enrichment, and RNA-seq analyses of chromosome regions of the stable MQTLs detected 52 potential CGs including those that have been cloned in previous studies. These genes encode proteins known to be involved in regulating grain yield including cytochrome P450, zinc fingers, MADs-box, AP2/ERF domain, F-box, ubiquitin ligase domain protein, homeobox domain, DEAD-box ATP domain, and U-box domain. This study provides the framework for molecular dissection of grain yield in rice. Moreover, the MQTLs and CGs identified could be useful for fine mapping, gene cloning, and marker-assisted selection to improve rice productivity.
Collapse
Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Aduragbemi Amo
- Institute of Plant Breeding, Genetics and Genomics University of Georgia, Athens, GA, United States
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
3
|
Shi S, Wang H, Nie L, Tan D, Zhou C, Zhang Q, Li Y, Du B, Guo J, Huang J, Wu D, Zheng X, Guan W, Shan J, Zhu L, Chen R, Xue L, Walling LL, He G. Bph30 confers resistance to brown planthopper by fortifying sclerenchyma in rice leaf sheaths. MOLECULAR PLANT 2021; 14:1714-1732. [PMID: 34246801 DOI: 10.1016/j.molp.2021.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/24/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Phloem-feeding insects cause massive losses in agriculture and horticulture. Host plant resistance to phloem-feeding insects is often mediated by changes in phloem composition, which deter insect settling and feeding and decrease viability. Here, we report that rice plant resistance to the phloem-feeding brown planthopper (BPH) is associated with fortification of the sclerenchyma tissue, which is located just beneath the epidermis and a cell layer or two away from the vascular bundle in the rice leaf sheath. We found that BPHs prefer to feed on the smooth and soft region on the surface of rice leaf sheaths called the long-cell block. We identified Bph30 as a rice BPH resistance gene that prevents BPH stylets from reaching the phloem due to the fortified sclerenchyma. Bph30 is strongly expressed in sclerenchyma cells and enhances cellulose and hemicellulose synthesis, making the cell walls stiffer and sclerenchyma thicker. The structurally fortified sclerenchyma is a formidable barrier preventing BPH stylets from penetrating the leaf sheath tissues and arriving at the phloem to feed. Bph30 belongs to a novel gene family, encoding a protein with two leucine-rich domains. Another member of the family, Bph40, also conferred resistance to BPH. Collectively, the fortified sclerenchyma-mediated resistance mechanism revealed in this study expands our understanding of plant-insect interactions and opens a new path for controlling planthoppers in rice.
Collapse
Affiliation(s)
- Shaojie Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huiying Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lingyun Nie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Di Tan
- The Institute of Technological Science, School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072, China
| | - Cong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qian Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jin Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaohong Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Guan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Junhan Shan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Longjian Xue
- The Institute of Technological Science, School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072, China
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of CaliforniaA, Riverside, CA 92521, USA
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
4
|
Aakanksha, Yadava SK, Yadav BG, Gupta V, Mukhopadhyay A, Pental D, Pradhan AK. Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies. FRONTIERS IN PLANT SCIENCE 2021; 12:721631. [PMID: 34603351 PMCID: PMC8481694 DOI: 10.3389/fpls.2021.721631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/16/2021] [Indexed: 01/07/2024]
Abstract
The exploitation of heterosis through hybrid breeding is one of the major breeding objectives for productivity increase in crop plants. This research analyzes the genetic basis of heterosis in Brassica juncea by using a doubled haploid (DH) mapping population derived from F1 between two heterotic inbred parents, one belonging to the Indian and the other belonging to the east European gene pool, and their two corresponding sets of backcross hybrids. An Illumina Infinium Brassica 90K SNP array-based genetic map was used to identify yield influencing quantitative trait loci (QTL) related to plant architecture, flowering, and silique- and seed-related traits using five different data sets from multiple trials, allowing the estimation of additive and dominance effects, as well as digenic epistatic interactions. In total, 695 additive QTL were detected for the 14 traits in the three trials using five data sets, with overdominance observed to be the predominant type of effect in determining the expression of heterotic QTL. The results indicated that the design in the present study was efficient for identifying common QTL across multiple trials and populations, which constitute a valuable resource for marker-assisted selection and further research. In addition, a total of 637 epistatic loci were identified, and it was concluded that epistasis among loci without detectable main effects plays an important role in controlling heterosis in yield of B. juncea.
Collapse
Affiliation(s)
- Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Bal Govind Yadav
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Akshay K. Pradhan
- Department of Genetics, University of Delhi South Campus, New Delhi, India
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| |
Collapse
|
5
|
Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S. Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross. Sci Rep 2020; 10:7766. [PMID: 32385410 PMCID: PMC7210974 DOI: 10.1038/s41598-020-64300-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/10/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.
Collapse
|
6
|
Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice. BMC Genomics 2020; 21:294. [PMID: 32272882 PMCID: PMC7146888 DOI: 10.1186/s12864-020-6702-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/25/2020] [Indexed: 11/29/2022] Open
Abstract
Background Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development. Results A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits. Conclusion This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.
Collapse
|
7
|
Khanal S, Dunne JC, Schwartz BM, Kim C, Milla-Lewis S, Raymer PL, Hanna WW, Adhikari J, Auckland SA, Rainville L, Paterson AH. Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids ( Cynodon dactylon x transvaalensis): Morphological Traits. G3 (BETHESDA, MD.) 2019; 9:2581-2596. [PMID: 31208957 PMCID: PMC6686926 DOI: 10.1534/g3.119.400061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11-19%), qLLS-7-1 (for LLS; R2 = 13-27%), qLEN-1-1 (for LLEN; R2 = 10-11%), and qLW-3-2 (for LW; R2 = 10-12%) were 'stable' across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.
Collapse
Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Jeffrey C Dunne
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susana Milla-Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Paul L Raymer
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 30224
| | - Wayne W Hanna
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Lisa Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606,
| |
Collapse
|
8
|
Development of High Yielding Glutinous Cytoplasmic Male Sterile Rice (Oryza sativa L.) Lines through CRISPR/Cas9 Based Mutagenesis of Wx and TGW6 and Proteomic Analysis of Anther. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8120290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Development of high yielding and more palatable glutinous rice is an important goal in breeding and long-standing cultural interaction in Asia. In this study, the TGW6 and Wx, major genes conferring 1000 grain weight (GW) and amylose content (AC), were edited in a maintainer line by CRISPR/Cas9 technology. Four targets were assembled in pYLCRISPR/Cas9Pubi-H vector and T0 mutant plants were obtained through Agrobacterium mediated transformation with 90% mutation frequency having 28% homozygous mutations without off-target effects in three most likely sites of each target and expression level of target genes in mutant lines was significantly decreased (P < 0.01), the GW and gel consistency (GC) were increased, and the AC and gelatinization temperature (GT) were decreased significantly and grain appearance was opaque, while there was no change in starch content (SC) and other agronomic traits. Mutations were inheritable and some T1 plants were re-edited but T2 generation was completely stable. The pollen fertility status was randomly distributed, and the mutant maintainer lines were hybridized with Cytoplasmic Male Sterile (CMS) line 209A and after subsequent backcrossing the two glutinous CMS lines were obtained in BC2F1. The identified proteins from anthers of CMS and maintainer line were closely associated with transcription, metabolism, signal transduction, and protein biosynthesis. Putative mitochondrial NAD+-dependent malic enzyme was absent in CMS line which caused the pollen sterility because of insufficient energy, while upregulation of putative acetyl-CoA synthetase and Isoamylase in both lines might have strong relationship with CMS and amylose content. High yielding glutinous CMS lines will facilitate hybrid rice breeding and investigations of proteins linked to male sterility will provide the insights to complicated metabolic network in anther development.
Collapse
|
9
|
Guo J, Xu C, Wu D, Zhao Y, Qiu Y, Wang X, Ouyang Y, Cai B, Liu X, Jing S, Shangguan X, Wang H, Ma Y, Hu L, Wu Y, Shi S, Wang W, Zhu L, Xu X, Chen R, Feng Y, Du B, He G. Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice. Nat Genet 2018; 50:297-306. [PMID: 29358653 DOI: 10.1038/s41588-018-0039-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/11/2017] [Indexed: 12/28/2022]
Abstract
The brown planthopper (BPH) and white-backed planthopper (WBPH) are the most destructive insect pests of rice, and they pose serious threats to rice production throughout Asia. Thus, there are urgent needs to identify resistance-conferring genes and to breed planthopper-resistant rice varieties. Here we report the map-based cloning and functional analysis of Bph6, a gene that confers resistance to planthoppers in rice. Bph6 encodes a previously uncharacterized protein that localizes to exocysts and interacts with the exocyst subunit OsEXO70E1. Bph6 expression increases exocytosis and participates in cell wall maintenance and reinforcement. A coordinated cytokinin, salicylic acid and jasmonic acid signaling pathway is activated in Bph6-carrying plants, which display broad resistance to all tested BPH biotypes and to WBPH without sacrificing yield, as these plants were found to maintain a high level of performance in a field that was heavily infested with BPH. Our results suggest that a superior resistance gene that evolved long ago in a region where planthoppers are found year round could be very valuable for controlling agricultural insect pests.
Collapse
Affiliation(s)
- Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunxue Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yan Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yongfu Qiu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoxiao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Baodong Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China
| | - Shengli Jing
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinxin Shangguan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huiying Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinhua Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Liang Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shaojie Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenliang Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuqi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Sun L, Xu X, Jiang Y, Zhu Q, Yang F, Zhou J, Yang Y, Huang Z, Li A, Chen L, Tang W, Zhang G, Wang J, Xiao G, Huang D, Chen C. Genetic Diversity, Rather than Cultivar Type, Determines Relative Grain Cd Accumulation in Hybrid Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1407. [PMID: 27708659 PMCID: PMC5030296 DOI: 10.3389/fpls.2016.01407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/02/2016] [Indexed: 05/26/2023]
Abstract
Cadmium (Cd) is a toxic element, and rice is known to be a leading source of dietary Cd for people who consume rice as their main caloric resource. Hybrid rice has dominated rice production in southern China and has been adopted worldwide. The characteristics of high yield heterosis of rice hybrids makes the public think intuitively that the hybrid rice accumulates more Cd in grain than do inbred cultivars. A detailed understanding of the genetic basis of grain Cd accumulation in hybrids and developing Cd-safe rice are one of the top priorities for hybrid rice breeders at present. In this study, we investigated genetic diversity and grain Cd levels in 617 elite rice hybrids collected from the middle and lower Yangtze River Valley in China and 68 inbred cultivars from around the world. We found that there are large variations in grain Cd accumulation in both the hybrids and their inbred counterparts. However, we found grain Cd levels in the rice hybrids to be similar to the levels in indica rice inbreds, suggesting that the hybrids do not accumulate more Cd than do the inbred rice cultivars. Further analysis revealed that the high heritability of Cd accumulation in the grain and the single indica population structure increases the risk of Cd over-accumulation in hybrid rice. The genetic effects of Cd-related QTLs, which have been identified in related Cd-QTL mapping studies, were also determined in the hybrid rice population. Four QTLs were identified as being associated with the variation in grain Cd levels; three of these loci exhibited obvious indica-japonica differentiations. Our study will provide a better understanding of grain Cd accumulations in hybrid rice, and pave the way toward effective breeding for high-yielding, low grain-Cd hybrids in the future.
Collapse
Affiliation(s)
- Liang Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Xiaxu Xu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Youru Jiang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Qihong Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Fei Yang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Jieqiang Zhou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Yuanzhu Yang
- Yuanlongping High-Tech Agriculture Co., LTDChangsha, China
| | - Zhiyuan Huang
- China National Hybrid Rice R&D CenterChangsha, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu ProvinceYangzhou, China
| | - Lianghui Chen
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Wenbang Tang
- Institute of Rice Science, Hunan Agricultural UniversityChangsha, China
| | - Guoyu Zhang
- Beishan Agricultural Service Center of Changsha CountyChangsha, China
| | - Jiurong Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Guoying Xiao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Daoyou Huang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| |
Collapse
|
12
|
Shang L, Wang Y, Wang X, Liu F, Abduweli A, Cai S, Li Y, Ma L, Wang K, Hua J. Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. G3 (BETHESDA, MD.) 2016. [PMID: 27342735 DOI: 10.1111/pbr.12352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
Collapse
Affiliation(s)
- Lianguang Shang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiaocui Wang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Abdugheni Abduweli
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Shihu Cai
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuhua Li
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingling Ma
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Jinping Hua
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| |
Collapse
|
13
|
Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. G3-GENES GENOMES GENETICS 2016; 6:2717-24. [PMID: 27342735 PMCID: PMC5015930 DOI: 10.1534/g3.116.031302] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
Collapse
|
14
|
Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci. BMC Genet 2015; 16:86. [PMID: 26243626 PMCID: PMC4526302 DOI: 10.1186/s12863-015-0249-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/09/2015] [Indexed: 11/26/2022] Open
Abstract
Background Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits. Results Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM. Conclusion Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0249-1) contains supplementary material, which is available to authorized users.
Collapse
|
15
|
Detection of Epistatic and Gene-Environment Interactions Underlying Three Quality Traits in Rice Using High-Throughput Genome-Wide Data. BIOMED RESEARCH INTERNATIONAL 2015; 2015:135782. [PMID: 26345334 PMCID: PMC4539430 DOI: 10.1155/2015/135782] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/20/2015] [Accepted: 03/24/2015] [Indexed: 11/18/2022]
Abstract
With development of sequencing technology, dense single nucleotide polymorphisms (SNPs) have been available, enabling uncovering genetic architecture of complex traits by genome-wide association study (GWAS). However, the current GWAS strategy usually ignores epistatic and gene-environment interactions due to absence of appropriate methodology and heavy computational burden. This study proposed a new GWAS strategy by combining the graphics processing unit- (GPU-) based generalized multifactor dimensionality reduction (GMDR) algorithm with mixed linear model approach. The reliability and efficiency of the analytical methods were verified through Monte Carlo simulations, suggesting that a population size of nearly 150 recombinant inbred lines (RILs) had a reasonable resolution for the scenarios considered. Further, a GWAS was conducted with the above two-step strategy to investigate the additive, epistatic, and gene-environment associations between 701,867 SNPs and three important quality traits, gelatinization temperature, amylose content, and gel consistency, in a RIL population with 138 individuals derived from super-hybrid rice Xieyou9308 in two environments. Four significant SNPs were identified with additive, epistatic, and gene-environment interaction effects. Our study showed that the mixed linear model approach combining with the GPU-based GMDR algorithm is a feasible strategy for implementing GWAS to uncover genetic architecture of crop complex traits.
Collapse
|
16
|
Dixit S, Huang BE, Sta Cruz MT, Maturan PT, Ontoy JCE, Kumar A. QTLs for tolerance of drought and breeding for tolerance of abiotic and biotic stress: an integrated approach. PLoS One 2014; 9:e109574. [PMID: 25314587 PMCID: PMC4196913 DOI: 10.1371/journal.pone.0109574] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/01/2014] [Indexed: 11/29/2022] Open
Abstract
Background The coupling of biotic and abiotic stresses leads to high yield losses in rainfed rice (Oryza sativa L.) growing areas. While several studies target these stresses independently, breeding strategies to combat multiple stresses seldom exist. This study reports an integrated strategy that combines QTL mapping and phenotypic selection to develop rice lines with high grain yield (GY) under drought stress and non-stress conditions, and tolerance of rice blast. Methodology A blast-tolerant BC2F3-derived population was developed from the cross of tropical japonica cultivar Moroberekan (blast- and drought-tolerant) and high-yielding indica variety Swarna (blast- and drought-susceptible) through phenotypic selection for blast tolerance at the BC2F2 generation. The population was studied for segregation distortion patterns and QTLs for GY under drought were identified along with study of epistatic interactions for the trait. Results Segregation distortion, in favour of Moroberekan, was observed at 50 of the 59 loci. Majority of these marker loci co-localized with known QTLs for blast tolerance or NBS-LRR disease resistance genes. Despite the presence of segregation distortion, high variation for DTF, PH and GY was observed and several QTLs were identified under drought stress and non-stress conditions for the three traits. Epistatic interactions were also detected for GY which explained a large proportion of phenotypic variance observed in the population. Conclusions This strategy allowed us to identify QTLs for GY along with rapid development of high-yielding purelines tolerant to blast and drought with considerably reduced efforts. Apart from this, it also allowed us to study the effects of the selection cycle for blast tolerance. The developed lines were screened at IRRI and in the target environment, and drought and blast tolerant lines with high yield were identified. With tolerance to two major stresses and high yield potential, these lines may provide yield stability in rainfed rice areas.
Collapse
Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - B. Emma Huang
- Computational Informatics, CSIRO, Dutton Park, Queensland, Australia
| | - Ma. Teresa Sta Cruz
- International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Paul T. Maturan
- International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | | | - Arvind Kumar
- International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- * E-mail:
| |
Collapse
|
17
|
Park GH, Kim JH, Kim KM. QTL Analysis of Yield Components in Rice Using a Cheongcheong/Nagdong Doubled Haploid Genetic Map. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.59130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
18
|
Jiang G, Zeng J, He Y. Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations. Gene 2013; 536:287-95. [PMID: 24361205 DOI: 10.1016/j.gene.2013.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 12/07/2013] [Accepted: 12/09/2013] [Indexed: 02/04/2023]
Abstract
Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F1 populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice.
Collapse
Affiliation(s)
- Gonghao Jiang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China; College of Life Science, Heilongjiang University, Haerbin 150080, China
| | - Jing Zeng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan 430070, PR China.
| |
Collapse
|
19
|
Liang YS, Zhan XD, Wang HM, Gao ZQ, Lin ZC, Chen DB, Shen XH, Cao LY, Cheng SH. Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice. Gene 2013; 526:331-5. [PMID: 23624393 DOI: 10.1016/j.gene.2013.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 11/29/2022]
Abstract
This study aimed to elucidate the genetics of the adult root system in elite Chinese hybrid rice. Several adult root traits in a recombinant inbred line (RIL) population of Xieyou 9308 and two backcross F1 (BCF1) populations derived from the RILs were phenotyped under hydroponic culture at heading stage for quantitative trait locus (QTL) mapping and other statistical analysis. There a total of eight QTLs detected for the root traits. Among of them, a pleiotropic QTL was repeatedly flanked by RM180 and RM5436 on the short arm of chromosome 7 for multiple traits across RILs and its BCF1 populations, accounting for 6.88% to 25.26% of the phenotypic variances. Only additive/dominant QTLs were detected for the root traits. These results can serve as a foundation for facilitating future cloning and molecular breeding.
Collapse
Affiliation(s)
- Yong Shu Liang
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses. PLoS One 2012; 7:e28463. [PMID: 22291881 PMCID: PMC3266898 DOI: 10.1371/journal.pone.0028463] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022] Open
Abstract
Background Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. Methodology/Principal Findings In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. Conclusions/Significance The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1–6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.
Collapse
|
21
|
Shi J, Li R, Zou J, Long Y, Meng J. A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.). PLoS One 2011; 6:e21645. [PMID: 21747942 PMCID: PMC3128606 DOI: 10.1371/journal.pone.0021645] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 06/07/2011] [Indexed: 01/12/2023] Open
Abstract
Although much research has been conducted, the genetic architecture of heterosis remains ambiguous. To unravel the genetic architecture of heterosis, a reconstructed F2 population was produced by random intercross among 202 lines of a double haploid population in rapeseed (Brassica napus L.). Both populations were planted in three environments and 15 yield-correlated traits were measured, and only seed yield and eight yield-correlated traits showed significant mid-parent heterosis, with the mean ranging from 8.7% (branch number) to 31.4% (seed yield). Hundreds of QTL and epistatic interactions were identified for the 15 yield-correlated traits, involving numerous variable loci with moderate effect, genome-wide distribution and obvious hotspots. All kinds of mode-of-inheritance of QTL (additive, A; partial-dominant, PD; full-dominant, D; over-dominant, OD) and epistatic interactions (additive × additive, AA; additive × dominant/dominant × additive, AD/DA; dominant × dominant, DD) were observed and epistasis, especially AA epistasis, seemed to be the major genetic basis of heterosis in rapeseed. Consistent with the low correlation between marker heterozygosity and mid-parent heterosis/hybrid performance, a considerable proportion of dominant and DD epistatic effects were negative, indicating heterozygosity was not always advantageous for heterosis/hybrid performance. The implications of our results on evolution and crop breeding are discussed.
Collapse
Affiliation(s)
- Jiaqin Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
| |
Collapse
|
22
|
Xu J, Wang B, Wu Y, Du P, Wang J, Wang M, Yi C, Gu M, Liang G. Fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo-sensitive genic male sterile gene in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:365-72. [PMID: 20938764 DOI: 10.1007/s00122-010-1452-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 09/08/2010] [Indexed: 05/07/2023]
Abstract
Photoperiod-thermo-sensitive genic male sterile (PTGMS) rice exhibits a number of desirable traits for hybrid rice production. The cloning genes responsible for PTGMS and those elucidating male sterility mechanisms and reversibility to fertility would be of great significance to provide a foundation to develop new male sterile lines. Guangzhan63S, a PTGMS line, is one of the most widely used indica two-line hybrid rice breeding systems in China. In this study, genetic analysis based on F(2) and BC(1)F(2) populations derived from a cross between Guangzhan63S and 1587, determined a single recessive gene controls male sterility in Guangzhan63S. Molecular marker techniques combined with bulked-segregant analysis (BSA) were used and located the target gene (named ptgms2-1) between two SSR markers RM12521 and RM12823. Fine mapping of the ptgms2-1 locus was conducted with 45 new Insertion-Deletion (InDel) markers developed between the RM12521 and RM12823 region, using 634 sterile individuals from F(2) and BC(1)F(2) populations. Ptgms2-1 was further mapped to a 50.4 kb DNA fragment between two InDel markers, S2-40 and S2-44, with genetic distances of 0.08 and 0.16 cM, respectively, which cosegregated with S2-43 located on the AP004039 BAC clone. Ten genes were identified in this region based on annotation results from the RiceGAAS system. A nuclear ribonuclease Z gene was identified as the candidate for the ptgms2-1 gene. This result will facilitate cloning the ptgms2-1 gene. The tightly linked markers for the ptgms2-1 gene locus will further provide a useful tool for marker-assisted selection of this gene in rice breeding programs.
Collapse
Affiliation(s)
- Jianjun Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, 225009, Yangzhou, Jiangsu Province, People's Republic of China
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G. Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 2010; 11:656. [PMID: 21106060 PMCID: PMC3091774 DOI: 10.1186/1471-2164-11-656] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/24/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics. RESULTS In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene. CONCLUSIONS The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
Collapse
Affiliation(s)
- Jianjun Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Qiang Zhao
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Peina Du
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Baohe Wang
- Lixiahe Region Agricultural Research Institute of Jiangsu, 225007, Yangzhou, PR China
| | - Qi Feng
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| |
Collapse
|
24
|
Hao W, Lin HX. Toward understanding genetic mechanisms of complex traits in rice. J Genet Genomics 2010; 37:653-66. [DOI: 10.1016/s1673-8527(09)60084-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 08/26/2010] [Indexed: 10/18/2022]
|
25
|
Li L, Lu K, Chen Z, Mou T, Hu Z, Li X. Gene actions at loci underlying several quantitative traits in two elite rice hybrids. Mol Genet Genomics 2010; 284:383-97. [PMID: 20862496 DOI: 10.1007/s00438-010-0575-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/07/2010] [Indexed: 11/25/2022]
Abstract
To understand the gene activities controlling nine important agronomic quantitative traits in rice, we applied a North Carolina design 3 (NC III design) analysis to recombinant inbred lines (RILs) in highly heterotic inter- (IJ) and intra-subspecific (II) hybrids by performing the following tasks: (1) investigating the relative contribution of additive, dominant, and epistatic effects for performance traits by generation means analysis and variance component estimates; (2) detecting the number, genomic positions, and genetic effects of QTL for phenotypic traits; and (3) characterizing their mode of gene action. Under an F∞-metric, generation means analysis and variance components estimates revealed that epistatic effects prevailed for the majority of traits in the two hybrids. QTL analysis identified 48 and 66 main-effect QTL (M-QTL) for nine traits in IJ and II hybrids, respectively. In IJ hybrids, 20 QTL (41.7%) showed an additive effect of gene actions, 20 (41.7%) showed partial-to-complete dominance, and 8 (16.7%) showed overdominance. In II hybrids, 34 QTL (51.5%) exhibited additive effects, 14 (21.2%) partial-to-complete dominance, and 18 (27.3%) overdominance. There were 153 digenic interactions (E-QTL) in the IJ hybrid and 252 in the II hybrid. These results suggest that additive effects, dominance, overdominance, and particularly epistasis attribute to the genetic basis of the expression of traits in the two hybrids. Additionally, we determined that the genetic causes of phenotypic traits and their heterosis are different. In the plants we studied, the phenotypic traits investigated and their heterosis were conditioned by different M-QTL and E-QTL, respectively, and were mainly due to non-allelic interactions (epistasis).
Collapse
Affiliation(s)
- Lanzhi Li
- College of Bio-Safety Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | | | | | | | | | | |
Collapse
|
26
|
Identification of main effects, epistatic effects and their environmental interactions of QTLs for yield traits in rice. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0786-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
Bian JM, Jiang L, Liu LL, Wei XJ, Xiao YH, Zhang LJ, Zhao ZG, Zhai HQ, Wan JM. Construction of a new set of rice chromosome segment substitution lines and identification of grain weight and related traits QTLs. BREEDING SCIENCE 2010. [PMID: 0 DOI: 10.1270/jsbbs.60.305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Jian Min Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Ling Long Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Xiang Jin Wei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Yue Hua Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Lu Jun Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Zhi Gang Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
| | - Hu Qu Zhai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
| | - Jian Min Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences
| |
Collapse
|
28
|
Yamamoto T, Yonemaru J, Yano M. Towards the understanding of complex traits in rice: substantially or superficially? DNA Res 2009; 16:141-54. [PMID: 19359285 PMCID: PMC2695773 DOI: 10.1093/dnares/dsp006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields.
Collapse
Affiliation(s)
- Toshio Yamamoto
- QTL Genomics Research Center, National Institute of Agrobiological Science, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
| | | | | |
Collapse
|
29
|
Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M. Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:881-90. [PMID: 18274726 DOI: 10.1007/s00122-008-0722-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 01/23/2008] [Indexed: 05/07/2023]
Abstract
To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment substitution lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.
Collapse
Affiliation(s)
- Tsuyu Ando
- Institute of the Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki, Japan
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Matsubara K, Ando T, Mizubayashi T, Ito S, Yano M. Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:179-86. [PMID: 17486310 DOI: 10.1007/s00122-007-0553-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2006] [Accepted: 04/10/2007] [Indexed: 05/09/2023]
Abstract
One outcome of hybrid breakdown is poor growth, which we observed as a reduction in the number of panicles per plant and in culm length in an F(2) population derived from a cross between the genetically divergent rice (Oryza sativa L.) cultivars 'Sasanishiki' (japonica) and 'Habataki' (indica). Quantitative trait locus (QTL) analysis of the two traits and two-way ANOVA of the detected QTLs suggested that the poor growth was due mainly to an epistatic interaction between genes at QTLs located on chromosomes 2 and 11. The poor growth was likely to result when a plant was homozygous for the 'Habataki' allele at the QTL on chromosome 2 and homozygous for the 'Sasanishiki' allele at the QTL on chromosome 11. The results suggest that the poor growth found in the F(2) population was due to hybrid breakdown of a set of complementary genes. To test this hypothesis and determine the precise chromosomal location of the genes causing the hybrid breakdown, we performed genetic analyses using a chromosome segment substitution line, in which a part of chromosome 2 from 'Habataki' was substituted into the genetic background of 'Sasanishiki'. The segregation patterns of poor growth in plants suggested that both of the genes underlying the hybrid breakdown were recessive. The gene on chromosome 2, designated hybrid breakdown 2 (hbd2), was mapped between simple sequence repeat markers RM3515 and RM3730. The gene on chromosome 11, hbd3, was mapped between RM5824 and RM1341.
Collapse
Affiliation(s)
- K Matsubara
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | | | | | | | | |
Collapse
|