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Zhang T, Xuan L, Mao Y, Hu Y. Cotton heterosis and hybrid cultivar development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:89. [PMID: 37000242 DOI: 10.1007/s00122-023-04334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Cotton, the most important economic crop in the world, displays strong hybrid vigor, and has long been a subject for hybrid cultivar breeding. Here, advances in the theoretical and applied research in cotton heterosis along with its hybrid cultivar development by hand-emasculation and pollination (HEP), cytoplasmic (CMS) and genic male sterile lines (GMS) mainly in China during the past few decades are presented in this review. Three types of hybrids produced by HEP, CMS and GMS facilitating hybrid seed production with hand-pollination have been developed and are being planted simultaneously in cotton production. However, most hybrids commercially planted in production are produced by HEP, therefore, F2 seeds are being extensively planted due to the high cost to produce F1 seed. F2 generations of these combinations exceed the check cultivars in yield usually up to 5~15%. GMS genes (ms2 and ms5ms6) used in hybrid seed production and casual mitochondrial genes for G. harknessii CMS have been cloned. Challenges and opportunities in cotton heterosis and future hybrid cultivar development in cotton are discussed.
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Affiliation(s)
- Tianzhen Zhang
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Lisha Xuan
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Mao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yan Hu
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Zhang C, Fu F, Lin C, Ding X, Zhang J, Yan H, Wang P, Zhang W, Peng B, Zhao L. MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean. Front Genet 2021; 12:654146. [PMID: 34054917 PMCID: PMC8153375 DOI: 10.3389/fgene.2021.654146] [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: 01/15/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is an important plant characteristic for exploiting heterosis to enhance crop traits during breeding. However, the CMS regulatory network remains unclear in plants, even though researchers have attempted to isolate genes associated with CMS. In this study, we performed high-throughput sequencing and degradome analyses to identify microRNAs (miRNAs) and their targets in a soybean CMS line (JLCMS9A) and its maintainer line (JLCMS9B). Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. A total of 280 miRNAs matched soybean miRNA sequences in miRBase, including mature miRNAs and pre-miRNAs. Of the 280 miRNAs, 30, 23, and 21 belonged to the miR166, miR156, and miR171 families, respectively. Moreover, 410 novel low-abundant miRNAs were identified in the JLCMS9A and JLCMS9B flower buds. Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. Moreover, all target genes were annotated with diverse functions related to biological processes, cellular components, and molecular functions, including transcriptional regulation, the nucleus, meristem maintenance, meristem initiation, cell differentiation, auxin-activated signaling, plant ovule development, and anther development. Finally, a network was built based on the interactions. Analyses of the miRNA, degradome, and transcriptome datasets generated in this study provided a comprehensive overview of the reproductive development of a CMS soybean line. The data presented herein represent useful information for soybean hybrid breeding. Furthermore, the study results indicate that miRNAs might contribute to the soybean CMS regulatory network by modulating the expression of CMS-related genes. These findings lay the foundation for future studies on the molecular mechanisms underlying soybean CMS.
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Affiliation(s)
- Chunbao Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Fuyou Fu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
| | - Chunjing Lin
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingyong Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Hao Yan
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Pengnian Wang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wei Zhang
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Bao Peng
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Limei Zhao
- Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun, China
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Reactive Oxygen Species Accumulation Strongly Allied with Genetic Male Sterility Convertible to Cytoplasmic Male Sterility in Kenaf. Int J Mol Sci 2021; 22:ijms22031107. [PMID: 33498664 PMCID: PMC7866071 DOI: 10.3390/ijms22031107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Male sterility (MS) plays a key role in the hybrid breed production of plants. Researchers have focused on the association between genetic male sterility (GMS) and cytoplasmic male sterility (CMS) in kenaf. In this study, P9BS (a natural GMS mutant of the kenaf line P9B) and male plants of P9B were used as parents in multiple backcross generations to produce P9SA, a CMS line with stable sterility, to explore the molecular mechanisms of the association between GMS and CMS. The anthers of the maintainer (P9B), GMS (P9BS), and CMS (P9SA) lines were compared through phenotypic, cell morphological, physiological, biochemical observations, and transcriptome analysis. Premature degradation of the tapetum was observed at the mononuclear stage in P9BS and P9SA, which also had lower activity of reactive oxygen species (ROS) scavenging enzymes compared with P9B. Many coexpressed differentially expressed genes were related to ROS balance, including ATP synthase, electron chain transfer, and ROS scavenging processes were upregulated in P9B. CMS plants had a higher ROS accumulation than GMS plants. The MDA content in P9SA was 3.2 times that of P9BS, and therefore, a higher degree of abortion occurred in P9SA, which may indicate that the conversion between CMS and GMS is related to intracellular ROS accumulation. Our study adds new insights into the natural transformation of GMS and CMS in plants in general and kenaf in particular.
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Differential transcript profiling alters regulatory gene expression during the development of Gossypium arboreum, G.stocksii and somatic hybrids. Sci Rep 2017; 7:3120. [PMID: 28600526 PMCID: PMC5466607 DOI: 10.1038/s41598-017-03431-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/02/2017] [Indexed: 11/20/2022] Open
Abstract
Polyploidy or genome doubling (i.e., the presence of two or more diploid parental genome sets within an organism) are very important in higher plants. Of particular interest are the mechanisms in the new microenvironment of the common nucleus, where doubled regulatory networks interact to generate a viable genetic system capable of regulating growth, development and responses to the environment. To determine the effects of whole genome merging and doubling on the global gene expression architecture of a new polyploid, derived from protoplast fusion of the A1A1 genome of Gossypium arboreum and the E1E1 genome of Gossypium stocksii, we monitored gene expression through cDNA-AFLP in the somatic hybrids (G. arboreum + G. stocksii). The genomic expression patterns of the somatic hybrids revealed that changes in expression levels mainly involved regulatory genes (31.8% of the gene expression profiles), and the AA and EE genomes contributed equally to genome-wide expression in the newly formed AAEE genome from additivity and dominance effects. These results provide a novel perspective on polyploid gene regulation and hint at the underlying genetic basis of allopolyploid adaption in the new microenvironmental nucleus.
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Fang W, Zhao F, Sun Y, Xie D, Sun L, Xu Z, Zhu W, Yang L, Zhao Y, Lv S, Tang Z, Nie L, Li W, Hou J, Duan Z, Yu Y, Yang X. Transcriptomic Profiling Reveals Complex Molecular Regulation in Cotton Genic Male Sterile Mutant Yu98-8A. PLoS One 2015; 10:e0133425. [PMID: 26382878 PMCID: PMC4575049 DOI: 10.1371/journal.pone.0133425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/26/2015] [Indexed: 01/13/2023] Open
Abstract
Although cotton genic male sterility (GMS) plays an important role in the utilization of hybrid vigor, its precise molecular mechanism remains unclear. To characterize the molecular events of pollen abortion, transcriptome analysis, combined with histological observations, was conducted in the cotton GMS line, Yu98-8A. A total of 2,412 genes were identified as significant differentially expressed genes (DEGs) before and during the critical pollen abortion stages. Bioinformatics and biochemical analysis showed that the DEGs mainly associated with sugars and starch metabolism, oxidative phosphorylation, and plant endogenous hormones play a critical and complicated role in pollen abortion. These findings extend a better understanding of the molecular events involved in the regulation of pollen abortion in genic male sterile cotton, which may provide a foundation for further research studies on cotton heterosis breeding.
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Affiliation(s)
- Weiping Fang
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
- * E-mail: (WPF); (XJY)
| | - Fu'an Zhao
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Yao Sun
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Deyi Xie
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Li Sun
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Zhenzhen Xu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agriculture Sciences, Anyang, Henan province, 455000, R.P. China
| | - Wei Zhu
- Agronomy College, Henan Agricultural University, Zhengzhou, Henan province, 450002, R.P. China
| | - Lirong Yang
- Plant Protection Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Yuanming Zhao
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Shuping Lv
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Zhongjie Tang
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Lihong Nie
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Wu Li
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Jianan Hou
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Zhengzheng Duan
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Yuebo Yu
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
| | - Xiaojie Yang
- Economic Crop Research Institute, Henan Academy of Agriculture Sciences, Zhengzhou, Henan province, 450002, R.P. China
- * E-mail: (WPF); (XJY)
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Differential proteomic studies of the genic male-sterile line and fertile line anthers of upland cotton (Gossypium hirsutum L.). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0176-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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LIU CHUANXIANG, YUAN DAOJUN, ZHANG XIANLONG, LIN ZHONGXU. Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. J Genet 2013. [DOI: 10.1007/s12041-013-0238-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Claverie M, Souquet M, Jean J, Forestier-Chiron N, Lepitre V, Pré M, Jacobs J, Llewellyn D, Lacape JM. cDNA-AFLP-based genetical genomics in cotton fibers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:665-683. [PMID: 22080217 DOI: 10.1007/s00122-011-1738-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 10/18/2011] [Indexed: 05/31/2023]
Abstract
Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum × G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD > 3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton.
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Affiliation(s)
- Michel Claverie
- UMR AGAP, CIRAD, Avenue Agropolis, 34398, Montpellier, France
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Martínez-Fernández M, Bernatchez L, Rolán-Alvarez E, Quesada H. Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis. BMC Evol Biol 2010; 10:356. [PMID: 21087461 PMCID: PMC2996406 DOI: 10.1186/1471-2148-10-356] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 11/18/2010] [Indexed: 12/22/2022] Open
Abstract
Background In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation. Results Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals. Conclusions At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.
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Affiliation(s)
- Mónica Martínez-Fernández
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Campus As Lagoas-Marcosende, Universidad de Vigo, 36310 Vigo, Spain
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