1
|
Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
Collapse
Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| |
Collapse
|
2
|
Ijaz B, Zhao N, Kong J, Hua J. Fiber Quality Improvement in Upland Cotton ( Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application. FRONTIERS IN PLANT SCIENCE 2019; 10:1585. [PMID: 31921240 PMCID: PMC6917639 DOI: 10.3389/fpls.2019.01585] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/12/2019] [Indexed: 05/17/2023]
Abstract
Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.
Collapse
Affiliation(s)
- Babar Ijaz
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua,
| |
Collapse
|
3
|
Tark-Dame M, Weber B, de Sain M, Anggoro DT, Bader R, Walmsley A, Oka R, Stam M. Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector. J Vis Exp 2018. [PMID: 29658919 DOI: 10.3791/57295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
When generating transgenic plants, generally the objective is to have stable expression of a transgene. This requires a single, intact integration of the transgene, as multi-copy integrations are often subjected to gene silencing. The Gateway-compatible binary vector based on bacterial artificial chromosomes (pBIBAC-GW), like other pBIBAC derivatives, allows the insertion of single-copy transgenes with high efficiency. As an improvement to the original pBIBAC, a Gateway cassette has been cloned into pBIBAC-GW, so that the sequences of interest can now be easily incorporated into the vector transfer DNA (T-DNA) by Gateway cloning. Commonly, the transformation with pBIBAC-GW results in an efficiency of 0.2-0.5%, whereby half of the transgenics carry an intact single-copy integration of the T-DNA. The pBIBAC-GW vectors are available with resistance to Glufosinate-ammonium or DsRed fluorescence in seed coats for selection in plants, and with resistance to kanamycin as a selection in bacteria. Here, a series of protocols is presented that guide the reader through the process of generating transgenic plants using pBIBAC-GW: starting from recombining the sequences of interest into the pBIBAC-GW vector of choice, to plant transformation with Agrobacterium, selection of the transgenics, and testing the plants for intactness and copy number of the inserts using DNA blotting. Attention is given to designing a DNA blotting strategy to recognize single- and multi-copy integrations at single and multiple loci.
Collapse
Affiliation(s)
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Mara de Sain
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | | | - Rechien Bader
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Aimee Walmsley
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Rurika Oka
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam;
| |
Collapse
|
4
|
Lv Y, Ma D, Liang W, Lv Y, Guo W, Hu Y, Zhang T. Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L. acc. TM-1. Mol Cytogenet 2015. [PMID: 26221184 PMCID: PMC4517413 DOI: 10.1186/s13039-015-0158-z] [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] [Indexed: 11/30/2022] Open
Abstract
Background The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to fiber fuzz, lethality, gland development and male sterility. In this study a physical map of the cotton TM-1 chromosome 12 was constructed. A number of large-insert cotton genome libraries are available, and genome-wide physical mapping using large insert segments combined with bacterial cloning is a thriving area of genome research. However, sequencing of the cotton genome is difficult due to sequence repeats and homoeologous regions. In order to effectively distinguish the homologous segments, a new method for adjusting the parameters of the FPC software was applied for contig map construction. Results All available markers on chromosomes A12 and D12 were used to screen the TM-1 BAC library by PCR. A total of 775 clones (387 for A12, 388 for D12) were obtained using Hind III fingerprinting and used for construction of the contig map. Seven pairs of SSR markers located on A12 and D12 were chosen for contig analysis. Following optimization of the tolerance (10) and cutoff (1e-12) parameters, combining all clones from A12 and D12 produced two separate contigs. Conclusions The BAC contig map of chromosomes A12 and D12 was constructed and FPC software parameters were optimized for analysis. The resulting approach is a powerful platform for genome-wide and evolutionary research on cotton.
Collapse
Affiliation(s)
- Yanhui Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dan Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenhua Liang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuanda Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yan Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
5
|
Buyyarapu R, Kantety RV, Yu JZ, Xu Z, Kohel RJ, Percy RG, Macmil S, Wiley GB, Roe BA, Sharma GC. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton. PLoS One 2013; 8:e76757. [PMID: 24116150 PMCID: PMC3792896 DOI: 10.1371/journal.pone.0076757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/28/2013] [Indexed: 11/19/2022] Open
Abstract
Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.
Collapse
Affiliation(s)
- Ramesh Buyyarapu
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - Ramesh V. Kantety
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| | - John Z. Yu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Zhanyou Xu
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Russell J. Kohel
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Richard G. Percy
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, Texas, United States of America
| | - Simone Macmil
- Gene Structure and Function Laboratory, University of Otago, Dunedin, New Zealand
| | - Graham B. Wiley
- Arthritis & Immunology Department, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Bruce A. Roe
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Govind C. Sharma
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama Agricultural & Mechanical University, Normal, Alabama, United States of America
| |
Collapse
|
6
|
Sierro N, van Oeveren J, van Eijk MJT, Martin F, Stormo KE, Peitsch MC, Ivanov NV. Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:880-9. [PMID: 23672264 PMCID: PMC3824204 DOI: 10.1111/tpj.12247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/22/2013] [Accepted: 05/09/2013] [Indexed: 05/08/2023]
Abstract
Genomics-based breeding of economically important crops such as banana, coffee, cotton, potato, tobacco and wheat is often hampered by genome size, polyploidy and high repeat content. We adapted sequence-based whole-genome profiling (WGP™) technology to obtain insight into the polyploidy of the model plant Nicotiana tabacum (tobacco). N. tabacum is assumed to originate from a hybridization event between ancestors of Nicotiana sylvestris and Nicotiana tomentosiformis approximately 200,000 years ago. This resulted in tobacco having a haploid genome size of 4500 million base pairs, approximately four times larger than the related tomato (Solanum lycopersicum) and potato (Solanum tuberosum) genomes. In this study, a physical map containing 9750 contigs of bacterial artificial chromosomes (BACs) was constructed. The mean contig size was 462 kbp, and the calculated genome coverage equaled the estimated tobacco genome size. We used a method for determination of the ancestral origin of the genome by annotation of WGP sequence tags. This assignment agreed with the ancestral annotation available from the tobacco genetic map, and may be used to investigate the evolution of homoeologous genome segments after polyploidization. The map generated is an essential scaffold for the tobacco genome. We propose the combination of WGP physical mapping technology and tag profiling of ancestral lines as a generally applicable method to elucidate the ancestral origin of genome segments of polyploid species. The physical mapping of genes and their origins will enable application of biotechnology to polyploid plants aimed at accelerating and increasing the precision of breeding for abiotic and biotic stress resistance.
Collapse
Affiliation(s)
- Nicolas Sierro
- Biological System Research, Philip Morris International R&D, Philip Morris Products SA Quai Jeanrenaud 5, 2000Neuchatel, Switzerland
| | - Jan van Oeveren
- Keygene NVAgro Business Park 90, 6708 PW, Wageningen, The Netherlands
| | | | - Florian Martin
- Biological System Research, Philip Morris International R&D, Philip Morris Products SA Quai Jeanrenaud 5, 2000Neuchatel, Switzerland
| | - Keith E Stormo
- Amplicon Express Inc.2345 NE Hopkins Court, Pullman, WA, 99163, USA
| | - Manuel C Peitsch
- Biological System Research, Philip Morris International R&D, Philip Morris Products SA Quai Jeanrenaud 5, 2000Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Biological System Research, Philip Morris International R&D, Philip Morris Products SA Quai Jeanrenaud 5, 2000Neuchatel, Switzerland
| |
Collapse
|
7
|
Lee MK, Zhang Y, Zhang M, Goebel M, Kim HJ, Triplett BA, Stelly DM, Zhang HB. Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). BMC Genomics 2013; 14:208. [PMID: 23537070 PMCID: PMC3623804 DOI: 10.1186/1471-2164-14-208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 02/11/2013] [Indexed: 11/25/2022] Open
Abstract
Background Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr. Results We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5). Conclusions The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii.
Collapse
Affiliation(s)
- Mi-Kyung Lee
- Department of Soil and Crop Sciences, 2474 TAMU, Texas A&M University, College Station, TX 77843-2474, USA
| | | | | | | | | | | | | | | |
Collapse
|