1
|
Szabała BM, Święcicka M, Łyżnik LA. Microinjection of the CRISPR/Cas9 editing system through the germ pore of a wheat microspore induces mutations in the target Ms2 gene. Mol Biol Rep 2024; 51:706. [PMID: 38824203 DOI: 10.1007/s11033-024-09644-w] [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: 04/03/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Microinjection is a direct procedure for delivering various compounds via micropipette into individual cells. Combined with the CRISPR/Cas9 editing technology, it has been used to produce genetically engineered animal cells. However, genetic micromanipulation of intact plant cells has been a relatively unexplored area of research, partly due to the cytological characteristics of these cells. This study aimed to gain insight into the genetic micromanipulation of wheat microspores using microinjection procedures combined with the CRISPR/Cas9 editing system targeting the Ms2 gene. METHODS AND RESULTS Microspores were first reprogrammed by starvation and heat shock treatment to make them structurally suitable for microinjection. The large central vacuole was fragmented and the nucleus with cytoplasm was positioned in the center of the cell. This step and an additional maltose gradient provided an adequate source of intact single cells in the three wheat genotypes. The microcapillary was inserted into the cell through the germ pore to deliver a working solution with a fluorescent marker. This procedure was much more efficient and less harmful to the microspore than inserting the microcapillary through the cell wall. The CRISPR/Cas9 binary vectors injected into reprogrammed microspores induced mutations in the target Ms2 gene with deletions ranging from 1 to 16 bp. CONCLUSIONS This is the first report of successful genome editing in an intact microspore/wheat cell using the microinjection technique and the CRISPR/Cas9 editing system. The study presented offers a range of molecular and cellular biology tools that can aid in genetic micromanipulation and single-cell analysis.
Collapse
Affiliation(s)
- Bartosz M Szabała
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland.
| | - Magdalena Święcicka
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
| | - Leszek A Łyżnik
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St, Warsaw, 02-787, Poland
| |
Collapse
|
2
|
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin RM, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong VE, Chai L. Transposable elements cause the loss of self-incompatibility in citrus. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1113-1131. [PMID: 38038155 PMCID: PMC11022811 DOI: 10.1111/pbi.14250] [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: 09/10/2023] [Revised: 10/25/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system.
Collapse
Affiliation(s)
- Jianbing Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Chenchen Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zezhen Du
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Furong Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Dan Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Nan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zhuangmin Wei
- Guangxi Subtropical Crops Research InstituteNanningP. R. China
| | - Jingdong Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zonghong Cao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Siqi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chenqiao Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Peng Chen
- Horticultural Institute, Hunan Academy of Agricultural SciencesChangshaChina
| | - Robert M. Larkin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zongcheng Lin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Lijun Chai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| |
Collapse
|
3
|
Yang Y, Zhang C, Li H, Yang Z, Xu Z, Tai D, Ni D, Wei P, Yi C, Yang J, Ding Y. An epi-allele of SMS causes Sanming dominant genic male sterility in rice. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2701-2710. [PMID: 37930474 DOI: 10.1007/s11427-023-2457-7] [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: 08/27/2023] [Accepted: 09/22/2023] [Indexed: 11/07/2023]
Abstract
Male sterility is an important trait in rice for hybrid rice (Oryza sativa) breeding. However, the factors involved in dominant male sterility are largely unknown. Here, we identified a gene from Sanming dominant genic male sterile rice, named Sanming dominant male sterility (SMS), and reported that an epi-allele of this locus contributes to male sterility. Segregation analysis attributed dominant male sterility to a single locus, SMS, which we characterized using a male-sterile near isogenic line (NIL) of rice cultivar 93-11. The SMS locus was heterozygous in the male-sterile 93-11 NIL, containing an epi-allele identical to that in 93-11, and an epi-allele identical to that in rice cultivar Nipponbare, which we refer to as SMS9 and SMSN, respectively. SMS9 is silent and hyper-methylated, whereas SMSN is expressed and hypo-methylated in the 93-11 NIL. Overexpressing SMSN led to male sterility. Mutations in SMS rescued the male sterility of the 93-11 NIL. Interestingly, we observed the duplication of SMSN in Nipponbare, but did not observe the duplication of SMS9 in 93-11. Together, these findings suggest that the reduced methylation and enhanced expression of the SMSN epi-allele in the 93-11 NIL is responsible for its role in conferring dominant male sterility.
Collapse
Affiliation(s)
- Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Cheng Zhang
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hao Li
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Zeyuan Yang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zuntao Xu
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Dewei Tai
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China
| | - Dahu Ni
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Pengcheng Wei
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Chengxin Yi
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China
| | - Jianbo Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230036, China.
| | - Yong Ding
- Institute of Health and Medicine, Hefei Comprehesive National Science Center, Hefei, 230031, China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| |
Collapse
|
4
|
Jia W, Li X, Wang R, Duan Q, He J, Gao J, Wang J. Disruption of the Contents of Endogenous Hormones Cause Pollen Development Obstruction and Abortion in Male-Sterile Hybrid Lily Populations. PLANTS (BASEL, SWITZERLAND) 2023; 12:3804. [PMID: 38005701 PMCID: PMC10674860 DOI: 10.3390/plants12223804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
Lilies are well-known flowers with large anthers and a high quantity of pollen that easily contaminates clothing and tepals. The anthers need to be artificially removed, leading to production problems. Cultivating male-sterile or pollen-free lilies could solve these problems. The key period of male sterility in a specific male-sterile hybrid lily population was determined through cytological observation. The contents of hormones, soluble sugar, soluble protein, and proline were determined by high-performance liquid chromatography, tandem mass spectrometry and colorimetry. Transcriptome sequencing was used to identify the genes with altered expression. The key period of male sterility was determined to be the microspore mother and tetrad stages. The hormone contents were abnormal in the sterile line compared with the fertile line. The indole-3-acetic acid (IAA) content was higher in the sterile line than in the fertile line at all stages, while the gibberellic acid 4 (GA4) content showed the opposite result. Abscisic acid (ABA) accumulated in the sterile line in both the microspore mother and tetrad stages, and the zeatin riboside (ZR) content in the sterile line increased at the microspore mother stage but decreased at the tetrad stage. The contents of soluble sugar, soluble protein and proline were higher in the fertile line than in the sterile line. Genes involved in auxin and ABA synthesis and signalling pathways were highly expressed in the male-sterile line. Our data suggested that abnormal contents of hormones in the microspore mother and tetrad stages resulted in pollen abortion in a male-sterile hybrid lily population, which indicated that the hormone balance in specific stages plays critical functions in pollen development in lilies.
Collapse
Affiliation(s)
- Wenjie Jia
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (W.J.); (R.W.)
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650000, China; (X.L.); (Q.D.)
| | - Xiang Li
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650000, China; (X.L.); (Q.D.)
| | - Rui Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (W.J.); (R.W.)
| | - Qing Duan
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650000, China; (X.L.); (Q.D.)
| | - Junna He
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (W.J.); (R.W.)
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (W.J.); (R.W.)
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming 650000, China; (X.L.); (Q.D.)
| |
Collapse
|
5
|
Lei D, Jian A, Huang X, Liu X, Chen L, Bai W, Cheng S, He X, Xiong Y, Yu X, Wang C, Zheng H, You S, Wang Q, Lu J, Hu Y, Xie Z, Jiang L, Zhang X, Ren Y, Lei C, Cheng Z, Lin Q, Wu C, Zhu S, Zhao Z, Wan J. Anther-specific expression of OsRIP1 causes dominant male sterility in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1932-1934. [PMID: 37551552 PMCID: PMC10502742 DOI: 10.1111/pbi.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Affiliation(s)
- Dekun Lei
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Anqi Jian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Xianbo Huang
- Sanming Academy of Agricultural ScienceSanming CityChina
| | - Xi Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Liangming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Wenting Bai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Siqi Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Xiaodong He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Yehui Xiong
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiaowen Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Chaolong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Hai Zheng
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Shimin You
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Qiming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Jiayu Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Yang Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Zhenwei Xie
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhigang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingChina
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences,Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| |
Collapse
|
6
|
Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [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: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
Collapse
Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| |
Collapse
|
7
|
Xu C, Xu Y, Wang Z, Zhang X, Wu Y, Lu X, Sun H, Wang L, Zhang Q, Zhang Q, Li X, Xiao J, Li X, Zhao M, Ouyang Y, Huang X, Zhang Q. Spontaneous movement of a retrotransposon generated genic dominant male sterility providing a useful tool for rice breeding. Natl Sci Rev 2023; 10:nwad210. [PMID: 37621414 PMCID: PMC10446136 DOI: 10.1093/nsr/nwad210] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/17/2023] [Accepted: 07/23/2023] [Indexed: 08/26/2023] Open
Abstract
Male sterility in plants provides valuable breeding tools in germplasm innovation and hybrid crop production. However, genetic resources for dominant genic male sterility, which hold great promise to facilitate breeding processes, are extremely rare in natural germplasm. Here we characterized the Sanming Dominant Genic Male Sterility in rice and identified the gene SDGMS using a map-based cloning approach. We found that spontaneous movement of a 1978-bp long terminal repeat (LTR) retrotransposon into the promoter region of the SDGMS gene activates its expression in anther tapetum, which causes abnormal programmed cell death of tapetal cells resulting in dominant male sterility. SDGMS encodes a ribosome inactivating protein showing N-glycosidase activity. The activation of SDGMS triggers transcription reprogramming of genes responsive to biotic stress leading to a hypersensitive response which causes sterility. The results demonstrate that an ectopic gene activation by transposon movement can give birth to a novel trait which enriches phenotypic diversity with practical utility.
Collapse
Affiliation(s)
- Conghao Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifeng Xu
- Ningde Inspection and Testing Centre for Agricultural Product Quality and Safety, Ningde 352100, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuying Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyan Lu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongwei Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingfu Zhao
- Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianbo Huang
- Sanming Institute of Agricultural Sciences, Shaxian 365509, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
8
|
Jiao C, Hao C, Li T, Bohra A, Wang L, Hou J, Liu H, Liu H, Zhao J, Wang Y, Liu Y, Wang Z, Jing X, Wang X, Varshney RK, Fu J, Zhang X. Fast integration and accumulation of beneficial breeding alleles through an AB-NAMIC strategy in wheat. PLANT COMMUNICATIONS 2023; 4:100549. [PMID: 36642955 DOI: 10.1016/j.xplc.2023.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 05/11/2023]
Abstract
Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross-nested association mapping plus inter-crossed population (AB-NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population. We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC. Notably, genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B (TraesCS7B03G1216700), which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB. Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.
Collapse
Affiliation(s)
- Chengzhi Jiao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tian Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Lanfen Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Hou
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yamei Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunchuan Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiwei Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jing
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Perth, WA 6150, Australia.
| | - Junjie Fu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xueyong Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| |
Collapse
|
9
|
Szabała BM. A bifunctional selectable marker for wheat transformation contributes to the characterization of male-sterile phenotype induced by a synthetic Ms2 gene. PLANT CELL REPORTS 2023; 42:895-907. [PMID: 36867203 DOI: 10.1007/s00299-023-02998-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/17/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE An engineered selectable marker combining herbicide resistance and yellow fluorescence contributes to the characterization of male-sterile phenotype in wheat, the severity of which correlates with expression levels of a synthetic Ms2 gene. Genetic transformation of wheat is conducted using selectable markers, such as herbicide and antibiotic resistance genes. Despite their proven effectiveness, they do not provide visual control of the transformation process and transgene status in progeny, which creates uncertainty and prolongs screening procedures. To overcome this limitation, this study developed a fusion protein by combining gene sequences encoding phosphinothricin acetyltransferase and mCitrine fluorescent protein. The fusion gene, introduced into wheat cells by particle bombardment, enabled herbicide selection, and visual identification of primary transformants along with their progeny. This marker was then used to select transgenic plants containing a synthetic Ms2 gene. Ms2 is a dominant gene whose activation in wheat anthers leads to male sterility, but the relationship between the expression levels and the male-sterile phenotype is unknown. The Ms2 gene was driven either by a truncated Ms2 promoter containing a TRIM element or a rice promoter OsLTP6. The expression of these synthetic genes resulted in complete male sterility or partial fertility, respectively. The low-fertility phenotype was characterized by smaller anthers than the wild type, many defective pollen grains, and low seed sets. The reduction in the size of anthers was observed at earlier and later stages of their development. Consistently, Ms2 transcripts were detected in these organs, but their levels were significantly lower than those in completely sterile Ms2TRIM::Ms2 plants. These results suggested that the severity of the male-sterile phenotype was modulated by Ms2 expression levels and that higher levels may be key to activating total male sterility.
Collapse
Affiliation(s)
- Bartosz M Szabała
- Institute of Biology, Department of Genetics, Breeding and Plant Biotechnology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166 St., 02-787, Warsaw, Poland.
| |
Collapse
|
10
|
Zhang R, Zhang S, Li J, Gao J, Song G, Li W, Geng S, Liu C, Lin Y, Li Y, Li G. CRISPR/Cas9-targeted mutagenesis of TaDCL4, TaDCL5 and TaRDR6 induces male sterility in common wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:839-853. [PMID: 36597709 PMCID: PMC10037139 DOI: 10.1111/pbi.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Phased, small interfering RNAs (phasiRNAs) are important for plant anther development, especially for male sterility. PhasiRNA biogenesis is dependent on genes like RNA polymerase 6 (RDR6), DICER-LIKE 4 (DCL4), or DCL5 to produce 21- or 24 nucleotide (nt) double-strand small RNAs. Here, we generated mutants of DCL4, DCL5 and RDR6 using CRISPR/Cas9 system and studied their effects on plant reproductive development and phasiRNA production in wheat. We found that RDR6 mutation caused sever consequence throughout plant development starting from seed germination and the dcl4 mutants grew weaker with thorough male sterility, while dcl5 plants developed normally but exhibited male sterility. Correspondingly, DCL4 and DCL5, respectively, specified 21- and 24-nt phasiRNA biogenesis, while RDR6 contributed to both. Also, the three key genes evolved differently in wheat, with TaDCL5-A/B becoming non-functioning and TaRDR6-A being lost after polyploidization. Furthermore, we found that PHAS genes (phasiRNA precursors) identified via phasiRNAs diverged rapidly among sub-genomes of polyploid wheat. Despite no similarity being found among phasiRNAs of grasses, their targets were enriched for similar biological functions. In light of the important roles of phasiRNA pathways in gametophyte development, genetic dissection of the function of key genes may help generate male sterile lines suitable for hybrid wheat breeding.
Collapse
Affiliation(s)
- Rongzhi Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Shujuan Zhang
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Jihu Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Jie Gao
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Guoqi Song
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Wei Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Cheng Liu
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Yanxiang Lin
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Yulian Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| | - Genying Li
- Crop Research InstituteShandong Academy of Agricultural SciencesJinanChina
- Ministry of Agriculture, Key Laboratory of Wheat Biology and Genetic Improvement on North Yellow and Huai River ValleyJinanChina
- National Engineering Research Center for Wheat and MaizeJinanChina
| |
Collapse
|
11
|
Dong J, Hu F, Guan W, Yuan F, Lai Z, Zhong J, Liu J, Wu Z, Cheng J, Hu K. A 163-bp insertion in the Capana10g000198 encoding a MYB transcription factor causes male sterility in pepper (Capsicum annuum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:521-535. [PMID: 36534067 DOI: 10.1111/tpj.16064] [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: 07/11/2022] [Revised: 10/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Male sterility provides an efficient approach for commercial exploitation of heterosis. Despite more than 20 genic male sterile (GMS) mutants documented in pepper (Capsicum annuum L.), only two causal genes have been successfully identified. Here, a novel spontaneous recessive GMS mutant, designated msc-3, is identified and characterized at both phenotypic and histological levels. Pollen abortion of msc-3 mutant may be due to the delayed tapetum degradation, leading to the non-degeneration of tetrads callosic wall. Then, a modified MutMap method and molecular marker linkage analysis were employed to fine mapping the msc-3 locus, which was delimited to the ~139.91-kb region harboring 10 annotated genes. Gene expression and structure variation analyses indicate the Capana10g000198, encoding a R2R3-MYB transcription factor, is the best candidate gene for the msc-3 locus. Expression profiling analysis shows the Capana10g000198 is an anther-specific gene, and a 163-bp insertion in the Capana10g000198 is highly correlated with the male sterile (MS) phenotype. Additionally, downregulation of Capana10g000198 in male fertile plants through virus-induced gene silencing resulted in male sterility. Finally, possible regulatory relationships of the msc-3 gene with the other two reported pepper GMS genes, msc-1 and msc-2, have been studied, and comparative transcriptome analysis reveals the expression of 16 GMS homologs are significantly downregulated in the MS anthers. Overall, our results reveal that Capana10g000198 is the causal gene underlying the msc-3 locus, providing important theoretical clues and basis for further in-depth study on the regulatory mechanisms of pollen development in pepper.
Collapse
Affiliation(s)
- Jichi Dong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Fang Hu
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Henry Fok School of Biology and Agricultural, Shaoguan University, Shaoguan, 512023, Guangdong, China
| | - Wendong Guan
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Fanchong Yuan
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Zepei Lai
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Jian Zhong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Jia Liu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, Guangdong, China
| |
Collapse
|
12
|
Qi X, Liu J, Liu Z, Chen C, Chen B, Guo S, Ni Z, Zhong Y, Chen S, Liu C. High-throughput haploid induction in species with bisexual flowers. PLANT COMMUNICATIONS 2023; 4:100454. [PMID: 36171721 PMCID: PMC9860177 DOI: 10.1016/j.xplc.2022.100454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 05/25/2023]
Affiliation(s)
- Xiaolong Qi
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Jinchu Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Zongkai Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Chen Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Baojian Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Shuwei Guo
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Yu Zhong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China.
| | - Shaojiang Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China.
| | - Chenxu Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; National Maize Improvement Center, China Agricultural University, Beijing 100193, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China.
| |
Collapse
|
13
|
Liang Z, Liu K, Jiang C, Yang A, Yan J, Han X, Zhang C, Cong P, Zhang L. Insertion of a TRIM-like sequence in MdFLS2-1 promoter is associated with its allele-specific expression in response to Alternaria alternata in apple. FRONTIERS IN PLANT SCIENCE 2022; 13:1090621. [PMID: 36643297 PMCID: PMC9834810 DOI: 10.3389/fpls.2022.1090621] [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: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Alternaria blotch disease, caused by Alternaria alternata apple pathotype (AAAP), is one of the major fungal diseases in apple. Early field observations revealed, the anther-derived homozygote Hanfu line (HFTH1) was highly susceptible to AAAP, whereas Hanfu (HF) exhibited resistance to AAAP. To understand the molecular mechanisms underlying the difference in sensitivity of HF and HFTH1 to AAAP, we performed allele-specific expression (ASE) analysis and comparative transcriptomic analysis before and after AAAP inoculation. We reported an important immune gene, namely, MdFLS2, which displayed strong ASE in HF with much lower expression levels of HFTH1-derived alleles. Transient overexpression of the dominant allele of MdFLS2-1 from HF in GL-3 apple leaves could enhance resistance to AAAP and induce expression of genes related to salicylic acid pathway. In addition, MdFLS2-1 was identified with an insertion of an 85-bp terminal-repeat retrotransposon in miniature (TRIM) element-like sequence in the upstream region of the nonreference allele. In contrast, only one terminal direct repeat (TDR) from TRIM-like sequence was present in the upstream region of the HFTH1-derived allele MdFLS2-2. Furthermore, the results of luciferase and β-glucuronidase reporter assays demonstrated that the intact TRIM-like sequence has enhancer activity. This suggested that insertion of the TRIM-like sequence regulates the expression level of the allele of MdFLS2, in turn, affecting the sensitivity of HF and HFTH1 to AAAP.
Collapse
Affiliation(s)
- Zhaolin Liang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Kai Liu
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Chunyang Jiang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - An Yang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Jiadi Yan
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Xiaolei Han
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Caixia Zhang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| | - Liyi Zhang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization), Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Xingcheng, China
| |
Collapse
|
14
|
Liu J, Xia C, Dong H, Liu P, Yang R, Zhang L, Liu X, Jia J, Kong X, Sun J. Wheat male-sterile 2 reduces ROS levels to inhibit anther development by deactivating ROS modulator 1. MOLECULAR PLANT 2022; 15:1428-1439. [PMID: 35864748 DOI: 10.1016/j.molp.2022.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/28/2022] [Accepted: 07/18/2022] [Indexed: 05/22/2023]
Abstract
Ms2 is an important dominant male-sterile gene in wheat, but the biochemical function of Ms2 and the mechanism by which it causes male sterility remain elusive. Here, we report the molecular basis underlying Ms2-induced male sterility in wheat. We found that activated Ms2 specifically reduces the reactive oxygen species (ROS) signals in anthers and thereby induces termination of wheat anther development at an early stage. Furthermore, our results indicate that Ms2 is localized in mitochondria, where it physically interacts with a wheat homolog of ROS modulator 1 (TaRomo1). Romo1 positively regulates the ROS levels in humans but has never been studied in plants. We found that single amino acid substitutions in the Ms2 protein that rescue the ms2 male-sterile phenotype abolish the interaction between Ms2 and TaRomo1. Significantly, Ms2 promotes the transition of TaRomo1 proteins from active monomers to inactive oligomers. Taken together, our findings unravel the molecular basis of Ms2-induced male sterility and reveal a regulatory mechanism in which ROS act as essential signals guiding the anther development program in wheat.
Collapse
Affiliation(s)
- Jie Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Chuan Xia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixue Dong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruizhen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
15
|
Zhang T, Xiang Y, Geng L, Jiang W, Cheng S, Zhao Y. A Non-Canonical MITE in the WOX11 Promoter Is Associated with Robust Crown Root development in Rice. PLANT & CELL PHYSIOLOGY 2022; 63:1052-1062. [PMID: 35727725 DOI: 10.1093/pcp/pcac075] [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: 10/27/2021] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The formation of tissues and organs in multicellular organisms is tightly controlled by transcriptional programs determined by temporal and spatial patterns of gene expression. As an important regulator of rice crown root development, WOX11 is essential for crown root formation and its transcript level is positively correlated with crown root biomass. However, how WOX11 is regulated during crown root primordium emergence and outgrowth still remains unknown. In this study, variations of the WOX11 genomic sequence were analyzed, and the highest genetic diversity was found within its promoter, which contained a non-canonical miniature inverted-repeat transposable element (ncMITE) sequence. Analysis of the WOX11 promoter-driven reporter gene GUS (β-glucuronidase) transgenic plants pWOX11(ncMITE+):GUS and pWOX11(ncMITE-):GUS uncovered higher GUS expression levels in crown roots of pWOX11(ncMITE+):GUS plants. Furthermore, pWOX11(ncMITE+):WOX11-FLAG in wox11 background could complement the crown root number and length compared to those of the wild type, while pWOX11(ncMITE-):WOX11-FLAG could not. These results suggested that the ncMITE was positively associated with WOX11 transcripts in rice crown roots. In addition, DNA methylation nearby the ncMITE region attenuated the activation effect of the ncMITE on WOX11 expression, which might also be the cause conferred to the root-specific expression of WOX11. This work provides novel insight into WOX11 expression regulation and reveals a promising target for genetic improvement of root architecture in rice.
Collapse
Affiliation(s)
- Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
- College of Bioengineering, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, No. 33 Xiangshan Avenue, Jingmen, Hubei 448000, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Wei Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Saifeng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan, Hubei 430070, China
| |
Collapse
|
16
|
Integrated Analysis of Microarray, Small RNA, and Degradome Datasets Uncovers the Role of MicroRNAs in Temperature-Sensitive Genic Male Sterility in Wheat. Int J Mol Sci 2022; 23:ijms23158057. [PMID: 35897633 PMCID: PMC9332412 DOI: 10.3390/ijms23158057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/10/2022] [Accepted: 07/17/2022] [Indexed: 01/27/2023] Open
Abstract
Temperature-sensitive genic male sterile (TGMS) line Beijing Sterility 366 (BS366) has been utilized in hybrid breeding for a long time, but the molecular mechanism underlying male sterility remains unclear. Expression arrays, small RNA, and degradome sequencing were used in this study to explore the potential role of miRNA in the cold-induced male sterility of BS366. Microspore observation showed defective cell plates in dyads and tetrads and shrunken microspores at the vacuolated stage. Differential regulation of Golgi vesicle transport, phragmoplast formation, sporopollenin biosynthesis, pollen exine formation, and lipid metabolism were observed between cold and control conditions. Pollen development was significantly represented in the 352 antagonistic miRNA-target pairs in the integrated analysis of miRNA and mRNA profiles. The specific cleavage of ARF17 and TIR1 by miR160 and miR393 were found in the cold-treated BS366 degradome, respectively. Thus, the cold-mediated miRNAs impaired cell plate formation through repression of Golgi vesicle transport and phragmoplast formation. The repressed expression of ARF17 and TIR1 impaired pollen exine formation. The results of this study will contribute to our understanding of the roles of miRNAs in male sterility in wheat.
Collapse
|
17
|
|
18
|
Wang Q, He Z, Wang L, Qi Z. 染色体工程在杂交小麦育种中的应用进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
19
|
Hao M, Zhang L, Huang L, Ning S, Yuan Z, Jiang B, Yan Z, Wu B, Zheng Y, Liu D. 渗入杂交与小麦杂种优势. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
20
|
Bai J, Wang Y, Liu Z, Guo H, Zhang F, Guo L, Yuan S, Duan W, Li Y, Tan Z, Zhao C, Zhang L. Global survey of alternative splicing and gene modules associated with fertility regulation in a thermosensitive genic male sterile wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2157-2174. [PMID: 34849734 DOI: 10.1093/jxb/erab516] [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: 05/10/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Thermosensitive genic male sterile (TGMS) wheat lines are the core of two-line hybrid systems. Understanding the mechanism that regulates male sterility in TGMS wheat lines is helpful for promoting wheat breeding. Several studies have obtained information regarding the mechanisms associated with male sterility at the transcriptional level, but it is not clear how the post-transcriptional process of alternative splicing might contribute to controlling male sterility. In this study, we performed genome-wide analyses of alternative splicing during the meiosis stage in TGMS line BS366 using PacBio and RNA-Seq hybrid sequencing. Cytological observations indicated that cytoskeleton assembly in pollen cells, calcium deposition in pollen and tapetal cells, and vesicle transport in tapetal cells were deficient in BS366. According to our cytological findings, 49 differentially spliced genes were isolated. Moreover, 25 long non-coding RNA targets and three bHLH transcription factors were identified. Weighted gene co-expression network analysis detected four candidate differentially spliced genes that had strong co-relation with the seed setting percentage, which is the direct representation of male sterility in BS366. In this study, we obtained comprehensive data regarding the alternative splicing-mediated regulation of male sterility in TGMS wheat. The candidates identified may provide the molecular basis for an improved understanding of male sterility.
Collapse
Affiliation(s)
- Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Yukun Wang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, NARA 630-0192, Japan
| | - Zihan Liu
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Haoyu Guo
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Fengting Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Liping Guo
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Shaohua Yuan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Wenjing Duan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yanmei Li
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Zhaoguo Tan
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Changping Zhao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| | - Liping Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- The Municipal Key Laboratory of Molecular Genetic of Hybrid Wheat, Beijing 10097, China
| |
Collapse
|
21
|
Zhao Y, Sun Y, Huang S, Liu Z, Feng H. Identification of an anther-specific promoter from a male sterile AB line in Chinese cabbage ( Brassica rapa L. ssp. pekinensis). 3 Biotech 2022; 12:104. [PMID: 35463043 PMCID: PMC8971320 DOI: 10.1007/s13205-022-03160-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/05/2022] [Indexed: 11/30/2022] Open
Abstract
The promoter of the male sterile gene is important for studying male sterility. In this study, BraA08g014780.3C which differentially expressed between male sterile and fertile plants was identified from a genetic male sterile AB line of Chinese cabbage by RNA-seq. qRT-PCR revealed that BraA08g014780.3C was mainly expressed in the early stage of floral bud development in fertile plants, and preferentially expressed in their anthers. The promoter of BraA08g014780.3C was cloned and analyzed. Cis acting element analysis showed that the promoter of BraA08g014780.3C contains POLLEN1LELAT52 and GTGANTG10, which are both pollen-specific expression elements. The BraA08g014780.3Cp::GUS vector was constructed, then transformed to Arabidopsis thaliana Col-0. PCR analysis and sequencing of the transgenic Arabidopsis revealed that the GUS gene driven by the BraA08g014780.3C promoter was successfully transformed to the Arabidopsis. GUS staining indicated that the promoter of BraA08g014780.3C was an anther-specific promoter. Identifying the anther-specific promoter laid a foundation for revealing BraA08g014780.3C function in male sterility of Chinese cabbage. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03160-z.
Collapse
Affiliation(s)
- Ying Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Ying Sun
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Shengnan Huang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhiyong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
22
|
Han Y, Gao Y, Li Y, Zhai X, Zhou H, Ding Q, Ma L. Chloroplast Genes Are Involved in The Male-Sterility of K-Type CMS in Wheat. Genes (Basel) 2022; 13:genes13020310. [PMID: 35205355 PMCID: PMC8871828 DOI: 10.3390/genes13020310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
The utilization of crop heterosis can greatly improve crop yield. The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.). The chloroplast genomes of two sterile lines and one maintainer were sequenced using second-generation high-throughput technology and assembled. The nonsynonymous mutated genes among the three varieties were identified, the expressed difference was further analyzed by qPCR, and finally, the function of the differentially expressed genes was analyzed by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method. A total of 16 genes containing 31 nonsynonymous mutations between K519A and 519B were identified. There were no base mutations in the protein-encoding genes between K519A and YS3038. The chloroplast genomes of 519B and K519A were closely related to the Triticum genus and Aegilops genus, respectively. The gene expression levels of the six selected genes with nonsynonymous mutation sites for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development. The seed setting rates of atpB-silenced or ndhH-silenced 519B plants by BSMV-VIGS method were significantly reduced. It can be concluded that atpB and the ndhH are likely to be involved in the reproductive transformation of 519B.
Collapse
Affiliation(s)
- Yucui Han
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yujie Gao
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Yun Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; (Y.H.); (Y.L.)
| | - Xiaoguang Zhai
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Hao Zhou
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Xianyang 712100, China
- Correspondence: (Q.D.); (L.M.)
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, China; (Y.G.); (X.Z.); (H.Z.)
- Correspondence: (Q.D.); (L.M.)
| |
Collapse
|
23
|
Esposito S, D'Agostino N, Taranto F, Sonnante G, Sestili F, Lafiandra D, De Vita P. Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis. Front Genet 2022; 13:1058471. [PMID: 36482886 PMCID: PMC9723387 DOI: 10.3389/fgene.2022.1058471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/07/2022] [Indexed: 03/22/2023] Open
Abstract
Although wheat (Triticum aestivum L.) is the main staple crop in the world and a major source of carbohydrates and proteins, functional genomics and allele mining are still big challenges. Given the advances in next-generation sequencing (NGS) technologies, the identification of causal variants associated with a target phenotype has become feasible. For these reasons, here, by combining sequence capture and target-enrichment methods with high-throughput NGS re-sequencing, we were able to scan at exome-wide level 46 randomly selected bread wheat individuals from a recombinant inbred line population and to identify and classify a large number of single nucleotide polymorphisms (SNPs). For technical validation of results, eight randomly selected SNPs were converted into Kompetitive Allele-Specific PCR (KASP) markers. This resource was established as an accessible and reusable molecular toolkit for allele data mining. The dataset we are making available could be exploited for novel studies on bread wheat genetics and as a foundation for starting breeding programs aimed at improving different key agronomic traits.
Collapse
Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | | | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
| |
Collapse
|
24
|
Liu YJ, Li D, Gong J, Wang YB, Chen ZB, Pang BS, Chen XC, Gao JG, Yang WB, Zhang FT, Tang YM, Zhao CP, Gao SQ. Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366. BMC Genomics 2021; 22:911. [PMID: 34930131 PMCID: PMC8686610 DOI: 10.1186/s12864-021-08163-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Known as the prerequisite component for the heterosis breeding system, the male sterile line determines the hybrid yield and seed purity. Therefore, a deep understanding of the mechanism and gene network that leads to male sterility is crucial. BS366, a temperature-sensitive genic male sterile (TGMS) line, is male sterile under cold conditions (12 °C with 12 h of daylight) but fertile under normal temperature (20 °C with 12 h of daylight). Results During meiosis, BS366 was defective in forming tetrads and dyads due to the abnormal cell plate. During pollen development, unusual vacuolated pollen that could not accumulate starch grains at the binucleate stage was also observed. Transcriptome analysis revealed that genes involved in the meiotic process, such as sister chromatid segregation and microtubule-based movement, were repressed, while genes involved in DNA and histone methylation were induced in BS366 under cold conditions. MethylRAD was used for reduced DNA methylation sequencing of BS366 spikes under both cold and control conditions. The differentially methylated sites (DMSs) located in the gene region were mainly involved in carbohydrate and fatty acid metabolism, lipid metabolism, and transport. Differentially expressed and methylated genes were mainly involved in cell division. Conclusions These results indicated that the methylation of genes involved in carbon metabolism or fatty acid metabolism might contribute to male sterility in BS366 spikes, providing novel insight into the molecular mechanism of wheat male sterility. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08163-3.
Collapse
Affiliation(s)
- Yong-Jie Liu
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Dan Li
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Jie Gong
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Yong-Bo Wang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zhao-Bo Chen
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bin-Shuang Pang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China
| | - Xian-Chao Chen
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian-Gang Gao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wei-Bing Yang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Feng-Ting Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Yi-Miao Tang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| | - Chang-Ping Zhao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| | - Shi-Qing Gao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing, 100097, China.
| |
Collapse
|
25
|
Bhowmik P, Bilichak A. Advances in Gene Editing of Haploid Tissues in Crops. Genes (Basel) 2021; 12:1410. [PMID: 34573392 PMCID: PMC8468125 DOI: 10.3390/genes12091410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 01/14/2023] Open
Abstract
Emerging threats of climate change require the rapid development of improved varieties with a higher tolerance to abiotic and biotic factors. Despite the success of traditional agricultural practices, novel techniques for precise manipulation of the crop's genome are needed. Doubled haploid (DH) methods have been used for decades in major crops to fix desired alleles in elite backgrounds in a short time. DH plants are also widely used for mapping of the quantitative trait loci (QTLs), marker-assisted selection (MAS), genomic selection (GS), and hybrid production. Recent discoveries of genes responsible for haploid induction (HI) allowed engineering this trait through gene editing (GE) in non-inducer varieties of different crops. Direct editing of gametes or haploid embryos increases GE efficiency by generating null homozygous plants following chromosome doubling. Increased understanding of the underlying genetic mechanisms responsible for spontaneous chromosome doubling in haploid plants may allow transferring this trait to different elite varieties. Overall, further improvement in the efficiency of the DH technology combined with the optimized GE could accelerate breeding efforts of the major crops.
Collapse
Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
| | - Andriy Bilichak
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
| |
Collapse
|
26
|
Genetic Mapping of ms1s, a Recessive Gene for Male Sterility in Common Wheat. Int J Mol Sci 2021; 22:ijms22168541. [PMID: 34445247 PMCID: PMC8395210 DOI: 10.3390/ijms22168541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 11/24/2022] Open
Abstract
The utilization of heterosis is an important way to improve wheat yield, and the production of wheat hybrid seeds mainly relies on male-sterile lines. Male sterility in line 15 Fan 03 derived from a cross of 72,180 and Xiaoyan 6 is controlled by a single recessive gene. The gene was mapped to the distal region of chromosome 4BS in a genetic interval of 1.4 cM and physical distance of 6.57 Mb between SSR markers Ms4BS42 and Ms4BS199 using an F2 population with 1205 individuals. Sterile individuals had a deletion of 4.57 Mb in the region presumed to carry the Ms1 locus. The allele for sterility was therefore named ms1s. Three CAPS markers were developed and verified from the region upstream of the deleted fragment and can be used for ms1s marker-assisted selection in wheat hybrid breeding. This work will enrich the utilization of male sterility genetic resources.
Collapse
|
27
|
Wang J, Li L, Li C, Yang X, Xue Y, Zhu Z, Mao X, Jing R. A transposon in the vacuolar sorting receptor gene TaVSR1-B promoter region is associated with wheat root depth at booting stage. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1456-1467. [PMID: 33555662 PMCID: PMC8313126 DOI: 10.1111/pbi.13564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/06/2021] [Accepted: 01/28/2021] [Indexed: 05/14/2023]
Abstract
Root depth, as an important component of root architecture, plays a significant role in growth, grain yield determination and abiotic stress tolerance in crop plants, but its genetic basis remains poorly elucidated. In this study, a panel composed of 323 wheat (Triticum aestivum L.) accessions was assessed for variation in root depth and genotyped with the Wheat 660K SNP Array. GWAS (genome-wide association study) detected significant association between a 125 bp miniature inverted-repeat transposable element (MITE) in the promoter of the TaVSR1-B gene with root depth at the booting stage. We showed that the MITE repressed TaVSR1-B expression by DNA methylation and H3K27 tri-methylation. The roles of TaVSR1-B in root growth were verified by altered expression of the gene in transgenic wheat, rice and a tavsr1 TILLING mutant. Increased TaVSR1-B expression made the root elongation zone shorter and the differentiation zone longer, leading to deeper root. This work provides novel insight into the genetic basis of variation in root depth and a promising target for genetic improvement of root architecture in wheat.
Collapse
Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xi Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yinghong Xue
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhi Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
28
|
Wang X, Miao Y, Cai Y, Sun G, Jia Y, Song S, Pan Z, Zhang Y, Wang L, Fu G, Gao Q, Ji G, Wang P, Chen B, Peng Z, Zhang X, Wang X, Ding Y, Hu D, Geng X, Wang L, Pang B, Gong W, He S, Du X. Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1110-1124. [PMID: 33369825 PMCID: PMC8196653 DOI: 10.1111/pbi.13532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Cotton seeds are typically covered by lint and fuzz fibres. Natural 'fuzzless' mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome-wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDELFZ , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDELFZ was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant-repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co-expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very-long-chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.
Collapse
Affiliation(s)
- Xiaoyang Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
- Crop Information CenterCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Gaofei Sun
- College of Computer Science and Information EngineeringAnyang Institute of TechnologyAnyangChina
| | - Yinhua Jia
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Song Song
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhaoe Pan
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yuanming Zhang
- Crop Information CenterCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Liyuan Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Guoyong Fu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Qiong Gao
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Gaoxiang Ji
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Pengpeng Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Baojun Chen
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhen Peng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiaomeng Zhang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiao Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Yi Ding
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Daowu Hu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiaoli Geng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Liru Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Baoyin Pang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Wenfang Gong
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
- Key Laboratory of Cultivation and Protection for Non‐Wood Forest TreesMinistry of EducationCentral South University of Forestry and Technology, Ministry of EducationChangshaChina
| | - Shoupu He
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Xiongming Du
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| |
Collapse
|
29
|
Yang G, Boshoff WHP, Li H, Pretorius ZA, Luo Q, Li B, Li Z, Zheng Q. Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat-Thinopyrum ponticum translocation line WTT34. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1587-1599. [PMID: 33677639 DOI: 10.1007/s00122-021-03796-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/16/2021] [Indexed: 05/12/2023]
Abstract
A novel Ug99-resistant wheat-Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat-Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat-Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).
Collapse
Affiliation(s)
- Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
30
|
Han Y, Zhang Y, Cao G, Shao L, Ding Q, Ma L. Dynamic expression of miRNAs and functional analysis of target genes involved in the response to male sterility of the wheat line YS3038. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:363-377. [PMID: 33730621 DOI: 10.1016/j.plaphy.2021.02.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Thermosensitive cytoplasmic male sterile (TCMS) lines play an important role in wheat breeding, heterosis utilization, and germplasm innovation. MicroRNAs (miRNAs) can regulate the expression level of target genes by inhibiting the translation of these genes. YS3038 is a wheat TCMS line. In this study, the fertility conversion mechanism of YS3038 was studied by examining the abortion characteristics of YS3038, the regulation pattern of miRNAs and the target genes of miRNAs in YS3038. MiRNA-seq was performed on three important stages of YS3038 under sterile and fertile conditions. Then, the clean reads were aligned with some databases to filter other ncRNAs and repeats. The known miRNAs and novel miRNAs were predicted by sequence comparison with known miRNAs from miRbase. Differential expression of miRNAs between different stages and between different fertile conditions was analyzed, and functional analysis of target genes with opposite expression patterns as those of the miRNAs was conducted. The Ubisch bodies and microspores of sterile anthers were covered with filamentous materials. The degradation of the tapetum cells, the chloroplast structure of endothecium cells, and the microspore structure were abnormal. Microspore development was hindered from the late uninucleate stage to the binucleate stage. Twenty, 52, and 68 differentially expressed miRNAs (DEmiRs) were identified at the early uninucleate, late uninucleate, and binucleate stages, respectively, and there were 0, 7, and 72 differentially expressed target genes (DETGs), respectively, at these three stages. At the binucleate stage, 29 DEmiRs had 41 target mRNAs in total, and the expression patterns of the 41 target mRNAs were opposite to those of the 29 miRNAs. Fifteen significantly enriched KEGG pathways were associated with the 41 target mRNAs. Leucine-rich repeat receptor-like kinases (LRR-RLKs) play important roles in plant developmental and physiological processes. Some studies have shown that the expression of LRR-RLKs is related to the differentiation of microsporocytes and tapetum cells and to male sterility. An LRR-RLK (TaeRPK) gene was silenced by the barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) method, and the seed setting rates of the TaeRPK-silenced plants (3.51%) were significantly lower than those of the negative control plants (88.78%) (P < 0.01). Thus, the TaeRPK gene is likely to be involved in the fertility conversion of YS3038.
Collapse
Affiliation(s)
- Yucui Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiyang Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guannan Cao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Leilei Shao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qin Ding
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Lingjian Ma
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
31
|
Dossa K, Zhou R, Li D, Liu A, Qin L, Mmadi MA, Su R, Zhang Y, Wang J, Gao Y, Zhang X, You J. A novel motif in the 5'-UTR of an orphan gene 'Big Root Biomass' modulates root biomass in sesame. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1065-1079. [PMID: 33369837 PMCID: PMC8131042 DOI: 10.1111/pbi.13531] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 05/06/2023]
Abstract
Developing crops with improved root system is crucial in current global warming scenario. Underexploited crops are valuable reservoirs of unique genes that can be harnessed for the improvement of major crops. In this study, we performed genome-wide association studies on seven root traits in sesame (Sesamum indicum L.) and uncovered 409 significant signals, 19 quantitative trait loci containing 32 candidate genes. A peak SNP significantly associated with root number and root dry weight traits was located in the promoter of the gene named 'Big Root Biomass' (BRB), which was subsequently validated in a bi-parental population. BRB has no functional annotation and is restricted to the Lamiales order. We detected the presence of a novel motif 'AACACACAC' located in the 5'-UTR of BRB in single and duplicated copy in accessions with high and small root biomass, respectively. A strong expression level of BRB was negatively correlated with high root biomass, and this was attributed to the gene SiMYB181 which represses the activity of BRB by binding specifically to the single motif but not to the duplicated one. Curiously, the allele that enhanced BRB expression has been intensively selected by modern breeding. Overexpression of BRB in Arabidopsis modulates auxin pathway leading to reduced root biomass, improved yield parameters under normal growth conditions and increased drought stress sensitivity. Overall, BRB represents a solid gene model for improving the performance of sesame and other crops.
Collapse
Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
- Laboratory of Genetics, Horticulture and Seed SciencesFaculty of Agronomic SciencesUniversity of Abomey‐CalaviCotonouBenin
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Lu Qin
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Marie A. Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Ruqi Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Yujuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
- Cotton Research CenterShandong Academy of Agricultural SciencesJinanChina
| | - Jianqiang Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhanChina
| |
Collapse
|
32
|
Genome editing of polyploid crops: prospects, achievements and bottlenecks. Transgenic Res 2021; 30:337-351. [PMID: 33846956 PMCID: PMC8316217 DOI: 10.1007/s11248-021-00251-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.
Collapse
|
33
|
Wan X, Wu S, Li X. Breeding with dominant genic male-sterility genes to boost crop grain yield in the post-heterosis utilization era. MOLECULAR PLANT 2021; 14:531-534. [PMID: 33582376 DOI: 10.1016/j.molp.2021.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 05/26/2023]
Abstract
Global food security is facing severe challenges from an ever-growing population, limited resources, and various stresses. Dominant genic male sterility (DGMS) technology combined with modern breeding strategies may create novel cultivation models with ~50% DGMS F1 hybrids for field production of cross-pollinated crops, boosting crop grain yield to ensure global food security and sustainable agriculture in the post-heterosis utilization era.
Collapse
Affiliation(s)
- Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTB, University of Science and Technology Beijing (USTB), Beijing 100024, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China.
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTB, University of Science and Technology Beijing (USTB), Beijing 100024, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| | - Xiang Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTB, University of Science and Technology Beijing (USTB), Beijing 100024, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd., Beijing 100192, China
| |
Collapse
|
34
|
Tang H, Liu H, Zhou Y, Liu H, Du L, Wang K, Ye X. Fertility recovery of wheat male sterility controlled by Ms2 using CRISPR/Cas9. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:224-226. [PMID: 32970905 PMCID: PMC7868981 DOI: 10.1111/pbi.13482] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/25/2020] [Accepted: 09/14/2020] [Indexed: 05/22/2023]
Affiliation(s)
- Huali Tang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
- College of AgronomyChina Agricultural UniversityBeijingChina
| | - Huiyun Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Yang Zhou
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Hongwei Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Lipu Du
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Ke Wang
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xingguo Ye
- Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
35
|
Tyrka M, Mokrzycka M, Bakera B, Tyrka D, Szeliga M, Stojałowski S, Matysik P, Rokicki M, Rakoczy-Trojanowska M, Krajewski P. Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach. BMC Genomics 2021; 22:81. [PMID: 33509072 PMCID: PMC7842024 DOI: 10.1186/s12864-020-07351-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/27/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach. RESULTS More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs. CONCLUSIONS Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.
Collapse
Affiliation(s)
- Mirosław Tyrka
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Monika Mokrzycka
- Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Beata Bakera
- Warsaw University of Life Sciences, Nowoursynowska 166, 02-787, Warszawa, Poland
| | - Dorota Tyrka
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Magdalena Szeliga
- Rzeszow University of Technology, Powstańców Warszawy 12, 35-959, Rzeszów, Poland
| | - Stefan Stojałowski
- West Pomeranian University of Technology Szczecin, Słowackiego 17, 71-434, Szczecin, Poland
| | - Przemysław Matysik
- Plant Breeding Strzelce Group IHAR Ltd., Kasztanowa 5, 63-004, Tulce, Poland
| | - Michał Rokicki
- Poznań Plant Breeding Ltd., Główna 20, 99-307, Strzelce, Poland
| | | | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Science, Strzeszyńska 34, 60-479, Poznań, Poland.
| |
Collapse
|
36
|
Jiao Z, Zhu X, Li H, Liu Z, Huang X, Wu N, An J, Li J, Zhang J, Jiang Y, Li Q, Qi Z, Niu J. Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility. PeerJ 2020; 8:e10275. [PMID: 33194433 PMCID: PMC7605228 DOI: 10.7717/peerj.10275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/08/2020] [Indexed: 11/20/2022] Open
Abstract
A dwarf, multi-pistil and male sterile dms mutant was previously reported by us. However, the genetic changes in this dms are unclear. To examine the genetic changes, single nucleotide polymorphism (SNP) association, chromosome counting, and high-resolution chromosome fluorescence in situ hybridization (FISH) techniques were employed. By comparing tall plants (T) with dwarf plants (D) in the offspring of dms mutant plants, SNP association analysis indicated that most SNPs were on chromosome 2A. There were three types in offspring of dms plants, with 42, 41 and 40 chromosomes respectively. High-resolution chromosome painting analysis demonstrated that T plants had all 42 wheat chromosomes; the medium plants (M) had 41 chromosomes, lacking one chromosome 2A; while D plants had 40 wheat chromosomes, and lacked both 2A chromosomes. These data demonstrated that dms resulted from a loss of chromosome 2A. We identified 23 genes on chromosome 2A which might be involved in the development of stamens or pollen grains. These results lay a solid foundation for further analysis of the molecular mechanisms of wheat male sterility. Because D plants can be used as a female parent to cross with other wheat genotypes, dms is a unique germplasm for any functional study of chromosome 2A and wheat breeding specifically targeting genes on 2A.
Collapse
Affiliation(s)
- Zhixin Jiao
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Xinxin Zhu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Huijuan Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zhitao Liu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China.,Sichuan Academy of Agricultural Sciences, Crop Research Institue, Chengdu, Sichuan, China
| | - Xinyi Huang
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Nan Wu
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Junhang An
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Junchang Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Jing Zhang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Yumei Jiang
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Qiaoyun Li
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| | - Zengjun Qi
- Nanjing Agricultural University, State key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing, Jiangsu, China
| | - Jishan Niu
- Henan Agricultural University, National Centre of Engineering and Technological Research for Wheat / National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou, Henan, China
| |
Collapse
|
37
|
Liu Y, Hou J, Wang X, Li T, Majeed U, Hao C, Zhang X. The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5794-5807. [PMID: 32803271 DOI: 10.1093/jxb/eraa333] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 05/20/2023]
Abstract
Starch is a major component of wheat (Triticum aestivum L.) endosperm and is an important part of the human diet. The functions of many starch synthesis genes have been elucidated. However, little is known about their regulatory mechanisms in wheat. Here, we identified a novel NAC transcription factor, TaNAC019-A1 (TraesCS3A02G077900), that negatively regulates starch synthesis in wheat and rice (Oryza sativa L.) endosperms. TaNAC019-A1 was highly expressed in the endosperm of developing grains and encoded a nucleus-localized transcriptional repressor. Overexpression of TaNAC019-A1 in rice and wheat led to significantly reduced starch content, kernel weight, and kernel width. The TaNAC019-A1-overexpression wheat lines had smaller A-type starch granules and fewer B-type starch granules than wild-type. Moreover, TaNAC019-A1 could directly bind to the 'ACGCAG' motif in the promoter regions of ADP-glucose pyrophosphorylase small subunit 1 (TaAGPS1-A1, TraesCS7A02G287400) and TaAGPS1-B1 (TraesCS7B02G183300) and repress their expression, thereby inhibiting starch synthesis in wheat endosperm. One haplotype of TaNAC019-B1 (TaNAC019-B1-Hap2, TraesCS3B02G092800) was positively associated with thousand-kernel weight and underwent positive selection during the Chinese wheat breeding process. Our data demonstrate that TaNAC019-A1 is a negative regulator of starch synthesis in wheat endosperm and provide novel insight into wheat yield improvement.
Collapse
Affiliation(s)
- Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
38
|
The unusual dRemp retrotransposon is abundant, highly mutagenic, and mobilized only in the second pollen mitosis of some maize lines. Proc Natl Acad Sci U S A 2020; 117:18091-18098. [PMID: 32661148 DOI: 10.1073/pnas.2010234117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The frequent mutations recovered recently from the pollen of select maize lines resulted from the meiotic mobilization of specific low-copy number long-terminal repeat (LTR) retrotransposons, which differ among lines. Mutations that arise at male meiosis produce kernels with concordant mutant phenotypes in both endosperm and embryo because the two sperms that participate in double fertilization are genetically identical. Those are in a majority. However, a small minority of kernels with a mutant endosperm carry a nonconcordant normal embryo, pointing to a postmeiotic or microgametophytic origin. In this study, we have identified the basis for those nonconcordant mutations. We find that all are produced by transposition of a defective LTR retrotransposon that we have termed dRemp (defective retroelement mobile in pollen). This element has several unique properties. Unlike the mutagenic LTR retrotransposons identified previously, dRemp is present in hundreds of copies in all sequenced lines. It seems to transpose only at the second pollen mitosis because all dRemp insertion mutants are nonconcordant yet recoverable in either the endosperm or the embryo. Although it does not move in most lines, dRemp is highly mobile in the Corn Belt inbred M14, identified earlier by breeders as being highly unstable. Lastly, it can be recovered in an array of structures, ranging from solo LTRs to tandem dRemp repeats containing several internal LTRs, suggestive of extensive recombination during retrotransposition. These results shed further light on the spontaneous mutation process and on the possible basis for inbred instability in maize.
Collapse
|
39
|
Guan J, Garcia DF, Zhou Y, Appels R, Li A, Mao L. The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:221-229. [PMID: 32561470 PMCID: PMC7801200 DOI: 10.1016/j.gpb.2019.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 08/15/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023]
Abstract
In the year 2018, the world witnessed the finale of the race to sequence the genome of the world's most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.
Collapse
Affiliation(s)
- Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Diego F Garcia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun Zhou
- Collaborative Innovation Center of Crop Stress Biology & Institute of Plant Stress Biology, School of Life Science, Henan University, Kaifeng 475004, China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, Melbourne, VIC 3083, Australia
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
40
|
Rasheed A, Takumi S, Hassan MA, Imtiaz M, Ali M, Morgunov AI, Mahmood T, He Z. Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1503-1520. [PMID: 31897516 DOI: 10.1007/s00122-019-03523-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.
Collapse
Affiliation(s)
- Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Muhammad Adeel Hassan
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Mohsin Ali
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Alex I Morgunov
- International Maize and Wheat Improvement Center (CIMMYT), Yenimahalle, Ankara, 06170, Turkey
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| |
Collapse
|
41
|
Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
Collapse
Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
42
|
Kalendar R, Raskina O, Belyayev A, Schulman AH. Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants. Int J Mol Sci 2020; 21:ijms21082931. [PMID: 32331257 PMCID: PMC7215508 DOI: 10.3390/ijms21082931] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.
Collapse
Affiliation(s)
- Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27 (Latokartanonkaari 5), FI-00014 Helsinki, Finland
- RSE “National Center for Biotechnology”, Korgalzhyn Highway 13/5, Nur-Sultan 010000, Kazakhstan
- Correspondence: (R.K.); (A.H.S.)
| | - Olga Raskina
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel;
| | - Alexander Belyayev
- Laboratory of Molecular Cytogenetics and Karyology, Institute of Botany of the ASCR, Zámek 1, CZ-252 43 Průhonice, Czech Republic;
| | - Alan H. Schulman
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
- Correspondence: (R.K.); (A.H.S.)
| |
Collapse
|
43
|
Milner MJ, Craze M, Bowden S, Bates R, Wallington EJ, Keeling A. Identification of genes involved in male sterility in wheat ( Triticum aestivum L.) which could be used in a genic hybrid breeding system. PLANT DIRECT 2020; 4:e00201. [PMID: 32181421 PMCID: PMC7063588 DOI: 10.1002/pld3.201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 05/12/2023]
Abstract
Wheat is grown on more land than any other crop in the world. Current estimates suggest that yields will have to increase sixty percent by 2050 to meet the demand of an ever-increasing human population; however, recent wheat yield gains have lagged behind other major crops such as rice and maize. One of the reasons suggested for the lag in yield potential is the lack of a robust hybrid system to harness the potential yield gains associated with heterosis, also known as hybrid vigor. Here, we set out to identify candidate genes for a genic hybrid system in wheat and characterize their function in wheat using RNASeq on stamens and carpels undergoing meiosis. Twelve genes were identified as potentially playing a role in pollen viability. CalS5- and RPG1-like genes were identified as pre- and post-meiotic genes for further characterization and to determine their role in pollen viability. It appears that all three homoeologues of both CalS5 and RPG1 are functional in wheat as all three homoeologues need to be knocked out in order to cause male sterility. However, one functional homoeologue is sufficient to maintain male fertility in wheat.
Collapse
Affiliation(s)
| | | | | | - Ruth Bates
- The John Bingham LaboratoryNIABCambridgeUK
| | | | | |
Collapse
|
44
|
A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation. Nat Commun 2020; 11:443. [PMID: 31974373 PMCID: PMC6978460 DOI: 10.1038/s41467-019-14265-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 12/20/2019] [Indexed: 12/22/2022] Open
Abstract
Callus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation. Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.
Collapse
|
45
|
Dong C, Zhang L, Chen Z, Xia C, Gu Y, Wang J, Li D, Xie Z, Zhang Q, Zhang X, Gui L, Liu X, Kong X. Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1249. [PMID: 32903549 PMCID: PMC7438552 DOI: 10.3389/fpls.2020.01249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/29/2020] [Indexed: 05/07/2023]
Abstract
The discovery of functional genes underlying agronomic traits is of great importance for wheat improvement. Here we designed a new wheat exome capture probe panel based on IWGSC RefSeq v1.0 genome sequence information and developed an effective algorithm, varBScore, that can sufficiently reduce the background noise in gene mapping and identification. An effective method, termed bulked segregant exome capture sequencing (BSE-Seq) for identifying causal mutations or candidate genes was established by combining the use of a newly designed wheat exome capture panel, sequencing of bulked segregant pools from segregating populations, and the robust algorithm varBScore. We evaluated the effectiveness of varBScore on SNP calling using the published dataset for mapping and cloning the yellow rust resistance gene Yr7 in wheat. Furthermore, using BSE-Seq, we rapidly identified a wheat yellow leaf mutant gene, ygl1, in an ethyl methanesulfonate (EMS) mutant population and found that a single mutation of G to A at 921 position in the wild type YGL1 gene encoding magnesium-chelatase subunit chlI caused the leaf yellowing phenotype. We further showed that mutation of YGL1 through CRISPR/Cas9 gene editing led to a yellow phenotype on the leaves of transgenic wheat, indicating that ygl1 is the correct causal gene responsible for the mutant phenotype. In summary, our approach is highly efficient for discovering causal mutations and gene cloning in wheat.
Collapse
Affiliation(s)
- Chunhao Dong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lichao Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
| | - Zhongxu Chen
- Department of Life Science, Chengdu Tcuni Technology, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Chuan Xia
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongqiang Gu
- Western Regional Research, United States Department of Agriculture-Agricultural Research Service, Albany, CA, United States
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Danping Li
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhencheng Xie
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueying Zhang
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixuan Gui
- Department of Life Science, Chengdu Tcuni Technology, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xu Liu
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
| | - Xiuying Kong
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lichao Zhang, ; Xu Liu, ; Xiuying Kong,
| |
Collapse
|
46
|
Huang S, Peng S, Liu Z, Li C, Tan C, Yao R, Li D, Li X, Hou L, Feng H. Investigation of the genes associated with a male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. Mol Genet Genomics 2019; 295:233-249. [PMID: 31673754 DOI: 10.1007/s00438-019-01618-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/16/2019] [Indexed: 12/15/2022]
Abstract
In Chinese cabbage, hybrid seed production is performed using male sterility lines, an important approach to heterosis utilization. In this study, a stably inherited male sterile mutant msm was obtained from the 'FT'-doubled haploid line of Chinese cabbage using isolated microspore culture combined with 60Co γ-ray mutagenesis. The genetic backgrounds of 'FT' and msm were highly consistent; however, compared with wild-type 'FT', msm exhibited completely degenerated stamens and no pollen phenotype. Other characters showed no significant differences. Cytological observations revealed that stamen abortion in msm begins during the tetrad period and that tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Genetic analysis indicated that the msm mutant phenotype is controlled by a single recessive nuclear gene. Comparative transcriptome analysis of 'FT' and msm flower buds using RNA-Seq technology revealed 1653 differentially expressed genes, among which, a large number associated with male sterility were detected, including 64 pollen development- and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes, and 16 transcription factor-related genes. An overwhelming majority of these genes were down-regulated in msm compared with 'FT'. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, 24,476 single-nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results will facilitate elucidation of the regulatory mechanisms underlying male sterility in Chinese cabbage.
Collapse
Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Shenling Peng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chengyu Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Chong Tan
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Runpeng Yao
- Department of Horticulture, Tonghua Horticulture Research Institute, Tonghua, 134000, People's Republic of China
| | - Danyang Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Xiang Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Li Hou
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
| |
Collapse
|
47
|
Identification, characterization and expression analysis of lineage-specific genes within Triticeae. Genomics 2019; 112:1343-1350. [PMID: 31401233 DOI: 10.1016/j.ygeno.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022]
Abstract
Lineage-specific genes (LSGs) are a set of genes in a given taxon without significant sequence similarity to genes and intergenic sequences of other taxa and are functional. The tribe Triticeae mainly includes species of different ploidy levels, such as staple food crops wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). This study is aimed at mining and characterizing the Triticeae-specific genes (TSGs) using expressed sequence data of wheat. A total of 3812 TSGs was identified and they were generally characterized by smaller size, fewer exons, shorter open reading frames and lower expression levels. Most TSGs were expressed with tissue preference and many of them were predominantly expressed in reproduction related tissues, especially in young stamen. Nearly one third of the TSGs were stress-responsive and inducible under abiotic and/or biotic stresses. A co-expression-based annotation supported the relevance of some TSGs with reproduction and stress responses, indicating their potential economic importance.
Collapse
|
48
|
Pallotta MA, Warner P, Kouidri A, Tucker EJ, Baes M, Suchecki R, Watson-Haigh N, Okada T, Garcia M, Sandhu A, Singh M, Wolters P, Albertsen MC, Cigan AM, Baumann U, Whitford R. Wheat ms5 male-sterility is induced by recessive homoeologous A and D genome non-specific lipid transfer proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:673-685. [PMID: 31009129 DOI: 10.1111/tpj.14350] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 05/22/2023]
Abstract
Nuclear male-sterile mutants with non-conditional, recessive and strictly monogenic inheritance are useful for both hybrid and conventional breeding systems, and have long been a research focus for many crops. In allohexaploid wheat, however, genic redundancy results in rarity of such mutants, with the ethyl methanesulfonate-induced mutant ms5 among the few reported to date. Here, we identify TaMs5 as a glycosylphosphatidylinositol-anchored lipid transfer protein required for normal pollen exine development, and by transgenic complementation demonstrate that TaMs5-A restores fertility to ms5. We show ms5 locates to a centromere-proximal interval and has a sterility inheritance pattern modulated by TaMs5-D but not TaMs5-B. We describe two allelic forms of TaMs5-D, one of which is non-functional and confers mono-factorial inheritance of sterility. The second form is functional but shows incomplete dominance. Consistent with reduced functionality, transcript abundance in developing anthers was found to be lower for TaMs5-D than TaMs5-A. At the 3B homoeolocus, we found only non-functional alleles among 178 diverse hexaploid and tetraploid wheats that include landraces and Triticum dicoccoides. Apparent ubiquity of non-functional TaMs5-B alleles suggests loss-of-function arose early in wheat evolution and, therefore, at most knockout of two homoeoloci is required for sterility. This work provides genetic information, resources and tools required for successful implementation of ms5 sterility in breeding systems for bread and durum wheats.
Collapse
Affiliation(s)
- Margaret A Pallotta
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Patricia Warner
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Allan Kouidri
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Elise J Tucker
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Mathieu Baes
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Nathan Watson-Haigh
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Takashi Okada
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Melissa Garcia
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Ajay Sandhu
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA, 50131-0552, USA
| | - Manjit Singh
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA, 50131-0552, USA
| | - Petra Wolters
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA, 50131-0552, USA
| | - Marc C Albertsen
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA, 50131-0552, USA
| | - A Mark Cigan
- DuPont Pioneer Hi-Bred International Inc., 7250 NW 62nd Avenue, Johnston, IA, 50131-0552, USA
| | - Ute Baumann
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Ryan Whitford
- School of Agriculture, Food & Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| |
Collapse
|
49
|
Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
Collapse
Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
50
|
Hu D, Zhang W, Zhang Y, Chang S, Chen L, Chen Y, Shi Y, Shen J, Meng J, Zou J. Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1106-1118. [PMID: 30467941 PMCID: PMC6523605 DOI: 10.1111/pbi.13041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 05/20/2023]
Abstract
Brassica napus (An An Cn Cn ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of Brassica rapa (Ar Ar ) and 74 accessions of Brassica carinata (Bc Bc Cc Cc ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high-throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses.
Collapse
Affiliation(s)
- Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenshan Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yikai Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Lunlin Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yingying Chen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yongdi Shi
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|