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Liu E, Zhu S, Du M, Lyu H, Zeng S, Liu Q, Wu G, Jiang J, Dang X, Dong Z, Hong D. LAX1, functioning with MADS-box genes, determines normal palea development in rice. Gene 2023; 883:147635. [PMID: 37442304 DOI: 10.1016/j.gene.2023.147635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Normal floral organ development in rice is necessary for grain formation. Many MADS-box family genes that belong to ABCDE model have been widely implicated in rice flower development. The LAX1 allele encodes a plant-specific basic helix-loop-helix (bHLH) transcription factor, which is the main regulator of axillary meristem formation in rice. However, the molecular mechanisms of LAX1 allele together with MADS-box family genes underlying palea development have not been reported. We found a short palea mutant plant in a population of indica rice variety 9311 treated with cobalt 60. We report the map-based cloning and characterization of lax1-7, identified as a new mutant allele of the LAX1 locus, and the role of its wild-type allele LAX1 in rice palea development. Through complementary experiments, combined with genetic and molecular biological analyses, the function of the LAX1 allele was determined. We showed that LAX1 allele is expressed specifically in young spikelets and encodes a nucleus-localized protein. In vitro and in vivo experiments revealed that the LAX1 protein physically interacts with OsMADS1, OsMADS6 and OsMADS7. The LAX1 allele is pleiotropic for the maintenance of rice palea identity via cooperation with MADS-box genes and other traits, including axillary meristem initiation, days to heading, plant height, panicle length and spikelet fertility.
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Affiliation(s)
- Erbao Liu
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shangshang Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyu Du
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Huineng Lyu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyuan Zeng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiangming Liu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Guocan Wu
- Ningde Institute of Agricultural Sciences, Ningde 355017, China
| | - Jianhua Jiang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Xiaojing Dang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Zhiyao Dong
- College of Life Sciences, Jilin Normal University, Jilin 136000, China
| | - Delin Hong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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Zhao X, Yi L, Zuo Y, Gao F, Cheng Y, Zhang H, Zhou Y, Jia X, Su S, Zhang D, Zhang X, Ren Y, Mu Y, Jin X, Li Q, Bateer S, Lu Z. High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement. PLANTS (BASEL, SWITZERLAND) 2023; 12:2773. [PMID: 37570928 PMCID: PMC10421198 DOI: 10.3390/plants12152773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023]
Abstract
Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.
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Affiliation(s)
- Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Liuxi Yi
- Agricultural College, Inner Mongolia Agricultural University, Hohhot 010019, China
| | - Yongchun Zuo
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Hohhot 010019, China
| | - Fengyun Gao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Hui Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yu Zhou
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiaoyun Jia
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Shaofeng Su
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Dejian Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yongfeng Ren
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Yanxin Mu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiaolei Jin
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Qiang Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Siqin Bateer
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
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Integrative Analysis of Transcriptomic and Proteomic Changes Related to Cytoplasmic Male Sterility in Spring Stem Mustard ( Brassica juncea var. tumida Tsen et Lee). Int J Mol Sci 2022; 23:ijms23116248. [PMID: 35682925 PMCID: PMC9180981 DOI: 10.3390/ijms23116248] [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: 05/02/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
The development of flower and pollen is a complex biological process that involves multiple metabolic pathways in plants. In revealing novel insights into flower and pollen development underlying male sterility (MS), we conducted an integrated profiling of gene and protein activities in developing buds in cytoplasmic male sterile (CMS) mutants of mustard (Brassica juncea). Using RNA-Seq and label-free quantitative proteomics, 11,832 transcripts and 1780 protein species were identified with significant differential abundance between the male sterile line 09-05A and its maintainer line 09-05B at the tetrad stage and bi-nucleate stage of B. juncea. A large number of differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) involved in carbohydrate and energy metabolism, including starch and sucrose metabolism, tricarboxylic acid (TCA) cycle, glycolysis, and oxidoreductase activity pathways, were significantly downregulated in 09-05A buds. The low expression of these DEGs or functional loss of DAPs, which can lead to an insufficient supply of critical substrates and ATP, could be associated with flower development, pollen development, and changes in fertility in B. juncea. Therefore, this study provided transcriptomic and proteomic information of pollen abortion for B. juncea and a basis for further research on the molecular regulatory mechanism of MS in plants.
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Xu B, Wu R, Shi F, Gao C, Wang J. Transcriptome profiling of flower buds of male-sterile lines provides new insights into male sterility mechanism in alfalfa. BMC PLANT BIOLOGY 2022; 22:199. [PMID: 35428186 PMCID: PMC9013074 DOI: 10.1186/s12870-022-03581-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The use of heterosis to produce hybrid seeds is a challenge to breeding for improved crop yield. In previous studies, we isolated a male sterile alfalfa hybrid and successfully obtained a genetically stable alfalfa male sterile line through backcrossing, henceforth named MS-4. In this study, we used RNA-seq technology to analyze the transcriptome profiles of the male sterile line (MS-4) and the male fertile line (MF) of alfalfa to elucidate the mechanism of male sterility. RESULTS We screened a total of 11,812 differentially expressed genes (DEGs) from both MS-4 and MF lines at three different stages of anther development. Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that these DEGs are mainly involved in processes such as energy metabolism, lipid and amino acid metabolism, carbohydrate metabolism, in addition to cell synthesis and aging. The results from protein-protein interaction (PPI) network analysis showed that the ribosomal protein (MS.Gene25178) was the core gene in the network. We also found that transcriptional regulation was an influential factor in the development of anthers. CONCLUSIONS Our findings provide new insights into understanding of the fertility changes in the male sterile (MS-4) of alfalfa.
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Affiliation(s)
- Bo Xu
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Rina Wu
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fengling Shi
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China.
| | - Cuiping Gao
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Jia Wang
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Qu Z, Jia Y, Duan Y, Chen H, Wang X, Zheng H, Liu H, Wang J, Zou D, Zhao H. Integrated Isoform Sequencing and Dynamic Transcriptome Analysis Reveals Diverse Transcripts Responsible for Low Temperature Stress at Anther Meiosis Stage in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:795834. [PMID: 34975985 PMCID: PMC8718874 DOI: 10.3389/fpls.2021.795834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Low temperatures stress is one of the important factors limiting rice yield, especially during rice anther development, and can cause pollen sterility and decrease grain yield. In our study, low-temperature stress decreased pollen viability and spikelet fertility by affecting the sugar, nitrogen and amino acid contents of anthers. We performed RNA-seq and ISO-seq experiments to study the genome-wide transcript expression profiles in low-temperature anthers. A total of 4,859 differentially expressed transcripts were detected between the low-temperature and control groups. Gene ontology enrichment analysis revealed significant terms related to cold tolerance. Hexokinase and glutamate decarboxylase participating in starch and sucrose metabolism may play important roles in the response to cold stress. Using weighted gene co-expression network analysis, nine hub transcripts were found that could improve cold tolerance throughout the meiosis period of rice: Os02t0219000-01 (interferon-related developmental regulator protein), Os01t0218350-00 (tetratricopeptide repeat-containing thioredoxin), Os08t0197700-00 (luminal-binding protein 5), Os11t0200000-01 (histone deacetylase 19), Os03t0758700-01 (WD40 repeat domain-containing protein), Os06t0220500-01 (7-deoxyloganetin glucosyltransferase), Pacbio.T01382 (sucrose synthase 1), Os01t0172400-01 (phospholipase D alpha 1), and Os01t0261200-01 (NAC domain-containing protein 74). In the PPI network, the protein minichromosome maintenance 4 (MCM4) may play an important role in DNA replication induced by cold stress.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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Hu J, Lan M, Xu X, Yang H, Zhang L, Lv F, Yang H, Yang D, Li C, He J. Transcriptome Profiling Reveals Molecular Changes during Flower Development between Male Sterile and Fertile Chinese Cabbage ( Brassica rapa ssp. pekinensis) Lines. Life (Basel) 2021; 11:life11060525. [PMID: 34199781 PMCID: PMC8227754 DOI: 10.3390/life11060525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/16/2022] Open
Abstract
Male sterility exists widely in flowering plants and is used as a fascinating tool by breeders for creating hybrid varieties. Herein, stamen samples from male sterile CCR20000 and male fertile CCR20001 lines during two developmental stages were employed to elucidate the molecular changes during flower development in fertile and sterile Chinese cabbage lines. RNA-seq revealed weak transcriptional activity in the sterile line, which may have led to the abnormal stamen development. The differentially expressed genes were enriched in plant hormone, carbon metabolism, and biosynthesis of amino acid pathways. Important genes with opposite patterns of regulation between the two lines have been associated with the male sterility trait. Members of the transcription factor families such as AP2, MYB, bHLH, and WRKY were highly active in the regulation of structural genes involved in pollen fertility. This study generated important genomic information to support the exploitation of the male sterility trait in Chinese cabbage breeding programs.
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Affiliation(s)
- Jingfeng Hu
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
| | - Mei Lan
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
| | - Xuezhong Xu
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
| | - Hongli Yang
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
| | - Liqin Zhang
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
| | - Fengxian Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (F.L.); (D.Y.); (C.L.)
| | - Huiju Yang
- Lijiang Teachers College, Lijiang 674100, China;
| | - Ding Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (F.L.); (D.Y.); (C.L.)
| | - Chongjuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (F.L.); (D.Y.); (C.L.)
| | - Jiangming He
- Institute of Horticultural Crops, Yunnan Academy of Agricultural Sciences, Yunnan Branch of the National Vegetable Improvement Center, Kunming 650205, China; (J.H.); (M.L.); (X.X.); (H.Y.); (L.Z.)
- Correspondence:
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Yang D, Xu H, Liu Y, Li M, Ali M, Xu X, Lu G. RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers. FRONTIERS IN PLANT SCIENCE 2021; 12:687826. [PMID: 34149789 PMCID: PMC8213351 DOI: 10.3389/fpls.2021.687826] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 05/26/2023]
Abstract
Cold stress is a serious threat to subtropical crop pollen development and induces yield decline. N6-methyladenosine (m6A) is the most frequent mRNA modification and plays multiple physiological functions in plant development. However, whether m6A regulates pollen development is unclear, and its putative role in cold stress response remains unknown. Here, we observed that moderate low-temperature (MLT) stress induced pollen abortion in tomato. This phenotype was caused by disruption of tapetum development and pollen exine formation, accompanied by reduced m6A levels in tomato anther. Analysis of m6A-seq data revealed 1,805 transcripts displayed reduced m6A levels and 978 transcripts showed elevated m6A levels in MLT-stressed anthers compared with those in anthers under normal temperature. These differentially m6A enriched transcripts under MLT stress were mainly related to lipid metabolism, adenosine triphosphatase (ATPase) activity, and ATP-binding pathways. An ATP-binding transcript, SlABCG31, had significantly upregulated m6A modification levels, which was inversely correlated to the dramatically downregulated expression level. These changes correlated with higher abscisic acid (ABA) levels in anthers and disrupted pollen wall formation under low-temperature stress. Our findings characterized m6A as a novel layer of complexity in gene expression regulation and established a molecular link between m6A methylation and tomato anther development under low-temperature conditions.
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Affiliation(s)
- Dandan Yang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Huachao Xu
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Yue Liu
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Mengzhuo Li
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Muhammad Ali
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Xiangyang Xu
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Gang Lu
- Department of Horticulture, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou, China
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Cai Y, Ma Z, Ogutu CO, Zhao L, Liao L, Zheng B, Zhang R, Wang L, Han Y. Potential Association of Reactive Oxygen Species With Male Sterility in Peach. FRONTIERS IN PLANT SCIENCE 2021; 12:653256. [PMID: 33936139 PMCID: PMC8079786 DOI: 10.3389/fpls.2021.653256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/08/2021] [Indexed: 05/11/2023]
Abstract
Male sterility is an important agronomic trait for hybrid vigor utilization and hybrid seed production, but its underlying mechanisms remain to be uncovered. Here, we investigated the mechanisms of male sterility in peach using a combined cytology, physiology, and molecular approach. Cytological features of male sterility include deformed microspores and tapetum cells along with absence of pollen grains. Microspores had smaller nucleus at the mononuclear stage and were compressed into belts and subsequently disappeared in the anther cavity, whereas tapetum cells were swollen and vacuolated, with a delayed degradation to flowering time. Male sterile anthers had an ROS burst and lower levels of major antioxidants, which may cause abnormal development of microspores and tapetum, leading to male sterility in peach. In addition, the male sterility appears to be cytoplasmic in peach, which could be due to sequence variation in the mitochondrial genome. Our results are helpful for further investigation of the genetic mechanisms underlying male sterility in peach.
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Affiliation(s)
- Yaming Cai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhishen Ma
- Shijiazhuang Pomology Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Lei Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ruoxi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Lu Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yuepeng Han,
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9
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Zhao H, Wang J, Qu Y, Peng R, Magwanga RO, Liu F, Huang J. Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background. BMC Genomics 2020; 21:859. [PMID: 33267770 PMCID: PMC7709281 DOI: 10.1186/s12864-020-07261-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Background Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B. Results We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background. Conclusion We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07261-y.
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Affiliation(s)
- Haiyan Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.,School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Jianshe Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.,School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yunfang Qu
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Renhai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Richard Odongo Magwanga
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Jinling Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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10
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Liu T, Duan W, Chen Z, Yuan J, Xiao D, Hou X, Li Y. Enhanced photosynthetic activity in pak choi hybrids is associated with increased grana thylakoids in chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2211-2224. [PMID: 32573878 DOI: 10.1111/tpj.14893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/01/2020] [Accepted: 06/12/2020] [Indexed: 05/12/2023]
Abstract
Increased photosynthetic activity is closely linked to heterosis in plants, but the underlying molecular mechanisms remain elusive. Pak choi (Brassica rapa ssp. chinensis) is a widely grown vegetable in Asia, and the most commercial cultivars are F1 hybrids. Here, the inbred pak choi lines WTC and 2Q, and their reciprocal F1 hybrids WQ and QW, were used to characterize the increased photosynthetic activity in these hybrids at the physiological, cellular and molecular levels. We found that the hybrids had larger leaves, with more grana thylakoids. Additionally, these hybrids had significantly increased net photosynthetic rates (Pn ) under both saturating and low irradiance conditions. These data indicate that the increased photosynthetic activity in pak choi hybrids was associated with an improved photosynthetic mechanism and larger leaves. Next, we obtained genome-wide data using transcriptome and bisulfite sequencing. Gene ontology (GO) analysis showed that the differentially expressed genes among the parents and hybrids were mostly enriched in the 'photosynthesis', 'thylakoid', and 'chloroplast' categories, indicating that the increased number of grana thylakoids contributes to the enhanced photosynthetic capacity in hybrids. Furthermore, we found that the increased number of grana thylakoids was associated with the upregulation of light-harvesting complex of photosystem II 1 (BrLhcb1). Yeast one-hybrid and transient assay showed that the BrLhcb1 promoter was directly bound by CIRCADIAN CLOCK ASSOCIATED 1 (BrCCA1), resulting in increased BrLhcb1 expression and enhanced carbon fixation in hybrids. Finally, our findings provide new insight into molecular mechanisms underlying enhanced photosynthesis in pak choi hybrids.
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Affiliation(s)
- Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Life science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zhongwen Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingping Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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11
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Zhang C, Wang H, Xu Y, Zhang S, Wang J, Hu B, Hou X, Li Y, Liu T. Enhanced Relative Electron Transport Rate Contributes to Increased Photosynthetic Capacity in Autotetraploid Pak Choi. PLANT & CELL PHYSIOLOGY 2020; 61:761-774. [PMID: 31904850 DOI: 10.1093/pcp/pcz238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Autopolyploids often show growth advantages over their diploid progenitors because of their increased photosynthetic activity; however, the underlying molecular basis of such mechanism remains elusive. In this study, we aimed to characterize autotetraploid pak choi (Brassica rapa ssp. chinensis) at the physiological, cellular and molecular levels. Autotetraploid pak choi has thicker leaves than its diploid counterparts, with relatively larger intercellular spaces and cell size and greater grana thylakoid height. Photosynthetic data showed that the relative electron transport rate (rETR) was markedly higher in autotetraploid than in diploid pak choi. Transcriptomic data revealed that the expressions of genes involved in 'photosynthesis' biological process and 'thylakoids' cellular component were mainly regulated in autotetraploids. Overall, our findings suggested that the increased rETR in the thylakoids contributed to the increased photosynthetic capacity of autotetraploid leaves. Furthermore, we found that the enhanced rETR is associated with increased BrPetC expression, which is likely altered by histone modification. The ectopic expression of BrPetC in Arabidopsis thaliana led to increased rETR and biomass, which were decreased in BrPetC-silenced pak choi. Autotetraploid pak choi also shows altered hormone levels, which was likely responsible for the increased drought resistance and the impaired powdery mildew resistance of this lineage. Our findings further our understanding on how autotetraploidy provides growth advantages to plants.
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Affiliation(s)
- Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiyu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyuan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuning Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bing Hu
- Department of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Department of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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12
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Cheng Q, Li T, Ai Y, Lu Q, Wang Y, Wu L, Liu J, Sun L, Shen H. Phenotypic, genetic, and molecular function of msc-2, a genic male sterile mutant in pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:843-855. [PMID: 31863155 DOI: 10.1007/s00122-019-03510-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Bulked segregant analysis and fine mapping delimited the pepper genic male sterile (msc-2) locus into a 336 kb region on chromosome 5. A strong candidate gene, Capana05g000766, a homolog of AtMS1, was indentified in this region. Genic male sterility (msc-2) is used to produce hybrid seeds in Northern China. However, no co-segregated markers have been reported or candidate genes controlling this trait have been cloned. Here, bulked segregant analysis and genotyping of an F2 population and a 18Q5431AB line were employed to fine map msc-2, which was delimited to a 336 kb region. In this region, Capana05g000766 was a homolog of AtMS1, which encodes a plant homeodomain finger involved in tapetum development. A "T" deletion in the Capana05g000766 locus leads to a premature stop codon, which may cause a loss-of-function mutation. Real-time PCR analysis revealed that Capana05g000766 was an anther-specific gene and down-regulation of the gene resulted in male sterility. Therefore, Capana05g000766 was identified as the strongest candidate gene for the msc-2 locus. Allelism tests showed that msc-1 and msc-2 were nonallelic, and bimolecular fluorescence complementation analysis indicated that the two genes did not interact directly with each other at the protein level. As msc-1 and msc-2 are homologs of AtDYT1 and AtMS1 in Arabidopsis, they may play similar roles in tapetum development in genic male sterile peppers, and Msc-1 might be up stream of Msc-2 in the regulation of other genes involved in tapetum development.
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Affiliation(s)
- Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yixin Ai
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Qiaohua Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yihao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lang Wu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jinqiu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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13
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Wang R, Lu C, Shu Z, Yuan X, Jiang H, Guo H. iTRAQ-based proteomic analysis reveals several key metabolic pathways associated with male sterility in Salvia miltiorrhiza. RSC Adv 2020; 10:16959-16970. [PMID: 35496921 PMCID: PMC9053177 DOI: 10.1039/c9ra09240d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/20/2020] [Indexed: 02/02/2023] Open
Abstract
Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops. In 2002, our team discovered a natural male sterile mutant of Salvia miltiorrhiza. It provided us with the possibility of obtaining stable and controllable quality. To study the molecular mechanism of male sterility in S. miltiorrhiza, we generated proteomic profiles comparing the male sterile mutant type (MT) and wild type (WT) using iTRAQ sequencing. We found a total of 639 differential abundant proteins (DAPs) between MT and WT buds. The DAPs associated with male sterility were mainly involved in (1) carbohydrate and energy metabolism, and (2) protein synthesis and degradation. Based on a comparison between the protein expression profiles of MT and WT, we elucidated a potential protein interaction network involved in male sterility. These results provide new potential biomarkers and insights into the molecular mechanism of male sterility in S. miltiorrhiza. Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops.![]()
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Affiliation(s)
- Ruihong Wang
- College of Chemistry and Pharmacy
- Northwest A&F University
- Yangling 712100
- China
- College of Life Sciences
| | - Congyu Lu
- Centre for Bioinformatics & Computational Biology
- University of Delaware
- Newark
- USA
| | - Zhiming Shu
- College of Chemistry and Pharmacy
- Northwest A&F University
- Yangling 712100
- China
| | - Xinbo Yuan
- College of Chemistry and Pharmacy
- Northwest A&F University
- Yangling 712100
- China
| | - Han Jiang
- College of Life Sciences
- Northwest A&F University
- Yangling 712100
- China
| | - Hongbo Guo
- College of Chemistry and Pharmacy
- Northwest A&F University
- Yangling 712100
- China
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14
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Rodríguez-Suárez C, Bagnaresi P, Cattivelli L, Pistón F, Castillo A, Martín AC, Atienza SG, Ramírez C, Martín A. Transcriptomics, chromosome engineering and mapping identify a restorer-of-fertility region in the CMS wheat system msH1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:283-295. [PMID: 31624874 DOI: 10.1007/s00122-019-03457-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/09/2019] [Indexed: 05/24/2023]
Abstract
An original RNA-seq mapping strategy, validated with chromosome engineering and physical mapping, identifies candidate genes for fertility restoration in the 6HchS chromosome of Hordeum chilense in the wheat msH1 system. Cytoplasmic male sterility (CMS) is a valuable trait for hybrid seed production. The msH1 CMS system in common wheat results from the incompatibility between the nuclear genome of wheat and the cytoplasm of the wild barley Hordeum chilense. This work aims to identify H. chilense candidate genes for fertility restoration in the msH1 system with a multidisciplinary strategy based on chromosome engineering, differential expression analysis and genome mapping. Alloplasmic isogenic wheat lines differing for fertility, associated with the presence of an acrocentric chromosome Hchac resulting from the rearrangement of the short arms of H. chilense chromosomes 1Hch and 6Hch, were used for transcriptome sequencing. Two novel RNA-seq mapping approaches were designed and compared to identify differentially expressed genes of H. chilense associated with male fertility restoration. Minichromosomes (Hchmi), new smaller reorganizations of the Hchac also restoring fertility, were obtained and used to validate the candidate genes. This strategy was successful identifying a putative restorer-of-fertility region on 6HchS, with six candidate genes, including the ortholog of the barley restorer gene Rfm1. Additionally, transcriptomics gave preliminary insights on sterility and restoration networks showing the importance of energy supply, stress, protein metabolism and RNA processing.
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Affiliation(s)
- Cristina Rodríguez-Suárez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain.
| | - Paolo Bagnaresi
- Research Centre for Genomics and Bioinformatics, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Luigi Cattivelli
- Research Centre for Genomics and Bioinformatics, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Fernando Pistón
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Almudena Castillo
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Azahara C Martín
- Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Carmen Ramírez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
| | - Antonio Martín
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Avda. Menéndez Pidal s/n, 14080, Córdoba, Spain
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15
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Liu E, Zeng S, Zhu S, Liu Y, Wu G, Zhao K, Liu X, Liu Q, Dong Z, Dang X, Xie H, Li D, Hu X, Hong D. Favorable Alleles of GRAIN-FILLING RATE1 Increase the Grain-Filling Rate and Yield of Rice. PLANT PHYSIOLOGY 2019; 181:1207-1222. [PMID: 31519786 PMCID: PMC6836814 DOI: 10.1104/pp.19.00413] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/01/2019] [Indexed: 05/12/2023]
Abstract
Hybrid rice (Oryza sativa) has been cultivated commercially for 42 years in China. However, poor grain filling still limits the development of hybrid japonica rice. We report here the map-based cloning and characterization of the GRAIN-FILLING RATE1 (GFR1) gene present at a major-effect quantitative trait locus. We elucidated and confirmed the function of GFR1 via genetic complementation experiments and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing in combination with genetic and molecular biological analyses. In addition, we conducted haplotype association analysis to mine the elite alleles of GFR1 among 117 rice accessions. We observed that GFR1 was constitutively expressed and encoded a membrane-localized protein. The allele of the rice accession Ludao (GFR1 Ludao) improved the grain-filling rate of rice by increasing Rubisco initial activity in the Calvin cycle. Moreover, the increased expression of the cell wall invertase gene OsCIN1 in the near isogenic line NIL-GFR1 Ludao promoted the unloading of Suc during the rice grain-filling stage. A yeast two-hybrid assay indicated that the Rubisco small subunit interacts with GFR1, possibly in the regulation of the rice grain-filling rate. Evaluation of the grain-filling rate and grain yield of F1 plants harboring GFR1 Ludao and the alleles of 20 hybrids widely cultivated commercially confirmed that favorable alleles of GFR1 can be used to further improve the grain-filling rate of hybrid japonica rice.
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Affiliation(s)
- Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyuan Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shangshang Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Guocan Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiming Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Zhiyao Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- China National Japonica Rice Research and Development Center, Tianjin 300457, China
| | - Dalu Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxiao Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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16
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Wu S, Tan H, Hao X, Xie Z, Wang X, Li D, Tian L. Profiling miRNA expression in photo-thermo-sensitive male genic sterility line (PTGMS) PA64S under high and low temperature. PLANT SIGNALING & BEHAVIOR 2019; 14:1679015. [PMID: 31610741 PMCID: PMC6866692 DOI: 10.1080/15592324.2019.1679015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/29/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Peiai64S (PA64S) is a photo-thermo-sensitive genic male sterile line (PTGMS), with wide application in hybrid seed production in rice (Oryza sativa L.). Micro-RNAs are 21-24 nt, endogenously expressed small RNAs that have been characterized in various developmental stages of rice, but none have been studied with respect to the regulation of TGMS in rice. Here, we employed high-throughput sequencing to identify expression profiles of miRNAs in the anthers of PA64S at high (PA64S-H) and low temperature (PA64S-L). Two small RNA libraries from PA64S-H and PA64-L anthers were sequenced, and 263 known and 321 novel candidate miRNAs were identified. Based on the number of sequencing reads, a total of 133 known miRNAs were found to be differentially expressed between PA64S-H and PA64S-L. Target prediction showed that the target genes encode MYB and TCP transcription factors, and bHLH proteins. These target genes are related to pollen development and male sterility, suggesting that miRNA/targets may play roles in regulating TGMS in rice. Further, starch and sucrose metabolism pathways, sphingolipid metabolism, arginine and proline metabolism, and plant hormone signal transduction pathways were enriched by KEGG pathway annotation. These findings contribute to our understanding of the role of miRNAs during anther development and TGMS occurrence in rice.
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Affiliation(s)
- Sha Wu
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Hang Tan
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohua Hao
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Zijing Xie
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Xiaohui Wang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Dongping Li
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
| | - Lianfu Tian
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha, P.R. China
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17
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Santiago JP, Sharkey TD. Pollen development at high temperature and role of carbon and nitrogen metabolites. PLANT, CELL & ENVIRONMENT 2019; 42:2759-2775. [PMID: 31077385 DOI: 10.1111/pce.13576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 05/11/2023]
Abstract
Fruit and seed crop production heavily relies on successful stigma pollination, pollen tube growth, and fertilization of female gametes. These processes depend on production of viable pollen grains, a process sensitive to high-temperature stress. Therefore, rising global temperatures threaten worldwide crop production. Close observation of plant development shows that high-temperature stress causes morpho-anatomical changes in male reproductive tissues that contribute to reproductive failure. These changes include early tapetum degradation, anther indehiscence, and deformity of pollen grains, all of which are contributing factors to pollen fertility. At the molecular level, reactive oxygen species (ROS) accumulate when plants are subjected to high temperatures. ROS is a signalling molecule that can be beneficial or detrimental for plant cells depending on its balance with the endogenous cellular antioxidant system. Many metabolites have been linked with ROS over the years acting as direct scavengers or molecular stabilizers that promote antioxidant enzyme activity. This review highlights recent advances in research on anther and pollen development and how these might explain the aberrations seen during high-temperature stress; recent work on the role of nitrogen and carbon metabolites in anther and pollen development is discussed including their potential role at high temperature.
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Affiliation(s)
- James P Santiago
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824
| | - Thomas D Sharkey
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824
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18
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Complementary Transcriptomic and Proteomic Analysis Reveals a Complex Network Regulating Pollen Abortion in GMS ( msc-1) Pepper ( Capsicum annuum L.). Int J Mol Sci 2019; 20:ijms20071789. [PMID: 30978924 PMCID: PMC6480423 DOI: 10.3390/ijms20071789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Pepper (Capsicum annuum L.) is a globally important horticultural crop. Use of the genic male-sterile (GMS) line enables efficient commercial hybrid pepper seed production. However, the mechanisms of pepper GMS functioning remain unclear. In this study, we used proteomic and transcriptomic analysis to identify proteins and genes related to genic male sterility. A total of 764 differentially expressed proteins (DEPs) and 1069 differentially expressed genes (DEGs) were identified in the proteomic and transcriptomic level respectively, and 52 genes (hereafter “cor-DEGs-DEPs” genes) were detected at both levels. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 13 DEPs and 14 DEGs involved in tapetum and pollen development. Among the 13 DEPs identified, eight were involved in pollen exine formation, and they were all up-regulated in the fertile line 16C1369B. For the 14 DEGs identified, ABORTED MICROSPORES (AMS) and DEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION1 (TDF1) were involved in tapetum development, and both are possibly regulated by Msc-1. All of these genes were detected and confirmed by qRT-PCR. The presence of these genes suggests their possible role in tapetum and pollen exine formation in GMS pepper. Most key genes and transcription factors involved in these processes were down-regulated in the sterile line 16C1369A. This study provides a better understanding of GMS (msc-1) molecular functioning in pepper.
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The initial deficiency of protein processing and flavonoids biosynthesis were the main mechanisms for the male sterility induced by SX-1 in Brassica napus. BMC Genomics 2018; 19:806. [PMID: 30404610 PMCID: PMC6223035 DOI: 10.1186/s12864-018-5203-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/25/2018] [Indexed: 12/14/2022] Open
Abstract
Background Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecular mechanism. In the present report, a multi-omics integrative analysis, including of the proteomic, transcriptomic and miRNAs, combined with morphological and physiological analysis were conducted. Results Earlier degeneration of the tapetosomes and elaioplasts, aberrantly stacking in tapetal cells and incompletely deposition in tryphine of pollen wall were observed in chemical hybridization agent (CHA) of SX-1 treated B. napus through SEM and TEM analysis. It was revealed that the deficiencies in protein processing in endoplasmic reticulum (ER) and flavonoids biosynthesis were occurred at early stage in the SX-1 treated materials. Subsequently, plant hormone signal transduction, biosynthesis of amino acids, fatty acids and steroid in anther at later stages were identified down-regulated after SX-1 treatment. 144 transcript factors (TFs) were also indentified to down-regulated at early stage, which suggested the early regulation in anther and pollen wall development were disordered in CHA treated B. napus. In addition, 7 important miRNAs were identified and 2 of the predicted target genes of miRNAs were Rf-like genes. Conclusions Taken together, an interaction network of candidate genes and the putative metabolism pathways were constructed based on the multi-omics integrative analysis, it provided a new insight into the male sterility induced by CHA of SX-1 in B. napus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5203-y) contains supplementary material, which is available to authorized users.
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Yang Y, Bao S, Zhou X, Liu J, Zhuang Y. The key genes and pathways related to male sterility of eggplant revealed by comparative transcriptome analysis. BMC PLANT BIOLOGY 2018; 18:209. [PMID: 30249187 PMCID: PMC6154905 DOI: 10.1186/s12870-018-1430-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 09/17/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Male sterility (MS) is an effective tool for hybrid production. Although MS has been widely reported in other plants, such as Arabidopsis and rice, the molecular mechanism of MS in eggplant is largely unknown. To understand the mechanism, the comparative transcriptomic file of MS line and its maintainer line was analyzed with the RNA-seq technology. RESULTS A total of 11,7695 unigenes were assembled and 19,652 differentially expressed genes (DEGs) were obtained. The results showed that 1,716 DEGs were shared in the three stages. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these DEGs were mainly involved in oxidation-reduction, carbohydrate and amino acid metabolism. Moreover, transcriptional regulation was also the impact effector for MS and anther development. Weighted correlation network analysis (WGCNA) showed two modules might be responsible for MS, which was similar to hierarchical cluster analysis. CONCLUSIONS A number of genes and pathways associated with MS were found in this study. This study threw light on the molecular mechanism of MS and identified several key genes related to MS in eggplant.
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Affiliation(s)
- Yan Yang
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014 China
| | - Shengyou Bao
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014 China
| | - Xiaohui Zhou
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014 China
| | - Jun Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014 China
| | - Yong Zhuang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014 China
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Liu H, Zhang G, Wang J, Li J, Song Y, Qiao L, Niu N, Wang J, Ma S, Li L. Chemical hybridizing agent SQ-1-induced male sterility in Triticum aestivum L.: a comparative analysis of the anther proteome. BMC PLANT BIOLOGY 2018; 18:7. [PMID: 29304738 PMCID: PMC5755283 DOI: 10.1186/s12870-017-1225-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/22/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Heterosis is widely used to increase the yield of many crops. However, as wheat is a self-pollinating crop, hybrid breeding is not so successful in this organism. Even though male sterility induced by chemical hybridizing agents is an important aspect of crossbreeding, the mechanisms by which these agents induce male sterility in wheat is not well understood. RESULTS We performed proteomic analyses using the wheat Triticum aestivum L.to identify those proteins involved in physiological male sterility (PHYMS) induced by the chemical hybridizing agent CHA SQ-1. A total of 103 differentially expressed proteins were found by 2D-PAGE and subsequently identified by MALDI-TOF/TOF MS/MS. In general, these proteins had obvious functional tendencies implicated in carbohydrate metabolism, oxidative stress and resistance, protein metabolism, photosynthesis, and cytoskeleton and cell structure. In combination with phenotypic, tissue section, and bioinformatics analyses, the identified differentially expressed proteins revealed a complex network behind the regulation of PHYMS and pollen development. Accordingly, we constructed a protein network of male sterility in wheat, drawing relationships between the 103 differentially expressed proteins and their annotated biological pathways. To further validate our proposed protein network, we determined relevant physiological values and performed real-time PCR assays. CONCLUSIONS Our proteomics based approach has enabled us to identify certain tendencies in PHYMS anthers. Anomalies in carbohydrate metabolism and oxidative stress, together with premature tapetum degradation, may be the cause behind carbohydrate starvation and male sterility in CHA SQ-1 treated plants. Here, we provide important insight into the mechanisms underlying CHA SQ-1-induced male sterility. Our findings have practical implications for the application of hybrid breeding in wheat.
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Affiliation(s)
- Hongzhan Liu
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Gaisheng Zhang
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Junsheng Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jingjing Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Yulong Song
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lin Qiao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Na Niu
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Junwei Wang
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shoucai Ma
- National Yangling Agricultural Biotechnology & Breeding Center / Yangling Branch of State Wheat Improvement Centre / Wheat Breeding Engineering Research Center, Ministry of Education /Key Laboratory of Crop Heterosis of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
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